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Douglas AP, Stewart AG, Halliday CL, Chen SCA. Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management. J Fungi (Basel) 2023; 9:1059. [PMID: 37998865 PMCID: PMC10672668 DOI: 10.3390/jof9111059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.
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Affiliation(s)
- Abby P. Douglas
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Adam G. Stewart
- Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women’s Hospital Campus, The University of Queensland, Herston, QLD 4006, Australia;
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
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Chaturvedi S, Victor TR, Marathe A, Sidamonidze K, Crucillo KL, Chaturvedi V. Real-time PCR assay for detection and differentiation of Coccidioides immitis and Coccidioides posadasii from culture and clinical specimens. PLoS Negl Trop Dis 2021; 15:e0009765. [PMID: 34529679 PMCID: PMC8486383 DOI: 10.1371/journal.pntd.0009765] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/01/2021] [Accepted: 08/25/2021] [Indexed: 11/19/2022] Open
Abstract
Coccidioidomycosis (Valley fever) is a pulmonary and systemic fungal disease with increasing incidence and expanding endemic areas. The differentiation of etiologic agents Coccidioides immitis and C. posadasii remains problematic in the clinical laboratories as conventional PCR and satellite typing schemes are not facile. Therefore, we developed Cy5- and FAM-labeled TaqMan-probes for duplex real-time PCR assay for rapid differentiation of C. immitis and C. posadasii from culture and clinical specimens. The RRA2 gene encoding proline-rich antigen 2, specific for Coccidioides genus, was the source for the first set of primers and probe. Coccidioides immitis contig 2.2 (GenBank: AAEC02000002.1) was used to design the second set of primers and probe. The second primers/probe did not amplify the corresponding C. posadasii DNA, because of an 86-bp deletion in the contig. The assay was highly sensitive with limit of detection of 0.1 pg gDNA/PCR reaction, which was equivalent to approximately ten genome copies of C. immitis or C. posadasii. The assay was highly specific with no cross-reactivity to the wide range of fungal and bacterial pathogens. Retrospective analysis of fungal isolates and primary specimens submitted from 1995 to 2020 confirmed 168 isolates and four primary specimens as C. posadasii and 30 isolates as C. immitis from human coccidioidomycosis cases, while all eight primary samples from two animals (rhesus monkey and rhinoceros) were confirmed as C. posadasii. A preliminary analysis of cerebrospinal fluid (CSF) and pleural fluid samples showed positive correlation between serology tests and real-time PCR for two of the 15 samples. The Coccidioides spp. duplex real-time PCR will allow rapid differentiation of C. immitis and C. posadasii from clinical specimens and further augment the treatment and surveillance of coccidioidomycosis.
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Affiliation(s)
- Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, University at Albany, Albany, New York, United States of America
- * E-mail: (SC); (VC)
| | - Tanya R. Victor
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Anuradha Marathe
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Ketevan Sidamonidze
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Kelly L. Crucillo
- Coccidioidomycosis Serology Laboratory, Department of Medical Microbiology and Immunology, University of California School of Medicine, Davis, California, United States of America
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- * E-mail: (SC); (VC)
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Reyes-Montes MDR, Frías-De-León MG, Victoriano-Pastelín I, Acosta-Altamirano G, Duarte-Escalante E. Design and evaluation of an AFLP molecular marker for the detection of Coccidioides spp. in biological samples. Braz J Infect Dis 2019; 23:322-330. [PMID: 31539511 PMCID: PMC9428003 DOI: 10.1016/j.bjid.2019.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 12/01/2022] Open
Abstract
At present, there is no standardized marker that is routinely used in clinical laboratories to diagnose coccidioidomycosis. Thus, the goals of this study were to obtain a sequence characterized amplified region (SCAR) marker for the identification of Coccidioides spp., evaluate its specificity and sensitivity in fungal DNA-spiked blood and sputum samples, and compare it with previously described molecular markers. Specific amplified fragment length polymorphism (AFLP) amplicons for Coccidioides immitis and Coccidioides posadasii were cloned into the vector pGEM® -T Easy vector and sequenced to develop a SCAR marker. Oligonucleotides were designed to identify Coccidioides spp. by polymerase chain reaction (PCR), and the specificity and sensitivity of these oligonucleotides were tested with the DNA from related pathogens. The specificity and sensitivity of the SCAR marker was evaluated with blood and sputum samples spiked with Coccidioides DNA and compared with other previously described markers (621, GAC2, and Ag2/PRA). In addition, the conditions for its use were established using biological samples. A specific marker named SCAR300 was obtained to identify Coccidioides spp. that exhibited good sensitivity and specificity. The results showed that all of the markers tested in this study can identify Coccidioides spp. However, the SCAR300 and 621 markers were the most sensitive, whereas the SCAR300 marker was the most specific. Thus, the SCAR300 marker is a useful tool to identify Coccidioides spp.
