Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry

Bacterial Identification and Susceptibility Testing

Works Count: 36365

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Description

This cluster of papers focuses on the advancements in microbial identification and diagnosis, particularly through the use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) and rapid diagnostic testing. It covers topics such as blood culture, antimicrobial susceptibility testing, bacterial identification, and molecular diagnosis in clinical microbiology, with a specific emphasis on bacteremia.

Keywords

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry; Microorganism Identification; Clinical Microbiology; Blood Culture; Antimicrobial Susceptibility Testing; Bacterial Identification; MALDI-TOF MS; Rapid Diagnostic Testing; Molecular Diagnosis; Bacteremia

Antibiotics in Laboratory Medicine.

1980-10-01

Víctor Lorian

The Breakpoint 1 Matthew A. Wikler, Paul G. Ambrose Antimicrobial Susceptibility on Solid Media 8 John D. Turnidge, Jan M. Bell Susceptibility Testing of Antimicrobials in Liquid Media 61 Daniel … The Breakpoint 1 Matthew A. Wikler, Paul G. Ambrose Antimicrobial Susceptibility on Solid Media 8 John D. Turnidge, Jan M. Bell Susceptibility Testing of Antimicrobials in Liquid Media 61 Daniel Amsterdam Antimicrobial Susceptibility Testing of Anaerobic Bacteria 144 David W. Hecht Antimycobacterial Agents: In Vitro Susceptibility Testing and Mechanisms of Action and Resistance 155 Clark B. Inderlied and Kevin A. Nash Antifungal Drugs: Mechanisms of Action, Drug Resistance, Susceptibility Testing, and Assays of Activity in Biological Fluids 226 Michael A. Pfaller, Daniel J. Diekema, and Michael G. Rinaldi Antimicrobial Susceptibility Testing for Some Atypical Microorganisms (Chlamydia, Mycoplasma, Rickettsia, Ehrlichia, Coxiella, and Spirochetes) 266 Jean-Marc Rolain, Didier Raoult Applications, Significance of, and Methods for the Measurement of Antimicrobial Concentrations in Human Body Fluids 290 Roger D. Klein and Stephen C. Edberg Antimicrobial Combinations 365 Satish K. Pillai, Robert C. Moellering, Jr., and George M. Eliopoulos Genetic and Biochemical Mechanisms of Bacterial Resistance to Antimicrobial Agents 441 Louis B. Rice and Robert A. Bonomo Molecular Methods for the Detection of Antibacterial Resistance Genes 509 Margareta Ieven Molecular Mechanisms of Action for Antimicrobial Agents: General Principles and Mechanisms for Selected Classes of Antibiotics 532 Charles W. Stratton The Antivirogram and the Modes of Action of Antiviral Agents, HIV, Hepatitis, Influenza, and Cytomegalovirus 564 Pierre Dellamonica, Vincent Calvez, Anne-Genevieve Marcelin, Albert Tran, Pierre-Marie Roger, Marie-Christine Mazeron, and Bruno Lina Disinfectants and Antiseptics, Modes of Action, Mechanisms of Resistance, and Testing 615 Joseph M. Ascenzi, Martin S. Favero Evaluation of Antimicrobials in Experimental Animal Infections 654 Terry O' Reilly, D. A. Andes, Ch. Ostergaard, N. Frimodt-Moller Extravascular Antimicrobial Distribution and the Respective Blood and Urine Concentrations in Humans 719 David M. Bamberger, John W. Foxworth, Darcie L. Bridwell, Christopher S. Shain, and Dale N. Gerding Epidemiology of Antimicrobial Resistance: Species Prevalence, Susceptibility Profiles, and Resistance Trends 815 Thomas R. Fritsche, Helio S. Sader, Ronald N. Jones Index 851

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Biochemical tests for identification of medical bacteria

1976-01-01

Jean F MacFaddin

Biochemical Tests for identification of medical bacteria , Biochemical Tests for identification of medical bacteria , کتابخانه دانشگاه علوم پزشکی و خدمات بهداشتی درمانی کرمان Biochemical Tests for identification of medical bacteria , Biochemical Tests for identification of medical bacteria , کتابخانه دانشگاه علوم پزشکی و خدمات بهداشتی درمانی کرمان

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

2015-08-05

Neelja Singhal , Manish Kumar , Pawan Kumar Kanaujia +1 more

Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years Matrix Assisted Laser Desorption Ionization-Time of Flight mass spectrometry (MALDI-TOF MS) has emerged … Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years Matrix Assisted Laser Desorption Ionization-Time of Flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses and fungi.

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Cowan and Steel's Manual for the Identification of Medical Bacteria

1993-01-28

S. T. Cowan

Cowan and Steel's Manual has for many years had an essential role in every laboratory of microbiology and bacteriology. This substantially revised new edition, which is modelled on the successful … Cowan and Steel's Manual has for many years had an essential role in every laboratory of microbiology and bacteriology. This substantially revised new edition, which is modelled on the successful pattern established in the previous two editions, has been fully updated and is suitable for all bacteriological laboratories using traditional diagnostic methods. It is essentially a practical manual with up-to-date contributions and key references by experts to the diagnostic characteristics of the bacteria likely to be encountered in public health and hospital microbiology laboratories, as well as in medical and veterinary practice. This edition contains new sections on rapid and mechanised test methods, and on the laboratory applications of computer theory and practice to the identification of bacteria. As in previous editions, the importance of laboratory quality control and proficiency procedures are emphasised. The Appendices give details of the laboratory methods and media for all the recommended diagnostic tests and, in addition, provide abstracts of the official guidelines for bacterial nomenclature.

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Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically : Approved standard

2006-01-01

Matthew A. Wikler , Clinical

1 Classical and Rapid Identification Methods for Medically Important Bacteria

1988-01-01

B Lányi

Manual of Methods for General Bacteriology

1981-09-01

Dylan M. Jones

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The Clinical Significance of Positive Blood Cultures in the 1990s: A Prospective Comprehensive Evaluation of the Microbiology, Epidemiology, and Outcome of Bacteremia and Fungemia in Adults

1997-04-01

Melvin P. Weinstein , Michael Towns , Seth M. Quartey +4 more

To assess changes since the mid-1970s, we reviewed 843 episodes of positive blood cultures in 707 patients with septicemia. The five most common pathogens were Staphylococcus aureus, Escherichia coli, coagulase-negative … To assess changes since the mid-1970s, we reviewed 843 episodes of positive blood cultures in 707 patients with septicemia. The five most common pathogens were Staphylococcus aureus, Escherichia coli, coagulase-negative staphylococci (CNS), Klebsiella pneumoniae, and Enterococcus species. Although CNS were isolated most often, only 12.4% were clinically significant. Half of all episodes were nosocomial, and a quarter had no recognized source. Leading identifiable sources included intravenous catheters, the respiratory and genitourinary tracts, and intraabdominal foci. Septicemia-associated mortality was 17.5%. Patients who received appropriate antimicrobial therapy throughout the course of infection had the lowest mortality (13.3%). Multivariate analysis showed that age (relative risk [RR], 1.80), microorganism (RR, 2.27), source of infection (RR, 2.86), predisposing factors (RR, 1.98), blood pressure (RR, 2.29), body temperature (RR, 2.04), and therapy (RR, 2.72) independently influenced outcome. Bloodstream infections in the 1990s are notable for the increased importance of CNS as both contaminants and pathogens, the proportionate increase in fungi and decrease in anaerobes as pathogens, the emergence of Mycobacterium avium complex as an important cause of bacteremia in patients with advanced human immunodeficiency virus infection, and the reduction in mortality associated with infection.

Manual of Clinical Microbiology

1991-12-01

Albert Balows , W.J. HAUSLER , Konrad Herrmann +2 more

General Issues in Clinical Microbiology Diagnostic Technologies in Clinical Microbiology Nosocomial and Community Infections: the Role of the Clinical Microbiology Laboratory Bacteria Fungi Parasites Viruses Rickettsiae and Chlamydiae Antimicrobial Agents … General Issues in Clinical Microbiology Diagnostic Technologies in Clinical Microbiology Nosocomial and Community Infections: the Role of the Clinical Microbiology Laboratory Bacteria Fungi Parasites Viruses Rickettsiae and Chlamydiae Antimicrobial Agents and Susceptibility Tests Quality Control, Media, Reagents and Stains.

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Manual of Clinical Microbiology, 7th ed.

2000-02-01

Albert Balows

The estimation of the bactericidal power of the blood

1938-11-01

A. A. Miles , S. S. Misra , J. O. Irwin

The survival rate, p , of a measured inoculum of Staph. aureus in a standard volume of denbrinated blood, is a reliable quantitative measure of the bactericidal power of blood. … The survival rate, p , of a measured inoculum of Staph. aureus in a standard volume of denbrinated blood, is a reliable quantitative measure of the bactericidal power of blood. The number of viable organisms in the inoculum and in the blood-bacterium mixture may be estimated with the necessary accuracy by counts of colonies developing from measured volumes of the fluids let fall on to the surface of solid media. Fildes' agar was the most suitable medium for this surface-viable count, and was selected on the basis of four criteria; of the media tested it yielded the highest counts, and the counts conformed most closely to a Poisson series; and on it the mean colony size was maximum, and the coefficient of variation of colony size was minimum. On this medium, the close conformity of the separate count values to a Poisson series enabled the standard error of the survival rate to be determined from a simplification of the general expression for the standard error of a ratio. The number of colonies growing from a sample of a blood-bacterium mixture may be reduced, not by killing of the individual cocci, but as a result of their aggregation either by agglutinins in the blood, or in the cytoplasm of leucocytes that are phagocytic but not bactericidal. It appears that these mechanisms are unlikely to operate in blood-bacterium mixture containing relatively few organisms; in such mixtures the survival rate is a reflexion of the killing power only. The immunological significance of p has not been investigated, but the range of values for healthy human adults differs significantly from that for sufferers from chronic staphylococcal infection. Moreover, by the technique employed differences may be detected between individual values of p that cannot reasonably be attributed to technical or sampling errors.

