Precise Dissection of an Escherichia coli O157:H7 Outbreak by Single Nucleotide Polymorphism Analysis

Turabelidze, George; Lawrence, Steven J.; Gao, Hongyu; Sodergren, Erica; Weinstock, George M.; Abubucker, Sahar; Wylie, Todd; Mitreva, Makedonka; Shaikh, Nurmohammad; Gautom, Romesh; Tarr, Phillip I.

doi:10.1128/jcm.01930-13

Cited by 37 publications

(34 citation statements)

References 30 publications

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“…S3). For presentation, we limited our displayed data to only a few key strains in the E. coli O157:H7 literature, several notable intermediates, and an outbreak from lettuce in salad bars in a multistate outbreak (37). This representation is not meant to suggest we have found the strains implicated in any outbreak directly, but simply to ascertain whether the genetic content of our strains is or is not similar to isolates that have caused outbreaks, thus providing evidence for their pathogenicity.…”

Section: Resultsmentioning

confidence: 99%

Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California

Worley

Flores

Yang

et al. 2017

Appl Environ Microbiol

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Escherichia coli serotype O157:H7 is a zoonotic food-and waterborne bacterial pathogen that causes a high hospitalization rate and can cause lifethreatening complications. Increasingly, E. coli O157:H7 infections appear to originate from fresh produce. Ruminants, such as cattle, are a prominent reservoir of E. coli O157:H7 in the United States. California is one of the most agriculturally productive regions in the world for fresh produce, beef, and milk. The close proximity of fresh produce and cattle presents food safety challenges on a uniquely large scale. We performed a survey of E. coli O157:H7 on 20 farms in California to observe the regional diversity and prevalence of E. coli O157:H7. Isolates were obtained from enrichment cultures of cow feces. Some farms were sampled on two dates. Genomes from isolates were sequenced to determine their relatedness and pathogenic potential. E. coli O157:H7 was isolated from approximately half of the farms. The point prevalence of E. coli O157:H7 on farms was highly variable, ranging from zero to nearly 90%. Within farms, generally one or a few lineages were found, even when the rate of isolation was high. On farms with high isolation rates, a single clonal lineage accounted for most of the isolates. Farms that were visited months after the first visit might have had the same lineages of E. coli O157:H7. Strains of E. coli O157:H7 may be persistent for months on farms.IMPORTANCE This survey of 20 cow-calf operations from different regions of California provides an in depth look at resident Escherichia coli O157:H7 populations at the molecular level. E. coli O157:H7 is found to have a highly variable prevalence, and with whole-genome sequencing, high prevalences in herds were found to be due to a single lineage shed from multiple cows. Few repeat lineages were found between farms in this area; therefore, we predict that E. coli O157:H7 has significant diversity in this area beyond what is detected in this survey. All isolates from this study were found to have pathogenic potential based on the presence of key virulence gene sequences. This represents a novel insight into pathogen diversity within a single subtype and will inform future attempts to survey regional pathogen populations.

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Section: Resultsmentioning

confidence: 99%

Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California

Worley

Flores

Yang

et al. 2017

Appl Environ Microbiol

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“…For example, Turabelidze and colleagues [16] sequenced pathogenic E. coli that was congregated by PFGE. It was reported that these isolates had identical PFGE band, but their differences were revealed by sequencing.…”

Section: Convergence Of E Coli Isolatesmentioning

confidence: 99%

Isolation and Characterization of <i>Escherichia coli</i> from Animals, Humans, and Environment

Lupindu¹

2017

≪i>Escherichia Coli

25
1
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Working on a diverse species of bacteria that have hundreds of pathotypes representing hundreds of strains and many closely related family members is a challenge. Appropriate research design is required not only to achieve valid desired outcome but also to minimize the use of resources, including time to outcome and intervention. This chapter outlines basics of Escherichia coli isolation and characterization strategies that can assist in research designing that matches the set objectives. Types of samples to be collected, collection and storage strategies, and processing of samples are described. Different approaches to isolation, confirmation and concentration of various E. coli strains are summarized in this chapter. Characterization and typing of E. coli isolates by biochemical, serological, and molecular methods have been explained so that an appropriate choice is made to suite a specific E. coli strain/pathotype. Some clues on sample and isolate preservation for future use are outlined, and general precautions regarding E. coli handling are also presented to the researcher to avoid improper planning and execution of E. coli-related research. Given different options, the best E. coli research design, however, should try as much as possible to shorten the length of time to outcomes.

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“…Nowadays, sequence-based typing approaches using whole-genome sequence (WGS) data are overcoming these obstacles. Several studies on various bacterial species have already shown that WGS-based typing, based either on single nucleotide variants (SNVs) (9,10) or on gene-by-gene allelic profiling of core genome genes, frequently named core genome MLST (cgMLST) (11)(12)(13), currently represents the ultimate tool for strain subtyping. Moreover, it was recently shown in an international ring trial that cgMLST is highly reproducible (14).…”

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confidence: 99%

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile
Bletz
¹
,
Janežič
²
,
Harmsen
³

et al. 2018
J Clin Microbiol
63
1
84
0
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, recently renamed , is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for Initially, we determined the breadth of the population based on all available MLST sequence types with Bayesian inference (BAPS). The resulting BAPS partitions were used in combination with clade information to select representative isolates that were subsequently used to define cgMLST target genes. Finally, we evaluated the novel cgMLST scheme with genomes from 3,025 isolates. BAPS grouping ( = 6 groups) together with the clade information led to a total of 11 representative isolates that were included for cgMLST definition and resulted in 2,270 cgMLST genes that were present in all isolates. Overall, 2,184 to 2,268 cgMLST targets were detected in the genome sequences of 70 outbreak-associated and reference strains, and on average 99.3% cgMLST targets (1,116 to 2,270 targets) were present in 2,954 genomes downloaded from the NCBI database, underlining the representativeness of the cgMLST scheme. Moreover, reanalyzing different cluster scenarios with cgMLST were concordant to published single nucleotide variant analyses. In conclusion, the novel cgMLST is representative for the whole population, is highly discriminatory in outbreak situations, and provides a unique nomenclature facilitating interlaboratory exchange.

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Precise Dissection of an Escherichia coli O157:H7 Outbreak by Single Nucleotide Polymorphism Analysis

Cited by 37 publications

References 30 publications

Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California

Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California

Isolation and Characterization of <i>Escherichia coli</i> from Animals, Humans, and Environment

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile

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