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Affiliation(s)
- María Del Rocío Reyes-Montes
- Facultad de Medicina (UNAM), Departamento de Microbiología y Parasitología, Laboratorio de Micología Molecular, Ciudad de México, Mexico
| | | | - Isai Victoriano-Pastelín
- Facultad de Medicina (UNAM), Departamento de Microbiología y Parasitología, Laboratorio de Micología Molecular, Ciudad de México, Mexico
| | - Gustavo Acosta-Altamirano
- Hospital Regional de Alta Especialidad de Ixtapaluca, Dirección de Investigación, Ixtapaluca, Mexico
| | - Esperanza Duarte-Escalante
- Facultad de Medicina (UNAM), Departamento de Microbiología y Parasitología, Laboratorio de Micología Molecular, Ciudad de México, Mexico.
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Verhasselt HL, Radke J, Schmidt D, Killengray D, Scharmann U, Rickerts V, Hansen W, Seidel D, Falces‐Romero I, Buer J, Rath P, Steinmann J. Comparison of genotyping methods forCunninghamella bertholletiae. Mycoses 2019; 62:519-525. [DOI: 10.1111/myc.12908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 01/30/2019] [Accepted: 02/18/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Hedda Luise Verhasselt
- Institute of Medical Microbiology University Hospital Essen University of Duisburg‐Essen Essen Germany
| | - Julia Radke
- Institute of Medical Microbiology University Hospital Essen University of Duisburg‐Essen Essen Germany
| | - Dirk Schmidt
- Institute of Medical Microbiology University Hospital Essen University of Duisburg‐Essen Essen Germany
| | - David Killengray
- Institute of Medical Microbiology University Hospital Essen University of Duisburg‐Essen Essen Germany
| | - Ulrike Scharmann
- Institute of Medical Microbiology University Hospital Essen University of Duisburg‐Essen Essen Germany
| | - Volker Rickerts
- FG 16: Erreger von Pilz‐, und Parasiteninfektionen und Mykobakteriosen, Konsiliarlabor für Kryptokokkose und seltene Systemmykosen Robert Koch‐Institut Berlin Germany
| | - Wiebke Hansen
- Institute of Medical Microbiology University Hospital Essen University of Duisburg‐Essen Essen Germany
| | - Danila Seidel
- Department I of Internal Medicine University Hospital of Cologne Cologne Germany
| | - Iker Falces‐Romero
- Clinical Microbiology Department Hospital Universitario La Paz Madrid Spain
| | - Jan Buer
- Institute of Medical Microbiology University Hospital Essen University of Duisburg‐Essen Essen Germany
| | - Peter‐Michael Rath
- Institute of Medical Microbiology University Hospital Essen University of Duisburg‐Essen Essen Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology University Hospital Essen University of Duisburg‐Essen Essen Germany
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology Hospital Nuremberg Paracelsus Medical University Nuremberg Germany
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Teixeira MM, Barker BM. Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides. Emerg Infect Dis 2018; 22:1022-30. [PMID: 27191589 PMCID: PMC4880095 DOI: 10.3201/eid2206.151565] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Although Coccidioides genotypes are highly genetically variable,
they cluster into discrete populations, which has implications for human
infections. During the past 20 years, a general picture of the genetic diversity and population
structure of Coccidioides, the causal agent of coccidioidomycosis
(Valley fever), has emerged. The genus consists of 2 genetically diverse species,
C. immitis and C. posadasii, each of which
contains 1 or more distinct populations with limited gene flow. Genotypic data
indicate that C. immitis is divided into 2 subpopulations (central
and southern California populations) and C. posadasii is divided
into 3 subpopulations (Arizona, Mexico, and Texas/South America populations).
