bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomy Updates for Anaerobes
Authors: Shannon Samantha K. , Pence Morgan A. 
Published: January 2025

Abstract
The International Committee on Systematics of Prokaryotes (ICSP) and the International Code of Nomenclature of Bacteria (ICNB) are responsible for the naming of prokaryotes, including anaerobes. ICSP and ICNB maintain a strict set of rules for naming and renaming bacteria. Not all proposed taxonomic changes that are published are in compliance with the ICNB. Thus, it is imperative to consult reliable sources to prevent adoption of invalid taxonomy. Taxonomic changes are frequently proposed by evolutionary microbiologists, and new taxonomic name proposals may have detrimental effects for clinical laboratories and hospitals. The Clinical and Laboratory Standards Institute is currently developing a document to address taxonomy changes and guidance for updating organism names for laboratory reporting. Microbiology laboratory leadership should discuss taxonomy changes with infectious diseases and other key clinician groups to determine if changes should be incorporated into laboratory reporting.
Introduction
Authors: McElvania Erin 
Published: January 2025

Abstract
There has been a revolution in the way clinical microbiology laboratories identify microorganisms with the advent of matrix‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI‐TOFMS). MALDI‐TOFMS identifies microorganisms based on their protein profile rather than traditional methods of phenotypic identification such as biochemical testing. MALDI‐TOFMS identification begins with colonies growing on solid agar or growing in liquid media. Cellular extracts of microorganism or direct application of a thin layer of organism from a colony are applied to the MALDI‐TOFMS target, followed by the application of matrix. Initial use of MALDI‐TOF in the clinical microbiology laboratory focused on bacterial identification from colonies growing on solid agar. Due to the ease of use, cost savings, and high accuracy, many laboratories had interest in using MALDI‐TOFMS for identification of other organism groups.
MALDI‐TOF MS for Identification of Bacteria and Yeast from Positive Blood Culture Broth
Authors: McElvania Erin 
Published: January 2025

Abstract
Identification of bacteria and yeast from blood culture is one of the most important functions of the microbiology laboratory due to the morbidity and mortality bloodstream infections inflict among patients. Matrix‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI‐TOF MS) provides identification of bacteria and yeast in under an hour. MALDI‐TOF MS performed directly from other patient specimens has not been implemented for routine use in clinical microbiology laboratories because the method does not perform well on polymicrobial specimens or those with a low burden of organisms. Blood culture broth is a complex specimen type due to the presence of RBCs and other blood components which must be separated from the bacteria or yeast to achieve high‐quality MALDI‐TOF MS spectra for accurate organism identification.
Oxacillin Salt Agar Test to Detect Methicillin (Oxacillin)‐Resistant
Staphylococcus aureus
Authors: Simner Patricia J. 
Published: January 2025

Abstract

The oxacillin salt agar test is an optional test for detecting
mec
A‐mediated methicillin (oxacillin) resistance in
Staphylococcus aureus
. A standard number of bacteria are inoculated onto Mueller‐Hinton agar containing 6 µg of oxacillin per ml and 4% NaCl. Following overnight incubation, the appearance of growth indicates that the
S. aureus
isolate is resistant to oxacillin, all other penicillins, carbapenems, beta‐lactam–beta‐lactamase inhibitor combinations, and cephems with the exception of ceftaroline. The chapter covers proper quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
Screen Tests to Detect High‐Level Aminoglycoside Resistance in
Enterococcus
spp.
Authors: Maris Alexander S. , Tao Lili 
Published: January 2025

Abstract
High‐level aminoglycoside resistance (HLAR) in enterococci is most commonly detected by assessing growth at high concentrations of gentamicin and sometimes streptomycin. Strains that show HLAR to gentamicin will not be synergistically killed with combinations of cell wall‐active drugs plus gentamicin. HLAR to gentamicin also means HLAR to tobramycin, netilmicin, amikacin, and kanamycin. This chapter describes the agar screen test in detail, and presents the reference to use of standard disk diffusion and broth microdilution MIC test procedures for detecting HLAR. It covers proper quality control principles for analytical tests. With postanalytical considerations, the chapter provides attention to common test limitations, interpretive challenges, and results reporting.
Serum Inhibitory and Bactericidal Titers
Authors: Alby Kevin 
Published: January 2025

Abstract
Schlichter and MacLean first used serum inhibitory titers (SIT) to assess the effectiveness of penicillin in the treatment of subacute bacterial endocarditis. Other recognized clinical indications for obtaining serum bactericidal titers (SBT) to monitor effective therapy are osteomyelitis, closed‐space infections such as meningitis or joint infection, and the use of oral antimicrobial agents after intravenous therapy. The SIT and SBT tests are designed to determine the activities of an antimicrobial agent(s) in a patient's serum against the patient's own infecting organism. The test integrates the pharmacokinetic and pharmacodynamic properties of the antimicrobial agent(s) that the patient is receiving. Doubling dilutions of the patient's serum are made, and a standard inoculum of the patient's organism is added to each tube or well and then incubated for 24 h at 35°C.
Quality Assurance Measures for Antimicrobial Susceptibility Testing
Authors: Cullen Sharon K. 
Published: January 2025

