bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disinfection and Sterilization
Authors: Arduino Matthew J. , McDonnell Gerald 
Published: January 2025

Abstract
The effective use of disinfection and sterilization procedures is important in patient care and laboratory settings. Inadequate disinfection and sterilization procedures may lead to health care‐associated and laboratory‐acquired infections. This chapter also discusses international consensus standards related to disinfection and sterilization in the health care environment. Cleaning is often an essential prerequisite to disinfection or sterilization to ensure the optimal activity of the antimicrobial effects of disinfectants or sterilization processes, as well as ensuring the lack of residual materials that may have other negative impacts. There are two major considerations in the use of any disinfection or sterilization product or process: antimicrobial expectations and safety. These safety practices include cleaning and disinfection of laboratory surfaces, sterilization, and hand hygiene. The chapter considers the most widely used sterilization method for clinical laboratory applications that is heat sterilization along with a brief explanation of alternative sterilization methods.
The Human Microbiome
Authors: Rao Meghana V. , Messina Julia A. , Surana Neeraj K. 
Published: January 2025

Abstract

Given the voluminous data regarding the microbiota and human health, this chapter focuses on exemplar data to highlight key findings that are often generalizable across body sites and disease states. The Human Microbiome Project, a landmark study that cataloged the microbiome in multiple anatomic sites in healthy adults, found that the composition of the microbiota differs by body site, there is tremendous interindividual variation, and the microbial gene content is relatively conserved irrespective of the body site or individual. The oropharyngeal microbiota translocates to the lower respiratory tract via normal microaspirations in healthy individuals. The ileal microbiota contains a number of
Streptococcus
spp. and other bacteria that are also found in the oral microbiota, a finding that suggests some continuity of microbes throughout the gastrointestinal tract. The skin microbiome is a diverse ecosystem with the greatest variation in microbial species over time and the greatest phylogenetic diversity of all anatomic sites.
Taxonomy of
Bacteria
and
Archaea
Authors: Lawson Paul A. 
Published: January 2025

Abstract

Taxonomy is more narrowly defined and can be considered to fall under the umbrella of systematics
per se
, consisting of classification, nomenclature, and identification. A reliable classification is a prerequisite for anyone dealing with microorganisms, whether in academia, industry, or health care. The establishment of orderly systems of classification is based on ranks, the highest of which is the domain; the domains of the prokaryotes are the
Archaea
and
Bacteria
. Even though phenotypic methods of numerical taxonomic identification were largely abandoned for the classification of new species, the determination of biochemical, nutritional, and physiological criteria remains a fundamental component of systematics and is routinely incorporated into the species description of published novel taxa. Genotypic information is derived from nucleic acids, whereas phenotypic information is derived from proteins and their functions, chemotaxonomic markers, and a wide range of other expressed features.
Specimen Collection, Transport, and Processing: Bacteriology
Authors: McElvania Erin , Singh Kamaljit 
Published: January 2025

Abstract

The clinical microbiology laboratory is responsible for providing guidance on how to select, collect, label, and transport specimens for processing in the laboratory. An improperly collected specimen can decrease the sensitivity of pathogen detection or introduce colonizing bacteria surrounding the site of infection, which complicates the laboratory workup of cultures and may result in unnecessary or inappropriate antimicrobial therapy. All specimen processing should be performed in a biosafety level 2 cabinet to prevent contamination of specimens, and staff should wear personal protective equipment, including a splash‐proof gown and gloves, to minimize accidental exposures. Superficial wound specimens are frequently submitted on swabs and often grow multiple organisms, including members of the commensal microbiota, which makes interpretation and treatment confusing for physicians. Detection of group A
Streptococcus
to diagnose pharyngitis is the most common test ordered for specimens from the upper respiratory tract.
Listeria
and
Erysipelothrix
Authors: Smith Kenneth P. , Harris Rebecca M. 
Published: January 2025