However, admixture within and among these populations and the current paucity of
environmental isolates limit our understanding of the population genetics of
Coccidioides. We assessed population structure of
Coccidioides in Arizona by analyzing 495 clinical and
environmental isolates. Our findings confirm the population structure as previously
described and indicate a finer scale population structure in Arizona. Environmental
isolates appear to have higher genetic diversity than isolates from human
patients.
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Kirkland TN, Fierer J. Coccidioides immitis and posadasii; A review of their biology, genomics, pathogenesis, and host immunity. Virulence 2018; 9:1426-1435. [PMID: 30179067 PMCID: PMC6141143 DOI: 10.1080/21505594.2018.1509667] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/31/2018] [Indexed: 11/24/2022] Open
Abstract
Coccidioides immitis and C. posadasii are two highly pathogenic dimorphic fungal species that are endemic in the arid areas of the new world, including the region from west Texas to southern and central California in the USA that cause coccidioidomycosis (also known as Valley Fever). In highly endemic regions such as southern Arizona, up to 50% of long term residents have been infected. New information about fungal population genetics, ecology, epidemiology, and host-pathogen interactions is becoming available. However, our understanding of some aspects of coccidioidomycosis is still incomplete, including the extent of genetic variability of the fungus, the genes involved in virulence, and how the changes in gene expression during the organism's dimorphic life cycle are related to the transformation from a free-living mold to a parasitic spherule. Unfortunately, efforts to develop an effective subunit vaccine have not yet been productive, although two potential live fungus vaccines have been developed.
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Affiliation(s)
- Theo N. Kirkland
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Joshua Fierer
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, San Diego, CA, USA
- VA Healthcare San Diego, San Diego, CA, USA
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Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How? Clin Microbiol Rev 2017; 30:671-707. [PMID: 28490578 DOI: 10.1128/cmr.00043-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for Candida spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Cryptococcus neoformans, Pneumocystis jirovecii, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.
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Del Rocío Reyes-Montes M, Pérez-Huitrón MA, Ocaña-Monroy JL, Frías-De-León MG, Martínez-Herrera E, Arenas R, Duarte-Escalante E. The habitat of Coccidioides spp. and the role of animals as reservoirs and disseminators in nature. BMC Infect Dis 2016; 16:550. [PMID: 27724885 PMCID: PMC5057265 DOI: 10.1186/s12879-016-1902-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 10/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coccidioidomycosis, a potentially fatal fungal infection, is considered an emergent mycotic disease because of the increased incidence of fungal infections registered over recent years. Infection occurs through the inhalation of arthroconidia from two main species of Coccidioides: Coccidioides immitis and C. posadasii, which are both endemic to arid and semi-arid regions of North America. Coccidioides species not only infect humans but can also infect other mammals (land, aquatic, wild or domestic), reptiles and birds. OBJECTIVE To obtain information regarding the habitat of Coccidioides spp. and the animals infected by this fungus and to identify the role that infected animals play as reservoirs and disseminators of this fungus in nature. MATERIALS A literature review was conducted to identify the habitat of Coccidioides spp. and the infected non-human animal species targeted by this fungus. RESULTS AND CONCLUSIONS This review allows us to suggest that Coccidioides spp. may be classified as halotolerant organisms; nevertheless, to perpetuate their life cycle, these organisms depend on different animal species (reservoirs) that serve as a link with the environment, by acting as disseminators of the fungi in nature.
