Disease surveillance in recombining pathogens: Multilocus genotypes identify sources of human<i>Coccidioides</i>infections

Fisher, Matthew C.; Rannala, Bruce; Chaturvedi, Vishnu; Taylor, John W.

doi:10.1073/pnas.132178099

Cited by 47 publications

(40 citation statements)

References 33 publications

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“…(9), and also for assigning unknown strains of Coccidioides to the corresponding species and population (8). The method has proven to be discriminative, reproducible, and easy to perform.…”

Section: Discussionmentioning

confidence: 99%

“…The higher mutation rates operating at the microsatellite loci (12) allow variations to accumulate at a high rate, leading to greater intrapopulation genetic diversity and improved typing (5,8,24).…”

Section: Discussionmentioning

confidence: 99%

“…Length polymorphism in microsatellites arises from variations in the number of repeated units (7,22). Indeed, these simple, tandem repeated oligonucleotides are highly polymorphic and amenable to precise, robust, and highly reproducible allelic characterization through the sizing or sequencing of PCR products (23), and it has been discovered that they can be used to identify several pathogenic fungi (1,8,9,13). Recently, the existence of microsatellite markers from a collection of unique random sequence tags that are representative of the genome composition has been described for P. brasiliensis (19).…”

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confidence: 99%

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Microsatellite Analysis of Three Phylogenetic Species of Paracoccidioides brasiliensis

et al. 2006

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Paracoccidioides brasiliensis is the etiological agent of paracoccidioidomycosis, an important human systemic mycosis in Latin America. Recently, the existence of three different phylogenetic species (S1, PS2, and PS3) of P. brasiliensis was demonstrated. Despite being genetically isolated, all three species were capable of inducing disease in both humans and animals, although lower virulence has been found with the PS2 species. The available molecular methods developed to characterize and type strains have not been useful for assigning isolates to the described species, creating the need for molecular markers capable of distinguishing genetically isolated groups. Here, we describe a PCR and sequencing-based microsatellite marker system that is stable, easy to assay, adaptable to large series of isolates, and discriminatory enough to be used as a typing system in identifying the three proposed species of P. brasiliensis. In addition, this system provides an unambiguous tool for strain discrimination between two (S1 and PS2) of the three phylogenetic species.

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“…(9), and also for assigning unknown strains of Coccidioides to the corresponding species and population (8). The method has proven to be discriminative, reproducible, and easy to perform.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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Microsatellite Analysis of Three Phylogenetic Species of Paracoccidioides brasiliensis

et al. 2006

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“…The occurrence of strongly spatially structured genotypes in this data set suggests that isolates of unknown ancestry can be assigned to a source population by using Bayesian assignment tests (BATs) (12). These statistical tests assign individuals to populations by calculating posterior probability densities for multilocus genotypes within all populations based on the observed allele frequencies, with assignment being made to the population with the highest posterior probability.…”

Section: Mlmtmentioning

confidence: 99%

Multilocus Microsatellite Typing System for Penicillium marneffei Reveals Spatially Structured Populations

et al. 2004

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For eukaryotic pathogens that have low levels of genetic variation, multilocus microsatellite typing (MLMT) offers an accurate and reproducible method of characterizing genetic diversity. Here, we describe the application of an MLMT system to the emerging pathogenic fungus Penicillium marneffei. Isolates used for this study were those held in the culture collections of the Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands, and the Chiang Mai University Department of Microbiology, Chang Mai, Thailand. High genetic diversity and extensive spatial structure were observed among clinical isolates, with the geographical area of origin for each isolate strongly correlating with the occurrence of two deeply divided clades. Within each clade, multilocus linkage associations were highly significant and could be explained by genetically differentiated populations or by an exclusively clonal reproductive mode, or both. Our results show that southeast Asian penicilliosis is caused by a fungus with a complex population genetic structure. Furthermore, this MLMT system generates digital data that can be easily queried against a centrally held database via the internet (http://pmarneffei.multilocus.net/); this provides a powerful epidemiological tool for analyzing the underlying parameters that are responsible for the emergence of P. marneffei in human immunodeficiency virus-positive populations.Penicillium marneffei is a mitosporic pathogenic fungus of the family Trichocomaceae that has emerged since 1990 as a significant human mycosis. Emergence of P. marneffei has occurred in concert with the explosive epidemic of AIDS in southeast Asia, where it is classified as an AIDS-related indicator disease (17). In northern Thailand, P. marneffei is the third most frequent opportunistic infectious disease organism, after tuberculosis and cryptococcosis (22).So far, the ecology and epidemiology of P. marneffei have remained enigmatic. The range of endemicity of the pathogen is confined to southeast Asia, where autochthonous isolations from northeast India, Thailand, the Guangxi region of China, Hong Kong, Taiwan, Vietnam, and Indonesia are known (1). In these regions, P. marneffei is a naturally occurring sylvatic infection in a high proportion of bamboo rat species (3-5). However, it is not known whether bamboo rats are (i) an obligate stage in P. marneffei's life cycle and (ii) a zoonotic focus for human infection. Furthermore, it is not known whether all lineages of P. marneffei are equally infectious to bamboo rats and humans or rather represent a subset of a wider, more genetically diverse population. In order to address these questions, there is an urgent need for well-characterized neutral markers with which to analyze the population genetic structure of P. marneffei.Studies of P. marneffei using molecular epidemiological techniques are still at an early stage of development, with previous differentiation of P. marneffei isolates relying on PCR amplification of anonymous loci (14) or enzyme-based restriction of nucle...

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“…Coccidioides immitis and C. posadasii are morphologically identical and their predicted proteins are more than 90% homologous [2]. They cannot be distinguished by serologic tests, but the two species can be distinguished by genetic polymorphisms, and some differences in growth characteristics have been reported [4,5]. C. posadasii has a larger population size, which is more diverse than C. immitis [6].…”

Section: Taxonomymentioning

confidence: 99%

Coccidioides immitis and posadasii; A review of their biology, genomics, pathogenesis, and host immunity

Kirkland

Fierer

2018

Virulence

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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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Disease surveillance in recombining pathogens: Multilocus genotypes identify sources of humanCoccidioidesinfections

Cited by 47 publications

References 33 publications

Microsatellite Analysis of Three Phylogenetic Species of Paracoccidioides brasiliensis

Microsatellite Analysis of Three Phylogenetic Species of Paracoccidioides brasiliensis

Multilocus Microsatellite Typing System for Penicillium marneffei Reveals Spatially Structured Populations

Coccidioides immitis and posadasii; A review of their biology, genomics, pathogenesis, and host immunity

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