Whole-genome sequencing and virulome analysis of Escherichia coli isolated from New Zealand environments of contrasting observed land use

<p>Generic <em>Escherichia coli</em> is commonly used as an indicator of fecal contamination to assess water quality and human health risk. Where measured <em>E. coli</em> exceedances occur, the presence of other pathogenic microorganisms, such as Shiga toxin-producing <em>E. coli</em> (STEC), is assumed, but confirmatory data are lacking. Putative <em>E. coli</em> isolates (<em>n</em> = 709) were isolated from water, sediment, soil, periphyton, and feces samples (<em>n</em> = 189) from five sites representing native forest and agricultural environments. Ten <em>E. coli</em> isolates (1.41%) were <em>stx</em>2 positive, 19 (2.7%) were <em>eae</em> positive, and <em>stx</em>1-positive isolates were absent. At the sample level, <em>stx</em>2-positive <em>E. coli</em> (5 of 189, 2.6%) and <em>eae</em>-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 (<em>stx</em>1, 23.9%; <em>stx</em>2, 31.4%; <em>eae</em>, 53.7%) and positively correlated with generic <em>E. coli</em> isolate numbers (<em>P</em> < 0.05) determined using culture-based methods. Whole-genome sequencing (WGS) was undertaken on a subset of 238 isolates with assemblies representing seven <em>E. coli</em> phylogroups (A, B1, B2, C, D, E, and F), 22 <em>Escherichia marmotae</em> isolates, and 1 <em>Escherichia ruysiae</em> isolate. Virulence factors, including those from extraintestinal pathogenic <em>E. coli</em>, 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 <em>E. coli</em> phylogroups. </p>