bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic Tests and Biochemical Procedures
Authors: Lee Philip A. 
Published: January 2025

Abstract
The oxidase test is used to determine if an organism possesses the enzyme cytochrome c oxidase as a component of the bacterial electron transport chain. During aerobic cellular respiration, bactericidal reactive oxygen species (ROS) are produced, including peroxide, superoxide, hydroxyl radical, and singlet oxygen. Catalase is an enzyme that protects against oxidative damage from ROS by catalyzing hydrogen peroxide into water and oxygen. The ability of an organism to split indole from the amino acid tryptophan is due to the presence of tryptophanase. In the rapid spot test, indole is detected directly from the colony growing on a medium rich in tryptophan. Beta‐lactamases are enzymes produced by many clinically significant bacteria and are major mediators of bacterial resistance to beta‐lactam agents. The motility test is used to detect the presence of flagella on bacteria, which allow them to travel in and out of the microscopic field or beyond their initial inoculation in agar.
Laboratory Accreditation and Compliance
Authors: Loeffelholz Michael , Samuel Linoj , Sharp Susan E. 
Published: January 2025

Abstract
The current laboratory regulatory framework for accreditation in the United States began with the Clinical Laboratory Improvement Act of 1967. The Clinical Laboratory Improvement Amendments (CLIA) program is administered by three agencies within the Department of Health and Human Services: Centers for Medicare and Medicaid Services, Centers for Disease Control and Prevention, and Food and Drug Administration. CLIA requires that all laboratories have a valid CLIA certificate unless they are CLIA exempt. CLIA inspectors may cite the laboratory for deficiencies based on the nature of the noncompliance. A quality management system is comprehensive; it involves all personnel and includes all phases of the testing workflow: preanalytical, analytical, and postanalytical. Quality control testing must be performed and reviewed after performance of significant maintenance on an instrument or replacement of any important part of the test system, including reagents.
Laboratory Detection of Bacteremia and Fungemia
Authors: T. Harrington Amanda , Jean Sophonie , Hilt Evann E. 
Published: January 2025

Abstract
Clinical microbiology laboratories play an essential role in establishing an etiologic diagnosis for sepsis and bloodstream infection. Diagnosis requires multiple steps, including one or more blood cultures drawn from different sites, recovery and identification of microorganisms detected in blood culture, antimicrobial susceptibility testing of clinically significant organisms, and interpretation of results in conjunction with other clinical, radiographic, and laboratory findings. This chapter provides a summary of the clinical importance of bacteremia and fungemia, the scientific and medical principles underlying current diagnostic methods, and diagnostic approaches. Determining the clinical significance can be difficult for coagulase‐negative staphylococci, as the identity of this organism group is of little or no help. Preparation for blood culture collection and transport to the laboratory includes a number of stepwise processes. Matrix‐assisted laser desorption ionization–time‐of‐flight mass spectrometry is an extensively studied approach to rapid microbial identification of blood culture isolates.
Molecular Techniques
Authors: Parikh Bijal A. , Hughes Andrew E. O. , Anderson Neil W. 
Published: January 2025

Abstract
Molecular methods for the diagnosis of infectious diseases can be broadly grouped into three categories: probe‐based methods without amplification, signal amplification methods, and target amplification methods. These methods differ significantly in terms of their technical requirements, analytical sensitivity, and specificity, which inform the role of individual techniques in specific clinical applications. Probe‐based methods without amplification are among the earliest‐described and simplest molecular tests. The analytical sensitivity of nucleic acid probes can be greatly enhanced through signal amplification, which allows the detection of low quantities of nucleic acid directly from clinical specimens. Transcription‐mediated amplification is a commonly utilized form of PCR‐free target amplification. Molecular assays all have some degree of susceptibility to inhibition by external substances. Quality assurance plans should be designed with consideration of the challenges and potential pitfalls of molecular testing. Molecular methods are exquisitely sensitive, making them very susceptible to false positivity due to environmental contamination.
Prevention of Health Care‐Associated Infections
Authors: Sullivan Kaede V. , Pfaller Michael A. , Diekema Daniel J. 
Published: January 2025

