Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks

Abstract

Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies.

Environmental adaptation and vertical dissemination of ESBL‐/pAmpC‐producing Escherichia coli in an integrated broiler production chain in the absence of an antibiotic treatment

“…In contrast, isolates of the parent flock were collected only 17 days earlier but the SNP differences between isolates of the parent flock and the fattening flock were about 10.5 SNPs Mbp −1 . The number of SNP differences between the strains of the fattening period is higher than the numbers published for clonal outbreaks of enterohemorrhagic E. coli (EHEC) (de Been et al ., 2014; Berenger et al ., 2015; Rusconi et al ., 2016) but overall lower than those described for interspecies transmissions of clonal ST‐410 E. coli strains (Schaufler et al ., 2016b). These findings suggest that ESBL‐/pAmpC‐resistant E. coli were more likely transferred from the parent flock into the production chain via an earlier event but not directly along the investigated batch of broiler chicken.…”

Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the EmergentXylella fastidiosaGenotype in Italy to Isolates from Central America

“…Genome-wide studies based on SNPs have been useful in tracking pathogen outbreaks, inferring evolution and spread pathways, in addition to identifying pathogenicity and host specificity determinants (Hendriksen et al 2011;Rusconi et al 2016). A previous SNP-based study was limited to only four complete X. fastidiosa genomes (Doddapaneni et al 2006).…”

Investigation of Respiratory Syncytial Virus Outbreak on an Adult Stem Cell Transplant Unit by Use of Whole-Genome Sequencing

“…Timely identification of the outbreak source is critical to allow implementation of infection control measures. Whole-genome sequencing (WGS) with next-generation sequencing technology has been increasingly applied to assess the epidemiological link between bacteria implicated in outbreaks (12)(13)(14). In the studies with bacterial pathogens, the targeted pathogen was first recovered by culture, and then wholegenome sequencing was performed with the nucleic acid extracted from the pure isolates.…”