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Affiliation(s)
- María Del Rocío Reyes-Montes
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Coyoacán, 04510, México Cd.Mx., Mexico
| | - María Ameyali Pérez-Huitrón
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Coyoacán, 04510, México Cd.Mx., Mexico
| | - Jorge Luis Ocaña-Monroy
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Coyoacán, 04510, México Cd.Mx., Mexico
| | - María Guadalupe Frías-De-León
- División de Investigación, Hospital Juárez de México, Edificio E. Av. Instituto Politécnico Nacional 5160, Col. Magdalena de las Salinas, 07760, México Cd.Mx., Mexico
| | - Erick Martínez-Herrera
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Coyoacán, 04510, México Cd.Mx., Mexico
| | - Roberto Arenas
- Unidad de Micología, Hospital General "Manuel Gea González", Av. Calzada de Tlalpan 4800, Tlalpan, 14080, México, Cd.Mx., Mexico
| | - Esperanza Duarte-Escalante
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Coyoacán, 04510, México Cd.Mx., Mexico.
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Local Population Structure and Patterns of Western Hemisphere Dispersal for Coccidioides spp., the Fungal Cause of Valley Fever. mBio 2016; 7:e00550-16. [PMID: 27118594 PMCID: PMC4850269 DOI: 10.1128/mbio.00550-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Coccidioidomycosis (or valley fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year. This infection is caused by two sibling species, Coccidioides immitis and C. posadasii, which are endemic to specific arid locales throughout the Western Hemisphere, particularly the desert southwest of the United States. Recent epidemiological and population genetic data suggest that the geographic range of coccidioidomycosis is expanding, as new endemic clusters have been identified in the state of Washington, well outside the established endemic range. The genetic mechanisms and epidemiological consequences of this expansion are unknown and require better understanding of the population structure and evolutionary history of these pathogens. Here we performed multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure in C. posadasii and demonstrate the presence of distinct geographic clades in central and southern Arizona as well as dispersed populations in Texas, Mexico, South America, and Central America. Although a smaller number of C. immitis strains were included in the analyses, some evidence of phylogeographic structure was also detected in this species, which has been historically limited to California and Baja, Mexico. Bayesian analyses indicated that C. posadasii is the more ancient of the two species and that Arizona contains the most diverse subpopulations. We propose a southern Arizona-northern Mexico origin for C. posadasii and describe a pathway for dispersal and distribution out of this region. Coccidioidomycosis, or valley fever, is caused by the pathogenic fungi Coccidioides posadasii and C. immitis. The fungal species and disease are primarily found in the American desert southwest, with spotted distribution throughout the Western Hemisphere. Initial molecular studies suggested a likely anthropogenic movement of C. posadasii from North America to South America. Here we comparatively analyze eighty-six genomes of the two Coccidioides species and establish local and species-wide population structures to not only clarify the earlier dispersal hypothesis but also provide evidence of likely ancestral populations and patterns of dispersal for the known subpopulations of C. posadasii.
