bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yersiniaceae
Authors: Kingry Luke C. , Gladney Lori , Petersen Jeannine M. 
Published: January 2025

Abstract

The family
Yersiniaceae
includes two well‐known pathogenic genera,
Serratia
and
Yersinia
, and multiple other genera which inhabit a wide range of ecological niches.
Serratia marcescens
is the
Serratia
species most often isolated from clinical specimens and can cause urinary tract infections, pneumonia, bloodstream infections, endocarditis, and wound infections. This chapter primarily focuses on the taxonomy, detection, and identification of
Serratia
and
Yersinia
.
Yersiniaceae
members are Gram‐negative rods that are non‐spore‐forming, oxidase‐negative, catalase‐positive facultative anaerobes which display nonfastidious growth. The
Yersiniaceae
are widely distributed throughout the environment and transmitted to humans via arthropod bites, contact with infected animals, ingestion of contaminated food or water, or exposure to hospital environments and medical procedures. Serology can be used as an adjunct in the diagnosis of disease due to
Yersinia enterocolitica
or
Yersinia pseudotuberculosis
. Many
S. marcescens
strains carry both chromosomally encoded and plasmid‐mediated resistance determinants for several different types of antimicrobials.
Pseudomonas
Authors: Høiby Niels , Bjarnsholt Thomas , Ciofu Oana 
Published: January 2025

Abstract

Pseudomonas
is a large and complex genus of Gram‐negative bacteria that is important because it includes species with both clinical and environmental implications.
Pseudomonas
spp. are conventionally described as aerobic species based on their growth in routine media used in the clinical microbiology laboratory, but several species are actually facultative aerobes. The identification of fluorescent and nonfluorescent pseudomonads has become less difficult with the availability of MALDI‐TOF MS technology, which has replaced conventional phenotypic identification systems in many clinical microbiology laboratories. However, phenotypic methods are still used in small laboratories, and it should be recognized that these methods also provide information about the physiological and biochemical capabilities of the bacteria, which may sometimes be important for the pathogenesis of infections. The frequent acquisition of antimicrobial resistance in
P. aeruginosa
limits the utility of antimicrobial susceptibility patterns as a tool in epidemiological typing.
Burkholderia
,
Stenotrophomonas
,
Ralstonia
,
Cupriavidus
,
Pandoraea
,
Brevundimonas
,
Comamonas
,
Delftia
, and
Acidovorax
Authors: Lipuma John J. , Currie Bart J. , Baird Robert W. , Vandamme Peter A. R. 
Published: January 2025

Abstract

Many of the bacteria discussed in this chapter formerly belonged to the genus Pseudomonas; others were described and named after the taxonomic dissection of this genus to conform to a modern phylogeny‐based taxonomy.
Burkholderia
,
Ralstonia
,
Cupriavidus
,
Pandoraea
,
Brevundimonas
,
Comamonas
,
Delftia
, and
Acidovorax
species are aerobic, non‐spore‐forming, straight or slightly curved Gram‐negative rods. Several molecular genetic methods are available to assess the relatedness of isolates of these genera during nosocomial or community outbreak investigations. Of the organisms discussed in this chapter, serologic tests have been used clinically to diagnose only infections with
B. pseudomallei
. Given the uncertainty regarding the role(s)
Delftia
,
Acidovorax
, and
Brevundimonas
play in human infection, antimicrobial susceptibility testing of isolates from human specimens as a matter of routine may not be warranted.
Acinetobacter
,
Chryseobacterium
,
Moraxella
,
Branhamella
and Other Nonfermentative Gram‐Negative Rods
Authors: Cools Piet , Nemec Alexandr , Abeele Anne‐Marie van den , Kämpfer Peter 
Published: January 2025

Abstract
This chapter covers the organisms which belong to a group of taxonomically and phylogenetically diverse, Gram‐negative, non‐fermentative rods and coccobacilli. Most of the organisms are found in the environment, that is, soil and water. For each group of closely related species, the chapter presents their taxonomic history, addresses the clinical importance of the species, and describes the phenotypic data that are useful to differentiate this group from other groups and to differentiate the species within this group. It discusses antibiotic susceptibility characteristics and treatment options. Decisions regarding the significance of GNF in a clinical specimen must consider the clinical condition of the patient and the source of the specimen submitted for culture. Identification of GNF may be important to document health care‐related outbreaks linked to hospital environments or medical devices.
Legionella
Authors: Lindsay Diane S. J. , Ricci Maria Luisa 
Published: January 2025