Abstract
This chapter discusses the impact of health care‐associated infections (HAIs) on patient outcomes and health care costs and the organization of the hospital infection prevention program (IPP) and describes the important role that the clinical microbiology laboratory (CML) plays in HAI prevention. An HAI is an infection that is acquired in a hospital or health care facility. The incidence of HAIs involving staphylococci and enterococci increased as these organisms became increasingly resistant to antibiotics. The responsibilities of the hospital IPP include surveillance and prevention of HAIs, continuing education of medical staff, outbreak control, protection of employees and visitors from infection, and providing advice on introduction of new products and procedures. The development and application of new technologies in the CML can greatly enhance infection prevention efforts. Close collaboration between CML and personnel from infection prevention and antimicrobial stewardship programs is required to ensure optimal HAI prevention, which saves money and lives.
Biothreat Agents
Authors: Mahlen Steven D. , Snyder James W. 
Published: January 2025

Abstract
The ideal qualities of a successful biothreat agent area high rate of illness in exposed persons/animals, a high case fatality rate, a short incubation period, and a paucity of immunity in the target population. The Laboratory Response Network forms an integrated network of more than 120 local and state public health, federal, and military laboratories that can respond to bioterrorism, chemical terrorism, and other public health emergencies. The Federal Select Agent Program was established in response to a heightened concern about the ease with which disease‐causing agents could be obtained. Select agent regulations were revised in October 2014 to designate “tier 1” agents with a documented risk of causing a high‐consequence event greater than those with other biological select agents and toxins. Natural forms of botulism include foodborne, wound, and intestinal botulism. Smallpox has a long history of use as a biothreat weapon.
Staphylococcus
,
Micrococcus
, and Other Catalase‐Positive Cocci
Authors: Becker Karsten , David Michael Z. , Skov Robert L. 
Published: January 2025

Abstract

Historically, the genera
Staphylococcus
and
Micrococcus
were placed together with the genera
Stomatococcus
and
Planococcus
in the family
Micrococcaceae
, containing Gram‐positive, catalase‐positive cocci. As staphylococci and micrococci are part of the microbiota of the skin and mucous membranes, careful procedures should be used to isolate organisms from the presumed focus of infection without collecting surrounding microbiota. Because serological testing for antistaphylococcal antibodies lacks specificity and predictive accuracy, it plays no role in the diagnosis of most staphylococcal diseases. A number of studies and reviews describing the antimicrobial and biocide susceptibilities of clinically important staphylococcal species have been published. Distinguishing contaminants and colonizers from staphylococcal and micrococcal isolates causing infection continues to be an important challenge for laboratorians and clinicians.
Aerococcus
, Abiotrophia, and Other Aerobic Catalase‐Negative, Gram‐Positive Cocci
Authors: Nielsen Xiaohui Chen , Christensen Jens Jørgen 
Published: January 2025

Abstract

The catalase‐negative, Gram‐positive cocci form a taxonomically diverse group of bacteria that are isolated infrequently as opportunistic agents of infection. Most of these organisms resemble other, better‐known clinical isolates and consequently may be mistaken for members of those genera. Some strains of
Aerococcus
may exhibit weakly positive catalase reactions due to nonheme catalase activity. Organisms in the genera
Abiotrophia
and
Granulicatella
are normal residents of the oral cavity and are recognized as agents of endocarditis involving both native and prosthetic valves.
Pediococcus
strains have been isolated from bacteremia and cases of sepsis and hepatic abscess in compromised patients.
Vagococci
are motile organisms that, like lactococci, express Lancefield group N antigen.
Weissella
strains are usually isolated in polymicrobial infections. Antimicrobial susceptibility studies on the organisms have generally employed dilution testing methods.
General Approaches to the Identification of Aerobic Gram‐Positive Rods
Authors: Bernard Kathryn A. 
Published: January 2025

Abstract
All strains of Gram‐positive rods can be grown on blood agar plates, with specific descriptions of growth requirements. Gram‐positive organisms demonstrating “regular” rods are those cells with usually parallel longitudinal edges. “Irregular” rods are those organisms with cells observed to have curved or coccoidal longitudinal edges which are not parallel; these taxa can produce yellowish‐pigmented, yellow‐pigmented, or orange‐pigmented colonies. Molecular methods may be required for definitive identification to genus and species level for bacteria which are poorly reactive biochemically and/or are under represented or absent from databases of commercial matrix‐assisted laser desorption ionization–time‐of‐flight mass spectrometry (MALDI‐TOF MS) systems. MALDI‐TOF MS technology is widely used in clinical microbiology, because that method has been found to provide rapid, cost‐effective, and accurate identifications of both common and rare pathogens.
Coryneform Gram‐Positive Rods
Authors: Mattos‐Guaraldi Ana Luíza , Santos Louisy Sanches dos , Vieira Verônica Viana 
Published: January 2025

