Abstract
Shiga toxin-producing Escherichia coli (STEC) are a leading cause of foodborne outbreaks of human disease, but they reside harmlessly as an asymptomatic commensal in the ruminant gut. STEC serogroup O145 are difficult to isolate as routine diagnostic methods are unable to distinguish non-O157 serogroups due to their heterogeneous metabolic characteristics, resulting in under-reporting which is likely to conceal their true prevalence. In light of these deficiencies, the purpose of this study was a twofold approach to investigate enhanced STEC O145 diagnostic culture-based methods: firstly, to use a genomic epidemiology approach to understand the genetic diversity and population structure of serogroup O145 at both a local (New Zealand) (n = 47) and global scale (n = 75) and, secondly, to identify metabolic characteristics that will help the development of a differential media for this serogroup. Analysis of a subset of E. coli serogroup O145 strains demonstrated considerable diversity in carbon utilisation, which varied in association with eae subtype and sequence type. Several carbon substrates, such as D-serine and D-malic acid, were utilised by the majority of serogroup O145 strains, which, when coupled with current molecular and culture-based methods, could aid in the identification of presumptive E. coli serogroup O145 isolates. These carbon substrates warrant subsequent testing with additional serogroup O145 strains and non-O145 strains. Serogroup O145 strains displayed extensive genetic heterogeneity that was correlated with sequence type and eae subtype, suggesting these genetic markers are good indicators for distinct E. coli phylogenetic lineages. Pangenome analysis identified a core of 3,036 genes and an open pangenome of >14,000 genes, which is consistent with the identification of distinct phylogenetic lineages. Overall, this study highlighted the phenotypic and genotypic heterogeneity within E. coli serogroup O145, suggesting that the development of a differential media targeting this serogroup will be challenging.
Highlights
Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens residing harmlessly in the gut of bovine reservoirs, but capable of causing human disease with a broad range of symptoms; from diarrhoea to life-threatening haemolytic uraemic syndrome (HUS) [1, 2]
We found considerable genetic heterogeneity within serogroup O145 strains according to the relative abundance of virulence factors, core genome SNPs, and pangenome analysis
The genetic heterogeneity within these strains provided evidence of a broad virulence continuum; stx2a- and eae-positive strains are implicated as the cause of severe human disease, both typical and atypical enteropathogenic E. coli (EPEC) are associated with mild diarrhoeal disease or asymptomatic carriage, while other serogroup O145 isolated from wolves lacked many STEC-associated virulence factors and appeared to be hostassociated and unlikely zoonoses
Summary
Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens residing harmlessly in the gut of bovine reservoirs, but capable of causing human disease with a broad range of symptoms; from diarrhoea to life-threatening haemolytic uraemic syndrome (HUS) [1, 2]. Most human infections are associated with sporadic outbreaks where risk factors include contact with cattle, animal manure, recreational waters [6] or consumption of contaminated food [7]. A cross-sectional study investigating the prevalence of STEC in young calves (2–21 days of age) throughout New Zealand (NZ) identified STEC O145 as the most prevalent serogroup (43%) at the dairy farm level compared with the other ‘Top 7’ serogroups [13]. These prevalence data indicate that, as a zoonotic pathogen, E. coli serogroup O145 represents both a risk to public health and a regulatory issue for NZ’s meat export industry
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