Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use

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dc.citation.issue9
dc.citation.volume88
dc.contributor.authorCookson AL
dc.contributor.authorMarshall JC
dc.contributor.authorBiggs PJ
dc.contributor.authorRogers LE
dc.contributor.authorCollis RM
dc.contributor.authorDevane M
dc.contributor.authorStott R
dc.contributor.authorWilkinson DA
dc.contributor.authorKamke J
dc.contributor.authorBrightwell G
dc.contributor.editorElkins CA
dc.coverage.spatialUnited States
dc.date.accessioned2024-01-11T20:09:36Z
dc.date.accessioned2024-07-25T06:48:49Z
dc.date.available2022-04-20
dc.date.available2024-01-11T20:09:36Z
dc.date.available2024-07-25T06:48:49Z
dc.date.issued2022-05-10
dc.description.abstractGeneric Escherichia coli is commonly used as an indicator of fecal contamination to assess water quality and human health risk. Where measured E. coli exceedances occur, the presence of other pathogenic microorganisms, such as Shiga toxin-producing E. coli (STEC), is assumed, but confirmatory data are lacking. Putative E. coli isolates (n = 709) were isolated from water, sediment, soil, periphyton, and feces samples (n = 189) from five sites representing native forest and agricultural environments. Ten E. coli isolates (1.41%) were stx2 positive, 19 (2.7%) were eae positive, and stx1-positive isolates were absent. At the sample level, stx2-positive E. coli (5 of 189, 2.6%) and eae-positive isolates (16 of 189, 8.5%) were rare. Using real-time PCR, these STEC-associated virulence factors were determined to be more prevalent in sample enrichments (stx1, 23.9%; stx2, 31.4%; eae, 53.7%) and positively correlated with generic E. coli isolate numbers (P < 0.05) determined using culture-based methods. Whole-genome sequencing (WGS) was undertaken on a subset of 238 isolates with assemblies representing seven E. coli phylogroups (A, B1, B2, C, D, E, and F), 22 Escherichia marmotae isolates, and 1 Escherichia ruysiae isolate. Virulence factors, including those from extraintestinal pathogenic E. coli, were extremely diverse in isolates from the different locations and were more common in phylogroup B2. Analysis of the virulome from WGS data permitted the identification of gene repertoires that may be involved in environmental fitness and broadly align with phylogroup. Although recovery of STEC isolates was low, our molecular data indicate that they are likely to be widely present in environmental samples containing diverse E. coli phylogroups. IMPORTANCE This study takes a systematic sampling approach to assess the public health risk of Escherichia coli recovered from freshwater sites within forest and farmland. The New Zealand landscape is dominated by livestock farming, and previous work has demonstrated that "recreational exposure to water" is a risk factor for human infection by Shiga toxin-producing Escherichia coli (STEC). Though STEC isolates were rarely isolated from water samples, STEC-associated virulence factors were identified more commonly from water sample culture enrichments and were associated with increased generic E. coli concentrations. Whole-genome sequencing data from both E. coli and newly described Escherichia spp. demonstrated the presence of virulence factors from E. coli pathotypes, including extraintestinal pathogenic E. coli. This has significance for understanding and interpreting the potential health risk from E. coli where water quality is poor and suggests a role of virulence factors in survival and persistence of E. coli and Escherichia spp.
dc.description.confidentialfalse
dc.edition.editionMay 2022
dc.format.paginatione0027722-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/35442082
dc.identifier.citationCookson AL, Marshall JC, Biggs PJ, Rogers LE, Collis RM, Devane M, Stott R, Wilkinson DA, Kamke J, Brightwell G. (2022). Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use.. Appl Environ Microbiol. 88. 9. (pp. e0027722-).
dc.identifier.doi10.1128/aem.00277-22
dc.identifier.eissn1098-5336
dc.identifier.elements-typejournal-article
dc.identifier.issn0099-2240
dc.identifier.numbere0027722
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70939
dc.languageeng
dc.publisherAmerican Society for Microbiology
dc.publisher.urihttps://journals.asm.org/doi/10.1128/aem.00277-22
dc.relation.isPartOfAppl Environ Microbiol
dc.rights(c) The author/sen
dc.rights.licenseCC BY 4.0en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectEscherichia
dc.subjectSTEC
dc.subjectenvironment
dc.subjectenvironmental microbiology
dc.subjectphylogroup
dc.subjectvirulome
dc.subjectwhole-genome sequencing
dc.subjectEscherichia coli Infections
dc.subjectEscherichia coli Proteins
dc.subjectFeces
dc.subjectHumans
dc.subjectNew Zealand
dc.subjectShiga-Toxigenic Escherichia coli
dc.subjectVirulence Factors
dc.titleWhole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use
dc.typeJournal article
pubs.elements-id452967
pubs.organisational-groupOther
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