bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevention of Laboratory‐Acquired Infections
Authors: Lagacé‐Wiens Philippe , Pentella Michael 
Published: January 2025

Abstract
Biosafety is protection of the laboratorian from acquiring illness due to pathogens handled in the laboratory. In contrast, biosecurity is protecting the pathogens from acquisition by those who would use them for harmful purposes. The foundational components of a biorisk management program are the performance of risk assessments, selection of mechanisms to mitigate risk, assessment of staff competency, training, an active biosafety committee, performance of safety audits, collaboration with the occupational health program, and continual improvement of the biosafety practices. The risk assessment is a critical tool to prevent laboratory‐acquired infections. Laboratory preparedness is the ability to recognize and respond to occupational, personal, and public health threats and hazards at all times. The blood‐borne pathogens most commonly associated with laboratory infections are hepatitis B virus, hepatitis C virus, and HIV. The investigation and management of laboratory exposures and laboratory infections vary considerably according to the pathogen and type of exposure.
Approaches to the Identification of Aerobic Gram‐Positive Cocci
Authors: Nielsen Xiaohui Chen , Christensen Jens Jørgen 
Published: January 2025

Abstract

The majority of aerobic, or facultatively anaerobic, Gram‐positive cocci isolated from clinical specimens are distributed among the genera
Staphylococcus
,
Streptococcus
, and
Enterococcus
. As new genera and species of aerobic Gram‐positive cocci are described and characterized, it becomes increasingly difficult to identify some of the less frequently isolated organisms solely on the basis of phenotypic traits. Nucleic acid amplification methods for identification of some of the commonly isolated aerobic Gram‐positive cocci are commercially available and designed for use in medium‐ to large‐volume clinical microbiology laboratories. One of the most useful methods for molecular characterization of aerobic Gram‐positive cocci of clinical interest is comparison of 16S rRNA gene sequences, although sequence comparison of other genes may also be helpful for identification.
Enterococcus
Authors: Teixeira Lúcia Martins , da Glória Siqueira Carvalho Maria , Facklam Richard R. , Shewmaker Patricia Lynn 
Published: January 2025

Abstract

The genus
Enterococcus
includes microorganisms that have a historical connection with the genus
Streptococcus
, as they were initially considered a distinct branch within the genus
Streptococcus
, including most of the serological group D streptococci. Transmission of vancomycin‐resistant enterococci represents a major public health concern. By using molecular typing approaches, the exogenous acquisition of enterococcal strains by direct and indirect contact among patients was demonstrated, breaking the traditional conception that enterococcal infections were endogenous. Serologic tests, in the form of Western blot assays, for detecting antibody responses to different enterococcal antigens have been proposed, but their usefulness in the clinical laboratory setting for the diagnosis or prognosis of enterococcal infections has not been demonstrated. The significance of a particular enterococcal isolate is a major factor in determining when antimicrobial testing should be done.
Bacillus
and Other Aerobic Endospore‐Forming Bacteria
Authors: Turenne Christine Y. , Alexander David C. 
Published: January 2025

Abstract

Historically, most aerobic endospore‐forming bacteria were classified as species of
Bacillus
.
Bacillus
is the type genus of the
Bacillaceae
and contains the largest number of species. Aerobic endospore‐forming bacteria are ubiquitous in nature. Cases of anthrax due to laboratory accidents, biological warfare, and bioterrorism events are also rare, but ongoing vigilance in the clinical microbiology laboratory is critical. This chapter describes the clinically significant infections involving
Bacillus
,
Brevibacillus
,
Lysinibacillus
, and
Paenibacillus
species. Members of the
B. cereus
group, other than
B. anthracis
,have been isolated from diverse ecological niches and are widely distributed in nature. Gastrointestinal anthrax is suspected only if an adequate history of the patient is known. Anthrax meningitis may occur on its own or, more frequently, as a complication of another form of the disease.
Escherichia
and
Shigella
Authors: Humphries Romney M. , Faron Matthew L. , Dekker John P. , Ledeboer Nathan A. , Buchan Blake W. 
Published: January 2025