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MANUAL FOR THE IDENTIFICATION OF MEDICAL BACTERIA

1965-12-01

E. Neter

MANUAL FOR THE IDENTIFICATION OF MEDICAL BACTERIA Erwin Neter CopyRight https://doi.org/10.2105/AJPH.55.12.2047-a Published Online: August 29, 2011 MANUAL FOR THE IDENTIFICATION OF MEDICAL BACTERIA Erwin Neter CopyRight https://doi.org/10.2105/AJPH.55.12.2047-a Published Online: August 29, 2011

Gram-Negative Bacteremia

1962-12-01

William R. McCabe

The pattern of life-threatening bacterial infections has changed since the introduction of potent antimicrobial agents. Infections caused by pneumococci and β-hemolytic streptococci are less frequent causes of potentially fatal infections, … The pattern of life-threatening bacterial infections has changed since the introduction of potent antimicrobial agents. Infections caused by pneumococci and β-hemolytic streptococci are less frequent causes of potentially fatal infections, and severe infections caused by staphylococci, other bacteria, and fungi are relatively more frequent.1-3The importance and increasing incidence of infections caused by Gram-negative bacilli have been pointed out by several investigators,1,4-7but infections caused by these microorganisms have received less attention than those due to staphylococci. This report reviews the experience with Gram-negative bacteremia during an 8-year period at the University of Illinois Research and Educational Hospitals. The etiology and some aspects of the ecology of these infections have been determined and are reported in this paper. Clinical manifestations, the effect of corticosteroid administration, and antibiotic prophylaxis and therapy of Gram-negative bacteremia are given in another report. <h3>Clinical Material</h3> All blood culture isolates of a species of

MANUAL OF CLINICAL MICROBIOLOGY

1970-08-01

Albert S. Klainer

An overview of nosocomial infections, including the role of the microbiology laboratory

1993-10-01

T.Grace Emori , Robert P. Gaynes

An estimated 2 million patients develop nosocomial infections in the United States annually. The increasing number of antimicrobial agent-resistant pathogens and high-risk patients in hospitals are challenges to progress in … An estimated 2 million patients develop nosocomial infections in the United States annually. The increasing number of antimicrobial agent-resistant pathogens and high-risk patients in hospitals are challenges to progress in preventing and controlling these infections. While Escherichia coli and Staphylococcus aureus remain the most common pathogens isolated overall from nosocomial infections, coagulase-negative staphylococci (CoNS), organisms previously considered contaminants in most cultures, are now the predominant pathogens in bloodstream infections. The growing number of antimicrobial agent-resistant organisms is troublesome, particularly vancomycin-resistant CoNS and Enterococcus spp. and Pseudomonas aeruginosa resistant to imipenem. The active involvement and cooperation of the microbiology laboratory are important to the infection control program, particularly in surveillance and the use of laboratory services for epidemiologic purposes. Surveillance is used to identify possible infection problems, monitor infection trends, and assess the quality of care in the hospital. It requires high-quality laboratory data that are timely and easily accessible.

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Bacteroides: the Good, the Bad, and the Nitty-Gritty

2007-10-01

Hannah M. Wexler

SUMMARY Summary: Bacteroides species are significant clinical pathogens and are found in most anaerobic infections, with an associated mortality of more than 19%. The bacteria maintain a complex and generally … SUMMARY Summary: Bacteroides species are significant clinical pathogens and are found in most anaerobic infections, with an associated mortality of more than 19%. The bacteria maintain a complex and generally beneficial relationship with the host when retained in the gut, but when they escape this environment they can cause significant pathology, including bacteremia and abscess formation in multiple body sites. Genomic and proteomic analyses have vastly added to our understanding of the manner in which Bacteroides species adapt to, and thrive in, the human gut. A few examples are (i) complex systems to sense and adapt to nutrient availability, (ii) multiple pump systems to expel toxic substances, and (iii) the ability to influence the host immune system so that it controls other (competing) pathogens. B. fragilis, which accounts for only 0.5% of the human colonic flora, is the most commonly isolated anaerobic pathogen due, in part, to its potent virulence factors. Species of the genus Bacteroides have the most antibiotic resistance mechanisms and the highest resistance rates of all anaerobic pathogens. Clinically, Bacteroides species have exhibited increasing resistance to many antibiotics, including cefoxitin, clindamycin, metronidazole, carbapenems, and fluoroquinolones (e.g., gatifloxacin, levofloxacin, and moxifloxacin).

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Antimicrobial Susceptibility Testing: A Review of General Principles and Contemporary Practices

2009-10-27

James H. Jorgensen , Mary Jane Ferraro

An important task of the clinical microbiology laboratory is the performance of antimicrobial susceptibility testing of significant bacterial isolates. The goals of testing are to detect possible drug resistance in … An important task of the clinical microbiology laboratory is the performance of antimicrobial susceptibility testing of significant bacterial isolates. The goals of testing are to detect possible drug resistance in common pathogens and to assure susceptibility to drugs of choice for particular infections. The most widely used testing methods include broth microdilution or rapid automated instrument methods that use commercially marketed materials and devices. Manual methods that provide flexibility and possible cost savings include the disk diffusion and gradient diffusion methods. Each method has strengths and weaknesses, including organisms that may be accurately tested by the method. Some methods provide quantitative results (eg, minimum inhibitory concentration), and all provide qualitative assessments using the categories susceptible, intermediate, or resistant. In general, current testing methods provide accurate detection of common antimicrobial resistance mechanisms. However, newer or emerging mechanisms of resistance require constant vigilance regarding the ability of each test method to accurately detect resistance.

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Health Care–Associated Bloodstream Infections in Adults: A Reason To Change the Accepted Definition of Community-Acquired Infections

2002-11-19

N. Deborah Friedman

Background: Bloodstream infections occurring in persons residing in the community, regardless of whether those persons have been receiving health care in an outpatient facility, have traditionally been categorized as community-acquired … Background: Bloodstream infections occurring in persons residing in the community, regardless of whether those persons have been receiving health care in an outpatient facility, have traditionally been categorized as community-acquired infections. Objective: To develop a new classification scheme for bloodstream infections that distinguishes among community-acquired, health care–associated, and nosocomial infections. Design: Prospective observational study. Setting: One academic medical center and two community hospitals. Patients: All adult patients admitted to the hospital with bloodstream infection. Measurements: Demographic characteristics, living arrangements before hospitalization, comorbid medical conditions, factors predisposing to bloodstream infection, date of hospitalization, dates and number of positive blood cultures, results of microbiological susceptibility testing, dates of hospital discharge or death, and mortality rates at 3 to 6 months of follow-up. Results: 504 patients with bloodstream infections were enrolled; 143 (28%) had community-acquired bloodstream infections, 186 (37%) had health care–associated bloodstream infections, and 175 (35%) had nosocomial bloodstream infections. Of the 186 patients with health care–associated bloodstream infection, 29 resided in a nursing home, 64 were receiving home health care, 78 were receiving intravenous or intravascular therapy at home or in a clinic, and 117 had been hospitalized in the 90 days before their bloodstream infection. Cancer was more common in patients with health care–associated or nosocomial bloodstream infection than in patients with community-acquired bloodstream infection. Intravascular devices were the most common source of health care–associated and nosocomial infections, and Staphylococcus aureus was the most frequent pathogen in these types of infections. Methicillin-resistant S. aureus occurred with similar frequency in the groups with health care–associated infection (52%) and nosocomial infection (61%) but was uncommon in the group with community-acquired bloodstream infection (14%) (P = 0.001). Mortality rate at follow-up was greater in patients with health care–associated infection (29% versus 16%; P = 0.019) or nosocomial infection (37% versus 16%; P < 0.001) than in patients with community-acquired infection. Conclusions: Health care–associated bloodstream infections are similar to nosocomial infections in terms of frequency of various comorbid conditions, source of infection, pathogens and their susceptibility patterns, and mortality rate at follow-up. A separate category for health care–associated bloodstream infections is justified, and this new category will have obvious implications for choices about empirical therapy and infection-control surveillance.

Executive Summary: Practice Guidelines for the Diagnosis and Management of Skin and Soft Tissue Infections: 2014 Update by the Infectious Diseases Society of America

2014-06-27

Dennis L. Stevens , Alan L. Bisno , Henry F. Chambers +7 more

A panel of national experts was convened by the Infectious Diseases Society of America (IDSA) to update the 2005 guidelines for the treatment of skin and soft tissue infections (SSTIs). … A panel of national experts was convened by the Infectious Diseases Society of America (IDSA) to update the 2005 guidelines for the treatment of skin and soft tissue infections (SSTIs). The panel's recommendations were developed to be concordant with the recently published IDSA guidelines for the treatment of methicillin-resistant Staphylococcus aureus infections. The focus of this guideline is the diagnosis and appropriate treatment of diverse SSTIs ranging from minor superficial infections to life-threatening infections such as necrotizing fasciitis. In addition, because of an increasing number of immunocompromised hosts worldwide, the guideline addresses the wide array of SSTIs that occur in this population. These guidelines emphasize the importance of clinical skills in promptly diagnosing SSTIs, identifying the pathogen, and administering effective treatments in a timely fashion.

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Antibiotic Susceptibility Testing by a Standardized Single Disk Method

1966-04-01

Alfred W. Bauer , William Kirby , J. C. Sherris +1 more

Journal Article Antibiotic Susceptibility Testing by a Standardized Single Disk Method Get access A. W. Bauer, M.D., A. W. Bauer, M.D. Departments of Microbiology and Medicine, University of Washington, School … Journal Article Antibiotic Susceptibility Testing by a Standardized Single Disk Method Get access A. W. Bauer, M.D., A. W. Bauer, M.D. Departments of Microbiology and Medicine, University of Washington, School of Medicine, Seattle, Washington 98105 Search for other works by this author on: Oxford Academic Google Scholar W. M. M. Kirby, M.D., W. M. M. Kirby, M.D. Departments of Microbiology and Medicine, University of Washington, School of Medicine, Seattle, Washington 98105 Search for other works by this author on: Oxford Academic Google Scholar J. C. Sherris, M.D., J. C. Sherris, M.D. Departments of Microbiology and Medicine, University of Washington, School of Medicine, Seattle, Washington 98105 Search for other works by this author on: Oxford Academic Google Scholar M. Turck, M.D. M. Turck, M.D. Departments of Microbiology and Medicine, University of Washington, School of Medicine, Seattle, Washington 98105 Search for other works by this author on: Oxford Academic Google Scholar American Journal of Clinical Pathology, Volume 45, Issue 4_ts, April 1966, Pages 493–496, https://doi.org/10.1093/ajcp/45.4_ts.493 Published: 01 April 1966 Article history Received: 17 August 1965 Published: 01 April 1966

Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology.

2002-05-01

Erko Stackebrandt , Wilhelm Frederiksen , George M Garrity +7 more

An ad hoc committee for the re-evaluation of the species definition in bacteriology met in Gent, Belgium, in February 2002. The committee made various recommendations regarding the species definition in … An ad hoc committee for the re-evaluation of the species definition in bacteriology met in Gent, Belgium, in February 2002. The committee made various recommendations regarding the species definition in the light of developments in methodologies available to systematists.

