Added Value of Genomic Surveillance of Virulence Factors in Shiga Toxin-Producing Escherichia coli in New South Wales, Australia

Abstract

The disease caused by Shiga toxin-producing Escherichia coli (STEC) remains a significant public health challenge globally, but the incidence of human STEC infections in Australia remains relatively low. This study examined the virulence characteristics and diversity of STEC isolates in the state of New South Wales between December 2017 and May 2020. Utilisation of both whole and core genome multi-locus sequence typing (MLST) allowed for the inference of genomic diversity and detection of isolates that were likely to be epidemiologically linked. The most common STEC serotype and stx subtype detected in this study were O157:H7 and stx1a, respectively. A genomic scan of other virulence factors present in STEC suggested interplay between iron uptake system and virulence factors that mediate either iron release or countermeasures against host defence that could result in a reduction of stx1a expression. This reduced expression of the dominant stx genotype could contribute to the reduced incidence of STEC-related illness in Australia. Genomic surveillance of STEC becomes an important part of public health response and ongoing interrogation of virulence factors in STEC offers additional insights for the public health risk assessment.

STECode: an automated virulence barcode generator to aid clinical and public health risk assessment of Shiga toxin-producingEscherichia coli

“…We showed that within our dataset, STEC of lower pathogenic potential were in circulation. This observation is consistent with the trend previously observed at the pre-lockdown period, both at the national or the state level, which showed that most clinical STEC had lower pathogenic potential (17, 70–75).…”

“…Prior to the COVID-19 border closures, it was reported that STEC isolated from clinical sources in NSW predominantly harboured stx genes of lower pathogenic potential (17). The COVID-19 lockdown provided an opportunity to interrogate the pathogenic potential STEC landscape without external influences.…”

“…STEC were isolated from clinical specimens by the Centre for Infectious Disease and Microbiology Laboratory Services (CIDMLS), Institute of Clinical Pathology and Medical Research (ICPMR), NSW Health Pathology, as per STEC control guidelines from Health Protection NSW (https://www.health.nsw.gov.au/Infectious/controlguideline/Pages/haemo.aspx). STEC studied (Supplementary Table S1) were isolated and processed for WGS on the Illumina NextSeq500 platform as previously described (17). All isolates were archived in Skim milk-Tryptone-Glucose-Glycerine (STGG) medium (48) at -80°C.…”

“…Tracking of this is beneficial for genomic surveillance as harbouring multiple isogenic stx copies has been associated with increased disease severity (18, 19). Computing this virulence barcode relied upon multiple manual curation steps and multiple database searches (17).…”

“…Previously, we proposed a STEC virulence barcode to capture subtyping information of both eae and stx (17). This 12-mer barcode is divided into three segments: segment 1 (2-mer) encodes the eae subtype, segment 2 (2-mer) encodes predicted multiple copies of isogenic stx genes, and segment 3 (8-mer) captures up to four stx subtypes within a single genome.…”