Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association

Strachan, Norval James Colin; Rotariu, Ovidiu; Lopes, Bruno Silvester; MacRae, Marion; Fairley, Susan; Laing, Chad R.; Gannon, Victor P. J.; Allison, Lesley; Hanson, Mary; Dallman, Tim; Ashton, Philip; Franz, Eelco; Hoek, Angela H.A.M. van; French, Nigel P.; George, Tessy; Biggs, Patrick J.; Forbes, Ken J.

doi:10.1038/srep14145

Cited by 52 publications

(51 citation statements)

References 45 publications

(58 reference statements)

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“…Similarly, a large-scale WGS study of Salmonella Typhi isolates from across the world identified a specific MDR clone that emerged in Asia and Africa with subsequent inter-and intracontinental transmission events (41). Importantly, our findings are also consistent with a WGS-based study (42) of Escherichia coli O157 isolates from different sources (e.g., animals, humans, and the environment/food) and different countries and continents. This study reported significant genetic differences among isolates from different geographical regions and hypothesized that a combination of local emergence events and international transmission leads to a "patchwork" of geographically confined and widely distributed clades.…”

Section: Discussionsupporting

confidence: 78%

Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations

Carroll

Bakker

Siler

et al. 2017

Appl Environ Microbiol

107

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Multidrug-resistant (MDR) Salmonella enterica can be spread from cattle to humans through direct contact with animals shedding Salmonella as well as through the food chain, making MDR Salmonella a serious threat to human health. The objective of this study was to use whole-genome sequencing to compare antimicrobial-resistant (AMR) Salmonella enterica serovars Typhimurium, Newport, and Dublin isolated from dairy cattle and humans in Washington State and New York State at the genotypic and phenotypic levels. A total of 90 isolates were selected for the study (37 S. Typhimurium, 32 S. Newport, and 21 S. Dublin isolates). All isolates were tested for phenotypic antibiotic resistance to 12 drugs using Kirby-Bauer disk diffusion. AMR genes were detected in the assembled genome of each isolate using nucleotide BLAST and ARG-ANNOT. Genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.2 and specificity of 85.2. Sulfamethoxazole-trimethoprim resistance was observed only in human isolates (P Ͻ 0.05), while resistance to quinolones and fluoroquinolones was observed only in 6 S. Typhimurium isolates from humans in Washington State. S. Newport isolates showed a high degree of AMR profile similarity, regardless of source. S. Dublin isolates from New York State differed from those from Washington State based on the presence/absence of plasmid replicons, as well as phenotypic AMR susceptibility/nonsusceptibility (P Ͻ 0.05). The results of this study suggest that distinct factors may contribute to the emergence and dispersal of AMR S. enterica in humans and farm animals in different regions.IMPORTANCE The use of antibiotics in food-producing animals has been hypothesized to select for AMR Salmonella enterica and associated AMR determinants, which can be transferred to humans through different routes. Previous studies have sought to assess the degree to which AMR livestock-and human-associated Salmonella strains overlap, as well as the spatial distribution of Salmonella's associated AMR determinants, but have often been limited by the degree of resolution at which isolates can be compared. Here, a comparative genomics study of livestock-and humanassociated Salmonella strains from different regions of the United States shows that while many AMR genes and phenotypes were confined to human isolates, overlaps between the resistomes of bovine and human-associated Salmonella isolates were observed on numerous occasions, particularly for S. Newport. We have also shown that whole-genome sequencing can be used to reliably predict phenotypic resistance across Salmonella isolated from bovine sources.

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Section: Discussionsupporting

confidence: 78%

Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations

Carroll

Bakker

Siler

et al. 2017

Appl Environ Microbiol

107

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“…), and 7·7% in Scotland (Strachan et al . ). In another study performed in Argentina on retail meat, and butcher shop environmental samples, Galli et al .…”

Section: Resultsmentioning

confidence: 97%

Virulence profile ofEscherichia coliO157 strains isolated from surface water in cattle breeding areas

Tanaro

Pianciola

D'Astek

et al. 2018

Lett Appl Microbiol

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The challenge for the growing global demand for food is to find sustained production strategies without collateral effects. Intensive livestock operations generate large volumes of manure that can contaminate a finite resource, the water. This study shows how water contaminated by confined feeding operations can transport dangerous pathogens and warns to pay more attention to control and sanitation systems to prevent this type of pollution.

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“…In principle, this should enable discovery of large numbers of markers (e.g. SNPs) which have the potential to achieve unprecedented source attribution accuracy [31][32][33][34][35][36] . The challenge lies in efficiently mining large data sets for source attribution.…”

Section: Introductionmentioning

confidence: 99%

Mining Whole Genome Sequence data to efficiently attribute individuals to source populations

Pérez‐Reche

Rotariu

Lopes

et al. 2020

Preprint

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Whole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that effectively mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as methods for optimally selecting loci. This was applied on WGS data to determine the source of human campylobacteriosis, the geographical origin of diverse biological species including humans and proteomic data to classify breast cancer tumours. The MMD method provides a highly accurate attribution which is computationally efficient for extended genotypes. These methods are generic, easy to implement for WGS and proteomic data and have wide application. set). ADMIXTURE was originally proposed as a method for unsupervised model-based estimation of ancestry of unrelated individuals 40 . This is the most widely used version of ADMIXTURE but, in fact, it was extended 48 for supervised learning in such a way that it can use prior knowledge on the population of origin of some individuals to infer the ancestry of other individuals. The supervised learning version of ADMIXTURE, however, was not designed to estimate the probability that individuals were sampled from a certain source, i.e., it was not designed to attribute individuals to sources but rather to infer their ancestry. In spite of that, one would expect some relationship between ancestry and source of individuals and it makes sense to explore the capability of ADMIXTURE as an attribution method (with applicability restricted to datasets consisting of SNP genotypes). GLOBETROTTER, another package to infer the ancestry of individuals, also has potential as a method for source attribution with extended SNP datasets 49 .Besides developing efficient methods for source attribution, selection of loci with high discriminatory power can also help deal with the computational challenge posed by extended genotypes. Several methods have been proposed to rank markers according to their importance for source attribution based on the intuitive idea that highly polymorphic markers should allow for higher genetic differentiation 50 . This can be achieved by measuring the importance of loci with diversity indices (e.g. expected heterozygosity, fixation index F ST or informativeness 5, 7,21,51,52 ). Other approaches propose focusing on the joint performance of sets of loci rather than considering performance of loci individually 53-55 . One would expect these approaches to be more appropriate than diversity-based methods when dealing with correlated markers (i.e. when linkage disequilibrium is important 56 ). However, they are computationally intensive and impractical to deal with extended genotypes and do not always improve on diversity-based methods 7 .Here, we address two of the challenges posed by extended genotypes for source attribution. First, we propose a fast method for source attribution which can deal with genotypes comprising thousands of loci with minimal computational effort. S...

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Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association

Cited by 52 publications

References 45 publications

Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations

Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations

Virulence profile ofEscherichia coliO157 strains isolated from surface water in cattle breeding areas

Mining Whole Genome Sequence data to efficiently attribute individuals to source populations

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