V.MFS.0440 - Molecular assessment and characterisation of Australian Shiga toxin-producing E. coli (STEC)

Summary

higa toxin producing E. coli (STEC) are traditionally classified by serotypes, and of the hundreds of types isolated to date from cattle, only a small percentage are known to be pathogenic. The US considers seven serotypes (Top 7) to be adulterants of manufacturing beef. Expert groups (JEMRA, NACMCF) have recently proposed alternative risk schemes for STEC based on their disease potential, whose adoption could impact the Australian red meat industry. To estimate this impact, a total of 923 historic and contemporary STEC isolates from Australian cattle, goat, sheep, and human sources were sequenced, analysed, and classified into the new schemes from low (group 5) to high (group 1) health risk. A genomics workflow was designed in-house for rapid, high-throughput and flexible risk profiling of STEC. Using this workflow, Australian isolates were shown to mostly fall into risk levels associated with medium to low human health risk. The JEMRA scheme was more likely to classify STEC into higher risk categories than NACMCF or FSIS risk schemes. This evidence-based data will prepare industry to make informed risk management decisions and to meet future export market requirements that may arise from the adoption of the new risk schemes.

Objectives

The project had three core objectives: (i) to describe the virulence profiles of historical Australian STEC (from CSIRO culture collection) according to internationally proposed risk classification schemes (ii) to conduct a survey of beef cattle faeces and manufacturing beef enrichment broths for the presence of E. coli harbouring priority virulence marker combinations as proposed by JEMRA and NACMCF and (iii) to characterise E. coli harbouring virulence markers of clinical relevance that were isolated from the survey of beef cattle faeces and manufacturing beef enrichment broths. The project achieved all three objectives, except for the survey sample target for calves, which was lowered due to challenges in sourcing samples from this animal class.

Key findings

National survey of STEC:
Beef cattle faeces and manufacturing beef enrichment broths were screened for the presence of E. coli harbouring priority virulence marker combinations (stx1, stx2, eae and aggR gene markers) as proposed by JEMRA and NACMCF. A total of 40,950 isolates were recovered from across 910 samples: 710 cattle faeces and 200 manufacturing beef enrichment broths. Of the 40,950 isolates, 1,978 (4.9%) were confirmed to possess one or both stx genes (1 or 2) either alone or in combination with eae. In total, 294 of 910 samples (32%) were confirmed to contain at least one stx-containing isolate. All STEC with unique virulence gene profiles from each sample were characterised as below.

STEC risk characterisation:
Two prominent international schemes (JEMRA and NACMCF) have been proposed to risk assess STEC into classes based on their estimated potential to cause disease. Using FSIS definitions, 36.5% of isolates were classified as adulterants while 60.5% were deemed non-adulterants. By comparison, using the JEMRA system, 17.8% of isolates were assigned to levels 1 or 2 which have the highest potential for severe disease, 41.9% were assigned levels 3 or 4 which are unlikely to cause haemolytic uremic syndrome (HUS) but may cause diarrhoea or bloody diarrhoea and the remaining 40.3% were assigned to level 5 which are predicted to cause diarrhoea but are unlikely to cause bloody diarrhoea or HUS. Using the NACMCF scheme, 0% of isolates were assigned to category 1 (highest health risk), 19% were assigned to category 2, 20% to category 3, 11.4% to category 4 and 49.1% were assigned to the lowest risk group, category 5.

Benefits to industry

The project generated a substantial database of whole genome sequences from a diverse set of Australian STEC, that will act as a valuable resource for genomic investigations into disease potential. The project also developed new tool kits that can be adapted and modified for the high-throughput whole genome sequence characterisation of STEC. We anticipate that risk classification data generated in this project will allow industry to assess the risk of STEC that are likely to be isolated through red meat testing, rapidly respond to changes to risk classifications and regulatory requirements from overseas customers and potentially lobby to reduce testing requirements and regulations around 'low risk' STEC.

Future research

Additional national surveys to collect STEC from animal groups and food sources that were underrepresented in this project should be undertaken. The further development of capability in the detection, isolation, and characterisation of STEC is recommended to support industry to evaluate/manage risk and meet future export market requirements of global customers of Australian red meat products. Collaboration with public health labs is recommended to gain access to data for comparing predicted disease potential of isolates with patient symptoms.