Abstract

Members of the genera
Escherichia
and
Shigella
are most often associated with infections of the gastrointestinal and urinary tracts, but may also cause more severe systemic or invasive infections including pneumonia, sepsis, and meningitis. This chapter provides an overview of each genus and discusses key aspects of taxonomy, epidemiology, and virulence, along with culture‐dependent and culture‐independent methodologies for the identification and classification of species within these genera. It discusses recent trends in antimicrobial resistance patterns and updates to recommended susceptibility testing modalities and interpretive criteria to understand the current best practice for treating active infections. The epidemiology and clinical impact of EIEC are difficult to ascertain because of its close relationship to
Shigella
and the difficulty in distinguishing EIEC from
Shigella
by using biochemical, phenotypic, and molecular methods. Appropriate transport of fecal specimens is essential for effective culture‐based recovery of bacterial pathogens associated with gastroenteritis.
Vibrio
and Related Organisms
Authors: Glover William A. , Boucher Yann F. , Lee Christine C. , Tarr Cheryl L. 
Published: January 2025

Abstract

Phylogenetic investigations indicate that multiple monophyletic clades (separate or distinct groups in a phylogenetic sense) exist within
Vibrio
, which has led to the reclassification of some species into different genera. The genera covered in this chapter are ubiquitous in aquatic environments, primarily marine waters. Pertinent clinical histories (when known) should accompany specimens to alert the laboratory to include appropriate isolation media for the
Vibrionaceae
in their stool workup; this is especially important in areas where the isolation of
Vibrio
is infrequent. Direct microscopic detection of vibrios in stool is not routinely recommended, since it may not be possible to distinguish pathogenic vibrios from other members of the enteric microbiota. Reagents for the serodiagnosis of cholera are available only in specialized reference laboratories, but titration of acute‐ and convalescent‐phase sera in agglutination, vibriocidal, or antitoxin tests is considered reliable.
Bordetella
and Related Genera
Authors: Kilgore Paul E. , Coenye Tom 
Published: January 2025

Abstract

Bordetellae are catalase positive and oxidize amino acids, but no carbohydrates are fermented.
Achromobacter
species are Gram‐negative, nonsporulating, small bacilli.
Alcaligenes
species are Gram‐negative, strictly aerobic rods or coccobacilli that possess oxidase and catalase activity. Cells of
Kerstersia
and
Advenella
species are Gram‐negative, small, and rod‐shaped or coccoid and occur alone, in pairs, or in short chains. Motility is strain dependent. Cells from
Paenalcaligenes
species are Gram‐negative, small rods. Many
Achromobacter
species have been recovered from clinical samples or from the hospital environment. Direct fluorescent‐antibody staining (DFA) on nasopharyngeal swabs or aspirates to detect
B. pertussis
or
B. parapertussis
is rapid and simple but lacks adequate sensitivity and specificity; for this reason, DFA is not recommended.
Francisella*
Authors: Dietrich Elizabeth A. , Petersen Jeannine M. 
Published: January 2025

Abstract

Francisella tularensis
is the causative agent of tularemia, an acute and fatal illness in animals and humans. Within the genus
Francisella
,
F. tularensis
is joined by several lesser‐known
Francisella
species which are largely environmental organisms.
F. novicida
,
F. philomiragia
,
F. hispaniensis
, and
F. opportunistica
cause rare opportunistic infections in immunocompromised individuals. The clinical spectrum of tularemia depends on the mode of transmission, the virulence of the infecting strain, the immune status of the host, and timely diagnosis and treatment. Once an isolate has been identified as a
Francisella
sp., supplemental tests can be used for additional characterization, including typing of species, subspecies, and strain. Agglutination testing, by either the tube agglutination or the microagglutination method, is a standard serological test for determining the presence of antibodies in tularemia.
Anaerobic Non‐Spore‐Forming Gram‐Positive Rods
Authors: Butler‐Wu Susan M. , She Rosemary C. 
Published: January 2025

Abstract

Anaerobic, Gram‐positive, non‐spore‐forming bacilli are widely distributed among the phyla
Actinomycetota
and
Bacillota
. The traditional genera
Actinomyces
,
Actinobaculum
,
Actinotignum
,
Mobiluncus
,and
Varibaculum
all belong to the family
Actinomycetaceae
. The large degree of taxonomic heterogeneity among members of the genus Actinomyces has been recognized for some time. Many Eubacterium species are closely related to clostridia.
Actinotignum schaalii
is the species most frequently implicated in human disease among the genera
Actinotignum
and
Actinobaculum
. The Gram‐variable, curved Gram‐positive rods of the genus
Mobiluncus
can be detected in samples from the female vaginal tract. The cutaneous group of propionibacteria, now reclassified as
Cutibacterium
species, are members of the skin microbiota.
Leptospira
Authors: Galloway Renee L. , Gulvik Christopher A. 
Published: January 2025