Delaying the Empiric Treatment of Candida Bloodstream Infection until Positive Blood Culture Results Are Obtained: a Potential Risk Factor for Hospital Mortality

2005-08-26

Matthew R. Morrell , Victoria J. Fraser , Marin H. Kollef

Fungal bloodstream infections are associated with significant patient mortality and health care costs. Nevertheless, the relationship between a delay of the initial empiric antifungal treatment until blood culture results are … Fungal bloodstream infections are associated with significant patient mortality and health care costs. Nevertheless, the relationship between a delay of the initial empiric antifungal treatment until blood culture results are known and the clinical outcome is not well established. A retrospective cohort analysis with automated patient medical records and the pharmacy database at Barnes-Jewish Hospital was conducted. One hundred fifty-seven patients with a Candida bloodstream infection were identified over a 4-year period (January 2001 through December 2004). Fifty (31.8%) patients died during hospitalization. One hundred thirty-four patients had empiric antifungal treatment begun after the results of fungal cultures were known. From the time that the first blood sample for culture that was positive was drawn, 9 (5.7%) patients received antifungal treatment within 12 h, 10 (6.4%) patients received antifungal treatment between 12 and 24 h, 86 (54.8%) patients received antifungal treatment between 24 and 48 h, and 52 (33.1%) patients received antifungal treatment after 48 h. Multiple logistic regression analysis identified Acute Physiology and Chronic Health Evaluation II scores (one-point increments) (adjusted odds ratio [AOR], 1.24; 95% confidence interval [CI], 1.18 to 1.31; P < 0.001), prior antibiotic treatment (AOR, 4.05; 95% CI, 2.14 to 7.65; P = 0.028), and administration of antifungal treatment 12 h after having the first positive blood sample for culture (AOR, 2.09; 95% CI, 1.53 to 2.84; P = 0.018) as independent determinants of hospital mortality. Administration of empiric antifungal treatment 12 h after a positive blood sample for culture is drawn is common among patients with Candida bloodstream infections and is associated with greater hospital mortality. Delayed treatment of Candida bloodstream infections could be minimized by the development of more rapid diagnostic techniques for the identification of Candida bloodstream infections. Alternatively, increased use of empiric antifungal treatment in selected patients at high risk for fungal bloodstream infection could also reduce delays in treatment.

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Nosocomial Bloodstream Infections in United States Hospitals: A Three‐Year Analysis

1999-08-01

Michael B. Edmond , Stephanie E Wallace , Donna K. McClish +3 more

Nosocomial bloodstream infections are important causes of morbidity and mortality. In this study, concurrent surveillance for nosocomial bloodstream infections at 49 hospitals over a 3-year period detected >10,000 infections. Gram-positive … Nosocomial bloodstream infections are important causes of morbidity and mortality. In this study, concurrent surveillance for nosocomial bloodstream infections at 49 hospitals over a 3-year period detected >10,000 infections. Gram-positive organisms accounted for 64% of cases, gram-negative organisms accounted for 27%, and 8% were caused by fungi. The most common organisms were coagulase-negative staphylococci (32%), Staphylococcus aureus (16%), and enterococci (11%). Enterobacter, Serratia, coagulase-negative staphylococci, and Candida were more likely to cause infections in patients in critical care units. In patients with neutropenia, viridans streptococci were significantly more common. Coagulase-negative staphylococci were the most common pathogens on all clinical services except obstetrics, where Escherichia coli was most common. Methicillin resistance was detected in 29% of S. aureus isolates and 80% of coagulase-negative staphylococci. Vancomycin resistance in enterococci was species-dependent—3% of Enterococcus faecalis strains and 50% of Enterococcus faecium isolates displayed resistance. These data may allow clinicians to better target empirical therapy for hospital-acquired cases of bacteremia.

16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls

2007-07-12

J. Michael Janda , Sharon L. Abbott

The use of 16S rRNA gene sequences to study bacterial phylogeny and taxonomy has been by far the most common housekeeping genetic marker used for a number of reasons. These … The use of 16S rRNA gene sequences to study bacterial phylogeny and taxonomy has been by far the most common housekeeping genetic marker used for a number of reasons. These reasons include (i) its presence in almost all bacteria, often existing as a multigene family, or operons; (ii) the function of

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Manual of Clinical Microbiology.

1980-12-01

The 11th edition of the Manual of Clinical Microbiology continues to set the standard for state-of-the-science laboratory practices as the most authoritative reference in the field of clinical microbiology. This … The 11th edition of the Manual of Clinical Microbiology continues to set the standard for state-of-the-science laboratory practices as the most authoritative reference in the field of clinical microbiology. This new edition presents the numerous microbial taxonomic changes and newer more powerful diagnostic approaches that have been developed since publication of the 10th edition. A collaborative team of editors and authors from around the world, all experienced practitioners, researchers, or public health experts, revised the Manual to include the latest applications of genomics and proteomics, producing an authoritative work of two volumes filled with current findings regarding infectious agents, leading-edge diagnostic methods, laboratory practices, and safety guidelines.

Nosocomial Bloodstream Infections in US Hospitals: Analysis of 24,179 Cases from a Prospective Nationwide Surveillance Study

2004-07-22

Hilmar Wisplinghoff , Thomas Bischoff , Sandra M. Tallent +3 more

Nosocomial bloodstream infections (BSIs) are important causes of morbidity and mortality in the United States.Data from a nationwide, concurrent surveillance study (Surveillance and Control of Pathogens of Epidemiological Importance [SCOPE]) … Nosocomial bloodstream infections (BSIs) are important causes of morbidity and mortality in the United States.Data from a nationwide, concurrent surveillance study (Surveillance and Control of Pathogens of Epidemiological Importance [SCOPE]) were used to examine the secular trends in the epidemiology and microbiology of nosocomial BSIs.Our study detected 24,179 cases of nosocomial BSI in 49 US hospitals over a 7-year period from March 1995 through September 2002 (60 cases per 10,000 hospital admissions). Eighty-seven percent of BSIs were monomicrobial. Gram-positive organisms caused 65% of these BSIs, gram-negative organisms caused 25%, and fungi caused 9.5%. The crude mortality rate was 27%. The most-common organisms causing BSIs were coagulase-negative staphylococci (CoNS) (31% of isolates), Staphylococcus aureus (20%), enterococci (9%), and Candida species (9%). The mean interval between admission and infection was 13 days for infection with Escherichia coli, 16 days for S. aureus, 22 days for Candida species and Klebsiella species, 23 days for enterococci, and 26 days for Acinetobacter species. CoNS, Pseudomonas species, Enterobacter species, Serratia species, and Acinetobacter species were more likely to cause infections in patients in intensive care units (P<.001). In neutropenic patients, infections with Candida species, enterococci, and viridans group streptococci were significantly more common. The proportion of S. aureus isolates with methicillin resistance increased from 22% in 1995 to 57% in 2001 (P<.001, trend analysis). Vancomycin resistance was seen in 2% of Enterococcus faecalis isolates and in 60% of Enterococcus faecium isolates.In this study, one of the largest multicenter studies performed to date, we found that the proportion of nosocomial BSIs due to antibiotic-resistant organisms is increasing in US hospitals.

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Ongoing Revolution in Bacteriology: Routine Identification of Bacteria by Matrix‐Assisted Laser Desorption Ionization Time‐of‐Flight Mass Spectrometry

2009-07-07

Piseth Seng , Michel Drancourt , Frédérique Gouriet +4 more

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry accurately identifies both selected bacteria and bacteria in select clinical situations. It has not been evaluated for routine use in the clinic.We … Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry accurately identifies both selected bacteria and bacteria in select clinical situations. It has not been evaluated for routine use in the clinic.We prospectively analyzed routine MALDI-TOF mass spectrometry identification in parallel with conventional phenotypic identification of bacteria regardless of phylum or source of isolation. Discrepancies were resolved by 16S ribosomal RNA and rpoB gene sequence-based molecular identification. Colonies (4 spots per isolate directly deposited on the MALDI-TOF plate) were analyzed using an Autoflex II Bruker Daltonik mass spectrometer. Peptidic spectra were compared with the Bruker BioTyper database, version 2.0, and the identification score was noted. Delays and costs of identification were measured.Of 1660 bacterial isolates analyzed, 95.4% were correctly identified by MALDI-TOF mass spectrometry; 84.1% were identified at the species level, and 11.3% were identified at the genus level. In most cases, absence of identification (2.8% of isolates) and erroneous identification (1.7% of isolates) were due to improper database entries. Accurate MALDI-TOF mass spectrometry identification was significantly correlated with having 10 reference spectra in the database (P=.01). The mean time required for MALDI-TOF mass spectrometry identification of 1 isolate was 6 minutes for an estimated 22%-32% cost of current methods of identification.MALDI-TOF mass spectrometry is a cost-effective, accurate method for routine identification of bacterial isolates in <1 h using a database comprising > or =10 reference spectra per bacterial species and a 1.9 identification score (Brucker system). It may replace Gram staining and biochemical identification in the near future.

Methods for in vitro evaluating antimicrobial activity: A review

2015-12-02

Mounyr Balouiri , Moulay Sadiki , Saâd Ibnsouda Koraichi

In recent years, there has been a growing interest in researching and developing new antimicrobial agents from various sources to combat microbial resistance. Therefore, a greater attention has been paid … In recent years, there has been a growing interest in researching and developing new antimicrobial agents from various sources to combat microbial resistance. Therefore, a greater attention has been paid to antimicrobial activity screening and evaluating methods. Several bioassays such as disk-diffusion, well diffusion and broth or agar dilution are well known and commonly used, but others such as flow cytofluorometric and bioluminescent methods are not widely used because they require specified equipment and further evaluation for reproducibility and standardization, even if they can provide rapid results of the antimicrobial agent's effects and a better understanding of their impact on the viability and cell damage inflicted to the tested microorganism. In this review article, an exhaustive list of in vitro antimicrobial susceptibility testing methods and detailed information on their advantages and limitations are reported.

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Manual of methods for general bacteriology.

1981-01-01

Philipp Gerhardt , R. G. E. Murray

Bergey's Manual of Systematic Bacteriology

2005-01-01

K. Kersters , Marc Vancanneyt

Antibiotic sensitivity testing. Report of an international collaborative study.

1971-01-01

Hans Ericsson , J. C. Sherris

An inocula replicating apparatus for routine testing of bacterial susceptibility to antibiotics.

