Summary

Verocytotoxin-producing E.coli (VTEC/STEC) confirmed by ERL in 2019. As of November 2018, approximately 80% of the country is now being tested for STEC via a number of different multiplex PCR methods. The ongoing increase in non-O157 STEC cases in NZ is due to changes in detection methods. STEC O157 case numbers have remained relatively stable over this time. See Appendix B: https://www.mpi.govt.nz/dmsdocument/47986-Annual-report-concerning-Foodborne-Diseases-in-New-Zealand-2020 On 1 August 2019, the Enteric Reference Laboratory transitioned to whole genome sequencing for all serotyping and fine typing of STEC. Subsequently, from this time there are minimal NT (not typable) results as the problems encountered in phenotypic typing such as auto-agglutination and poor phenotypic expression are overcome by the genomic method. From 1 August 2019, toxin subtyping and Achtman 7-gene Multi Locus Sequencing Type (ST) have been routinely reported on individual patient reports. In many cases, the ST type is uniform across a serotype, with just a small number of isolates showing variation (eg the majority of STEC O157 are ST 11; and the majority of STEC O26 are ST 21). ST type differs within an O type if there is a different H result – eg O103:H2 (ST 17) and O103:H25 (ST343). As part of the introduction of routine WGS all O157 and O26 isolates are being routinely cluster typed via a SNP based method, which is much more precise than previously used clustering methods. Each week a cluster comparison is done at SNP difference level on O157 and O26 isolates. Our third most common serotype – O128:H2 is a heterogeneous group, so far comprising seven different ST types, which allows ready differentiation within this type. Ten cases of dual serotype infections were noted in 2019 – there are likely to have been more as ESR's current method will only detect multiple serotypes if each has a have different toxin profile. These dual serotypes included: O38:H26 + ONT:H8; O38:H26+ ONT:H7; O128:H2 + O149:H2; O128:H2 + O174:H8; O128:H2 + ONT:H7; O156:H25 + O177:H25; O157:H7 + O26:H11; O157:H7 + O123:H2; O176:H4 + ONT:H2; ONT:H14 + ONT:H2. Use of WGS enabled the recognition of three dual toxicity STEC in 2019 – all three were STEC by way of stx2 toxin positivity and ETEC by way of heat stable enterotoxin positivity. Serotypes of these isolates were O100:H20; O15:H16 and O148:H7. National typing data is incomplete for the 2019 year as a laboratory testing 1/6 of the NZ's samples ceased referral of STEC isolates in November 2018 but resumed referrals in June 2019. A genomic cluster of 28 STEC O157 cases predominantly from the Auckland region was noted in March 2019. A cause/source was not confirmed.