Abstract

The family
Legionellaceae
is composed of a single genus,
Legionella
, and comprises 66 validly named species and three subspecies.
Legionella pneumophila
,
Legionella micdadei
,
Legionella bozemanii
, and
Legionella longbeachae
are the most important species from a clinical standpoint, with
L. pneumophila
causing more than 90% of Legionnaires' disease (LD) globally, apart from Australia and New Zealand, where
L. longbeachae
predominates. LD is a type of bacterial pneumonia caused by
L. pneumophila
and other
Legionella spp
. Identification of
Legionella spp
. in a clinical laboratory is optimally performed by observation of visual morphology, agglutination methods, and matrix‐assisted laser desorption ionization–time of flight mass spectrometry. Antimicrobial agents regarded as effective for treatment of LD are macrolides, fluoroquinolones, and, rarely, rifampin, all achieving adequate intracellular concentrations.
Approaches to the Identification of Anaerobic Bacteria
Authors: Boyanova Lyudmila , Medeiros José Augusto da Silva 
Published: January 2025

Abstract
This chapter focuses on important requirements of anaerobic microbiology and methods and techniques used in the diagnostic workflow. Anaerobic bacteria (anaerobes) can cause infections in all tissues and organs of the human body. The chapter summarizes some important recommendations for specimen collection and handling for diagnosing anaerobic infections. Moreover, since antibiotic resistance in anaerobes and the proportion of patients with immunosuppressive diseases or immunosuppressive therapy are constantly increasing, anaerobic microbiology is becoming increasingly important and must not be neglected in any hospital center or country. The disk diffusion method may facilitate susceptibility testing of anaerobes. However, all microbiology laboratories should, at the minimum, be able to culture and perform basic identification of anaerobes and refer uncommon isolates to a reference laboratory. Both clinicians and laboratory staff should be familiar with the requirements for collection and transport of clinical samples for anaerobic microbiology.
Clostridium, Clostridioides
, and Other Clostridia
Authors: Kuijper Ed J. , Reubsaet Frans A. G. , Barbut Frédéric 
Published: January 2025

Abstract

The genus
Clostridium
comprises obligately anaerobic (or occasionally aerotolerant), Gram‐positive rods commonly found in soil, water, and gastrointestinal tracts of insects and animals, as well as humans. Accurate, definitive identification is needed to better define the role of clostridia in disease, to aid the clinician in selecting optimal treatment, and for public health purposes (e.g., hospital‐acquired
Clostridioides difficile disease
). The isolation of a
Clostridium
species from a clinical specimen, even a blood culture, may or may not be significant clinically, and culture results should be interpreted in relation to the clinical findings for the patient. Identification of clostridia in specimens from sites of infection due to mixed organisms can be time‐consuming and expensive. Typing of
Clostridioides difficile
fosters understanding of the epidemiology of infections and has become increasingly important with the emergence of outbreaks caused by hypervirulent strains.
Helicobacter
Authors: Couturier Marc R. 
Published: January 2025

Abstract

The genus
Helicobacter
is classified in the family
Helicobacteriaceae
of the class
Epsilonproteobacteria
, formerly known as the epsilon subclass of the
Proteobacteria
, with
Helicobacter pylori
as the type species. There are five other genera in the family:
Sulfuricurvum
,
Sulfurimonas
,
Sulfurovum
,
Thiovulum
, and
Wolinella
. Phylogenetic analyses reliant on 16S rRNA gene sequences alone are insufficient for distinguishing closely related helicobacters, which have a high degree of natural transformation and genetic plasticity.
Helicobacter
species are isolated from the gastrointestinal and hepatobiliary tracts of a variety of mammalian and avian hosts. Laboratory tests requiring the collection of other types of specimen have been developed to assist in the diagnosis of
H. pylori
infection and may be undertaken under some circumstances.
H. pylori
is readily isolated by culture from gastric biopsy specimens.
Mycoplasma
and
Ureaplasma
Authors: Waites Ken B. , Bébéar Cécile 
Published: January 2025