1959-05-01

Edward Steers , Elwood L. Foltz , Bianca Graves

Manual of Clinical Microbiology

2011-05-16

Clinical Microbiology Procedures Handbook

2010-08-01

Methods for antimicrobial dilution and disk susceptibility testing of infrequently isolated or fastidious bacteria; approved guideline

2006-01-01

James H. Jorgensen , Clinical

Gram-negative bacteremia

1980-03-01

Bernard E. Kreger , Donald E. Craven , William R. McCabe

Performance standards for antimicrobial susceptibility testing

2019-01-01

Melvin P. Weinstein , Clinical

Bergey’s Manual of Systematic Bacteriology

2010-01-01

Brown , Séverine Tasker , JB Messick +1 more

Bergey's Manual of Systematic Bacteriology

1989-09-01

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Manual of Clinical Microbiology

1991-08-01

Microbiology Laboratory Manual

1945-06-01

Marie E. Conklin , Ethel J. Odegard

Bergey's Manual of Determinative Bacteriology

1923-12-01

dren is given, also, instruction in the care of the sick infant.Part of this chapter is de- voted to poisons and their antidotes.In the back of the book are height … dren is given, also, instruction in the care of the sick infant.Part of this chapter is de- voted to poisons and their antidotes.In the back of the book are height and weight charts, also eventful dates and memorandum sheets.Most of the " Nursery Guide " would be very helpful to the mothers of young babies.However, a criticism might be made where stotnach washing and tube feeding is recommended.It would seem that this treatment is rather tech- nical for the lay person to attempt with safety.

Bergey's Manual of Determinative Bacteriology

1958-02-22

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor … Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal

Manual of Clinical Microbiology.

1970-09-01

Manual of Clinical Microbiology

1970-12-01

Jacob Blair , E H Lennette , J P Truant

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Rapid Multi-Omics for Bacterial Identification Using Flow Injection–Ion Mobility–Mass Spectrometry

2025-06-24

Hannah M. Hynds , Jana M. Carpenter , Kelly M. Hines | Analytical Chemistry

The implementation of mass spectrometry (MS) in clinical microbiology has made a significant improvement in the turnaround time from positive culture to identification, but current protein-based approaches can struggle with … The implementation of mass spectrometry (MS) in clinical microbiology has made a significant improvement in the turnaround time from positive culture to identification, but current protein-based approaches can struggle with species-level identification because of the high degree of homology within a genus. However, other MS-based strategies for bacterial identification that are based on lipids and small molecules have shown promise toward species-level identification and detection of specific phenotypes, including those related to antibiotic resistance. We are leveraging rapid gas-phase ion mobility (IM) separations coupled to MS to simultaneously detect the lipids and metabolites in bacterial pathogens. Using flow-injection (FI) rather than liquid chromatography (LC), we instead rely more directly on the structural separation of the IM dimension to resolve features from different biochemical classes and aid in identification. A head-to-head comparison demonstrates that the FI-IM-MS multiomic strategy performs similarly to LC-IM-MS in its ability to distinguish 24 strains of the high-concern ESKAPE pathogens, while shortening overall analysis time from 17 to 2 min per injection. We demonstrate that the IM dimension has excellent stability and reproducibility, which enables extracted IM peak areas to be used in lieu of chromatographic peak areas. Furthermore, the same features that are important for the discrimination of bacterial species and strains are found within both the FI-IM-MS and HILIC-IM-MS data sets. These results showcase the capabilities of mobility-enabled rapid multiomics and open the possibility to detect subtle strain-level differences and resistance phenotypes in bacterial pathogens by including additional classes of biomolecules.

Detection of pathogenic microorganisms using metagenomic next generation sequencing for patients with suspected infection presenting in the emergency department

2025-06-24

Tobias Schroeder , Mélissa Vanwynsberghe , Albion Dervishi +1 more | European Journal of Emergency Medicine

MicroBIS - An integrated AI laboratory Assistant for Bacteria and Antimicrobial Resistance Identification

2025-06-24

Hyun Seung Lim , Alexander Kwakye , Chul‐Sung Huh +1 more | Wellcome Open Research

<ns3:p>Antimicrobial Resistance (AMR) represents a major global health challenge, placing considerable strain on both clinical and public health systems—a burden projected to escalate without substantial intervention. Surveillance programs like the … <ns3:p>Antimicrobial Resistance (AMR) represents a major global health challenge, placing considerable strain on both clinical and public health systems—a burden projected to escalate without substantial intervention. Surveillance programs like the Pfizer Antimicrobial Testing Leadership and Surveillance (ATLAS) initiative play a critical role in addressing this challenge by providing valuable data to advance AMR research. In clinical settings, machine learning (ML)-based, data-driven tools have been proposed to aid bacterial identification and antibiotic prescription decision-making, aiming to minimize the human error inherent in these processes. In this work, we integrate the Pfizer-ATLAS dataset into MicroBIS, a novel ML-based platform for bacterial identification, and antibiotic susceptibility profiling. MicroBIS employs a Random Forest model trained on both simulated biochemical test results and real-world data obtained from Pfizer ATLAS program. Our results show that MicroBIS achieves a 79% accuracy rate in predicting bacterial species from 20-panel biochemical tests and a 31% accuracy from 8-panel biochemical tests. When identifying the top 5 bacterial species out of 133 candidates, MicroBIS achieved accuracies of 99% and 74% for the 20-panel and 8-panel biochemical tests, respectively. Additionally, MicroBIS predicted antimicrobial susceptibility profiles with an overall accuracy of 56% using the Pfizer ATLAS dataset. We developed MicroBIS as an integrated pipeline that combines bacterial identification with antibiotic susceptibility prediction, providing a clinically oriented platform that leverages simple laboratory inputs. MicroBIS offers significant potential to enhance clinical decision-making, bolster public health surveillance, and support AMR research efforts, especially in resource-limited settings.</ns3:p>

Bacterial microorganisms isolated in blood cultures of patients in a tertiary care hospital

2025-06-24

Álvaro J. Montiel‐Jarquín , Arturo García-Galicia , Brenda A. Olguin-Rincon +5 more | Anales Médicos de la Asociación Médica del Centro Médico ABC

Experience of use of dalbavancin for the treatment of unlicensed indications in a UK tertiary infectious diseases setting

2025-06-23

Christopher A Darlow , J. D. Parsons , Danielle C Lucy +4 more | Infection

Dalbavancin is a long-acting lipoglycopeptide with Gram-positive activity, licensed for the treatment of acute bacterial skin and skin-structure infections (ABSSSIs), although off-licence use is increasingly prevalent. We describe our experience … Dalbavancin is a long-acting lipoglycopeptide with Gram-positive activity, licensed for the treatment of acute bacterial skin and skin-structure infections (ABSSSIs), although off-licence use is increasingly prevalent. We describe our experience in Liverpool of using dalbavancin for off-licence indications and as a risk-reduction strategy in patients at risk of premature hospital discharge. Patients receiving dalbavancin in the period 1/9/2020-30/4/2024 in Liverpool were identified. Data was extracted by review of patient notes. Primary outcomes were clinical success (resolution of infection without re-admission or further antibiotics) and 90-day mortality. Ninety-five individual dalbavancin courses were identified. 24/95 were for licensed indications (i.e., ABSSSI without bacteraemia). Off-licence indications included bone and joint infections (BJIs) (30/95), infective endocarditis (IE) (13/95) and Staphylococcus aureus bacteraemia (SAB) (27/95). The clinical success rate and 90-day mortality for ABSSSI without bacteraemia were 91.67% and 4.17%, respectively. BJI without bacteraemia and SAB outcomes were similar (p > 0.999). However, IE had worse rates of clinical success (61.5%, p = 0.072) and 90-day mortality (30.8%, p = 0.042). 10/18 PWIDs who were prematurely discharged achieved clinical success; 17/18 were alive at 90 days. The data in this retrospective analysis adds to the growing body of evidence that dalbavancin is safe and effective for the treatment of BJIs and SABs. It also reinforces the uncertainty in the literature over the efficacy of use in IE. Additionally, these data demonstrate that dalbavancin may be used successfully as a risk mitigation strategy for PWIDs who may be prematurely discharged from an inpatient stay.

A Nationwide Survey on Standard Blood Culture Protocols and Quality Improvement for the Diagnosis of Sepsis

2025-06-23

Sae Am Song , Sunggyun Park , Kwang‐Sook Woo +3 more | Laboratory Medicine Online

Association between Charlson Comorbidity Index and positive blood cultures at a tertiary-care hospital in Indonesia

2025-06-23

Patricia M. Tauran , Mansyur Arif , Direk Limmathurotsakul +2 more | PLOS Global Public Health

Blood culture (BC) tests are a scarce resource in low- and middle-income countries (LMICs); therefore, prioritization based on likelihood of positive results might be beneficial. We aimed to determine whether … Blood culture (BC) tests are a scarce resource in low- and middle-income countries (LMICs); therefore, prioritization based on likelihood of positive results might be beneficial. We aimed to determine whether comorbidities in the Charlson Comorbidity Index (CCI) were associated with positive BC tests among patients with suspected hospital-acquired bacteremia. We analysed a retrospective cohort from health records at Dr. Wahidin Sudirohusodo Hospital, Makassar, Indonesia from 2015-2018. We applied multivariable logistic regression to identify associations between CCI score and the outcome of the first BC taken two calendar days after admission, adjusting for confounders. The primary analysis considered BCs positive for all pathogens. Of 3,875 adult patients who had their first BCs taken two calendar days after hospital admissions, 786 (20.3%) had their first BCs positive for any pathogen. Those included 371 patients who had their first BCs positive for Staphylococcus aureus (n = 133; 35.9%), Acinetobacter spp. (n = 84; 22.6%), Klebsiella. pneumoniae (n = 58; 15.6%), Escherichia coli (n = 63; 17.0%) and Pseudomonas aeruginosa (n = 33; 8.9%). There was no association between increasing CCI score and positive BC (OR 1.01, 95%CI: 0.96-1.06, p = 0.69) after adjustment for age, sex and other potential confounders. There was some indication that antibiotic use prior to BC test acted as an effect modifier between CCI score and positivity of BC (p = 0.17). In this single-hospital study, no significant association was observed between CCI score and positive BC taken two calendar days after hospital admission. We suggest that other factors need to be investigated to guide BC testing, and that improving diagnostic and antibiotic stewardship, including increasing resources for BC testing prior to antibiotics among hospitalized patients are needed in LMICs.

Biofilm formation and associated gene detection in Staphylococcus spp. isolated from urinary tract infection patients

2025-06-22

Sara Hadi Jassim , Zainab Rashaid Hameed , Ragad Hameed Khaleefa | International Journal of Health Sciences

Objectives: The study aimed to investigate the ability of Staphylococcus species isolated from urinary tract infection (UTI) patients to form biofilms, and to detect the presence of the biofilm regulatory … Objectives: The study aimed to investigate the ability of Staphylococcus species isolated from urinary tract infection (UTI) patients to form biofilms, and to detect the presence of the biofilm regulatory genes icaA and icaD. Methods: Urine samples were collected from 100 UTI-diagnosed patients at [Baladrouz Hospital] over six months under aseptic conditions. The collected specimens were inoculated onto Mannitol Salt Agar (MSA) and Blood Agar. Biofilm formation was evaluated using the crystal violet staining method. The presence of the icaR gene was detected by polymerase chain reaction (PCR) in Staphylococcus aureus isolates obtained from urine samples of patients with inflammatory conditions. Antimicrobial susceptibility was assessed by the disc diffusion method. Results: Different Staphylococcus species exhibited varying biofilm-forming capacities, with the highest observed in S. capitis and the lowest in S. lugdunensis. All tested S. aureus strains were positive for the icaR gene. Most isolates displayed broad-spectrum antibiotic resistance, particularly among coagulase-negative Staphylococci (CoNS). Conclusion: These findings highlight the role of biofilm formation in antibiotic resistance among Staphylococcus species, especially in CoNS. Understanding these mechanisms is crucial for developing effective treatment strategies for UTIs and reducing the incidence of persistent infections.

