Summary

Verocytotoxin-producing E.coli (VTEC/STEC) confirmed by ERL in 2020. The year 2020 has been unusual at best for everyone and the enteric data for 2020 will always stand apart from other years due the multiple effects of our COVID 19 response on our national data. When NZ locked down at the end of March 2020, diagnostic laboratories staff and resources were given over to the task of establishing and performing testing for COVID 19. Therefore, diagnostic laboratories were actively discouraging referral of other, more routine work. This coupled with people staying home in small bubbles; not eating out; and not being able to readily access face-to-face medical assistance meant that for a period of two months there were very few enteric pathogens received at ESR for typing. Once NZ moved back to Alert Level 2, enteric testing and isolate referral gradually recommenced and STEC numbers returned to the levels expected compared with previous years, suggesting that the vast majority of NZ cases are locally acquired. As of April 2020, >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. Diagnostic laboratories are requested to culture samples to selective media and refer these cultures to ESR for testing. When we receive these plates we test up 12 colonies per faecal sample seeking stx + organisms. If no stx + colonies are identified this in no way refutes the original finding of the diagnostic laboratory. Reasons for failure to isolate by this method include: 1) The STEC is no longer viable in the sample. 2) The STEC is inhibited by the method used (method improvement is ongoing). 3) The STEC is present in insufficient numbers to be selected by the methods currently available. Hence the number of typed STEC is less than the number of notified cases. All isolates confirmed as STEC isolates underwent whole genome sequencing; therefore, minimal samples remain not typable, a problem often encountered using phenotypic typing due to auto-agglutination and poor phenotypic expression. Toxin subtyping and Achtman 7-gene Multi Locus Sequencing Type (ST) are 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). 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 full cluster comparison is done at single nucleotide polymorphism (SNP) difference level on serotypes O157 and O26. Our third most common serotype – O128:H2 is a heterogeneous group, so far comprising at least 10 different ST types, which allows ready differentiation within this type. Five cases of dual serotype infections were noted in 2020 – 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: O128:H2 + O130:H11; O146:H21 + O38:H26; O111:H2 + O157:H7; O128:H2 + O88:H8; O153:H2 + O174:H21. Use of WGS enabled the recognition of two dual toxicity STEC in 2020 – both were STEC by way of stx2g toxin positivity and ETEC by way of heat stable enterotoxin positivity. Both of these were serotype O51:H24.