Abstract

The genus
Leptospira
comprises spiral‐shaped bacteria with hooked ends. This genus, along with the genera
Leptonema
and
Turneriella
, makes up the family
Leptospiraceae
in the order
Spirochaetales
and class
Spirochaetes
of the phylum
Spirochaetae
. Leptospires are divided into serovars defined by agglutination after cross‐absorption with homologous antigen. Leptospires are ubiquitous, either free‐living in water or wet soil, or associated with renal colonization of mammals. Knowledge of the prevalent serovars and their maintenance hosts is essential for understanding the epidemiology of the disease. The clinical presentation of leptospirosis is biphasic, with a septicemic phase lasting about a week, followed by the immune phase, characterized by antibody production and excretion of leptospires in the urine. Nucleic acid amplification tests, such as PCR, have been widely used for detection of leptospires. Leptospiral DNA has been amplified from blood, plasma, serum, urine, aqueous humor, cerebrospinal fluid, and tissues obtained at autopsy or biopsy.
Mechanisms of Resistance to Antibacterial Agents
Authors: Bradford Patricia A. , Castanheira Mariana 
Published: January 2025

Abstract
Bacterial pathogens have developed resistance to antibacterial agents via multiple routes. The emergence of antimicrobial resistance phenotypes is directly linked to the use of any given anti microbial agent. Resistance to aminoglycosides occurs by several different mechanisms that can coexist in the same bacterial cell. β‐Lactam antibiotics act by inhibiting penicillin‐binding proteins, which are transpeptidases and transglycosylases that synthesize the peptidogly can that composes the bacterial cell wall. The main bacterial resistance mechanism against fluoroquinolonesis is the alteration of their target in the deoxyribonucleic acid synthesis process. Tetracyclines are bacteriostatic antibiotics that inhibit bacterial growth by binding to the ribosome, thereby preventing protein synthesis. Nitrofurantoin is a synthetic antibacterial agent that is only used in the treatment of urinary tract infections. Rifampin is particularly active against Gram‐positive bacteria and mycobacteria. Daptomycin is a cyclic lipopeptide antibiotic with activity exclusively against Gram‐positive bacteria.
Antimicrobial Susceptibility Test Methods: Dilution and Disk Diffusion Methods
Authors: Koeth Laura M. , Miller Linda A. 
Published: January 2025

Abstract
The performance of antimicrobial susceptibility tests (ASTs) to help guide patient therapy is one of the most important functions of a clinical microbiology laboratory. The most commonly used AST methods to date can be categorized into dilution methods that generate minimum inhibitory concentration values and disk diffusion methods that generate a zone diameter result. Most clinical microbiology laboratories in the United States and in many developed countries utilize manual or automated commercial dilution products that provide AST results which are demonstrated to correspond to the International Organization for Standardization/Clinical and Laboratory Standards Institute broth microdilution reference method. This chapter provides descriptions, context, advantages, and disadvantages for each of the methods: broth microdilution, broth macrodilution, agar dilution, and disk diffusion. The convenience afforded by the availability of sterile microdilution trays with round or conical bottoms for use in dilution susceptibility testing led to the widespread use of broth microdilution methods.
A Practical Guide to the Taxonomy, Classification, and Characterization of Clinically Important Viruses
Authors: Drews Steven D. 
Published: January 2025

Abstract
This chapter focuses on the characterization, classification, and taxonomy of viruses that infect humans, both pathogens that infect humans alone and those that infect humans but may also infect other mammalian or nonmammalian genera and species. While other forms of life encode genetic information within double‐stranded DNA (dsDNA), viruses encode their genetic information within genomes that may be composed of single‐stranded RNA, double‐stranded RNA, single‐stranded DNA, and dsDNA. The Baltimore classification, a nonhierarchical approach, categorizes viruses into seven groups and is based on the genome present in virions and type of replication. Classification of viruses below the level of species is not standardized across all species by the International Committee on Taxonomy of Viruses, but in some cases, subspecies standardization does occur. Between 2016 and 2021, a series of changes have occurred in the taxonomy of viruses that infect humans.
Respiratory Syncytial Virus and Human Metapneumovirus
Authors: Berry Gregory J. , Babady N. Esther 
Published: January 2025

