bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Herpesvirus 8
Authors: Dollard Sheila C. , Gunthel Clifford J. 
Published: December 2024

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: December 2024

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: December 2024

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.
Prion Diseases
Authors: Appleby Brian S. , Safar Jiri G. 
Published: December 2024

Abstract
Prion diseases, originally called transmissible spongiform encephalopathies, are invariably fatal neurodegenerative diseases that affect humans and animals. The unusual biological and biochemical properties of the infectious agent causing the disease were first recognized in studies of scrapie in sheep, which is the prototypic prion disease. Most cases of prion disease in humans arise sporadically, but some are attributed to PRNP mutations, and still others are caused by zoonotic or iatrogenic transmission. The differential diagnosis of prion disease includes rapidly progressive variants of dementias that are usually chronic and slowly progressive, autoimmune diseases, vascular disease, metabolic diseases, vitamin deficiency, malignancy, and infection. Autopsy is currently the gold standard for the diagnosis and classification of prion diseases and the determination of disease origin. The diagnosis or exclusion of prion disease should be based on the whole clinical picture, including clinical and family history, symptomatology, neurological signs, radiographic findings, and laboratory results.
Mechanisms of Resistance to Antiviral Agents
Authors: Shafer Robert W. , Boivin Guy , Howe Anita Y. M. , Chou Sunwen 
Published: December 2024

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.
Susceptibility Test Methods: Viruses
Authors: Pinsky Benjamin A. 
Published: December 2024

Abstract
Testing for viral susceptibility, primarily via genotypic drug resistance mutation testing, is now standard practice for the management of viral infections for optimum patient care. Antiviral resistance is expressed as a drop in the efficacy of a drug to inhibit viral replication. The virus being treated is inherently resistant to the drug(s) being given. Alternatively, host biological and socio‐behavioral factors or inadequate dosing may influence therapeutic success. Host physiologic factors can interfere with a successful clinical response. Viral susceptibility testing can identify resistance and guide patient management strategies. The clinical category and status of the patient are important in determining whether antiviral resistance testing is indicated. Genotypic viral susceptibility testing requires knowledge of the mutations that confer antiviral resistance. FDA‐cleared genotypic antiviral resistance tests include software to analyze the raw sequence and render a resistance interpretation. The pharmaceutical industry is actively investigating and developing new antiviral drugs.
Specimen Collection, Transport, and Processing: Mycology
Authors: Berkow Elizabeth L. , Sexton D. Joseph 
Published: December 2024

Abstract
As in bacteriology, the goals of a good mycology laboratory are to accurately isolate and identify fungi suspected of causing infection. It is the laboratory's responsibility to ensure that specimens are appropriate for the requested test and to provide submitters with the guidelines for proper specimen selection, collection, and transport to the laboratory. This chapter provides general information related to fungal culture from various specimens and is based on historical practice that has been successful. Pretreatment of several specimen types is necessary to maximize the recovery of fungi. Abscess specimens should be collected from the active peripheral edge of open abscesses or aspirated from closed abscesses by use of a syringe. There are presently a wide variety of manual, biphasic, automated, and continuously monitoring systems for blood cultures, but no single commercial system or culture medium can detect all potential blood pathogens.
Reagents, Stains, and Media: Mycology
Authors: Lindsley Mark D. 
Published: December 2024

Abstract

A variety of stains, media, and reagents are available to the mycology laboratory for the detection, isolation, characterization, and identification of yeasts and moulds. Familiarity with the composition and characteristics of these materials is critical to the diagnostic approach when processing specimens from patients with suspected mycotic diseases. Many media are available for the primary inoculation and cultivation of fungi from clinical specimens. Chloramphenicol or gentamicin inhibits most bacterial contaminants, while cycloheximide inhibits most saprobic moulds. Dithiothreitol is a mucolytic agent that can be purchased commercially and has been used to prepare sputum specimens for detection of
Pneumocystis jirovecii
. Alcian blue is a mucopolysaccharide stain useful for visualizing the polysaccharide capsule produced by
Cryptococcus
species in histological sections of tissue. Methenamine silver stains are the most useful stains for visualizing fungi in tissue. Acetate ascospore agar is used for the cultivation of ascosporogenous yeasts such as
Saccharomyces cerevisiae
.
General Approaches for Direct and Indirect Detection and Identification of Fungi
Authors: Fida Madiha , Wengenack Nancy L. , Theel Elitza S. 
Published: December 2024