Comparative study of the microbiological activity of pazufloxacin, levofloxacin and moxifloxacin

2025-06-22

О. В. Кондратенко , R. R. Galieva | Meditsinskiy sovet = Medical Council

Introduction. Increasing antibiotic resistance is an important global problem. One of the most common classes of antibacterial drugs used in therapeutic practice are fluoroquinolones. Such drugs as levofloxacin, moxifloxacin, and … Introduction. Increasing antibiotic resistance is an important global problem. One of the most common classes of antibacterial drugs used in therapeutic practice are fluoroquinolones. Such drugs as levofloxacin, moxifloxacin, and pazufloxacin are the most promising for the treatment of a wide range of infections. Pazufloxacin has a good clinical effect in the treatment of infections resistant to other antibiotics. With respect to levofloxacin and moxifloxacin, there are criteria for determining sensitivity and significant experience in clinical and microbiological studies indicating their effectiveness, but with respect to pazufloxacin, there are few such studies and currently there are no criteria for interpreting the diameters of growth retardation zones and/or indicators of the values of the minimum suppressive concentration (MSC). Aim. To evaluate the distribution of the values of the minimum suppressive concentrations of drugs of the fluoroquinolone group: pazufloxacin, levofloxacin, moxifloxacin in relation to 200 clinical isolates of microorganisms. Materials and methods. We selected 200 bacterial strains isolated from patients from various regions of the Russian Federation. Among them are 20 strains of Pseudomonas aeruginosa , excluding MBL producers, 20 – Klebsiella pneumoniae , excluding MBL producers, 20 – Streptococcus pneumoniae , 20 – Enterococcus faecalis , 20 – Enterococcus faecium , 20 – Escherichia coli , excluding MBL producers, 20 – Proteus spp ., excluding MBL producers, 20 – Staphylococcus aureus , including MRSA, 20 – Haemophilus influenzae , 20 – Moraxella catarrhalis . Results and discussion. According to the data obtained, it was found that some of the studied strains have a high level of sensitivity to the drugs levofloxacin and moxifloxacin, and some, on the contrary, retain a high level of resistance. The criteria for evaluating the MSC of pazufloxacin in relation to the studied isolates have not been determined, but it is worth noting that most cultures have demonstrated an achievable value of MSC indicators. This suggests a high level of efficacy of the drug in clinical use. Conclusions. According to the results of the study, sensitivity to low values of pazufloxacin was revealed in relation to a number of cultures, in the absence of sensitivity to other drugs of the fluoroquinolone group, this also indicates the absence of crossresistance with drugs of this group.

Performance and workflow comparison of the VITEK MS PRIME and Bruker Biotyper MALDI-TOF MS systems

2025-06-20

Rachel E. Bosserman , Nicole J. Tarlton , Kelly Alvarado +2 more | Journal of Clinical Microbiology

ABSTRACT Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used for rapid identification of bacteria and yeast in clinical labs. The VITEK MS PRIME (“PRIME”) is the … ABSTRACT Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used for rapid identification of bacteria and yeast in clinical labs. The VITEK MS PRIME (“PRIME”) is the latest MALDI-TOF MS system from bioMérieux. This study evaluated PRIME’s performance and workflow timing against the MALDI Biotyper CA System by Bruker (“Biotyper”). We compared a collection of 154 bacteria and yeast clinical isolates from various specimen types using three methods: Biotyper target with a toothpick, PRIME target with the PICKME nib, and PRIME target with a loop. Positive blood culture isolates were also analyzed using these methods, with high-experience (HEU, n = 300) and low-experience users (LEU, n = 50) after short (6–8 h) and routine (18–24 h) incubation on agar plates. Workflow timing, from sample processing to organism identification, was assessed to identify time savings. PRIME identified 96% (PICKME) and 95% (Loop) of challenge isolates to genus level, compared with Biotyper at 99%. Short incubation of positive blood culture isolates demonstrated similar species-level identification rates across all methods (Biotyper: 84%, PRIME PICKME: 80%, PRIME Loop: 81%), although more repeats were needed compared with routine incubation. No difference in species identification occurred between users for any method at short incubation (89%–91%, HEU, vs 79%–85% LEU). Single-target process times were comparable for all methods (55–59 min), whereas PRIME methods had shorter hands-on times for analysis of multiple targets (Biotyper: 53 min, PRIME PICKME: 39 min, PRIME Loop: 40 min). These findings highlight the comparable performance of the PRIME and Biotyper systems while demonstrating the potential for time savings with PRIME workflows, particularly in high-throughput settings. IMPORTANCE This study provides a critical evaluation of the new VITEK MS PRIME MALDI-TOF MS system, comparing its performance and workflow efficiency against the Bruker MALDI Biotyper. The study investigates the success rate of isolate identification from short incubation of positive blood cultures, illustrating the utility of this technique for downstream workflows such as faster reporting of results for patient management and isolate identification for interpretation of rapid phenotypic AST. Analysis of different workflows demonstrated areas for potential time savings, particularly in high-throughput settings. These findings highlight the importance of optimizing MALDI-TOF MS workflows in the era of workforce shortages and lab centralization to enhance rapid pathogen identification and improve patient care.

Accurate zone of inhibition measurement for rapid antimicrobial susceptibility testing

2025-06-20

B. Esther Sunanda , D. R. Ramesh Babu | Biomedical Signal Processing and Control

Rapid identification of Carbapenem-Resistant bacteria by MALDI-TOF-MS via a specifically designed probe

2025-06-19

Jiarui Li , Hao Wang , Nan Zhao +3 more | Microchemical Journal

Hospital-onset bacteraemia and fungaemia as a novel automated surveillance indicator: results from four European university hospitals, 2018 to 2022

2025-06-19

Seven Johannes Sam Aghdassi , Suzanne D. van der Werff , Gaud Catho +7 more | Eurosurveillance

BACKGROUND Conventional manual surveillance of healthcare-associated infections is labour-intensive and therefore often restricted to areas with high-risk patients. Fully automated surveillance of hospital-onset bacteraemia and fungaemia (HOB) may facilitate hospital-wide … BACKGROUND Conventional manual surveillance of healthcare-associated infections is labour-intensive and therefore often restricted to areas with high-risk patients. Fully automated surveillance of hospital-onset bacteraemia and fungaemia (HOB) may facilitate hospital-wide surveillance. AIM To develop an algorithm and minimal dataset (MDS) required for automated surveillance of HOB and apply it to real-life routine data in four European hospitals METHODS Through consensus discussion, a HOB definition with MDS suitable for automated surveillance was developed and applied in a retrospective multicentre observational study including all adult patients admitted to hospitals in the Netherlands, Germany, Sweden and Switzerland (2018–22). Annual HOB rates were calculated per 1,000 patient days for hospital, intensive care unit (ICU) and non-ICU settings. RESULTS HOB was defined as a positive blood culture with a recognised pathogen 2 or more days after hospital admission. For common commensals, two blood cultures with the same commensal within 2 days were required. HOB rates were comparable between the four hospitals (1.0–2.2/1,000 patient days). HOB rates were substantially higher in ICU than non-ICU settings, and HOB with common commensals accounted for 14.8–28.2% of all HOB. HOB rates per 1,000 patient days were consistent over time, but higher in 2020–21. HOB caused by Staphylococcus aureus comprised 8.4–16.0% of all HOB. CONCLUSION Automated HOB surveillance using a common definition was feasible and reproducible across four European hospitals. Future studies should investigate clinical relevance and preventability of HOB, and focus on strategies to make the automated HOB metric an actionable infection control tool.

A European survey on anaerobes from paediatric blood cultures: a comparative analysis with adults

2025-06-19

Matteo Boattini , Arianna Aceti , Paulo Bastos +7 more | European Journal of Clinical Microbiology & Infectious Diseases

Empiric and targeted antibiotic therapy for bloodstream infections in internal medicine patients in Poland: a three-year analysis in a single centre using the AWaRe classification

2025-06-19

Piotr Piekiełko , Dariusz A Hareza , Ewa Stawowczyk +2 more | Pharmacological Reports

Bloodstream infection (BSI), defined as bacteraemia accompanied by sepsis or septic shock, is a frequent cause of hospitalization in departments of internal medicine (DIM). This study aimed to characterize the … Bloodstream infection (BSI), defined as bacteraemia accompanied by sepsis or septic shock, is a frequent cause of hospitalization in departments of internal medicine (DIM). This study aimed to characterize the epidemiology, microbiological profile, and antibiotic treatment patterns of BSIs in a DIM setting in 2021-2023 in Polish hospital. A three-year, single-centre retrospective analysis was conducted at a DIM in Southern Poland. Medical records from 2021 to 2023 were reviewed for patients diagnosed with sepsis (ICD-10 codes A40-A41) with microbiological confirmation. Antibiotic use was assessed using Days of Therapy (DOT) and Length of Therapy (LOT). Empiric and targeted therapies were classified according to the WHO AWaRe (Access, Watch, Reserve) framework. A total of 124 BSI cases were identified, with an incidence rate of 5.8%. Community-acquired BSIs accounted for 84.3% of cases, while 15.7% were hospital-acquired. The predominant pathogens were Escherichia coli and Staphylococcus aureus. The median LOT for empiric therapy was 3 days (IQR 2-4), with third-generation cephalosporins being the most frequently used agents (78 patients; 43.3%, 228 DOTs; 43.9%). Targeted therapy had a median LOT of 8 days (IQR 5-10), most commonly involving penicillins (33 patients; 28.4%, 291 DOTs; 34.5%). Access group antibiotics were significantly more prevalent in targeted therapy compared to empiric therapy (p < 0.001). Microbiological confirmation of BSI facilitates a safe de-escalation from broad-spectrum empiric antibiotics to narrow-spectrum targeted therapy, supporting antimicrobial stewardship in internal medicine settings.

Integrating Rapid Diagnostics, AI Technologies, and Omics Approaches for Sepsis Management and Antimicrobial Stewardship

2025-06-18

Kaneez Fatima , Hiba Haroon , Ifra Laraib +3 more | Journal of medical & health sciences review.