Abstract

Mollicutes
are eubacteria that have evolved from
Clostridium
‐like Gram‐positive cells through genome reduction. The term “mycoplasma” is often used in a trivial way to refer to any members of the class
Mollicutes
, irrespective of whether they actually belong to the genus
Mycoplasma
. Mycoplasmas and ureaplasmas of human origin can be classified according to whether they utilize glucose, arginine, or urea. Attachment of
Mycoplasma pneumoniae
to host cells in the respiratory tract of humans is a prerequisite for colonization and infection. Urogenital mycoplasmas of clinical importance include
Mycoplasma genitalium
, a sexually transmitted pathogen, and
Mycoplasma hominis
and
Ureaplasma
spp., commensals of the human urogenital tract.
Ureaplasma
species have been shown to cause systemic and sometimes fatal infections leading to hyperammonemia in immunosuppressed persons who have undergone lung transplantation. Serology has been the most common laboratory means for diagnosis of
M. pneumoniae
respiratory tract infections.
Tropheryma whipplei
Authors: Geißdörfer Walter , Moter Annette , Bogdan Christian 
Published: January 2025

Abstract

Tropheryma whipplei
is the agent of classical Whipple disease, an infection originally described by the American pathologist George Hoyt Whipple in 1907 as intestinal lipodystrophy. Reasons are the rarity of the disease, the diversity and nonspecificity of symptoms, the fastidious nature of the pathogen, and the lack of serological tests. Data from two sequenced
T. whipplei
genomes reveal a small genome lacking key biosynthetic pathways. Whipple disease is a rare condition, with an estimated annual incidence of 1 case per 100,000 to 1,000,000. In classical Whipple disease, infection with
T. whipplei
probably occurs years before clinical manifestations point to the diagnosis.
T. whipplei
was detected in urine sediments by nucleic acid amplification testing in 9 of 12 patients and 10 of 13 patients with classical Whipple disease and in one patient with isolated endocarditis, but not in control persons, including healthy carriers.
Specimen Collection, Transport, and Processing: Virology
Authors: Dunn James J. , Pinsky Benjamin A. 
Published: January 2025

Abstract
This chapter describes preanalytical steps for viral diagnostics involving specimen selection, collection, transport, and processing, as well as details for collection of specific sample types. Depending on the specimen source and type of testing requested, it may be appropriate to place the sample in viral transport medium (VTM). Liquid specimens, such as amniotic fluid, blood, cerebrospinal fluid, urine, and bronchoalveolar lavage fluid, do not generally require VTM. Eye specimens include swabs or scrapings of the conjunctiva, corneal scrapings, and vitreous and aqueous fluids. An oral specimen provides a noninvasive means of detecting infection, and for some viruses, the onset of salivary shedding can indicate recent acquisition. Nonsterile specimens (e.g., upper respiratory tract, skin, lower genital tract, and stool) are obtained from sites that contain normal microbiota, or they are obtained from sterile sites but contact with nonsterile sites is unavoidable during specimen collection.
Reagents, Stains, Media, and Cell Cultures: Virology
Authors: Binnicker Matthew J. 
Published: January 2025

Abstract
This chapter describes the cell lines, reagents, stains, and media used in association with traditional tube and rapid viral culture techniques. In the era of molecular detection and quantification of viral pathogens, the applicability of viral isolation has been questioned. Quality control (QC) in the diagnostic virology laboratory is one component of quality assurance program and refers to the measures included in each assay to verify that the test is working properly and to ensure that a laboratory consistently produces accurate results. Essential to the QC process are the use of internal and external control material and the verification that these controls are performed in accordance with manufacturer criteria for acceptability, adherence to appropriate incubation time and temperatures for the assay, and ensuring that test kits are used prior to expiration. Several commercial sources provide reliable QC material for purchase, including specific strains, purified nucleic acid, antigens, antibodies, and other biological reagents.
Enteroviruses and Parechoviruses
Authors: Stellrecht Kathleen A. , Lamson Daryl M. , Romero José R. 
Published: January 2025

