Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways

Harris, Simon R.; Okoro, Chinyere K.

doi:10.1016/bs.mim.2014.07.003

Cited by 5 publications

(3 citation statements)

References 75 publications

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“…Genotypic assays, like the Cepheid Xpert MTB/RIF (Cepheid, Sunnyvale, CA, USA) and Hain line-probe (Hain Lifescience, Nehren Germany) assays, provide a short turnaround time (less than a day) in the identification of mycobacteria; but they are not able to detect all resistance conferring mutations [94]. In our work, we used WGS to identify SNP differences in MTC species and determined those that had multi-drug resistance genes [81,94,95,96,97]. A total of 7250 SNPs was used to generate the phylogenetic tree that enabled us to determine the relatedness of the sequenced genomes to reference strains.…”

Section: Discussionmentioning

confidence: 99%

Retrospective Analysis of Archived Pyrazinamide Resistant Mycobacterium tuberculosis Complex Isolates from Uganda—Evidence of Interspecies Transmission

et al. 2019

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The contribution of Mycobacterium bovis to the proportion of tuberculosis cases in humans is unknown. A retrospective study was undertaken on archived Mycobacterium tuberculosis complex (MTBC) isolates from a reference laboratory in Uganda to identify the prevalence of human M. bovis infection. A total of 5676 isolates maintained in this repository were queried and 136 isolates were identified as pyrazinamide resistant, a hallmark phenotype of M. bovis. Of these, 1.5% (n = 2) isolates were confirmed as M. bovis by using regions of difference PCR analysis. The overall size of whole genome sequences (WGSs) of these two M. bovis isolates were ~4.272 Mb (M. bovis Bz_31150 isolated from a captive chimpanzee) and 4.17 Mb (M. bovis B2_7505 from a human patient), respectively. Alignment of these genomes against 15 MTBC genome sequences revealed 7248 single nucleotide polumorphisms (SNPs). Theses SNPs were used for phylogenetic analysis that indicated a strong relationship between M. bovis and the chimpanzee isolate (Bz_31150) while the other M. bovis genome from the human patient (B2_7505) analyzed did not cluster with any M. bovis or M. tuberculosis strains. WGS analysis also revealed multidrug resistance genotypes; these genomes revealed pncA mutations at positions H57D in Bz_31150 and B2_7505. Phenotypically, B2_7505 was an extensively drug-resistant strain and this was confirmed by the presence of mutations in the major resistance-associated proteins for all anti-tuberculosis (TB) drugs, including isoniazid (KatG (S315T) and InhA (S94A)), fluoroquinolones (S95T), streptomycin (rrs (R309C)), and rifampin (D435Y, a rare but disputed mutation in rpoB). The presence of these mutations exclusively in the human M. bovis isolate suggested that these occurred after transmission from cattle. Genome analysis in this study identified M. bovis in humans and great apes, suggesting possible transmission from domesticated ruminants in the area due to a dynamic and changing interface, which has created opportunity for exposure and transmission.

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Section: Discussionmentioning

confidence: 99%

Retrospective Analysis of Archived Pyrazinamide Resistant Mycobacterium tuberculosis Complex Isolates from Uganda—Evidence of Interspecies Transmission

et al. 2019

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“…The strains were stored on dry ice and sent to Biomarker Technologies (Beijing, China) for bacterial genome sequencing (Harris & Okoro, 2014).…”

Section: Jin4 Whole Genome Sequencing Analysismentioning

confidence: 99%

Isolation, identification, and genome of a Bacillus velezensis JIN4 exhibiting biocontrol activity against kiwifruit bacterial canker

Zhao,

Zhai,

et al. 2023

Preprint

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Kiwifruit bacterial canker is a devastating disease in production. This study aimed to screen antagonistic bacteria that might be used to control this disease. Strain JIN4 showed significant antifungal activity against Pseudomonas syringae pv. Actinidiae (Psa) and seven other phytopathogenic bacteria isolated from kiwifruit branches. Based on morphological, physiological, and biochemical characteristics, 16S rDNA sequence analysis, and gyrA sequence analysis, JIN4 was identified as Bacillus velezensis. In field prevention experiments, the control efficiency of strain JIN4 reached 60.22%. Our results indicate that B. velezensis JIN4 has broad-spectrum antifungal resistance, and its genome contains many genes encoding enzymes involved in the synthesis of antimicrobial metabolites. In addition, JIN4 has three antibiotic-resistance genes and a cluster of nine genes used in the synthesis of secondary metabolites with antimicrobial activity. In conclusion, B. velezensis JIN4 can be used as a potential biocontrol agent against kiwifruit bacterial canker, but further work is required to improve its efficacy.

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“…Major data gaps in LICs stem from inadequate national monitoring and surveillance programs. Whole-genome sequencing (WGS) can provide accurate information on foodborne pathogens (2). The availability of molecular data is crucial for improving food safety outcomes in LICs and understanding foodborne outbreaks and transmission pathways.…”

mentioning

confidence: 99%

Draft Genome Sequences of 81 Salmonella enterica Strains from Informal Markets in Cambodia

Schwan

Trinetta

Balkey

et al. 2020

Microbiol Resour Announc

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Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways

Cited by 5 publications

References 75 publications

Retrospective Analysis of Archived Pyrazinamide Resistant Mycobacterium tuberculosis Complex Isolates from Uganda—Evidence of Interspecies Transmission

Retrospective Analysis of Archived Pyrazinamide Resistant Mycobacterium tuberculosis Complex Isolates from Uganda—Evidence of Interspecies Transmission

Isolation, identification, and genome of a Bacillus velezensis JIN4 exhibiting biocontrol activity against kiwifruit bacterial canker

Draft Genome Sequences of 81 Salmonella enterica Strains from Informal Markets in Cambodia

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