bluuebunny/crossref_metadata_2025 huggingface dataset:
Ehrlichia
,
Anaplasma
, and Related Intracellular Bacteria
Authors: Theel Elitza S. , Pritt Bobbi S.
Published: December 2024

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 Herpesvirus 8
Authors: Dollard Sheila C. , Gunthel Clifford J.
Published: December 2024

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Objective

Patients 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.

Methods

We 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.

Results

We 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).

Conclusion

RA 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.
Bifunctional Catalysts with Separated and Tunable Sites on Zeolites for Relay Catalysis of the Oxidative Dehydrogenation of Propane Using CO2
Authors: Li Wanting , Wang Tianchang , Cao Xinxin , Li Yuze , Miao Gai , Sun Nannan , Li Jiong , Han Wei , Wei Wei , Chen Xinqing
Published: December 2024

The oxidative dehydrogenation of propane using CO2 (CO2‐ODH) technology has broad application prospects in the production of propylene and the utilization of CO2, and the development of efficient CO2‐ODH catalysts is of great significance. However, it remains a challenge to develop a highly efficient catalyst that can activate both C─H and C═O. Herein, a PtZn/Co@S‐1 catalyst with a very low precious metal content of 0.2 wt.% is reported. Benefiting from the PtZn4 nanoclusters dispersed on the surface of Silicalite‐1 zeolite and tetrahedrally coordinated Co2+ in the Silicalite‐1 zeolite framework via relay catalysis, the independent dual sites structure (PtZn/Co@S‐1) greatly promotes CO2‐ODH reaction with a high conversion rate of both C3H8 (59.7%) and CO2 (44.3%), and propylene selectivity of 94.9%, thus upsetting the equilibrium for direct dehydrogenation of propane. Experimental measurements and density functional theory calculations suggest that the PtZn4 and Co2+ interfaces are likely propane dehydrogenation and carbon dioxide hydrogenation active sites respectively.
Embedded Bioprinting of Breast Cancer–Adipose Composite Tissue Model for Patient‐Specific Paracrine Interaction Analysis
Authors: Jeong Wonwoo , Han Jonghyeuk , Choi Jeonghan , Kang Hyun‐Wook
Published: December 2024

The interaction between breast cancer and stromal tissues varies significantly from patient to patient, greatly impacting cancer prognosis. However, conventional models struggle to accurately replicate these patient‐specific interactions. Herein, a novel breast cancer–adipose composite tissue model capable of precisely adjusting the inter‐tissue interaction is developed. The composite tissue model is produced through precise embedded bioprinting of breast‐cancer spheroids and live‐adipose‐tissue ink. This model possessed not only precisely patterned cancer spheroids but also well‐preserved intrinsic extracellular matrices (ECMs) and heterogeneous cell populations of adipose tissue (AT). Evaluation results successfully demonstrated that the bioprinted composite model can precisely regulate adipokine secretion, drug resistance, and cancer‐cell invasion characteristics by adjusting the distance between the cancer spheroids and adipose tissue. The utility of the model is validated using adipokine‐targeted therapies (C‐compound/SC600125 (SC), AG 490 (AG), and Metformin (MET)). Interestingly, the inhibition of cancer cell proliferation and invasion by these adipokine‐targeted drugs nearly doubled as the tissue distance decreased. This suggests that the efficacy of the drugs can be precisely evaluated using the new model. These findings underscore the potential of the developed composite model to replicate patient‐specific crosstalk, thereby offering a promising platform for the sophisticated evaluation of various breast‐cancer therapies.
Deep Learning‐Assisted Design of Novel Donor–Acceptor Combinations for Organic Photovoltaic Materials with Enhanced Efficiency
Authors: Zhang Shizhao , Li Shuixing , Song Siqin , Zhao Yang , Gao Liang , Chen Hongzheng , Li Hanying , Lin Jiaping
Published: December 2024

Designing donor (D) and acceptor (A) structures and discovering promising D‐A combinations can effectively improve organic photovoltaic (OPV) device performance. However, to obtain excellent power conversion efficiency (PCE), the trial‐and‐error structural design in the infinite chemical space is time‐consuming and costly. Herein, a deep learning (DL)‐assisted design framework for OPV materials is proposed. To effectively digitally represent the D and A structures, a structure representation method, polymer fingerprints, is developed, and a database of OPV materials is constructed. By applying an end‐to‐end graph neural network modeling method, high‐precision DL models for predicting OPV performance are established. After combining the existing structures, ≈0.6 million virtual D‐A combinations are generated. Then, the OPV performance of these candidate combinations is predicted by the well‐trained models, and numbers of novel D‐A combinations with high efficiency are identified. Experimental validations confirm that the prediction accuracy is greater than 93% and one of the screened combinations (i.e., D18:BTP‐S11) exhibits an efficiency above 19.3% in single‐junction organic solar cells. Finally, based on the structural gene analysis, the design rules to guide experimental explorations are suggested. The developed DL‐assisted approach can accelerate the design of D‐A combinations with ultrahigh efficiency and bring property breakthroughs for OPV devices.
Enhance Photo‐Stability of Up‐Scalable Organic Solar Cells: Suppressing Radical Generation in Polymer Donors
Authors: Xiao Mengfei , Wang Chen , Xu Yujie , Zhang Wenqing , Fu Zhen , Qiao Jiawei , Wang Hao , Xia Xinxin , Zhang Maojie , Qin Wei , Hao Xiaotao , Du Xiaoyan
Published: December 2024

The power conversion efficiency (PCE) of single‐junction organic solar cells (OSCs) has been promoted above 20%. Device up‐scaling draws more and more research attentions. Besides the high PCE for devices with up‐scalable fabrication methods and conditions, achieving high stability simultaneously is essential for pushing industrialization of this technology. Here, the stability of the state‐of‐the‐art OSCs blade‐coated in air with non‐halogenated solvents in a wide thickness range is thoroughly investigated. The losses in short‐circuit current density under photo‐thermal stress strongly depend on processing conditions. Devices with less crystalline phases in unit thickness show faster generation of trap states and hence strongly reduced charge collection efficiency. Through in‐depth photo‐chemical, photo‐physical, and morphological characterizations during ageing, faster generation of radicals in PM6 for active layers with more amorphous structures is identified as the cause for device degradation. Increasing the crystallinity of active layer films for suppressing radical generation in polymer donors is critical to enhance the photo‐thermal stability of devices processed in air with a wide thickness range.