Abstract
The frequency with which invasive fungal infections (IFIs) occur has markedly increased over the past decade. The ability to rapidly detect and identify the causative fungal agents is essential for the successful management of IFIs. The ability to detect fungi in clinical material depends on several factors, including the quality of the specimen that is received into the laboratory. Microscopic examination of specimens can be carried out with either unfixed specimens or fixed, stained specimens. The use of unfixed specimens has the advantages of being quick and relatively simple to carry out; the use of fixed, stained specimens may highlight features specific to certain fungi and also the host response in tissue, but they take longer to process and hence may delay reporting. Detection of antibodies targeting fungal pathogens may be useful in a range of IFIs, particularly when they occur in immunocompetent patients; however, these assays may have limited use in significantly immunocompromised patients.
Pneumocystis Jirovecii
Authors: Cushion Melanie T. , Smulian A. George , Powers‐Fletcher Margaret V. 
Published: December 2024

Abstract

Fungi in the genus
Pneumocystis
are extracellular, hostobligate, mostly host‐specific, and typically restricted to the lung tissues of mammals, although extrapulmonary manifestations have been reported.
Pneumocystis
species all appear to contain similar life cycle stages, although the clusters of organisms removed from the lungs of the different host species can vary in presentation and size. There is no consensus for a typing system for
P. jirovecii
. Serological assays to detect anti‐
P. jirovecii
antibodies are useful for epidemiological studies, but not for diagnosis of
Pneumocystis pneumonia
. The microscopic demonstration of
P. jirovecii
in tissue and fluids by staining with Gomori methenamine silver or a rapid variant of the Wright‐Giemsa stain, by immunofluorescent assay, or by other stains such as Papanicolaou stain should be considered sufficient for diagnosis.
Fusarium
and Other Opportunistic Hyaline Fungi
Authors: Zhang Sean X. , O'Donnell Kerry , Wiederhold Nathan P. , Cañete‐Gibas Connie F. 
Published: December 2024

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.
Agents of Systemic and Subcutaneous Mucormycosis and Entomophthoromycosis
Authors: Garcia‐Hermoso Dea , Alanio Alexandre , Lanternier Fanny , Lortholary Olivier 
Published: December 2024

Abstract
Mucormycosis and entomophthoromycosis are invasive fungal infections caused by environmental pauciseptate filamentous fungi. Entomophthoromycosis presents as subcutaneous infections with favorable outcome after prolonged azole therapy without surgery, although it is potentially associated with disfiguring lesions. Mucormycosis can develop in HIV‐infected patients and in intravenous‐drug users. The diagnosis of mucormycosis should be considered an emergency, because delaying therapy will affect outcome. One of the major differences between mucormycosis and entomophthoromycosis is that the former occurs mainly in predisposed individuals, whereas the latter occurs mostly in apparently immunocompetent hosts. Culture results should always be interpreted in light of the clinical presentation and along with the results of direct examination and/or histopathology. Therapeutic strategies for basidiobolomycosis and conidiobolomycosis are not standardized because of the lack of clinical trials for these rare infections.
Antifungal Agents
Authors: Lockhart Shawn R. , Berkow Elizabeth L. 
Published: December 2024

Abstract

This chapter summarizes the comparative activities of the major systemic antifungal agents against important groups of fungi. It discusses the characteristics of the several other agents that can be used for the oral or parenteral treatment of superficial, subcutaneous, or systemic fungal infections. The allylamines are a group of synthetic antifungal compounds effective in the topical and oral treatment of dermatophytoses. Terbinafine is a lipophilic drug that is available for oral or topical administration. With the exception of fluconazole and isavuconazole, food has a significant effect on the absorption of azole antifungals. Itraconazole is a lipophilic triazole drug available for oral or parenteral administration. Ketoconazole is a lipophilic drug formulated for oral or topical use. The echinocandins are semisynthetic lipopeptide antifungal agents that target the fungal cell wall. Micafungin is a water‐soluble antifungal agent, derived from a fermentation product of
Coleophoma empetri
.
Susceptibility Test Methods: Yeasts and Filamentous Fungi
Authors: Johnson Elizabeth M. , Arendrup Maiken Cavling 
Published: December 2024