The most recent developments in microbiological diagnostics are highlighted in this review, with an emphasis on quick and precise techniques that are essential for treating critically sick patients who may … The most recent developments in microbiological diagnostics are highlighted in this review, with an emphasis on quick and precise techniques that are essential for treating critically sick patients who may have bacterial infections. Rapid, accurate diagnostic tools that go beyond conventional culture-based methods are desperately needed, especially in light of the growing problem of antibiotic resistance and the high morbidity and mortality linked to sepsis in intensive care units. Improved pathogen identification and resistance profiling are promised by emerging technologies such as sophisticated omics techniques, nucleic acid amplification, direct-from-blood testing, and quick antigen detection. Diagnostic speed and accuracy are being revolutionized by AI-enhanced techniques like SepsetER and the Sepsis ImmunoScore, as well as cutting-edge platforms like T2 magnetic resonance and nanopore sequencing. However, these techniques still depends on their incorporation into strong antimicrobial stewardship initiatives and validation through well planned clinical trials. The potential of these new technologies is rigorously evaluated in this review, along with the crucial actions needed to turn them into improved patient outcomes.

Performance of direct-from-blood-culture disk diffusion antibiotic susceptibility testing and its impact on antibiotic adjustment in bloodstream infections at a Malaysian tertiary center

2025-06-18

Chee Lan Lau , Ramliza Ramli , Petrick Periyasamy +7 more | Microbiology Spectrum

ABSTRACT Delayed antibiotics increase mortality in bloodstream infection (BSI). Direct-from-blood-culture disk diffusion antibiotic susceptibility testing (dAST) forecasts susceptibility earlier than conventional susceptibility testing (cAST). The study aimed to evaluate dAST … ABSTRACT Delayed antibiotics increase mortality in bloodstream infection (BSI). Direct-from-blood-culture disk diffusion antibiotic susceptibility testing (dAST) forecasts susceptibility earlier than conventional susceptibility testing (cAST). The study aimed to evaluate dAST performance and its impact on antibiotic adjustment in BSI. In this Malaysian single-center prospective study, dAST was performed and interpreted according to breakpoints by Clinical and Laboratory Standards Institute (CLSI) guidelines. The turnaround time (TAT), categorical agreements (CA), and predictive values of dAST for susceptibility by cAST were determined among positive blood cultures (PBC) between November 2022 and November 2023. The active and WHO AWaRe antibiotics administered before and after dAST results were compared. Of the 318 PBCs, the median of TAT was earlier than cAST by 35 hours. The CA for 3,561 organism-antibiotics combinations was 91.5%, with 3.6% very major errors (VME), 3.3% major errors (ME), and 5.2% minor errors (mE). The dAST achieved CA above 90% for Staphylococcus aureus with cefoxitin (98.5%), Pseudomonas aeruginosa with ceftazidime (100%), and Acinetobacter baumannii with ampicillin/sulbactam (100%). For Enterobacterales, most combinations were above 90%, including ampicillin (95.1%), ceftriaxone (95.7%), and meropenem (95.7%), though those of the aminopenicillin/inhibitor combinations were above 80%. Most errors were attributed to mEs. Among 159 BSI, the prescribing of active antibiotics improved significantly following dAST (73.0% versus 89.3%, P < 0.001) but not WHO Access antibiotics (35.8% versus 35.2%, P = 0.188). dAST had good CAs for most antibiotics, allowing earlier improvement in active antibiotics. The modest change in WHO Access antibiotics prescribing reveals practice gaps in need of antimicrobial stewardship. IMPORTANCE Global deaths attributable to antimicrobial resistance are rising. Hence, rapid susceptibility testing is essential for timely antibiotic de-escalation to mitigate antimicrobial resistance (AMR) development from exposure to broad-spectrum antibiotics. Compared to the costly advanced technology, direct disk diffusion from blood culture (diffusion antibiotic susceptibility testing [dAST]) is an affordable method that can be quickly adopted. However, the reliability of dAST in informing susceptibility was mainly reported from Western countries and scarcely from other regions, including Southeast Asia, where the AMR burden is high. This study from Malaysia adds insights into the performance of dAST and the potential to apply it in similar resource-limited settings from the same region. Furthermore, assessing the dAST's influence on antibiotic prescribing identifies the gap in implementation to guide areas of improvement for optimizing clinical utility.

Direct Identification of IMP and VIM Metallo‐β‐Lactamases in Gram‐Negative Bacteria Using A‐MALDI

2025-06-17

Dong Huey Cheon , Seohyun Hwang , Yoon Kyung Choi +6 more | Rapid Communications in Mass Spectrometry

ABSTRACT Rationale Rapid and accurate identification of carbapenemase‐producing Enterobacteriaceae (CPE) is crucial for effective infection control and patient treatment. However, accurate identification of VIM and IMP metallo‐β‐lactamases remains still challenging … ABSTRACT Rationale Rapid and accurate identification of carbapenemase‐producing Enterobacteriaceae (CPE) is crucial for effective infection control and patient treatment. However, accurate identification of VIM and IMP metallo‐β‐lactamases remains still challenging using MALDI‐TOF MS. Methods The A‐MALDI method which incorporates sequential lysis steps and internal mass calibration, was used for the identification of IMP and VIM carbapenemases. Two Escherichia coli standard strains and 26 clinical isolates harboring IMP or VIM genes were tested by A‐MALDI along with corresponding negative controls. Previously published carbapenemases‐negative data ( n = 112) were used to check the specificity of IMP and VIM identification. Results For IMP‐positive isolates, proteoforms corresponding to amino acid residues 20–246 showed distinct peaks for IMP. For VIM‐positive isolates, unique single peaks corresponding to amino acid residues 27–266 allowed clear identification of VIM. Clinical evaluation of A‐MALDI demonstrated 93.9% accuracy for IMP identification (100% sensitivity, 93.3% specificity) and 100% accuracy for VIM identification. Conclusions This study successfully expands the direct identification capabilities for VIM and IMP, achieving comprehensive identification of all six carbapenemases using A‐MALDI. We anticipate that A‐MALDI will provide clinical laboratories with a powerful tool for rapid identification of all types of carbapenemases in bacterial infections.

Reducing Blood Culture Contamination Rates Below 1%

2025-06-17

Samantha Biddle , Jo Whitis | Clinical Nurse Specialist

The American Society for Microbiology’s evidence-based laboratory medicine practice guidelines for the diagnosis of bloodstream infections using rapid tests: a systematic review and meta-analysis

2025-06-16

Donna M. Wolk , J. Scott Parrott , N. Esther Babady +7 more | Clinical Microbiology Reviews

SUMMARY Bloodstream infections (BSIs) are a significant cause of mortality and morbidity. Rapid identification of pathogens and detection of a few resistance markers from positive blood cultures are now possible … SUMMARY Bloodstream infections (BSIs) are a significant cause of mortality and morbidity. Rapid identification of pathogens and detection of a few resistance markers from positive blood cultures are now possible through the increased availability of commercial rapid diagnostic tests, including nucleic acid amplification tests and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. This document describes the clinical utility of rapid diagnostics performed on positive blood cultures and provides evidence-based laboratory medicine guidelines for using rapid tests to diagnose BSIs in hospitalized adult and pediatric patients. This guideline was developed for use by medical (a.k.a. clinical) microbiologists, medical laboratory professionals, infectious disease clinicians, pharmacists, hospital administrators, healthcare providers, and other stakeholders associated with BSIs. A panel of experts, including medical microbiologists and experts in systematic literature review, was assembled to formulate the Population–Intervention–Comparison–Outcome (PICO) question, review the literature, and provide recommendations for using rapid tests to diagnose BSI and improve patient outcomes. A comprehensive literature search of four electronic bibliographic databases (MEDLINE, Embase, CINAHL, and Cochrane) was conducted to identify studies with measurable outcomes. The panel followed a systematic process, which included a standardized methodology for rating the certainty of the evidence and strength of recommendations using the GRADE (Grading of Recommendations, Assessment, Development, and Evaluation) approach. The panel evaluated the literature to answer the question: Does using rapid diagnostic tests improve clinical outcomes in adult and pediatric patients hospitalized with a BSI? Peer-reviewed literature was available to address three outcomes, including time to targeted therapy, mortality, and length of hospital stay. In general, the quality of the evidence was low to moderate due to the paucity of controlled, randomized clinical trial studies. However, eight recommendations were made based on evidence derived from the systematic review of the published literature. To answer the PICO question, the expert committee recommended using rapid diagnostic tests combined with active communication to decrease the time to targeted therapy and length of stay (strong recommendation). While the strength of the evidence for the impact on mortality is low, the panel supports using rapid tests to impact these outcomes. A summary of the recommendations is listed in the Executive Summary, which includes a detailed description of the background, methods, evidence summary, and rationale that supports each recommendation in the full text.

A Retrospective Study on the Prevalence and Antimicrobial Susceptibility of Gram-Positive Cocci in a Pediatric Department: A Single-Center Report from Egypt

2025-06-14

Mona Moheyeldin AbdelHalim , Shimaa Abdel Salam , Marwa O. Elgendy +4 more | Medicina

Background and Objectives: The rising prevalence of drug-resistant organisms presents a significant challenge to healthcare, underscoring the importance of implementing effective antimicrobial stewardship programs. The success of these programs depends … Background and Objectives: The rising prevalence of drug-resistant organisms presents a significant challenge to healthcare, underscoring the importance of implementing effective antimicrobial stewardship programs. The success of these programs depends on access to accurate, evidence-based data reflecting local patterns of antibiotic resistance. This study aims to assess the antimicrobial susceptibility profiles of gram-positive bacteria isolated from pediatric patients in a tertiary care hospital in Egypt. Materials and Methods: We carried out a retrospective study over a five-year period, from January 2018 to December 2022, using microbiology laboratory records. Clinical samples included blood, urine, respiratory secretions, pus, wound, cerebrospinal fluid (CSF), and pleural fluid. The analysis focused on the resistance patterns of gram-positive pathogens identified through routine culture procedures. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disc diffusion method, and vancomycin MIC was confirmed using the VITEK 2 system. Results: A total of 3223 gram-positive bacterial isolates were identified. Staphylococcus aureus, including 82.5% methicillin-resistant strains (MRSA), exhibited high resistance to erythromycin (47.3%) and gentamicin (low potency) (32.1%). Coagulase-negative staphylococci (CoNS) showed the highest erythromycin resistance (up to 88.3%), while Enterococcus spp. demonstrated declining susceptibility to vancomycin, levofloxacin, and erythromycin. Across all isolates, vancomycin and gentamicin (high potency) showed the highest overall susceptibility. Resistance to cotrimoxazole and doxycycline declined over the five-year period. Conclusions: While a decline in resistance was noted for some agents, persistent resistance to key antibiotics (particularly erythromycin and gentamicin) among MRSA and CoNS remains concerning. These findings underscore the importance of targeted antimicrobial stewardship interventions and continuous surveillance to inform empirical therapy in pediatric settings.