Abstract

Enteroviruses (EVs) are members of the
Picornaviridae
family, with “pico” meaning very small, “rna” indicating an RNA genome, and “viridae” signifying viruses. Traditional criteria for taxonomy and identification of EVs to subgroups were based on patterns of replication in cell cultures, clinical syndromes, or disease and on disease manifestations in suckling mice. EVs and Parechoviruses (PeVs) cause a wide array of both localized and systemic infections that affect many organ systems in patients of all ages. Specimen selection is important for making a diagnosis of EV infection, as asymptomatic shedding, especially in stool, is common. Nucleic acid amplification tests, such as reverse transcriptase PCR, are the recommended method for the detection of EV and PeV because of their enhanced sensitivity and rapid turnaround times. In the clinical setting, situations may arise where EV serology is requested; such is the case for myocarditis and determination of congenital infection in pregnant women.
Coronaviruses
Authors: Mostafa Heba H. , Pinsky Benjamin A. 
Published: January 2025

Abstract
Coronaviruses (CoVs) are so called due to their striking crown of surface projections, reminiscent of the solar corona, which can be seen by electron microscopy. CoVs have been found in a wide range of domestic and wild mammals and birds; however, the particular diversity of strains found in birds and bats suggests that these animals are the natural reservoirs of CoVs, although this may also be the result of sampling bias. The major transmission route of HCoV is likely to be respiratory, although many animal CoVs also have a fecal‐oral route of transmission and can replicate in epithelial cells in both the respiratory and gastrointestinal tracts. HCoVs can be detected by nucleic acid amplification testing in a range of routine upper and lower respiratory tract specimens, such as nasopharyngeal (NP) swabs, NP aspirates, sputum, and bronchoalveolar lavage fluid.
Hepatitis C Virus
Authors: Slev Patricia 
Published: January 2025

Abstract

Hepatitis C virus (HCV) is classified within the family
Flaviviridae
in its own genus
Hepacivirus
. Phylogenetic analysis of helicase sequences has been used to probe its relatedness to other viruses in the family. Serum and plasma are acceptable for HCV nucleic acid amplification tests (NAATs) and serology tests. HCV core antigen detection/quantification tests have been developed as alternatives to HCV RNA assays. HCV genotypes and subtypes can be determined by commercial and laboratory‐developed NAATs based on a variety of biochemical methods. With the emergence of the simplified pangenotypic treatment algorithms for the treatment naive, the clinical utility of baseline testing for the presence of resistance‐associated substitutions (RASs) that are associated with direct‐acting antiviral (DAA) therapy failures has been greatly reduced. Sequencing is the diagnostic method of choice for RAS detection. Initiating DAA therapy is recommended for both acute and pediatric HCV infections.
Herpes Simplex Viruses and Herpes B Virus
Authors: Greninger Alexander L. , Morrow Rhoda Ashley , Jerome Keith R. 
Published: January 2025

Abstract
This chapter provides taxonomy, description of the agent, epidemiology and transmission, clinical significance, direct detection, isolation procedures, identification and typing, serologic tests, and antiviral susceptibilities of Herpes Simplex viruses (HSVs) and Herpes B virus. HSV infections occur worldwide with no seasonal distribution. Most HSV‐1 infections are acquired early in childhood as subclinical or unrecognized infections. Young children may present with classic primary HSV‐1 infection characterized by gingivostomatitis, fever, and marked submandibular lymphadenopathy. Herpes B virus is similar to HSV in terms of genome size and structure and in terms of virion morphology. Herpes B virus can be cultured in monkey kidney and chicken embryo cells. Detection of virus in patient samples without an intervening culture amplification step provides the most rapid diagnosis. Serodiagnosis of herpes B virus infections has been complicated by extensive cross‐reactivity with HSV‐1 and HSV‐2.
Human Herpesviruses 6A, 6B, and 7
Authors: Greninger Alexander L. , Sedlak Ruth Hall , Jerome Keith R. 
Published: January 2025

Abstract

Human herpesvirus (HHV) 6A, HHV‐6B, and HHV‐7 are three distinct virus species that make up the
Roseolovirus
genus. Like HHV‐6, HHV‐7 infection is highly prevalent and infects most individuals during childhood. HHV‐7 DNA has been detected more frequently and at higher loads in affected tissues from non‐immunocompromised patients with interstitial pneumonia. Interpreting HHV‐6 detection by PCR in clinical specimens is complicated by both the ubiquity of subclinical reactivation and inherited chromosomally integrated forms. HHV‐6A and HHV‐6B can be typed through the use of species‐specific monoclonal antibodies and species‐specific PCR assays. The most usual setting for HHV‐6 testing is in the context of immunosuppression, especially hematopoietic cell or solid organ transplantation. Like all herpesviruses, HHV‐7 establishes latency after primary infection, and thus reactivation can later occur, particularly in the setting of immunodeficiency. Cytomegalovirus viremia is also more frequent among recipients with inherited chromosomally integrated HHV‐6.
Human Herpesvirus 8
Authors: Dollard Sheila C. , Gunthel Clifford J. 
Published: January 2025