Abstract

This chapter presents Coryneform bacteria comprising aerobically or facultatively anaerobically growing, asporogenous, non‐acid fast Gram‐positive rods with irregular morphology. Establishing the clinical significance of coryneform bacteria can be difficult for caregivers and microbiologists.
Corynebacterium
spp. form the predominant group and include diphtheria toxin (DT)‐producing
Corynebacterium diphtheriae
, the causative agent of classic diphtheria, which was once a major cause of illness and death among children. Laboratory procedures for identification of
Corynebacterium
spp. and other coryneform bacteria include collection and transport of clinical samples, isolation practices, culture conditions, phenotypic and molecular assays, as well as antimicrobial susceptibility testing. Molecular techniques have been increasingly used in microbiology laboratories for the identification of
Corynebacterium
species and other coryneform bacteria. Detection of antibodies directed against DT is the only established serologic test for coryneform bacteria.
Nocardia
,
Rhodococcus
,
Gordonia
,
Actinomadura
,
Streptomyces
, and Other Aerobic Actinomycetes
Authors: Brown‐Elliott Barbara A. , Zelazny Adrian M. , Conville Patricia S. 
Published: January 2025

Abstract

The anaerobic organisms now in the genus
Actinomyces
and the aerobic organisms grouped together as the “aerobic actinomycetes” were previously presumed to be related to one another on the basis of shared features of microscopic and colonial morphology. The microscopic and colonial morphologies of organisms in the genus
Actinomadura
, which contains more than 100 validly named species or subspecies, are very similar to those in the genus
Streptomyces
. Species in the genus
Saccharopolyspora
were initially thought to be related to
Nocardia
and
Streptomyces
by biochemical characteristics but are phylogenetically distinct from those genera. However, an unknown number of
Gordonia
infections may be missed, either because the isolate is considered an insignificant coryneform Gram‐positive rod or because the isolate is misidentified by biochemical methods as belonging to another genus, such as
Nocardia
or
Rhodococcus
.
Mycobacterium tuberculosis
Complex
Authors: Rowlinson Marie‐Claire , Musser Kimberlee A. , Khare Reeti 
Published: January 2025

Abstract

Tuberculosis (TB) is caused by a group of closely related slowly growing mycobacteria, collectively named the
Mycobacterium tuberculosis
complex (MTBC). Members of the MTBC have undergone several taxonomic reclassifications, which has resulted in confusing nomenclature. Mycobacterial culture is currently considered the reference standard for MTBC detection. Until the early 1990s, typing of MTBC strains was limited to mycobacterial phage typing and drug resistance patterns, methods which have low discriminatory power that have been replaced by molecular genotypic methods. Antimicrobial susceptibility testing is a critical element of the MTBC laboratory workup. While cell‐based immunodiagnostics, such as tuberculin skin testing or interferon‐gamma release assays, can be used as part of establishing a diagnosis of active TB disease, they are mainly used as tests for latent TB infection and to determine exposure to TB.
Approaches to the Identification of Aerobic Gram‐Negative Bacteria
Authors: Nørskov‐Lauritsen Niels , Chuvochina Maria 
Published: January 2025

Abstract
The description of aerobic Gram‐negative bacteria is long established, based on culture conditions and the failure to retain crystal violet‐iodine complex by Gram's staining method. This chapter shows dichotomous phenotypic and biochemical identification algorithms for Gram‐negative bacteria that are fastidious and grow poorly or not at all on sheep blood agar. The use of KIA/TSI slants as part of the workup of Gram‐negative organisms has largely been discontinued due to the introduction of matrix‐assisted laser desorption ionization‐time of flight mass spectrometry, which provides more rapid and specific identification. The major limitation of analyzing the 16S‐23S ribosomal RNA (rRNA) region for bacterial identification and community profiling is the current lack of a reference database containing combined 16S rRNA and 23S rRNA gene sequences.
Salmonella
Authors: Dekker John P. , Faron Matthew L. , Humphries Romney M. , Buchan Blake W. , Ledeboer Nathan A. 
Published: January 2025