Abstract

Accurate and predictive antifungal susceptibility testing has become imperative and is widely accepted as a useful tool for informing decision making during the management of patients with invasive fungal infections that recommendations for testing appear in management guidelines. Clinical and Laboratory Standards Institute and European Committee for Antimicrobial Susceptibility Testing have both set clinical breakpoints for a number of antifungal agents and fungal species. Breakpoints are species specific, which makes accurate species identification a vital part of breakpoint interpretation. Quality control of minimal inhibitory concentration tests is essential to good laboratory practice. Standardized broth macrodilution and microdilution methods are available for testing molds and yeasts, as are standardized disk diffusion methods for systemically active antifungal drugs. The application of molecular methods to the detection of resistance in isolates of filamentous fungi has proved to be easier in
Aspergillus
isolates than in
Candida
because resistance mechanisms appear to be fewer.
Taxonomy and Classification of Human Eukaryotic Parasites
Authors: Adl Sina M. , Mathison Blaine A. 
Published: December 2024

Abstract
The eukaryotic parasites of medical importance are classically known as protozoan, arthropod, and helminthic parasites; the last includes nematodes, cestodes, trematodes, and acanthocephalans. The modern classification of biological species intends to reflect an evolutionary history of living organisms. Eukaryotes are divided into five monophyletic lineages called supergroups, of which four include human parasites: SAR, Excavata, Amoebozoa, and Opisthokonta. These supergroups replace the previous kingdoms that encompassed the eukaryotes. The chapter outlines basic characters of the parasitic protists by clade and the state of their classification at the level of family and genus. Species are identified by sequencing of the 18S small rRNA gene regions and phylogenetic analysis, and the species identification is verified against reference sequences. Modern specimen analysis is discovering new opportunistic pathogens related to known pathogenic groups, but others unrelated to known pathogenic genera will continue to be encountered.
Leishmania
and
Trypanosoma
Authors: da Silva Alexandre J. , Ndao Momar 
Published: December 2024

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.
Toxoplasma
Authors: Robert‐Gangneux Florence 
Published: December 2024

Abstract

Toxoplasmosis is a worldwide zoonosis caused by infection with the parasite
Toxoplasma gondii
. It is one of the most common parasitic infections in humans and is most typically asymptomatic.
T. gondii
is a protozoan parasite classified in the Apicomplexa: Conoidasida: Coccidia: Eimeriorina, genus Toxoplasma. Serologic prevalence data indicate that toxoplasmosis is one of the most common infections of humans throughout the world. Serologic screening of organ donors and recipients allows the identification of patients at risk of donor‐derived primary infection. Toxoplasmosis can be categorized into four clinical groups: infection acquired in the immunocompetent patient; infection acquired or reactivated in the immunodeficient patient; congenital infection; and ocular infection. Diagnosis of toxoplasmosis is critical in four clinical settings: pregnant women with infection during gestation, newborns with suspected congenital toxoplasmosis, patients with retinochoroiditis, and immunocompromised patients.
Pathogenic and Opportunistic Free‐Living Amebae
Authors: Cope Jennifer R. , Ali Ibne Karim M. , Visvesvara Govinda S. 
Published: December 2024