Abstract

Human herpesvirus 8 (HHV‐8) is classified in the genus
Rhadinovirus
of the subfamily
Gammaherpesvirinae
based on sequence and biological properties. The HHV‐8 genome is double‐stranded DNA approximately 160 kb long and contains over 85 genes, including several genes of host derivation. HHV‐8 is in the small group of DNA viruses that cause cancer in humans, along with Epstein‐Barr virus, human papillomavirus, and hepatitis B virus. Serum and plasma can be used interchangeably in most HHV‐8 serologic tests, and standard procedures for collection and storage of serum and plasma apply. Kaposi's sarcoma is normally a clinical diagnosis that does not involve laboratory testing other than possible histological examination of a lesion biopsy.
Adenoviruses
Authors: Heim Albert , Kajon Adriana E. 
Published: January 2025

Abstract

In 1953, Rowe and colleagues described an “adenoid degeneration agent” that induced spontaneous deterioration of tissue cultures prepared from adenoids of children. In the mid1960s, human adenoviruses (HAdV) were found to cause tumors in rodents, prompting studies that revealed fundamental processes of molecular biology but failed to link the virus convincingly to human cancer. HAdV belong to the
Adenoviridae
family,
Mastadenovirus
genus. Adenoviruses are large, nonenveloped, icosahedral viruses 70 to 90 nm in diameter. Adenovirus infections can be epidemic, endemic, or sporadic, with the pattern of circulation, specific syndrome, and severity varying by type, population, and route of exposure. Adenovirus‐associated gastroenteritis is caused primarily by types 40 and 41 of species HAdV‐F, which are also known as the “enteric adenoviruses.”
Poxviruses
Authors: Satheshkumar P. S. , Olson Victoria A. , Damon Inger K. 
Published: January 2025

Abstract

All poxviruses belong to the family
Poxviridae
and subfamily
Chordopoxviridae
. All naturally occurring poxviruses that infect humans are sporadic zoonotic agents except the
Molluscipoxvirus
MCV, which is transmitted strictly between humans. The clinical appearance of human monkeypox, typified by that seen with the Congo Basin virus, is much like that of smallpox, with fever, a centrifugally distributed vesiculopustular rash, respiratory distress, and in some cases, death from systemic shock. In humans, cowpox lesions occur mainly on the fingers, with reddening and swelling. Human parapoxvirus infection is normally associated with an exposure to sheep, goats, and/or cattle. Electron microscopy could be a method for laboratory diagnosis of poxvirus infections. Serologic methods currently used to detect antibodies against human orthopoxviruses include enzyme‐linked immunosorbent assays, the virus neutralization test, Western blotting, and hemagglutination inhibition. The description of an orthopoxvirus immunoglobulin M assay offers great promise to enhance investigations of orthopoxvirus infection outbreaks, which are often semi‐retrospective.
Mechanisms of Resistance to Antiviral Agents
Authors: Shafer Robert W. , Boivin Guy , Howe Anita Y. M. , Chou Sunwen 
Published: January 2025

Abstract
Understanding the mechanisms of viral drug resistance is critical for clinical management of individuals receiving antiviral therapy, for developing new antiviral drugs, and for drug resistance surveillance. This chapter reviews the mechanisms of resistance to antiviral drugs used to treat infections by eight common viruses: herpes simplex, cytomegalovirus, varicella‐zoster virus, human immunodeficiency virus type 1, influenza A and B, hepatitis B, hepatitis C, and severe acute respiratory syndrome coronavirus 2. Drug‐resistant virus subpopulations may exist at low levels in clinical isolates or may arise only during drug exposure. The error‐prone polymerases in RNA viruses render the development of resistance more frequent than in DNA viruses. Drug‐resistant viruses are identified by in vitro passage experiments in which wild‐type viruses are cultured in increasing concentrations of an inhibitory drug and by ex vivo analysis of virus isolates obtained from individuals receiving antiviral therapy.