Abstract

Salmonella typhi
has one of the largest sets of universal genetic markers common to
Salmonella enterica
serotypes but also contains among the fewest genetic markers defining a subspecies. This chapter discusses traditional classification schemes based on antigenic typing, pulsed‐field gel electrophoresis, and multilocus sequence typing (MLST) and covers newer molecular and next‐generation sequencing‐based approaches, including ribosomal MLST, whole‐genome and core‐genome MLST, and whole‐genome single‐nucleotide variant‐based strain tracking. Nontyphoidal
Salmonella
is a common inhabitant of the gastrointestinal tract of wild and domestic poultry, which serves as an important reservoir for infection, but is also frequently isolated from warm‐blooded mammals and reptiles. Use of appropriate isolation media along with novel diagnostic techniques is improving understanding of the epidemiology of the genus
Salmonella
and will ultimately help meet the goal of improving patient care. Determination of antimicrobial susceptibility is valuable for surveillance purposes to monitor the development and spread of antimicrobial resistance among
Salmonella
isolates.
Peptostreptococcus
,
Finegoldia
,
Anaerococcus
,
Peptoniphilus
,
Parvimonas
,
Murdochiella
,
Veillonella
, and Other Anaerobic Cocci
*
Authors: Veloo Alida C. M. , Johnson Crystal N. 
Published: January 2025

Abstract

Gram‐positive anaerobic cocci (GPAC) belong to the Firmicutes phylum and have been known to most bacteriologists as peptococci or peptostreptococci. The genera
Anaerococcus
,
Anaerosphaera
,
Fastidiophila
,
Finegoldia
,
Gallicola
,
Murdochiella
,
Parvimonas
,
Peptococcus
,
Peptoniphilus
, and
Peptostreptococcus
are Gram‐positive, coccobacillary or occasionally coccoid cells. The genera
Veillonella
, Acidaminococcus,
Megasphaera
,
Anaeroglobus
, and
Negativicoccus
are Gram‐negative cocci. The polymicrobial nature of GPAC infections, in addition to inadequate classification, has most likely contributed to neglect the clinical significance of individual species of GPAC. A variety of microscopic, immunologic, and molecular techniques have been developed for direct examination of GPAC. New information regarding the antimicrobial susceptibilities of individual GPAC is increasing due to the improvement in classification and identification.
Antibacterial Agents
Authors: Lewis James S. , Bush Karen 
Published: January 2025

Abstract

Antimicrobial chemotherapy has played a vital role in the treatment of human infectious diseases since the discovery of penicillin in the 1920s. This chapter provides an overview of the antibacterial agents currently marketed in the United States, with major emphasis on their mechanisms of action, spectra of activity, important pharmacologic parameters, and toxicities. The major antibacterial action of penicillins is derived from their ability to inhibit multiple bacterial enzymes, namely, penicillin‐binding proteins (PBPs), that catalyze the last steps of peptidoglycan synthesis. The penicillins have antibacterial activity against most Gram‐positive and many Gram‐negative and anaerobic organisms. Like the penicillins, cephalosporins act by binding to PBPs of susceptible organisms, thereby interfering with the synthesis of peptidoglycan of the bacterial cell wall. Clavulanic acid is a naturally occurring weak antimicrobial agent found initially in cultures of
Streptomyces clavuligerus
. Streptomycin, neomycin, kanamycin, tobramycin, and gentamicin are naturally occurring aminoglycosides.
Antimicrobial Susceptibility Testing Systems
Authors: Karlowsky James A. , Richter Sandra S. , Patel Jean B. 
Published: January 2025

Abstract
This chapter focuses primarily on commercial Antimicrobial Susceptibility Testing (AST) systems currently available in the United States. Only one semiautomated system for disk diffusion testing is marketed in the United States; additional systems are available in other countries. AST systems include data management software that may be interfaced with a laboratory information system and offer various levels of expert system and epidemiological analyses. The manual broth microdilution systems facilitate the visual reading and recording of minimal inhibitory concentrations. The semiautomated broth microdilution systems use automated devices to read susceptibility and identification tests after offline incubation. New technology provided by the Accelerate Pheno system generates AST results directly from positive blood cultures in less time than testing performed on isolates. In the future, the time required to complete AST testing may also be reduced with the application of molecular techniques.
Susceptibility Test Methods: Anaerobic Bacteria
Authors: Schuetz Audrey N. , Carpenter Darcie E. 
Published: January 2025

