Biology subjects

M'ikanatha, N. M.

Publications and source records attributed to M'ikanatha, N. M..

2 recordsLinked to original sources

bioRxiv2018

Whole genome sequencing of antimicrobial-resistant Shigella sonnei associated with infection acquired from international and domestic setting reveals gene allelic variants that predict Global Lineages

Shigella spp. are a major cause of gastroenteritis worldwide, and S. sonnei is the most common species isolated within the United States. Recently, advancements in technology have made whole genome sequencing (WGS) readily available, and as such, laboratories are moving to implement WGS in outbreak analysis, surveillance, and antimicrobial resistance (AMR) monitoring of major foodborne pathogens. Accordingly, our study examined a collection of 22 antimicrobial resistant S. sonnei isolates from patients who either acquired the infections within the United States or when travelling to international locations between 2009 to 2014. We applied WGS to investigate both the relatedness of these isolates and the genetic determinants of AMR to address the phenotypic differences seen in previous observations. We analyzed the phylogeny of these strains and observed segmentation based on the previously described Global Lineages of S. sonnei. Following these results, 17 gene sequences with lineage specific single nucleotide polymorphisms (SNPs) were identified and developed into a lineage prediction test to determine the Global Lineage of uncharacterized S. sonnei, which accurately predicted phylogenetic segmentation and additionally showed specificity for S. sonnei genomes (97% accuracy, 38/39 genomes). Lastly, to determine differences between either the international or domestic isolates or between the Global Lineages, the AMR determinants were identified. We found a variety of AMR determinants within the genomes, and while the international and domestic S. sonnei carried similar resistance determinants, differences between Global Lineages were observed.

microbiology↗

bioRxiv2018

Retrospective whole-genome sequencing analysis distinguished PFGE and drug resistance matched retail meat and clinical Salmonella isolates

Non-typhoidal Salmonella are a leading cause of outbreak and sporadic-associated foodborne illnesses in the U.S. These infections have been associated with a range of foods, including retail meats. Traditionally, pulsed-field gel electrophoresis (PFGE) and antibiotic susceptibility testing (AST) have been used to facilitate public health investigations of Salmonella infections. However, whole-genome sequencing (WGS) has emerged as an alternative tool that can be routinely implemented. To assess its potential in enhancing integrated surveillance in Pennsylvania, WGS was used to directly compare the genetic characteristics of 7 retail meat and 43 clinical historic Salmonella isolates, subdivided into three subsets based on PFGE and AST results, to retrospectively resolve their genetic relatedness and identify antimicrobial resistance (AMR) determinants. Single nucleotide polymorphism (SNP) analyses revealed the retail meat isolates within S. Heidelberg, S. Typhimurium var. O5- subset 1, and S. Typhimurium var. O5- subset 2 were separated from each primary PFGE pattern-matched clinical isolate by 6-12, 41-96, and 21-81 SNPs, respectively. Fifteen resistance genes were identified across all isolates, including fosA7, a gene only recently found in a limited number of Salmonella and a [≥] 95% phenotype to genotype correlation was observed for all tested antimicrobials. Moreover, AMR was primarily plasmid-mediated in S. Heidelberg and S. Typhimurium var. O5- subset 2; whereas, AMR was chromosomally-carried in S. Typhimurium var. O5- subset 1. Similar plasmids were identified in both the retail meat and clinical isolates. Collectively, these data highlight the utility of WGS in retrospective analyses and enhancing integrated surveillance of Salmonella from multiple sources.

microbiology↗