Abstract

Free‐living amebae belonging to the genera
Naegleria
,
Acanthamoeba
, and
Balamuthia
can infect humans and other animals and cause potentially severe, life threatening disease. This chapter presents a list of clinical syndromes caused by free‐living amebae infections. Free‐living amebae can be cultivated in axenic conditions or in the presence of a mammalian cell culture for research purposes. The real‐time multiplex PCR assay is a fast, sensitive, and robust assay that detects all three pathogenic free‐living amebae,
Acanthamoeba
spp.,
B. mandrillaris
, and
N. fowleri
, simultaneously in a single specimen and has many advantages over conventional PCR. All clinical specimens should first be examined microscopically, and if amebae are visualized, then the clinician should be immediately notified.
Nematodes
Authors: Sheorey Harsha , Biggs Beverley‐Ann , Bradbury Richard S. 
Published: December 2024

Abstract

Nematodes are unsegmented cylindrical worms with a body cavity containing an alimentary canal and genital system; the sexes are separate. They have longitudinal muscles, which allow them to move by flexing their bodies. Molecular diagnosis for intestinal nematodes is increasingly being introduced in diagnostic laboratories. There are a variety of morphological features and DNA sequences which form the basis for taxonomy of nematodes. The primary diagnosis of infection is by demonstration of
A. lumbricoides
eggs in feces. Albendazole is the first choice for treating
A. lumbricoides
, and mebendazole is also effective. Any helminth eggs or larvae found in feces are significant, and treatment is recommended even if the patient is asymptomatic. There is no need to quantitate helminth parasites in a diagnostic context, as this does not necessarily correlate with clinical illness.
Trematodes
Authors: Jones Malcolm K. , A. Gordon Catherine , Mcmanus Donald P. 
Published: December 2024

Abstract

This chapter focuses on members of the clade Digenea of the phylum Platyhelminthes. At least 70 species of digenean trematodes have been recorded as adult parasites in humans. These species are endoparasitic, occupying a variety of tissue sites. Members of the genus
Schistosoma
are blood flukes responsible for the important human disease schistosomiasis. The second strategy, evident in the remainder of the human‐infecting species, is foodborne transmission, and parasites that use this strategy can be termed collectively the foodborne digeneans. For these species, the human‐infective stage, a metacercaria, is ingested with food. The impact of these foodborne trematodes on human health is large. The primary epidemiological features governing human infection include the distribution of suitable snail intermediate hosts, human food consumption behaviors, the presence of suitable zoonotic hosts, and the potential for water contamination with human or animal excreta.
Risk of Incident Heart Failure and Heart Failure Subtypes in Patients With Rheumatoid Arthritis
Authors: Kawano Yumeko , Weber Brittany N. , Weisenfeld Dana , Jeffway Mary I. , Cai Tianrun , McDermott Gregory C. , Liu Qing , Sparks Jeffrey A. , Stuart Jennifer , Joseph Jacob , Cai Tianxi , Liao Katherine P. 
Published: December 2024

ObjectivePatients with rheumatoid arthritis (RA) are at increased risk of cardiovascular disease (CVD) including heart failure (HF). However, little is known regarding the relative risks of HF subtypes such as HF with preserved ejection fraction (HFpEF) or reduced ejection fraction (HFrEF) in RA compared with non‐RA.MethodsWe identified patients with RA and matched non‐RA comparators among participants consenting to broad research from two large academic centers. We identified incident HF and categorized HF subtypes based on EF closest to the HF incident date. Covariates included age, sex, and established CVD risk factors. Cox proportional hazards models were used to estimate the hazard ratios (HRs) for incident HF and HF subtypes.ResultsWe studied 1,445 patients with RA and 4,335 matched non‐RA comparators (mean age 51.4 and 51.7 years, respectively; 78.7% female). HFpEF was the most common HF subtype in both groups (65% in RA vs 59% in non‐RA). Patients with RA had an HR of 1.79 (95% confidence interval [CI] 1.38–2.32) for incident HF compared with those without RA after adjusting for CVD risk factors. Patients with RA had a higher rate of HFpEF (HR 1.99, 95% CI 1.43–2.77), but there was no statistical difference in the HFrEF rate (HR 1.45, 95% CI 0.81–2.60).ConclusionRA was associated with a higher rate of HF overall compared with non‐RA, even after adjustment for established CVD risk factors. The elevated risk was driven by HFpEF, supporting a role for inflammation in HFpEF and highlighting potential opportunities to address this excess risk in RA.