Abstract

Listeria
and
Erysipelothrix
are genera of small, non‐sporeforming, Gram‐positive bacilli that include the opportunistic human pathogens
Listeria monocytogenes
and
Erysipelothrix rhusiopathiae
. The clinical presentation of an individual exposed to
Listeria
varies from asymptomatic to mild gastroenteritis to life‐threatening illness, depending on a combination of factors that include bacterial virulence, inoculum size, and underlying host defenses. Isolation of
Listeria
can be achieved from clinical specimens from normally sterile sites, including blood and cerebrospinal fluid. Typing of
Erysipelothrix
is used for the analysis of outbreaks in farmed animals and other epidemiologic purposes but has little clinical relevance in humans. Historically, strain typing was performed by serologic testing based on somatic and flagellar antigens. Due to the lack of resistant strains, breakpoints exist for susceptible results only.
Mycobacterium
: Laboratory Characteristics of Slowly Growing Mycobacteria Other than
Mycobacterium tuberculosis
Authors: Caulfield Adam J. , Richter Elvira , Brown‐Elliott Barbara A. , Wengenack Nancy L. 
Published: January 2025

Abstract

This chapter describes the clinically significant, slowly growing nontuberculous mycobacteria (SGM). Pulsed‐Field Gel Electrophoresis has been a useful technique for strain typing of the SGM. It is important to recognize that an unidentified mycobacterial isolate should be treated as if it is
M. tuberculosis
and that appropriate safety measures, including biosafety level 3 practices and facilities, should be used until
M. tuberculosis
is ruled out. One of the first, easiest, and least expensive means of detecting the presence of mycobacteria in clinical samples is microscopic examination. Matrix‐assisted laser desorption ionization‐time‐of‐flight mass spectrometry has revolutionized the identification of microorganisms, including mycobacteria. Not all laboratories may have the necessary funds, facilities, or instrumentation to provide molecular testing in mycobacteriology. Antimicrobial susceptibility testing of clinically relevant mycobacteria is important for the treatment of infections caused by many mycobacterial species.
Neisseria
Authors: Lâm Thiên‐Trí , Vogel Ulrich , Claus Heike 
Published: January 2025

Abstract

Microaerobic growth by denitrification of nitrite via nitric oxide has also been shown for
Neisseria meningitidis
. The species
N. gonorrhoeae
and
N. meningitidis
are exclusively human pathogens. Identification of the serogroup of invasive
N. meningitidis
isolates is of interest with respect to vaccination of close contacts of the index case. A further level of differentiation to analyze local epidemiology is achieved by DNA sequence‐based typing schemes of hypervariable outer membrane proteins, which have been harmonized throughout Europe. Cultivation of
N. gonorrhoeae
is best performed on chocolate agar, which supports the growth of many other commensal bacteria. DNA‐based methods used for typing of
N. gonorrhoeae
include gel‐based methods such as
opa
typing and restriction fragment length polymorphism analysis by pulsed‐field gel electrophoresis. Serologic tests are used for the determination of protection against invasive meningococcal disease after vaccination or for seroepidemiological studies. First‐catch urine is recommended for the molecular detection of genitourinary
N. gonorrhoeae
infections in men.
Aeromonas*
Authors: Lamy Brigitte 
Published: January 2025

Abstract

Members of the genus
Aeromonas
are Gram‐negative facultative anaerobes that are straight, coccobacillary to bacillary cells with rounded ends.
Aeromonas
species are environmental opportunistic pathogens, involved in numerous types of diseases, including gastroenteritis and infections at a variety of extraintestinal sites, of which blood and wounds are the most common. Most clinical infections with aeromonads are related to an exposure to some type of aquatic source, whether the clinical specimen is feces or extraintestinal, and to a lesser extent to the ingestion of foods. Aeromonads survive well in specimens, and any of the widely used transport media are acceptable for transport, with Cary‐Blair generally considered to be the best for feces transportation. Whole‐genome sequencing is the reference method to identify aeromonads or to describe a novel species. Strains show a propensity to acquire resistance genes and to disseminate them to other bacteria. Antimicrobial susceptibility testing of local isolates is necessary because of emerging resistance.
Bacteroides
,
Porphyromonas
,
Prevotella
,
Fusobacterium
, and Other Anaerobic Gram‐Negative Rods
Authors: Conrads Georg , Nagy Elisabeth , Könönen Eija 
Published: January 2025