Abstract

Human respiratory syncytial virus (RSV) is a member of the genus
Orthopneumovirus
, family
Pneumoviridae
, order
Mononegavirales
. Most general viral specimen collection principles also apply to specimen collection for RSV detection and culture. Although RSV can be visualized by electron microscopy, its application has been limited to research laboratories. However, characteristic syncytial cytopathic effects in lung biopsies can facilitate the diagnosis. Human metapneumovirus (HMPV) virus belongs to the order
Mononegavirales
, the family
Pneumoviridae
, and the genus
Metapneumovirus
, which also includes avian metapneumovirus, also known as turkey rhinotracheitis virus, a cause of respiratory tract infections in turkeys, ducks, and chickens. HMPV is the only human pathogen within the genus
Metapneumovirus
.
Orthopneumovirus
, the other genus in the family
Pneumoviridae
, includes the closely related human RSV.
Gastroenteritis Viruses
Authors: Hindiyeh Musa , Das Shubhagata , Dunbar Sherry 
Published: January 2025

Abstract

Acute viral gastroenteritis (AVG) is a common self‐limiting illness affecting infants, children, and adults worldwide. In developed countries, AVG is associated with significant morbidity in children and the elderly, while in developing countries these infections have been associated with high morbidity and mortality, especially in infants. The clinical manifestation of AVG is due to the effects that the virus and its specific cytotoxins exert on the enterocytes of the intestine. AVG can be triggered by many viruses, most often rotavirus, caliciviruses, enteric adenoviruses 40/41, and astroviruses. The luciferase immunoprecipitation system assay, a liquid‐phase immunoassay that quantifies antigen‐specific serum antibodies, has also been used for the quantitation of
Norovirus
antibodies. Antibody‐neutralization assays have been used for evaluating antibodies induced post RV vaccination. The major advantage of molecular diagnostic methods is the increased sensitivity and specificity for common viruses, such as rotaviruses and adenoviruses, and the ability to detect uncultivable viruses such as noroviruses, astroviruses, and sapoviruses.
Rabies Lyssavirus
Authors: Orciari Lillian A. , Yager Pamela A. , Satheshkumar P. S. 
Published: January 2025

Abstract

This chapter provides information on taxonomy, description of the agent, epidemiology and transmission, clinical significance, collection, transport, and storage of specimens, direct detection methods, isolation procedures, typing systems, serologic tests, and antiviral susceptibilities of Rabies Lyssavirus infection. There are numerous etiologic agents in the genus
Lyssavirus
that result in an acute, fatal viral encephalomyelitis known as rabies in both humans and animals. Rabies is a zoonotic disease. All mammals are susceptible. The main route of transmission is introduction of saliva containing RABV into a wound via the bite of a rabid animal. Direct methods may be used to detect histopathological changes and viral antigen (inclusions) and to observe virion morphology. These methods include: microscopy, antigen detection, and nucleic acid detection. Identification of a
Lyssavirus
infection is made typically by direct examination of brain impressions and demonstration of specific viral inclusions by DFA testing.
Arboviruses
Authors: Hunsperger Elizabeth A. , Hughes Holly R. , Ritter Jana M. , Brault Aaron C. 
Published: January 2025

Abstract

Arthropod‐borne viruses are transmitted to vertebrate hosts through the bites of infected arthropods and cause over 80 diseases in humans. The medically important arboviruses are found primarily within the families
Togaviridae
,
Flaviviridae
,
Peribunyaviridae
,
Phenuiviridae
, and
Nairoviridae
. Arboviruses are RNA viruses of either positive or negative polarity. Arbovirus replication takes place in the cytoplasm of susceptible cells following viral entry. Many mosquito‐borne arboviruses are most commonly transmitted in tropical and subtropical regions of the world and are highly dependent on the presence of the vector and an amplifying host. Virus isolation serves as a confirmatory test for reverse transcription‐PCR‐positive specimens, helps to further characterize circulating strains for molecular epidemiology studies, and serves to identify novel or emerging arboviral agents. The hemagglutination inhibition assay is a classic test used for arbovirus diagnostics and was the basis for virus family classification prior to genome sequencing.
Human Papillomaviruses
Authors: Cuschieri Kate , Unger Elizabeth R. 
Published: January 2025