Abstract
Quality control (QC) is performed to ensure proper performance of antimicrobial susceptibility tests (AST) in order to provide accurate, reproducible, and timely results. The basic QC procedure used in clinical laboratories involves testing reference strains that have defined characteristics of susceptibility to the antimicrobial agent(s) tested. These strains must be properly maintained in order to ensure their reliable performance. Testing the QC strains controls many parameters of the AST; however, testing the QC strains alone does not always ensure reliable results when testing patients' isolates. Inclusion of supplemental control strains (particularly if recommended in the manufacturer's instructions when using a commercial test system), evaluation of susceptibility profiles on patients' isolates, verification of technologist competency, and review of cumulative susceptibility statistics are some of the additional measures that can be taken to further ensure quality of AST results.
Creation of an Antibiogram and Verification of Data
Authors: Johnson J. Kristie , Cullen Sharon K. 
Published: January 2025

Abstract
The antimicrobial susceptibility data that are generated by clinical microbiology laboratories from testing individual patient isolates can be utilized by different health care disciplines. These individual patient isolate data can be combined into a cumulative antimicrobial susceptibility test database, also referred to as an antibiogram, and utilized to determine empiric antibiotics at the local level, to observe increase in resistance, or to compare against local or national data. This chapter gives an overview on how to gather, validate, create, and distribute data based on the Clinical and Laboratory Standards Institute guidelines found in M39‐A5. These guidelines were designed to gather data for the selection of the most appropriate agents for initial empiric antimicrobial therapy. The quality of the data extracted in antibiogram reports is highly dependent on the accuracy and completeness of data entry into the lab information system.
Preparation of Broth Microdilution MIC Trays
Authors: Lonsway David R. 
Published: January 2025

Abstract
Broth microdilution MIC trays may be prepared in‐house for performance of quantitative antimicrobial susceptibility studies. The medium preparation would be similar to what is used for conventional MICs, but there are a few differences in the MIC plate preparation. These include using higher drug stock concentrations for the instrument to automatically create the serial doubling dilution concentrations and the addition of a dispersal or wetting agent to the antimicrobial agent stock solution(s) to enhance accurate release of the antimicrobial agent from the HP D300e's disposable dispense head cassette into the 96‐well tray. This system is usually reserved for producing small numbers of MIC trays and experimental checkerboard drug combinations. If large numbers of trays are required, dilutions of the antimicrobial agents are made in large volumes and generally dispensed in 0.1‐ml amounts into microdilution trays by using a commercial dispensing apparatus.
Examination and Evaluation of Primary Cultures
Authors: Zhang Sean X. , Memon Warda 
Published: January 2025

Abstract
Several key characteristics of a fungus may be discerned from primary cultures. For the yeasts, these include the presence of a capsule, budding characteristics, size, morphology, and colony color. If CHROMagar or another chromogenic medium was used in the primary setup, presumptive identification of a yeast may be possible. For molds, helpful features include colony characteristics, sporulation characteristics, the presence of septa, and hyphal or conidial color. CHROMagar contains enzymatic substrates that are linked to chromogenic compounds. Blood cultures or fluid cultures incubated in broth that have fungal elements upon Gram staining should be subcultured onto appropriate mycology media. One of the more controversial issues regarding primary cultures is quantitation. While for yeasts, quantitation is generally reported using criteria similar to those used in bacteriology for deciding clinical significance, the situation is different for molds, because they grow as contiguous cells that may break off into fragments.
Presumptive Identification Tests for Yeasts Isolated on Primary Culture
Authors: Leal Sixto M. , Azar Marwan M. 
Published: January 2025

Abstract

The presumptive tests assume that yeast inocula are from pure cultures or from single colonies. Tests such as the
Candida albicans
screen require multiple colonies to prepare the inoculum. Sabouraud dextrose agar is the best medium to isolate yeasts for germ tube production; sheep blood agar is an acceptable substitute. Some
Candida tropicalis
isolates produce pseudohyphae, and some also produce germ tubes that require careful observation to discriminate them from those of
C. albicans
. Frequently, isolates of
C. albicans
produce colonies described as “yeasts with feet” in recognition of a peripheral fringe. If a single presumptive test is used for preliminary reporting purposes, then the report should indicate that the identification is presumptive; for example, “yeast, presumptive
Cryptococcus neoformans
”. This chapter covers proper quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
Identification of Molds on Primary Culture
Authors: Azar Marwan M. , Leal Sixto M. 
Published: January 2025