Abstract

With increasing use of sequencing techniques, obligate anaerobic Gram‐negative rods are increasingly detected in clinical infections, such as brain or liver abscesses with
Prevotella
and
Fusobacterium
species predominating. Production of pigment is visible characteristic valuable in presumptive identification; the pigmented Gram‐negative anaerobic rods are composed of saccharolytic and asaccharolytic species of the genera
Prevotella
and
Porphyromonas
and pigment‐producing
Alistipes
species.
Bacteroides
species can be involved in part in polymicrobial necrotizing soft tissue infections, and the
B. fragilis
group is, after Gram‐positive anaerobic cocci, one of the most common anaerobes found in infected moderate to severe diabetic foot wounds. Antimicrobial resistance among Gram‐negative anaerobes continues to rise. The chapter gives characteristics of anaerobic Gram‐negative genera that have grown from clinical specimens.
Algorithms for Identification of Curved and Spiral‐Shaped Gram‐Negative Rods
Authors: Nachamkin Irving 
Published: January 2025

Abstract

Curved and spiral‐shaped bacteria have a common microscopic morphology but represent diverse bacterial pathogens. These organisms are curved, helical, or spiral‐shaped Gram‐negative rods. Most bacteria in this group of organisms are isolated from patients with gastrointestinal tract‐related infections, but may be isolated from blood cultures, wound cultures, or other less common specimen types. Increased hydrogen levels in the microaerobic environment are important for isolation of some
Campylobacter
and
Helicobacter
species. Many clinical laboratories use rapid identification systems such as matrix‐assisted laser desorption/ionization–time of flight mass spectrometry for quick identification of bacterial agents isolated in primary culture, or use multiplex molecular amplification systems for direct detection of common enteric pathogens in fecal samples. The chapter describes few laboratories perform conventional biochemical identification of the organisms.
Treponema
and
Brachyspira
Authors: Seña Arlene C. , Pillay Allan , Radolf Justin D. 
Published: January 2025

Abstract

Spirochetal phylotypes identified in the human mouth belong exclusively to the genus
Treponema
.
Brachyspira
spp. are oxygen‐tolerant anaerobes differentiated by phenotypic growth characteristics and degree of beta‐hemolysis. The epidemiologic importance of
Treponema denticola
and other oral treponemes arises to a great extent from their occurrence as members of the polymicrobial consortium that causes gingivitis and periodontitis. Two Brachyspira species,
Brachyspira aalborgi
and
Brachyspira pilosicoli
, have been associated definitively with human intestinal spirochetosis. The method used for direct detection of
Treponema pallidum
depends upon the stage of disease, the clinical presentation, and the type of specimen obtained.
T. pallidum
can be detected in lesion exudate by darkfield microscopy or nucleic acid amplification tests. Most infants with congenital syphilis are asymptomatic at birth. Serologic tests play an important role in syphilis diagnosis by supplementing direct detection methods for early syphilitic lesions, for diagnosing latent infection, and confirming suspected tertiary disease.
General Approaches to Identification of
Mycoplasma
,
Ureaplasma
, and Obligately Intracellular Bacteria
Authors: Bébéar Cécile , Dumler J. Stephen 
Published: January 2025

Abstract

This chapter focuses on
Mycoplasma
and
Ureaplasma
species, and provides characterization of
Coxiella burnetii
and
Tropheryma whipplei
, a requirement for intracellular growth. The most frequently used tests in clinical microbiology laboratories, Gram staining and culture on artificial media, are often unable to detect these organisms if they are present in clinical samples. Diagnosis of infections caused by these bacteria has traditionally been accomplished by Giemsa and Wright stains of clinical samples, by detection of antibody responses to infection using a variety of serologic tests, or by histopathologic analysis of biopsy samples. Molecular diagnostic tools and enhanced culture methods have significantly improved the ability to detect these agents and to diagnose the diseases they cause. The chapter summarizes the epidemiology of these infections and the diagnostic tests most often used for detection of the causative bacteria.
Rickettsia
and
Orientia
Authors: Blanton Lucas S. , Walker David H. , Bouyer Donald H. 
Published: January 2025