Abstract
Anaerobic bacterial pathogens cause serious infections, particularly in the hospital environment. Antimicrobials are a mainstay of treatment, and as with aerobic pathogens, resistance in anaerobic bacteria is increasingly becoming problematic. This chapter covers resistance in specific anaerobe‐antimicrobial agent combinations. It outlines susceptibility testing methods and emphasizes the advantages and disadvantages of each approach. The chapter summarizes susceptibility data for major antimicrobials within four groups of anaerobic pathogens (Gram‐negative bacilli, Gram‐positive spore‐forming bacilli, Gram‐positive non‐spore‐forming bacilli, and cocci). It presents pertinent trends of increasing resistance for each group, and reviews specific recommendations for testing and reporting. A quality control program is designed to monitor the accuracy and precision of the susceptibility testing process being performed. Clinical laboratories should provide susceptibility testing of anaerobes to optimize patient care. More frequent susceptibility testing of anaerobes will lead to a better understanding of the epidemiology of resistance.
Human T‐Cell Lymphotropic Viruses
Authors: Switzer William M. , Heneine Walid , Owen S. Michele 
Published: January 2025

Abstract

Human T‐cell lymphotropic virus types 1 and 2 (HTLV‐1 and HTLV‐2) are members of the
Deltaretrovirus
genus in the
Retroviridae
family. Classification of HTLV groups using Roman numerals was replaced over a decade ago with Arabic numerals, following the guidelines of the International Committee on Taxonomy of Viruses. Many molecular epidemiologic studies have shown HTLV proviruses to be remarkably stable genetically, which has allowed strong resolution of HTLV phylogenies and molecular dating of these viruses. Serum or plasma is suitable for use in serologic assays for HTLV detection and can be drawn at the time of presentation. Isolation of HTLV has been difficult since these viruses are cell associated. Testing for antibodies to HTLV‐1 and HTLV‐2 should be performed for all blood donors and patients presenting with relevant clinical signs and symptoms.
Parainfluenza and Mumps Viruses
Authors: Relich Ryan F. 
Published: January 2025

Abstract

The human parainfluenza viruses (HPIVs) and mumps virus (MuV) are currently classified among the genera
Respirovirus
and
Orthorubulavirus
within the family
Paramyxoviridae
, order
Mononegavirales
. All the viruses described in this chapter are enveloped and possess helical nucleocapsids. Virus isolation and RNA detection have also been recommended for mumps diagnosis in individuals with a documented immunization history. Diagnosis of mumps does not typically involve direct microscopic examination of clinical specimens. However, microscopic examination of affected salivary glands reveals an edematous interstitium diffusely infiltrated by macrophages, lymphocytes, and plasma cells, which compress acini and ducts. The accepted laboratory criteria for the diagnosis of MuV infection are isolation of the virus from clinical specimens, detection of MuV RNA via molecular methods, a significant rise between acute‐ and convalescent‐phase antibody titers in serum, or a positive IgM result for mumps.
Measles and Rubella Viruses
Authors: Crooke Stephen N. , Coughlin Melissa M. , Perelygina Ludmila M. 
Published: January 2025

Abstract

Measles virus is the prototypic member of the genus
Morbillivirus
in the family
Paramyxoviridae
, and it is the only member of the genus that causes human disease. Characteristic cytopathic effects of measles virus infection include giant multinucleated cells (Warthin‐Finkeldey giant cells) as well as intracytoplasmic and intranuclear cellular inclusions. Rubella virus was historically classified in the family
Togaviridae
as the sole member of the genus
Rubivirus
; however, in 2018, rubella virus (and the genus
Rubivirus
) was reclassified as the sole member the new family
Matonaviridae
. The present description of laboratory testing for rubella emphasizes identification of postnatal and congenital rubella cases. However, in the United States, much of the testing is for assessing immunity to rubella, since health care providers should test all pregnant women for immunity by a serum IgG test at the earliest prenatal visit.