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Affiliation(s)
- Eric R. G. Lewis
- Pathogen Genomics Division, Translational Genomics Institute, Flagstaff, Arizona, United States of America
- Northern Arizona Center for Valley Fever Research, Translational Genomics Institute, Flagstaff, Arizona, United States of America
- * E-mail: (ERGL); (JRB); (BMB)
| | - Jolene R. Bowers
- Pathogen Genomics Division, Translational Genomics Institute, Flagstaff, Arizona, United States of America
- * E-mail: (ERGL); (JRB); (BMB)
| | - Bridget M. Barker
- Pathogen Genomics Division, Translational Genomics Institute, Flagstaff, Arizona, United States of America
- Northern Arizona Center for Valley Fever Research, Translational Genomics Institute, Flagstaff, Arizona, United States of America
- Center for Microbial Genetic and Genomics, Department of Biology, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail: (ERGL); (JRB); (BMB)
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Recent advances in our understanding of the environmental, epidemiological, immunological, and clinical dimensions of coccidioidomycosis. Clin Microbiol Rev 2014; 26:505-25. [PMID: 23824371 DOI: 10.1128/cmr.00005-13] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Coccidioidomycosis is the endemic mycosis caused by the fungal pathogens Coccidioides immitis and C. posadasii. This review is a summary of the recent advances that have been made in the understanding of this pathogen, including its mycology, genetics, and niche in the environment. Updates on the epidemiology of the organism emphasize that it is a continuing, significant problem in areas of endemicity. For a variety of reasons, the number of reported coccidioidal infections has increased dramatically over the past decade. While continual improvements in the fields of organ transplantation and management of autoimmune disorders and patients with HIV have led to dilemmas with concurrent infection with coccidioidomycosis, they have also led to advances in the understanding of the human immune response to infection. There have been some advances in therapeutics with the increased use of newer azoles. Lastly, there is an overview of the ongoing search for a preventative vaccine.
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Duarte-Escalante E, Zúñiga G, Frías-De-León MG, Canteros C, Castañón-Olivares LR, Reyes-Montes MDR. AFLP analysis reveals high genetic diversity but low population structure in Coccidioides posadasii isolates from Mexico and Argentina. BMC Infect Dis 2013; 13:411. [PMID: 24004977 PMCID: PMC3766708 DOI: 10.1186/1471-2334-13-411] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 08/30/2013] [Indexed: 01/29/2023] Open
Abstract
Background Coccidioides immitis and C. posadasii cause coccidioidomycosis, a disease that is endemic to North and South America, but for Central America, the incidence of coccidioidomycosis has not been clearly established. Several studies suggest genetic variability in these fungi; however, little definitive information has been discovered about the variability of Coccidioides fungi in Mexico (MX) and Argentina (AR). Thus, the goals for this work were to study 32 Coccidioides spp. isolates from MX and AR, identify the species of these Coccidioides spp. isolates, analyse their phenotypic variability, examine their genetic variability and investigate the Coccidioides reproductive system and its level of genetic differentiation. Methods Coccidioides spp. isolates from MX and AR were taxonomically identified by phylogenetic inference analysis using partial sequences of the Ag2/PRA gene and their phenotypic characteristics analysed. The genetic variability, reproductive system and level of differentiation were estimated using AFLP markers. The level of genetic variability was assessed measuring the percentage of polymorphic loci, number of effective allele, expected heterocygosity and Index of Association (IA). The degree of genetic differentiation was determined by AMOVA. Genetic similarities among isolates were estimated using Jaccard index. The UPGMA was used to contsruct the corresponding dendrogram. Finally, a network of haplotypes was built to evaluate the genealogical relationships among AFLP haplotypes. Results All isolates of Coccidioides spp. from MX and AR were identified as C. posadasii. No phenotypic variability was observed among the C. posadasii isolates from MX and AR. Analyses of genetic diversity and population structure were conducted using AFLP markers. Different estimators of genetic variability indicated that the C. posadasii isolates from MX and AR had high genetic variability. Furthermore, AMOVA, dendrogram and haplotype network showed a small genetic differentiation among the C. posadasii populations analysed from MX and AR. Additionally, the IA calculated for the isolates suggested that the species has a recombinant reproductive system. Conclusions No phenotypic variability was observed among the C. posadasii isolates from MX and AR. The high genetic variability observed in the isolates from MX and AR and the small genetic differentiation observed among the C. posadasii isolates analysed, suggest that this species could be distributed as a single genetic population in Latin America.
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Affiliation(s)
- Esperanza Duarte-Escalante
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No, 3000, México, D, F, 04510, México.