Abstract
Molds may be polymorphic, and therefore any visible structures present must be demonstrated to be produced by a single fungus. Contaminating bacteria and yeasts may interfere with the development of key characteristics of a mold, so a pure culture is optimal for identification. Most medically relevant molds cultured in nutritive media and appropriate conditions in the clinical laboratory will undergo asexual reproduction in culture. Pathogenic molds and contaminants may demonstrate only vegetative/nonreproductive hyphae requiring subculture on nutrient‐poor media to induce sporulation. Matrix‐assisted laser desorption ionization‐time of flight mass spectrometry may also enable mold identification. Filamentous fungi isolated in the laboratory must be accurately identified, and their significance must be assessed, before being reported to the clinician. The rate of growth of a mold may not be reliable on initial culture, but after subculture onto standardized medium, it may be a useful characteristic.
Molecular Identification of Yeasts and Molds
Authors: Cañete‐Gibas Connie F. , Wiederhold Nathan P. 
Published: January 2025

Abstract
Identification of fungi to the species level is becoming increasingly reliant upon molecular methods, such as DNA sequence analysis. Historically, species identification was performed by phenotypic characteristics, including assessment of the colony and microscopic morphologies, biochemical assays, temperature studies, and growth characteristics on different types of medium. Correct identification to the species level can have clinical implications. It may influence interpretations of antifungal susceptibility testing results, which are species specific, as are epidemiologic cutoff values. The nature of the fungal cell walls can prevent efficient lysis, thereby reducing recovery of nucleic acids. The results of DNA sequence analysis for fungal species identification should be in agreement with the phenotypic/morphologic characteristics that are observed.
Detection of Blood Parasites
Authors: Davis Richard E. , Garcia Lynne S. 
Published: January 2025

Abstract
Identification of blood parasites most often utilizes either or both of two types of stained blood films, also known as smears: a thin film and a thick film. With some key differences in practice, the principles of preparing and handling the combination film derive from the thin and thick film procedures. The traditional stain used to detect parasites on blood films is a Giemsa stain, which if used at a pH of 7.0 to 7.2 is optimal for visualizing characteristic parasite features. Delafield's hematoxylin stain particularly improves the visibility of the microfilaria sheath if present. Wright's stain can be used to stain blood films for detecting parasites, but it is generally considered to be inferior to Giemsa. It is important to report the level of parasitemia when blood films are examined and found to be positive for malaria parasites.
Appendixes
Authors: Pritt Bobbi S. , Garcia Lynne S. 
Published: January 2025

Abstract
This chapter provides illustrations and color images that show the differences among different organisms and human cells. However, unlike the ova‐and‐parasite examination, which facilitates the recovery of many different parasites, the fecal immunoassays are limited to one or two organisms only. The selection of any particular immunoassay format will often depend on the workflow options within the laboratory; different laboratories may select different formats for the rapid tests available. The composition of a quality control manual should allow for flexibility; the content should include a description of the laboratory's goals, policies, procedures, roles, responsibilities, and monitoring process for each of the quality system components. OSHA also requires each laboratory to develop a comprehensive, written chemical hygiene plan. OSHA requires monitoring for formaldehyde vapor wherever formaldehyde is used in the workplace.
Selection, Collection, Transport, and Processing of Specimens for Viral Diagnosis
Authors: Graf Erin H. 
Published: January 2025

Abstract
Optimal use of all diagnostic testing for viral infections, but especially recovery of viruses in culture, requires careful consideration of preanalytical factors, including selection, collection, transport, assessment, and processing of patient specimens. Specimen selection relates to more than just the specimen type or source; it also includes the appropriate clinical indications for which virus culture may be warranted. The laboratory must provide written guidelines to collection sites detailing which viruses can and should be tested by the laboratory, including specific information on the limitations of virus culture‐based methods compared to molecular and/or immunologic testing, as well as instructions for submitting specimens. It is important to ensure that the collection facility has access to all required transport media and has processes in place to store the media under required conditions, with appropriate quality assurance mechanisms in place.
Biosafety in the Clinical Virology Laboratory
Authors: Cárdenas Ana María 
Published: January 2025

Abstract
Laboratory biosafety is fundamental to protecting medical and public health laboratory workers and preventing unintentional exposures and acute infectious disease threats. Performing diagnostic testing and research‐related activities in the clinical virology laboratory requires special emphasis in defined areas. These areas include: general safety rules; biohazard signs and warning labels; specimen transportation, receipt, and storage; work area safety; personal protective equipment; laboratory equipment; biosafety related to virus cell cultures; biosafety considerations for virus antigen detection assays; biosafety related to molecular virology work areas; and so on. This procedure enables implementation of sustainable laboratory biosafety practices that are relevant to diagnostic virology laboratory circumstances and priorities. Facilities handling biological agents have an obligation to perform a risk assessment and implement appropriate risk control measures as well as putting into practice personnel competence and training plans to ensure continuous safe laboratory practices.
Isolation of
Chlamydia
spp. in Cell Culture
Authors: Peterson Ellena M. 
Published: January 2025