Pediatric Blood Culture Contamination Rates and Risk Factors in a Large Integrated Health System

2025-06-13

Kelsey Childress , Michael Hartmann , Gizely Teixeira Fernandes +3 more | Hospital Pediatrics

INTRODUCTION Contaminated blood cultures result in unnecessary use and antibiotic exposure. US studies have found contamination rates of 0.6 to 6; however, the rates and risk factors of blood culture … INTRODUCTION Contaminated blood cultures result in unnecessary use and antibiotic exposure. US studies have found contamination rates of 0.6 to 6; however, the rates and risk factors of blood culture contamination (BCC) across age groups in children are not well understood. OBJECTIVE The objective of this study was to calculate rates of BCC by pediatric age groups and identify risk factors for BCC. METHODS This was a retrospective cohort study of 89 948 blood cultures obtained from 2014 to 2022 in outpatient and hospital settings within a multicenter health care system. Cultures with commensal organisms were considered contaminated after excluding patients with immunodeficiencies, history of malignancy, and indwelling catheters. Multivariable logistic regression models estimated odds ratios (OR) and 95% CIs for the association of risk factors and odds of BCC. RESULTS Among 89 948 total blood cultures, 1594 (1.8%) were identified as likely contaminants. The BCC rate was greatest in infants: 2.0% in the 0- to 28-day-old age group, 5.4% in 29- to 90-day-old age group, and 2.7% in the 90-day- to 1-year age group. Emergency department (ED) nurses had the highest odds of contamination compared with phlebotomists (OR = 2.79, 95% CI: 2.47–3.15). Inpatient nurses had lower odds of contamination compared with phlebotomists for newborns aged 0 to 28 days (OR = 0.36, 95% CI: 0.28–0.46) but had higher odds for patients aged older than 1 year. Inpatient nurses had the highest odds compared with phlebotomists for patients aged 5 to 12 years (OR = 6.90, 95% CI: 4.08–11.75). CONCLUSIONS Younger patient age and ED nurse blood cultures had greater odds of contamination. Results can inform focused training on quality collection and testing techniques, as well as the creation of enhanced staffing models to increase phlebotomist collections.

Evaluating rapid antimicrobial susceptibility testing directly from positive blood cultures for Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa in Chinese hospitals

2025-06-13

Zhu Mei , Xinlu Bai , Dongmei Huang +2 more | Laboratory Medicine

Abstract Introduction We sought to assess whether rapid antimicrobial susceptibility testing (AST) directly from positive blood culture bottles for Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa can be used in … Abstract Introduction We sought to assess whether rapid antimicrobial susceptibility testing (AST) directly from positive blood culture bottles for Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa can be used in Chinese hospitals. Methods Rapid AST was performed on each positive blood culture bottle. Categorical rapid AST results at 8 to 10 and 16 to 18 hours were compared with those from the VITEK 2 system (bioMérieux). Minimum inhibitory concentrations and zone diameter were interpreted according to Clinical and Laboratory Standards Institute (CLSI) standard M100-S34, published in 2024. Results At 8 to 10 hours, the overall categorical agreement for E coli, K pneumoniae, and P aeruginosa was 99.1%, 98.4%, and 95.8%, respectively. At 16 to 18 hours, these rates were 97.4%, 98.9%, and 99.1%, respectively. For E coli, the categorical agreement ranged from 97.2% (ceftazidime at 8-10 hours) to 100% (ampicillin and meropenem at 8-10 and 16-18 hours and ciprofloxacin at 16-18 hours). The categorical agreement for K pneumoniae varied from 96.5%with ceftazidime at 8 to 10 hours to 100% with meropenem and ciprofloxacin at 16 to 18 hours. For P aeruginosa, the categorical agreement ranged from 93.7% (meropenem at 8-10 hours) to 100% (ciprofloxacin at 16-18 hours). Discussion The CLSI rapid AST method is reliable for E coli, K pneumoniae, and P aeruginosa in Chinese hospitals.

Evaluation of the I-dOne System for Rapid Bacterial Identification: A Diagnostic Accuracy Study

2025-06-12

Felipe Francisco Tuon , Paula Hansen Suss , Gabriel Burato Orthis +1 more | Diagnostic Microbiology and Infectious Disease

Limitations of MALDI-TOF MS in identifying anaerobic bacteremia: challenges in polymicrobial infections and the role of whole-genome sequencing

2025-06-12

Takuya Hosoda , Masahiro Suzuki , Takahiro Matsuno +3 more | Microbiology Spectrum

ABSTRACT With the widespread use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), the number of identifiable bacterial species has increased. However, anaerobic bacteremia remains challenging to accurately … ABSTRACT With the widespread use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), the number of identifiable bacterial species has increased. However, anaerobic bacteremia remains challenging to accurately diagnose due to the diverse range of anaerobic bacteria and the frequent occurrence of polymicrobial infections. Consequently, MALDI-TOF MS often fails to achieve accurate species-level identification in such cases. To address this limitation, we evaluated whole-genome sequencing (WGS) as an alternative method for identifying anaerobic bacteria in blood cultures. Over a 4-year period (April 2020 to March 2024), 69 cases of anaerobic bacteremia were identified, involving 85 bacterial strains. WGS successfully identified 73 strains (89%) at the species level. MALDI-TOF MS accurately identified 43 strains (59%) at the species level and 6 strains (8.2%) at the genus level. Among the 24 discordant strains, 9 species were not included in the database, and 6 species had limited prior reports of bloodstream infections. Additionally, 21 of the 69 cases (30%) were polymicrobial, and WGS revealed 9 cases (13%) in which multiple species had not been identified by MALDI-TOF MS. These results highlight the limitations of MALDI-TOF MS in anaerobic bacterial identification, particularly in polymicrobial infections, and suggest that alternative molecular approaches are necessary to improve diagnostic accuracy. IMPORTANCE Accurate identification of anaerobic bacteria remains a significant challenge despite the widespread use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry. While this technology has improved the detection of many bacterial species, some anaerobes remain unidentified due to their absence from reference databases and the difficulties associated with their isolation, particularly in polymicrobial infections. Whole-genome sequencing (WGS) has revealed previously unreported anaerobes and identified polymicrobial infections that were initially misclassified as monomicrobial. Our findings underscore the importance of implementing molecular approaches such as WGS- or PCR-based methods in clinical diagnostics to improve the detection of anaerobic pathogens.

Evaluation of the identification performance of MALDI-TOF MS Smart MS 5020 from Zhuhai DL Biotech

2025-06-12

Blanca Carrasco , Elena Hidalgo , Ángela Iniesta +1 more | Microbiology Spectrum

ABSTRACT Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a reliable technique, is rapid and precise in the identification of pathogens, and is essential in clinical microbiology laboratories. … ABSTRACT Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a reliable technique, is rapid and precise in the identification of pathogens, and is essential in clinical microbiology laboratories. The aim of this project is to evaluate the identification performance of the MALDI-TOF MS Smart MS 5020 system (Zhuhai DL Biotech) by comparing the identification results with those of the MALDI-TOF MS Biotyper Microflex LT system (Bruker Daltonics). A total of 612 clinical isolates were analyzed in parallel: 494 routine species and 118 species not commonly isolated in routine practice, previously isolated and frozen in our hospital’s strain collection. This collection included gram-negative bacteria, gram-positive bacteria, anaerobes, and fungi. Concordance at genus and species level identification was evaluated, and 16S rRNA gene sequencing was performed for strains unidentified or with discordant results. Both systems, Smart MS 5020 and Biotyper Microflex LT, achieved high identification rates (100% and 98.9%, respectively). The concordance between the systems was 98.9% at the genus level and 97.2% at the species level. Correct species-level identification was 96.9% for the Smart MS 5020 and 96.6% for the Biotyper Microflex LT. The MALDI-TOF MS Smart MS 5020 and Biotyper Microflex LT systems offer high efficacy in identifying a wide variety of clinical isolates, both demonstrating excellent performance. IMPORTANCE Accurate identification of microorganisms in clinical microbiology laboratories is essential for the effective diagnosis and treatment of patients. This study evaluates the performance of the Smart MS 5020 matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) system in comparison to the widely used Biotyper Microflex LT system. As a new entrant to the market, independent validation of the Smart MS 5020 system is crucial for laboratories considering its implementation. By analyzing 612 clinical isolates, including both routine and rare species, this study provides valuable data on the concordance rates between the two systems. The results confirm the Smart MS 5020 high accuracy and reinforce the reliability of MALDI-TOF MS technology. The high concordance rate between the two systems establishes the Smart MS 5020 as a promising, cost-effective alternative for routine diagnostics. These results expand the evidence base on MALDI-TOF MS platforms and can inform procurement decisions in clinical laboratories worldwide.

Evaluating the cost-effectiveness of rapid diagnostic testing for the identification of pathogens and resistance genes in bloodstream infections

2025-06-12

James Karichu , M. Ross Pennington , Xue Bao +3 more | medRxiv (Cold Spring Harbor Laboratory)

