Core and Accessory Genome Comparison of Australian and International Strains of O157 Shiga Toxin-Producing Escherichia coli

Abstract

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen, and serotype O157:H7 is typically associated with severe disease. Australian STEC epidemiology differs from many other countries, as severe outbreaks and HUS cases appear to be more often associated with non-O157 serogroups. It is not known why Australian strains of O157 STEC might differ in virulence to international strains. Here we investigate the reduced virulence of Australian strains. Multiple genetic analyses were performed, including SNP-typing, to compare the core genomes of the Australian to the international isolates, and accessory genome analysis to determine any significant differences in gene presence/absence that could be associated with their phenotypic differences in virulence. The most distinct difference between the isolates was the absence of the stx2a gene in all Australian isolates, with few other notable differences observed in the core and accessory genomes of the O157 STEC isolates analyzed in this study. The presence of stx1a in most Australian isolates was another notable observation. Acquisition of stx2a seems to coincide with the emergence of highly pathogenic STEC. Due to the lack of other notable genotypic differences observed between Australian and international isolates characterized as highly pathogenic, this may be further evidence that the absence of stx2a in Australian O157 STEC could be a significant characteristic defining its mild virulence. Further work investigating the driving force(s) behind Stx prophage loss and acquisition is needed to determine if this potential exists in Australian O157 isolates.

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

“…Three different virulence barcodes ( Table 2 ) were associated with O157:H7 with the majority being 06-00-1A-2C-00-00 ( n = 17) followed by 06-00-1A-00-00-00 ( n = 3) and 06-00-2A-00-00-00 ( n = 2). All O157:H7 isolates harboured a γ1 subtype eae consistent with previous reports ( Oswald et al, 2000 ; Blanco et al, 2005 ) and majority harboured stx 1a either alone or in combination with stx 2c, an stx genotype common in Australian STEC O157 ( Fegan and Desmarchelier, 2002 ; Mellor et al, 2012 , 2013 , 2015 ; Ingle et al, 2019 ; Pintara et al, 2020 ).…”

“…The predominant subtype detected in our dataset was Stx1a, which is known to be less cytotoxic than the subtypes Stx2a, Stx2d, and Stx2c ( Friedrich et al, 2002 ; Orth et al, 2007 ). Previous reports, albeit with a STEC O157:H7 bias, have also shown that Stx1a was the predominant Stx subtype circulating in Australia ( Mellor et al, 2012 , 2015 ; Ingle et al, 2019 ; Pintara et al, 2020 ). While the lower potency of Stx1a could explain the lower virulence of STEC in Australia, we would like to posit a possible genomic contributing factor to reduced virulence, at least in Stx1a-producing STEC.…”

“…However, these non-motile O157 did encode an intact fliC , the target for in silico H-antigen typing, and as such would be genomically identified as O157:H7 when typed in silico ( Pintara et al, 2018 ). Australian STEC O157 isolates typically harbour stx 1a and stx 2c either alone or in combination ( Fegan and Desmarchelier, 2002 ; Mellor et al, 2012 , 2015 ) and have been reported to be genetically distinct from international collections of isolates ( Leotta et al, 2008 ; Mellor et al, 2012 , 2013 , 2015 ; Ingle et al, 2019 ; Pintara et al, 2020 ). It remains unknown if the other non-O157 STEC were also geographically and genetically distinct.…”

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)(71)(72)(73)(74)(75).…”

Genomic analysis of an outbreak of toxin gene bearing Corynebacterium diphtheriae in Northern Queensland, Australia reveals high level of genetic similarity

“…Whole genome sequencing was performed on the isolates listed in Supplementary Table S1 using the procedure described in our previous studies [14,15]. Briefly, DNA was prepared for sequencing using the Nextera XT kit (Illumina, San Diego, USA) and sequenced on the NextSeq500 using the NextSeq 500 Mid Output v2 kit (300 cycles) (Illumina), according to the manufacturer's instructions.…”