Abstract

The family
Rickettsiaceae
comprises two genera of small, obligately intracellular bacteria that reside free within the host cell's cytosol, namely,
Rickettsia
and
Orientia
. Pathogenic
Rickettsia
spp. reside in an arthropod host for at least a part of their life cycle, during which they are maintained by transovarian transmission and/or cycles involving horizontal transmission to vertebrate hosts. Nucleic acid amplification testing has been applied to the amplification of the DNA of spotted fever group and typhus group rickettsiae, usually from peripheral blood, buffy coat, or plasma and occasionally from fresh, frozen, or paraffin‐embedded tissue and from swabs of the ulcerated bases of eschars. The limited quantities of circulating rickettsial DNA during infection greatly hinder the clinical sensitivity of molecular detection from peripheral blood specimens. Species identification of rickettsial isolates was performed by microimmunofluorescence serotyping. Enzyme immunoassay has become an increasingly used method to detect antibodies reactive against
Orientia tsutsugamushi
.
Special Phenotypic Methods for Detecting Antibacterial Resistance
Authors: Simner Patricia J. , Humphries Romney M. 
Published: January 2025

Abstract
Special phenotypic tests may be performed as an adjunct or surrogate to standard antimicrobial susceptibility testing methods to help characterize an isolate's antimicrobial susceptibility to a drug or drug class or detect a particular resistance mechanism or phenotype. Special phenotypic susceptibility tests are categorized into supplemental tests, screening tests, surrogate agent tests, and equivalent agent tests. Phenotypic methods for the detection of resistance have been developed for use with both clinical specimens and cultured growth. Resistance to streptomycin is mediated by a different resistance mechanism, and consequently, streptomycin resistance must be determined separately from gentamicin resistance. Although erythromycin and clindamycin are in separate antimicrobial agent classes, i.e., macrolides and lincosamides, respectively, their mechanisms of action and mechanisms of resistance are similar. Antimicrobial resistance among Gram‐negative bacilli, and especially resistance to β‐lactam agents, is a serious public health concern worldwide.
Susceptibility Test Methods: Mycobacteria,
Nocardia
, and Other Actinomycetes
Authors: Brown‐Elliott Barbara A. , Cirillo Daniela‐Maria , Musser Kimberlee A. , Rowlinson Marie‐Claire 
Published: January 2025

Abstract

This chapter includes a description of the main laboratory tools for the detection of antimicrobial resistance (drug resistance) in tuberculosis (TB), other mycobacterial infections, and aerobic actinomycetes. Nontuberculous mycobacteria (NTM) and aerobic actinomycetes can also cause substantial disease in humans. The incidence of NTM infection continues to increase, particularly in certain patient populations, and AST for NTM and aerobic actinomycetes is an important component of optimal patient care. The chapter discusses the antimicrobial agents that are used in treating mycobacterial infections. It discusses antimicrobial agents in alphabetical order. For TB, first‐line drugs are less toxic, can be given orally using short‐course therapy, and are used to treat pulmonary TB disease susceptible to those agents.
Nocardia
spp. and other aerobic actinomycetes can cause serious disease in immunocompromised and occasionally even healthy hosts. In vitro susceptibility testing should be performed on all clinically significant isolates to serve as a guide for therapy and to monitor for resistance.
Influenza Viruses
Authors: Atmar Robert L. 
Published: January 2025

Abstract

The influenza viruses are members of the family
Orthomyxoviridae
. The transmission of influenza viruses to people from avian and swine species highlights the need for vigilant surveillance for such events. Antigen detection assays are used in a variety of formats to rapidly detect influenza viruses in clinical specimens and to confirm the identity of isolates grown in culture. Influenza viruses have been detected in clinical specimens by direct and indirect visualization of their typical morphological appearance by electron microscopy. Influenza virus isolation procedures should be performed under biosafety level 2 conditions. Influenza virus infections are also identified by serologic methods. The pandemic strain may develop because of genetic reassortment following coinfection of a susceptible host with human and animal influenza viruses or through gradual adaptation of an avian strain to mammalian hosts.
Rhinoviruses
Authors: Landry Marie Louise , Lu Xiaoyan 
Published: January 2025