Abstract

Papillomaviruses are in the family
Papillomaviridae
. Human papillomavirus (HPV) initiates infection in primitive basal‐like epithelial cells, accessed through minor trauma or at specialized sites of epithelial transition, particularly the squamocolumnar junction. The epidemiology and transmission of genital and nongenital infections differ significantly. Nongenital infections manifesting as hand and foot warts are most common in children and adolescents. The epidemiology and natural history of genital or mucosal HPV differ by anatomic site, by sex, and by age. Warts are more common in immunocompromised individuals, including organ transplant recipients, those infected with HIV, and pregnant women. Recurrent respiratory papillomatosis is a rare condition characterized by benign papillomatous lesions of the larynx and other parts of the upper respiratory tract that are characteristically resistant to treatment. Nucleic acid amplification technologies are the mainstay of clinical HPV tests, particularly those designed to inform screening and management of cervical disease.
Parvovirus B19V, Bocaviruses, and Other Human Parvoviruses
Authors: Söderlund‐Venermo Maria 
Published: January 2025

Abstract

Parvoviruses are small, nonenveloped icosahedral viruses with a linear single‐stranded‐DNA (ssDNA) genome in the family
Parvoviridae
in the realm
Monodnaviria
. The family
Parvoviridae
is divided into three subfamilies,
Parvovirinae
,
Densovirinae
, and the new
Hamaparvovirinae
, on the basis of their ability to infect vertebrates, invertebrates, or both, respectively, and their NS1 amino acid sequences. The first human parvoviruses identified were the nonpathogenic adeno‐associated viruses of the genus
Dependoparvovirus
, which are increasingly used in gene therapy. Human bocavirus (HBoV1) has the typical structure of a member of the
Parvoviridae
. The most common test for diagnosis of HBoV1 infection is DNA detection by qualitative PCR. Parvoviruses are unable to induce cells to divide, so they require actively dividing cells for their replication.
Antiviral Agents
Authors: Santos Carlos A.Q. , Reyna Quito Manuela Jannet 
Published: January 2025

Abstract
There are five classes of antiviral agents for the treatment of human immunodeficiency virus type 1 (HIV‐1): nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs/NtRTIs), nonucleoside reverse transcriptase inhibitors, protease inhibitors (PIs), entry/fusion inhibitors, and integrase strand transfer inhibitors. PIs are commonly used in combined antiretroviral therapy regimens in combination with NRTI and/or NtRTIs for maximum antiretroviral activity and to minimize the development of resistance. Integrase Strand Transfer Inhibitors a class of antiretroviral drugs, target the HIV‐1 integrase enzyme that mediates transfer of the reverse‐transcribed HIV‐1 DNA into the host chromosome. The common target for antiviral drugs active against both viruses is the reverse transcriptase function of the HIV and hepatitis B virus (HBV) replication enzymes. Chronic HBV infection plays an important role in the morbidity and mortality of HIV‐infected patients. Most of the antiviral compounds that are approved to treat the eight human herpesviruses are nucleoside or nucleotide analogues, which inhibit DNA replication.
Leishmania
and
Trypanosoma
Authors: da Silva Alexandre J. , Ndao Momar 
Published: January 2025

Abstract

Leishmania
spp. and
Trypanosoma
spp. belong to the Trypanosomatida in the eukaryote supergroup Excavata. Although microcopy techniques cannot be used to identify
Leishmania
spp. to the species level, the microscopic detection of
Leishmania
amastigotes in clinical specimens continues to be invaluable. Serologic tests including indirect fluorescent‐antibody testing, enzyme‐linked immunoassays, and immunoblot tests may give mixed results when applied to the diagnosis of leishmaniasis. The likelihood of a positive skin test increases with parasite burden and the time the patient has been infected with
Leishmania
parasites. Although vectorial transmission is considered the most important mode of transmission, leishmaniasis can also be transmitted by direct contact with an infected lesion or mechanically through bites by stable flies/dog flies. Molecular techniques for the detection of leishmanial nucleic acid have been used for diagnosis, predicting prognosis, and species identification.