Genetic typing of isolates of Rickettsia typhi

Kato, Cecilia Y.; Chung, Ida H; Robinson, Lauren K; Eremeeva, Marina E.; Dasch, Gregory A.

doi:10.1371/journal.pntd.0010354

Cited by 3 publications

(2 citation statements)

References 51 publications

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“…Several research groups have recently developed single nucleotide polymorphisms (SNP)-based genotyping approaches, e.g. , to investigate Mycobacterium species ( Kim et al, 2021 ; Napier et al, 2020 ), attribute hosts for Chlamydia psittaci ( Vorimore et al, 2021 ) and Campylobacter coli ( Jehanne et al, 2020 ), distinguish Rickettsia typhi from different continents ( Kato et al, 2022 ), identify Escherichia coli of specific serotype ( Rahman, Lim & Park, 2022 ), and track the spread of drug resistance in Plasmodium falciparum infections ( Jacob et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data

Hoon

Holt

Auburn

et al. 2023

PeerJ

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Here, we present the R package, minSNPs. This is a re-development of a previously described Java application named Minimum SNPs. MinSNPs assembles resolution-optimised sets of single nucleotide polymorphisms (SNPs) from sequence alignments such as genome-wide orthologous SNP matrices. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to determine all sequences from all other sequences, i.e., to maximise diversity. MinSNPs encompasses functions that facilitate rapid and flexible SNP mining, and clear and comprehensive presentation of the results. The minSNPs’ running time scales in a linear fashion with input data volume and the numbers of SNPs and SNPs sets specified in the output. MinSNPs was tested using a previously reported orthologous SNP matrix of Staphylococcus aureus and an orthologous SNP matrix of 3,279 genomes with 164,335 SNPs assembled from four S. aureus short read genomic data sets. MinSNPs was shown to be effective for deriving discriminatory SNP sets for potential surveillance targets and in identifying SNP sets optimised to discriminate isolates from different clonal complexes. MinSNPs was also tested with a large Plasmodium vivax orthologous SNP matrix. A set of five SNPs was derived that reliably indicated the country of origin within three south-east Asian countries. In summary, we report the capacity to assemble comprehensive SNP matrices that effectively capture microbial genomic diversity, and to rapidly and flexibly mine these entities for optimised marker sets.

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Section: Introductionmentioning

confidence: 99%

minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data

Hoon

Holt

Auburn

et al. 2023

PeerJ

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“…While whole genome analysis is now widely applied directly to public health, clinical, and research microbiology, targeted genetic analyses may be complementary to whole genome analysis for purposes such as high-volume, low-cost surveillance, analysis of primary specimens, and/or analyses performed outside the laboratory environment. Several research groups have recently developed SNP-based genotyping approaches, e.g., to investigate Mycobacterium species (1, 2), attribute host for Chlamydia psittaci (3) and Campylobacter coli (4) , distinguish Rickettsia typhi from different continents (5), identify Escherichia coli of specific serotype (6), and track the spread of drug resistance in Plasmodium falciparum infections (7).…”

Section: Introductionmentioning

confidence: 99%

MinSNPs: an R package for derivation of resolution-optimised SNP sets from microbial genomic data

Hoon

Holt

Auburn

et al. 2022

Preprint

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Here we present the R package - MinSNPs. This is designed to assemble resolution optimised sets of single nucleotide polymorphisms (SNPs) from alignments such as genome wide orthologous SNP matrices. We also demonstrate a pipeline for assembling such matrices from multiple bio-projects, so as to facilitate SNP set derivation from globally representative data sets. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to discriminate all from all, i.e., to maximise diversity. MinSNPs encompasses functions that facilitate rapid and flexible SNP mining, and clear and comprehensive presentation of the results. The MinSNPs running time scales in a linear fashion with input data volume, and the numbers of SNPs and SNPs sets specified in the output. MinSNPs was tested using a previously reported orthologous SNP matrix of Staphylococcus aureus. and an orthologous SNP matrix of 3,279 genomes with 164,335 SNPs assembled from four S. aureus short read genomic data sets. MinSNPs demonstrated efficacy in deriving discriminatory SNP sets for potential surveillance targets and in identifying SNP sets optimised to discriminate isolates from different clonal complexes (CC). MinSNPs was also tested with a large Plasmodium vivax orthologous SNP matrix. A set of five SNPs was derived that reliably indicated the country of origin within 3 south-east Asian countries. In summary, we report the capacity to assemble comprehensive SNP matrices that effectively capture microbial genomic diversity, and to rapidly and flexibly mine these entities for optimised surveillance marker sets.

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Murine Typhus: A Review of a Reemerging Flea-Borne Rickettsiosis with Potential for Neurologic Manifestations and Sequalae

Blanton

2023

Infectious Disease Reports

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Murine typhus is an acute febrile illness caused by Rickettsia typhi, an obligately intracellular Gram-negative coccobacillus. Rats (Rattus species) and their fleas (Xenopsylla cheopis) serve as the reservoir and vector of R. typhi, respectively. Humans become infected when R. typhi-infected flea feces are rubbed into flea bite wounds or onto mucous membranes. The disease is endemic throughout much of the world, especially in tropical and subtropical seaboard regions where rats are common. Murine typhus is reemerging as an important cause of febrile illness in Texas and Southern California, where an alternate transmission cycle likely involves opossums (Didelphis virginiana) and cat fleas (Ctenocephalides felis). Although primarily an undifferentiated febrile illness, a range of neurologic manifestations may occur, especially when treatment is delayed. Serology is the mainstay of diagnostic testing, but confirmation usually requires demonstrating seroconversion or a fourfold increase in antibody titer from acute- and convalescent-phase sera (antibodies are seldom detectable in the first week of illness). Thus, early empiric treatment with doxycycline, the drug of choice, is imperative. The purpose of this review is to highlight murine typhus as an important emerging and reemerging infectious disease, review its neurologic manifestations, and discuss areas in need of further study.

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Genetic typing of isolates of Rickettsia typhi

Cited by 3 publications

References 51 publications

minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data

minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data

MinSNPs: an R package for derivation of resolution-optimised SNP sets from microbial genomic data

Murine Typhus: A Review of a Reemerging Flea-Borne Rickettsiosis with Potential for Neurologic Manifestations and Sequalae

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