Abstract

Members of the genus
Chlamydia
are obligately intracellular bacteria that contain RNA and DNA, have a cell wall resembling those of Gram‐negative bacteria, and multiply by binary fission in a manner distinct from those of other bacteria.
Chlamydia trachomatis
,
Chlamydia psittaci
, and
Chlamydia pneumoniae
are the three species that are most often associated with human infections. The majority of laboratory tests to detect
Chlamydia
are for the diagnosis of sexually transmitted diseases. Nucleic acid amplification tests for the detection of genital infections with
C. trachomatis
have largely replaced cell culture. This is for a variety of reasons, including their sensitivity, ease of specimen collection with urine and vaginal swabs being acceptable, and convenient specimen transport. Cell culture may still be preferred or recommended for certain situations, such as laboratory testing in cases of sexual abuse, medicolegal situations, pneumonia, and ophthalmia neonatorum.
Serologic Diagnosis of Group A Streptococcal Infections
Authors: Murray David 
Published: January 2025

Abstract

The bacterial pathogen
Streptococcus
(group A
Streptococcus
[GAS]) pyogenes is associated with a diverse range of human diseases. These include infections such as pharyngitis, impetigo, and invasive infections, as well as post‐infective pathologies, particularly acute rheumatic fever and poststreptococcal glomerulonephritis. Important to indicate is that streptococcal serology is unhelpful and should not be used for the diagnosis of purulent, acute infections caused by GAS. GAS have a wide array of extracellular and cellular virulence factors, and a number of these antigens have been the focus of assay development for streptococcal serology. Most individuals produce either anti‐streptolysin O or anti‐DNase B antibodies in response to GAS infection. The chapter covers proper quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
SARS‐CoV‐2 Serologic Testing
Authors: Theel Elitza S. 
Published: January 2025

Abstract
Serologic assays for detection of antibodies against SARS‐CoV‐2 were developed quickly following onset of the pandemic in early 2020. From the diagnostic perspective, serologic tests for SARS‐CoV‐2 can also be used to help identify COVID‐19‐related sequelae, including multisystem inflammatory syndrome in children. The majority of commercially available serologic assays for SARS‐CoV‐2 are designed for the detection of antibodies in serum and plasma, with some rapid lateral flow immunoassays also able to be performed on finger‐stick whole blood. Qualitative SARS‐CoV‐2 serologic assay results are typically determined by comparing the signal‐to‐cutoff value (S/Co) of the patient sample to the S/Co of the kit calibrator, which has been established by the manufacturer as the reactivity threshold. Values above the calibrator S/Co value are considered positive and, depending on the kit, may have an additional equivocal/indeterminate S/Co range, whereas values below the calibrator S/Co are considered negative.
Management of Laboratory Accidents
Authors: Buchan Blake W. 
Published: January 2025

Abstract
Ensuring the safety of laboratory workers is of paramount importance to creating a positive work environment and preventing time loss or severe long‐term injury or disability. The implementation of various control measures, including engineering controls, procedural controls, and use of PPE, and the conduct of a thorough risk assessment, can greatly reduce the risk of these events; however, total elimination of laboratory accidents is an unrealistic goal. Therefore, there is a need to develop a plan for the reporting and management of laboratory accidents. Physical hazards posing a risk for accidental injury abound in the clinical laboratory. They may take the form of physical obstructions that pose a risk for slip, trip, or fall, such as unsecured electrical cords, boxes, or rugs in a walkway, aqueous or chemical spills, and paraffin wax. Accidents due to physical hazards may require review of instrument‐specific or general laboratory safety policies.
Management of Infectious Waste
Authors: Relich Ryan F. 
Published: January 2025

Abstract
For effective and efficient management of infectious wastes, a comprehensive waste management plan is essential for ensuring the safety of the employees handling wastes, compliance with various regulatory requirements, meeting the standards of The Joint Commission and the guidelines of other groups such as the CLSI, and implementation of cost‐effective strategies for waste disposal. Microbiology laboratories generate various types of wastes, including infectious waste, chemical waste (some of which is probably hazardous per Resource Conservation and Recovery Act of 1976 regulations), and wastes with mixed hazards, in addition to general trash and wastewater. Most laboratories in the United States use red‐colored sharps containers and biohazardous waste bags for disposal of infectious wastes that are treated and disposed of by specialized waste contractors. Soft wastes such as intact culture plates, gloves, and specimen bags can be discarded in color‐coded plastic bags marked with the international biohazard symbol and verbal warnings.