bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anaerobic Non‐Spore‐Forming Gram‐Positive Rods
Authors: Butler‐Wu Susan M. , She Rosemary C. 
Published: December 2024

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.
Bacteroides
,
Porphyromonas
,
Prevotella
,
Fusobacterium
, and Other Anaerobic Gram‐Negative Rods
Authors: Conrads Georg , Nagy Elisabeth , Könönen Eija 
Published: December 2024

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: December 2024

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.
General Approaches to Identification of
Mycoplasma
,
Ureaplasma
, and Obligately Intracellular Bacteria
Authors: Bébéar Cécile , Dumler J. Stephen 
Published: December 2024

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: December 2024

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
.
Ehrlichia
,
Anaplasma
, and Related Intracellular Bacteria
Authors: Theel Elitza S. , Pritt Bobbi S. 
Published: December 2024

Abstract

The family
Anaplasmataceae
in the order
Rickettsiales
is composed of several genera of clinically significant bacteria encompassing both human and veterinary pathogens. Members of the genera
Ehrlichia
and
Anaplasma
are the best known, having been recognized as agents of veterinary importance for over a century and as human pathogens since 1987. This chapter focuses on the clinically relevant members of the
Anaplasmataceae
, with particular emphasis on
Anaplasma phagocytophilum
and
Ehrlichia chaffeensis
, the most common human pathogens in this family. The family
Anaplasmataceae
contains small, nonmotile, pleomorphic, obligately intracellular bacteria that reside and propagate within host membrane‐derived vacuoles in the host cell cytoplasm. Like other rickettsiae, members of the
Anaplasmataceae
have a reduced genome size and rely on host cell machinery for survival. As with anaplasmosis, the spectrum of clinical presentations of
Ehrlichia chaffeensis
ehrlichiosis ranges from subclinical infection to life‐threatening disease.
Antibacterial Agents
Authors: Lewis James S. , Bush Karen 
Published: December 2024

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: December 2024

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.
Special Phenotypic Methods for Detecting Antibacterial Resistance
Authors: Simner Patricia J. , Humphries Romney M. 
Published: December 2024

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: Fastidious Bacteria
Authors: Humphries Romney M. , Bard Jennifer Dien 
Published: December 2024

Abstract

Most fastidious bacteria do not grow satisfactorily in standard
in vitro
susceptibility test systems that use unsupplemented media. This chapter summarizes the standard methods recommended by CLSI and EUCAST for antimicrobial susceptibility testing of
Streptococcus
spp.,
H. influenzae
,
N. gonorrhoeae
, and
N. meningitidis
. It summarizes methods for testing the infrequently isolated or fastidious bacteria included in CLSI guideline M45‐A3 and/or EUCAST clinical breakpoint tables. The chapter provides test methods and indications for testing and the reporting of results. Regional and global surveillance studies for antimicrobial resistance among respiratory pathogens including
H. influenzae
,
S. pneumoniae
, and
Moraxella catarrhalis
were conducted regularly. Several bacterial agents are identified as potential agents of bioterrorism by the CDC. The antimicrobial susceptibility patterns for most of these organisms are predictable, so susceptibility testing of naturally occurring isolates is often not necessary.
Susceptibility Test Methods: Mycobacteria,
Nocardia
, and Other Actinomycetes
Authors: Brown‐Elliott Barbara A. , Cirillo Daniela‐Maria , Musser Kimberlee A. , Rowlinson Marie‐Claire 
Published: December 2024

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.
Human T‐Cell Lymphotropic Viruses
Authors: Switzer William M. , Heneine Walid , Owen S. Michele 
Published: December 2024

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: December 2024

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.
Enteroviruses and Parechoviruses
Authors: Stellrecht Kathleen A. , Lamson Daryl M. , Romero José R. 
Published: December 2024

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: December 2024

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 A and E Viruses
Authors: Izopet Jacques , Kamar Nassim 
Published: December 2024

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.
Hepatitis C Virus
Authors: Slev Patricia 
Published: December 2024

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.
Gastroenteritis Viruses
Authors: Hindiyeh Musa , Das Shubhagata , Dunbar Sherry 
Published: December 2024

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.
Arboviruses
Authors: Hunsperger Elizabeth A. , Hughes Holly R. , Ritter Jana M. , Brault Aaron C. 
Published: December 2024

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.
Arenaviruses and Filoviruses
Authors: Raabe Vanessa N. , Gilchrist Alison , Kraft Colleen 
Published: December 2024

Abstract

This chapter focuses on the viruses capable of causing viral hemorrhagic fever (VHF) from two taxa, the families
Arenaviridae
and
Filoviridae
. Some members of these virus families can cause severe VHF with high mortality in localized areas of the world. Continuing detection and isolation of new arenavirus and filovirus species from new geographic locations remains important for public health. Human infection with filoviruses and arenaviruses can cause a wide spectrum of illness. For virus isolation, antigen detection, and RT‐PCR, serum, heparinized plasma, or whole blood should be collected during the acute, febrile stages of illness and frozen on dry ice or in liquid nitrogen vapor. Most arenavirus and filovirus species grow well in cell culture. Early diagnosis of arenavirus and filovirus infections is desirable since specific monoclonal antibody treatments and appropriately selected antiviral drugs are, in certain cases, effective when treatment is initiated soon after onset.
Herpes Simplex Viruses and Herpes B Virus
Authors: Greninger Alexander L. , Morrow Rhoda Ashley , Jerome Keith R. 
Published: December 2024

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.