Abstract Objectives Bloodstream infections (BSI) are a leading cause of mortality worldwide. Rapid detection of the causative pathogen can help optimise therapy, reduce mortality, curb antimicrobial resistance, and lower healthcare … Abstract Objectives Bloodstream infections (BSI) are a leading cause of mortality worldwide. Rapid detection of the causative pathogen can help optimise therapy, reduce mortality, curb antimicrobial resistance, and lower healthcare costs. This study evaluates the cost-effectiveness of adding molecular rapid diagnostic tests (mRDTs) to microbiology standard-of-care (SoC) methods. mRDTs evaluated include the Cobas ® Eplex blood culture identification (BCID) panels, BioFire ® BCID panel, BioFire ® BCID2 panel, Accelerate PhenoTest ™ blood culture (BC) kit and Diasorin Verigene ® BCID panels. Methods A decision-tree model was built to quantify the incremental costs and outcomes associated with adding mRDTs to the SoC. The inputs were derived from the published literature. The analysis considered a population aged 65 years and 45% female, admitted to a United States (US) hospital with a suspected BSI. Model outcomes included costs, 30-day mortality, quality-adjusted life years (QALYs) and adverse events ( Clostridioides difficile infection and acute kidney injury [AKI]). A United Kingdom (UK) setting in place of the US setting was also considered in the scenario analysis. Results A strategy involving the Cobas Eplex BCID panels as an adjunct test to the SoC dominated SoC alone without Cobas Eplex BCID panels, saving $164 per patient and averting 24 deaths per 10,000 patients. Earlier optimisation of ineffective empiric therapy generated half of the lives saved, with the majority of the remainder from reductions in AKI. This strategy was also dominant compared with other mRDTs. In a UK setting, Cobas Eplex BCID panels remained cost-effective, saving £51 compared with SoC. Results were robust to scenarios varying key model inputs including time to pathogen identification with SoC. Conclusions The model demonstrated improved patient survival and reduced average total costs with mRDT. The Cobas Eplex BCID panels, which has the largest pathogen coverage, reduced both mortality and overall costs compared with other mRDTs. Key points for decision makers Rapid identification of BSI pathogens enables early optimisation of antimicrobial therapy, which can improve patient outcomes, reduce healthcare costs, and mitigate antimicrobial resistance. Conventional methods, including culture followed by MALDI-ToF MS, are time intensive. In contrast, mRDTs can identify pathogens within hours, facilitating earlier treatment optimisation. Evidence on the cost-effectiveness of mRDTs is limited, despite their potential to reduce overall costs by reducing length of stay (LOS). This study provides a comprehensive assessment of the cost-effectiveness of adding mRDTs to SoC. Cost savings from reductions in LOS and adverse events arising from broad-spectrum antimicrobial therapy are more than sufficient to offset the cost of procuring the mRDTs. Hence the use of mRDTs improves patient outcomes and contributes to antibiotic stewardship, alongside lowering costs. The Cobas Eplex BCID panels, with broadest coverage of pathogens, dominated other mRDTs. Plain Language Summary Bloodstream infections (BSI) are responsible for significant morbidity and mortality, causing 250,000 deaths each year in Europe and the United States (US) [1]. Rapid treatment with an effective antimicrobial is potentially one of the most important elements of care for patients with BSI, and patients are typically treated with two broad-spectrum antimicrobials rapidly (within an hour) if BSI is suspected. Conventional methods to identify the cause of the BSI require culturation of blood culture bottles followed by Gram stain and sub-culture onto solid agar plates to isolate individual colonies. Molecular rapid diagnostic tests (mRDTs) allow detection of a range of different pathogens causing BSIs within a few hours of a blood culture bottle flagging positive [2]. These tests offer the potential to improve care by reducing time to appropriate therapy which in turn can save lives and lower costs. This analysis used a decision-tree model to evaluate the costs and benefits of adding mRDTs to conventional methods. The study finds that mRDTs save lives and generate lower overall costs compared with standard of care (SoC) methods alone. Among the mRDTs, the Cobas ® Eplex BCID panels, which detect the broadest spectrum of pathogens, were associated with the highest reduction in mortality and overall costs compared with other mRDTs. Declarations I. Funding COBAS and EPLEX are trademarks of Roche. All other product names and trademarks are the property of their respective owners. Financial support for this research analysis was provided by GenMark Diagnostics (A member of the Roche Group) to Source Health Economics—content experts (MP, XB, KL), and medical writing support was provided by Dr. Dom Partridge of Source Health Economics. II. Conflicts of Interest JKK and AT are employees of Roche Molecular Systems (RMS). JKK and AT hold Roche stock options. TS is an employee of Roche Diagnostics Corporation (RDC). III. Availability of data and material The analysis used secondary data sources which are publicly available. No primary individual patient data was collected or used. IV. Ethics approval The analysis used secondary data sources. No individual patient data was collected or used. Consequently, ethical approval for the study was not required. V. Consent to participate No individual patient data was collected or used, and hence consent was not required. VI. Code availability The economic model is considered commercially sensitive and we are unable to provide access to it. VII. Author contributions JKK and AT conceived the study. MP, JKK, AT and KL designed the study. MP, JKK, AT, TS and XB compiled the data. MP, JKK, AT, TS, KL and XB reviewed the results. MP drafted the manuscript. MP, JKK, AT, TS, KL and XB reviewed the manuscript.

Pre-analytical delay of blood cultures which hinders the management of sepsis and fosters the emergence of antimicrobial resistance is an adverse effect of laboratory centralisation.

2025-06-11

M Noone | medRxiv (Cold Spring Harbor Laboratory)

Abstract Background The clinical diagnosis of sepsis is based on non-specific criteria and blood culture remains the gold standard confirmatory test. While early results are of wide clinical benefit delayed … Abstract Background The clinical diagnosis of sepsis is based on non-specific criteria and blood culture remains the gold standard confirmatory test. While early results are of wide clinical benefit delayed reports lead to prolonged anti-microbial therapy which fosters the emergence of antimicrobial resistance. Pre-analytical delay of a blood culture delays or decreases the chance of a positive report and a maximal four-hour delay between collection and incubation of the specimen is recommended by the United Kingdom Standards for Microbiology Investigations (UK SMI). This retrospective observational study documents compliance with this quality standard by National Health Service (NHS) hospitals across England. An appraisal is undertaken of the policies which governed laboratory centralisation and their impact on the microbiology service. Methods Freedom of Information (FOI) applications were submitted to 116 NHS Trusts in England requesting retrospective audit data showing compliance with the recommended pre-analytical standard for blood cultures. Information relating to the configuration of microbiology services and global laboratory costs were also requested. Results Reports were received from 89 Trusts (76.7%) comprising 146 acute hospitals. Only four hospitals (2.7%) showed full compliance with the four-hour pre-analytical standard. Service configurations varied widely. The anticipated savings resulting from centralisation have not been realised. Conclusions There was poor compliance with the quality standard for pre-analytical delay of blood cultures. Evidence is presented to show that the poor compliance rates reported are a result of the approach taken and the guiding policies applied when laboratory centralisation was imposed by NHS England. Reversal of these adverse effects will require mandatory implementation of UK SMIs and computing the cost of quality measures in the context of the overall health care benefit to the patient.

Diagnostic Stewardship in Antimicrobial Stewardship

2025-06-11

Crisel Margaret Machuca | Pediatric Infectious Disease Society of the Philippines Journal

On a global scale, infec/ons are a leading contributor to morbidity and mortality. Use of diagnos/c tests for pa/ents with suspected infec/ons are known to improve pa/ent care. Hence, there … On a global scale, infec/ons are a leading contributor to morbidity and mortality. Use of diagnos/c tests for pa/ents with suspected infec/ons are known to improve pa/ent care. Hence, there has been an increasing use of acute phase reactants (APRs) to guide treatment of infec/ons since the presence of these markers signify injury and inflamma/on.1 According to Zakhour et al there has been an overuse of diagnos/c tests, par/cularly in pa/ents who are cri/cally ill or immunocompromised.2 The overuse of tests applies even to mild infec/ons where unnecessary tes/ng lead to inappropriate treatment for colonizers iden/fied through culture. Diagnos/c stewardship plays a key role to help physicians request the right tests for the right pa/ent at the right /me. This involves providing coordinated guidance and interven/ons to ensure that tests especially cultures, are used appropriately and promptly to produce clinically relevant results. This guides medical decisions, while also conserving healthcare resources. Diagnos/c stewardship therefore serves as a complement to An/microbial Stewardship (AMS).3 The objec/ve of this review is to look into Diagnos/c Stewardship as a component of An/microbial Stewardship. The discussion will focus on the use of inflammatory markers including erythrocyte sedimenta/on rate (ESR), C-Reac/ve Protein (CRP), and procalcitonin. The role of blood culture and a PCR based pneumonia panel in will also be examined.

Evaluation of EUCAST rapid antibiotic susceptibility testing for positive blood cultures in the Autobio BC60 blood culture system

2025-06-04

Serap Süzük Yıldız , Esra Tavukcu , Mert Emre Ölmez +6 more | Diagnostic Microbiology and Infectious Disease

Bacteremia detected on peripheral blood smear in small animal patients presenting to the Emergency Department and its association with prognosis to discharge

2025-06-04

Sally E. Ford , Megan Whelan , Patty J. Ewing +1 more | Frontiers in Veterinary Science

Objective Detection of bacteremia on peripheral blood smear (PBS) is rare and may be a poor prognostic indicator for small animal patients. This study aimed to determine the relationship between … Objective Detection of bacteremia on peripheral blood smear (PBS) is rare and may be a poor prognostic indicator for small animal patients. This study aimed to determine the relationship between bacteremia on PBS and survival to discharge in clinically ill patients presenting through the Emergency Department (ED). Methods This retrospective study analyzed data from two veterinary tertiary care facilities from 2014 to 2024. Records from 16 client-owned animals presenting to the ED with PBS-detected bacteremia were reviewed. The primary outcome was survival to discharge. Secondary outcomes evaluated associations between survival in these patients with glucose level, leukocyte count, toxic change, band neutrophils, total bilirubin, blood pressure, and antibiotic use. Statistical comparisons between categorical data were made using Fisher’s exact test. A p -value of &lt;0.05 was considered significant. Results In-hospital mortality of the 16 patients was 75% (12/16). Hyperglycemia was positively associated with survival ( p = 0.0099). All survivors were cats. No other parameters showed statistical significance between survivors and non-survivors. Conclusion PBS-detected bacteremia in clinically ill small animals was associated with a high in-hospital mortality in this study. Further investigation is warranted to better understand its clinical relevance and potential diagnostic utility.

Evaluation of antimicrobial adsorption capacity in blood culture medium

2025-06-03

Ning Mao , Li Ma , Ying Ren +7 more | Research Square (Research Square)

<title>Abstract</title> <bold>Objective:</bold>To evaluate the adsorption capacity of Merieux BacT/ALERT (FA Plus and FN Plus) bottles and HAPYEAR (aerobic and anaerobic) bottles for antimicrobial agents. <bold>Method</bold>: In simulated adult blood cultures, … <title>Abstract</title> <bold>Objective:</bold>To evaluate the adsorption capacity of Merieux BacT/ALERT (FA Plus and FN Plus) bottles and HAPYEAR (aerobic and anaerobic) bottles for antimicrobial agents. <bold>Method</bold>: In simulated adult blood cultures, microbial-antimicrobial combinations were added to compare the inactivation capacity of commercial blood culture medium. The antibiotics used were imipenem, cefoxitin, vancomycin, cefoperazone/sulbactam, piperacillin/tazobactam, penicillin and micafungine. <bold>Result:</bold> The Merieux blood culture vial (bacteria + antibiotics) experimental group was all positive and had adsorption capacity for the antibiotics used in the experiment.However, the HAPYEAR results were partially positive, which only had adsorption capacity for piperacillin/tazobactam and micafungine, and had no adsorption capacity for most other antibiotics. In terms of the time to report positive results, the Merieux blood culture vial group (bacteria + antibiotics) was reported earlier. Among them, the average time of Merieux blood culture vial in the (Pseudomonas aeruginosa + piperacillin/Tazobactam) group was 8.4 hours earlier than that in the HAPYEAR group. The average time of the Merieux blood culture vial in the (Candida albicans + Micafunzin) group was 64.8 hours earlier than that in the HAPYEAR group. <bold>Conclusion: </bold>BacT/ALERT (FA Plus and FN Plus) culture medium have a relative advantage, but not an absolute advantage. Its detection rate is high, TAT is short, it can be selectively applied to patients who have used antibiotics in the past, and then take the blood culture samples.