STEC/VTEC isolates

Shiga-toxin producing Escherichia coli (E.coli) (STEC) isolate data from ESR's enteric reference laboratory.

Note: also known as Verocytotoxin producing E.coli (VTEC).

We welcome the use of this surveillance data with the following acknowledgement, 

New Zealand surveillance data provided by ESR, funded by the Ministry of Health with the cooperation of the diagnostic laboratories.

 

The last five years of data is available here. For older data please visit the Archive.

  • 2022

    2022 report will be coming soon.

  • 2021

    2021 - STEC/VTEC isolates

    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 notification data and notification data which do not include laboratory typing information.

    All isolates confirmed as STEC undergo whole genome sequencing and toxin subtyping and Achtman 7-gene Multi Locus Sequencing Type (ST) are routinely reported on individual patient reports. In most cases, the ST 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 some 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.

  • 2020

    2020 - STEC/VTEC isolates

    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:

    • 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

    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.

  • 2019

    2019 - STEC/VTEC isolates

    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.

  • 2018

    2018 - STEC/VTEC isolates

    STEC/VTEC confirmations continue to increase as another two laboratories commenced culture independent testing for this organism in January and November 2018. Thus, more than 75% of clinical samples in New Zealand are now being screened routinely for stx genes.

    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.

    The 10 most common STEC O types confirmed in 2018 were: O157, O26, O128, O146, O38, O123/186, O103, O174, O176, and O91.

    Note: the USA "Top 7" serotypes only include O157, O26 and O103 from NZ's top 10. However, some of NZ's common types are being regularly seen elsewhere in the world.

    stx2+ STEC O26 continues to emerge as a significant pathotype with 15 isolates confirmed in 2018.

    The number of samples from which an organism has not been able to be isolated is similar to 2017, and comprehensive typing is not currently possible without a pure culture isolate. Work to improve organism isolation is ongoing and the upcoming introduction of routine WGS will add to our understanding of this group of organisms.