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Brilhante RSN, de Lima RAC, Ribeiro JF, de Camargo ZP, Castelo-Branco DDSCM, Grangeiro TB, Cordeiro RDA, Gadelha Rocha MF, Sidrim JJC. Genetic diversity of Coccidioides posadasii from Brazil. Med Mycol 2012; 51:432-7. [PMID: 23167705 DOI: 10.3109/13693786.2012.731711] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Studies of the genetic variation within populations of Coccidioides posadasii are scarce, especially for those recovered from South America. Understanding the distribution of genotypes among populations is important for epidemiological surveillance. This study evaluated the genetic diversity of 18 Brazilian strains of C. posadasii through the sequencing of the 18-28S region of nuclear rDNA, as well as through RAPD and M13-PCR fingerprinting techniques. The sequences obtained were compared to Coccidioides spp. previously deposited in GenBank. The MEGA5 program was used to perform phylogenetic analyses. Within the C. posadasii clade, a single cluster was observed, containing seven isolates from Ceará, which presented a single nucleotide polymorphism. These isolates were from the same geographical area. The strains of C. posadasii showed a lower rate of genetic diversity in the ITS1 and ITS2 regions. The results of M13 and RAPD-PCR fingerprinting indicated a similar electrophoretic profile. No differences between clinical and environmental isolates were detected. This was the first study assessing the genetic variability of a larger number of C. posadasii isolates from Brazil.
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Barker BM, Tabor JA, Shubitz LF, Perrill R, Orbach MJ. Detection and phylogenetic analysis of Coccidioides posadasii in Arizona soil samples. FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2011.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Engelthaler DM, Chiller T, Schupp JA, Colvin J, Beckstrom-Sternberg SM, Driebe EM, Moses T, Tembe W, Sinari S, Beckstrom-Sternberg JS, Christoforides A, Pearson JV, Carpten J, Keim P, Peterson A, Terashita D, Balajee SA. Next-generation sequencing of Coccidioides immitis isolated during cluster investigation. Emerg Infect Dis 2011; 17:227-32. [PMID: 21291593 PMCID: PMC3204756 DOI: 10.3201/eid1702.100620] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Next-generation sequencing enables use of whole-genome sequence typing (WGST) as a viable and discriminatory tool for genotyping and molecular epidemiologic analysis. We used WGST to confirm the linkage of a cluster of Coccidioides immitis isolates from 3 patients who received organ transplants from a single donor who later had positive test results for coccidioidomycosis. Isolates from the 3 patients were nearly genetically identical (a total of 3 single-nucleotide polymorphisms identified among them), thereby demonstrating direct descent of the 3 isolates from an original isolate. We used WGST to demonstrate the genotypic relatedness of C. immitis isolates that were also epidemiologically linked. Thus, WGST offers unique benefits to public health for investigation of clusters considered to be linked to a single source.
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Sheff KW, York ER, Driebe EM, Barker BM, Rounsley SD, Waddell VG, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS, Keim PS, Engelthaler DM. Development of a rapid, cost-effective TaqMan Real-Time PCR Assay for identification and differentiation of Coccidioides immitis and Coccidioides posadasii. Med Mycol 2010; 48:466-9. [PMID: 20370360 DOI: 10.3109/13693780903218990] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Coccidioidomycosis is an infection caused by Coccidioides immitis or C. posadasii. We developed a TaqMan real-time PCR assay that rapidly and accurately differentiates the species. This assay can be used as a tool to improve disease surveillance, increase understanding of the natural history of the infection, and assist in clinical differentiation studies.
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Affiliation(s)
- Kelly W Sheff
- Translational Genomics Research Institute, Pathogen Genomics Division (TGen North), 3051 West Shamrell Boulevard, Flagstaff, Arizona, USA
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Baden LR, Digumarthy SR, Guimaraes ASR, Branda JA. Case records of the Massachusetts General Hospital. Case 35-2009. A 60-year-old male renal-transplant recipient with renal insufficiency, diabetic ketoacidosis, and mental-status changes. N Engl J Med 2009; 361:1980-9. [PMID: 19907046 DOI: 10.1056/nejmcpc0900645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Lindsey R Baden
- Division of Infectious Disease, Brigham and Women's Hospital, USA
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