Abstract

Human rhinoviruses (RVs) are members of the family
Picornaviridae
. RVs derive their name from the predominant site of their replication and symptomatology, the nose. The wider use of molecular methods in viral diagnostics has led to the discovery of a novel group of RVs identified in patients with lower respiratory tract disease. Symptoms of RV infection parallel the rise and fall of chemical mediators of inflammation. Psychological stress and inadequate sleep appear to increase susceptibility and the development of clinical symptoms. A presumptive diagnosis of RV isolates in cell culture is made by the appearance and progression of characteristic cytopathic effects in the appropriate cell lines. Serotyping of RV isolates by neutralization with type‐specific antisera used to be the gold standard for RV identification. Molecular typing based on reverse transcription polymerase chain reaction and amplicon sequencing has essentially replaced serotyping for type‐specific identification of RVs.
Hepatitis A and E Viruses
Authors: Izopet Jacques , Kamar Nassim 
Published: January 2025

Abstract

Hepatitis A virus (HAV) is a species of the genus
Hepatovirus
within the family
Picornaviridae
. HAV has a primitive capsid related to picorna‐like viruses, which infect insects. Hepatitis E virus (HEV) belongs to the
Hepeviridae
family. HAV is a small RNA virus with an icosahedral capsid. Close contact between infected and susceptible people is the most common mode of HAV transmission in developing and developed countries. HAV can be transmitted by transfusion of blood or blood products on rare occasions. HAV and HEV are both transmitted mainly by the fecal‐oral route. Occurrence of clinical manifestations of hepatitis E in immunocompetent individuals is associated with high viral load. Enzyme or chemiluminescent immunoassays for anti‐HAV IgM and IgG are commercially available in microplate and multiparametric automated formats. Regarding HEV infection, the availability of high‐performance serologic and molecular tools allowed a significant change in the understanding of global epidemiology and pathology.
Aspergillus
,
Talaromyces
, and
Penicillium
Authors: Chen Sharon C.‐A. , Meyer Wieland , Sorrell Tania C. , Halliday Catriona L. 
Published: January 2025

Abstract

The genus
Aspergillus
is classified in the family Trichocomaceae of the Ascomycota. The majority of human infections due to known
Aspergillus
species are caused by
A. fumigatus
, followed by
A. flavus
,
A. terreus
, and
A. niger
, with recognition that these designations represent complexes of closely related species.
Aspergillus
species are environmental saprophytes that thrive in decaying vegetation and are readily cultured from soil, water, certain foods, and air.
Aspergillus
DNA can be detected in clinical specimens either by nucleic acid amplification methods specifically targeting
Aspergillus
or by panfungal PCR assays followed by DNA sequencing for species identification.
Penicillium sensu lato
is associated with two teleomorphic genera:
Eupenicillium
and
Talaromyces
. Assays have been developed to detect antibodies to
Talaromyces marneffei
,
Talaromyces marneffei
antigen, or both in serum and other body fluids in various test formats, including immunodiffusion, indirect immunofluorescence, and enzyme‐linked immunosorbent assay.
Fusarium
and Other Opportunistic Hyaline Fungi
Authors: Zhang Sean X. , O'Donnell Kerry , Wiederhold Nathan P. , Cañete‐Gibas Connie F. 
Published: January 2025

Abstract

The opportunistic hyaline or lightly colored molds constitute a phylogenetically diverse group of common to rare fungi, some of which are only known to reproduce asexually while others possess sexual and asexual life cycles. Serologic procedures currently have little clinical utility in the diagnosis of uncommon hyaline opportunistic fungi. Identification of uncommon hyaline molds should always be evaluated considering the patient's immune status as well as the anatomic site of recovery and frequency of isolation. This chapter describes the salient colony and microscopic features of medically important species in the genus
Fusarium
and other select hyaline opportunists. As for
Aspergillus
and
Candida
, multilocus DNA typing systems have been developed to identify clinically and veterinary important isolates of
Fusarium
. The typical antifungal susceptibility profiles of
Fusarium
species are of relative resistance to most antifungal agents.