STEC Isolates 2021

Friday 2nd December 2022


Summary

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:

• The STEC is no longer viable in the sample
• The STEC is inhibited by the method used (method improvement is ongoing)
• The STEC is present in insufficient numbers to be selected by the methods currently available

Once the case is laboratory notified it is then investigated by the relevant Public Health team who may deem it to not be a case as it fails to fulfil the clinical criteria. The New Zealand Communicable Disease Control manual states (last updated 2018):

asymptomatic infection or presentations with milder bowel symptoms (eg, occasional loose stools) and/or non-diarrhoeal abdominal symptoms do not meet the case definition.

Thus, there are laboratory STEC confirmations which are not included in Episurv data and Episurv data which do not include laboratory typing information.

All isolates confirmed as STEC undergo whole genome sequencing and toxin subtyping and Achtman 7-gene MLST typing (ST type) are routinely reported on individual patient reports. In most 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 serogroup 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 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 comprising at least 15 different ST types, which allows differentiation within this type.

Eight cases of dual serotype infections were reported in 2021 – there are likely to have been more as ESR's current method will only detect multiple serotypes if each has a different toxin profile. These dual serotypes included: O103:H2 + O8:H9; O38:H26 + O91:H14; O146:H21 + O157:H7; O146:H21 + O174:H8; O130:H11 + O157:H7; O26:H11 + O5:HNT (x 2); O26:H11 + O38:H26.

Use of WGS enabled the recognition of a single case of dual toxicity STEC in 2021: STEC by way of stx1c toxin positivity and ETEC by way of heat stable enterotoxin gene positivity. This was serotype O187:H52, ST642.

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STEC Isolates 2021

 

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STEC Isolates 2021

Ph: +64 4 914 0700 Fax: +64 4 914 0770 Email: survqueries@esr.cri.nz