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19 Sep 2016

Public Health Night recap: antimicrobial resistance in microorganisms

Insight by Mary Valcanis

Last month, approximately 80 people attended Public Health Night at the Doherty Institute in partnership with the Australian Society for Microbiology – Victoria branch. The theme for the presentations was ‘antimicrobial resistance (AMR) in microorganisms’, chaired by University of Melbourne Professor, Tim Stinear.

The keynote speaker, the University of Adelaide’s Professor John Turnidge, summarised the content of ‘AURA 2016: first Australian report on antimicrobial use and resistance in human health’, which provides a comprehensive picture of AMR, antimicrobial use and appropriateness of prescribing in Australia to date. This report sets a starting point from where AMR trends will be monitored over time and highlights areas where future work will inform action to prevent the spread of AMR.

The University of Melbourne’s Kerrie Stevens and Courtney Lane from the Doherty Institute presented an update on Carbapenemase-producing Enterobacteriaceae (CPE) in Victoria. Carbapenemase-producing Enterobacteriaceae (CPE) are bacteria that can produce enzymes that degrade carbapenems, antibiotics used to treat infections due to multi-drug resistant (MDR), gram-negative bacteria. CPE infections are associated with high rates of mortality and pose serious infection control risks within healthcare facilities.

In December 2015, the Victorian Guideline on CPE was released, which requires clinical microbiology laboratories to refer all suspected CPE to the Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL) at the Doherty Institute for confirmatory testing, and characterisation through whole genome sequencing. All confirmed cases also undergo epidemiological follow up. Between 1 January and 30 June 2016, 40 CPE infections or colonisations were identified in Victoria, of which 21 (53%) were associated with overseas travel, particularly to Asia, including India. Local acquisition of KPC-2 and IMP-4 producing organisms has been observed, with centralised epidemiological and microbiological investigation pivotal in early identification of transmission within healthcare facilities, allowing targeted intervention. 

The Royal Melbourne Hospital’s Dr. Doris Chibo from the Doherty Institute gave an overview on the mechanisms that drive the development of resistance to current HIV antiretrovirals, which included laboratory aspects of HIV drug resistance genotype testing to identify the presence of drug resistance mutations guiding clinicians to make targeted treatment choices.

The University of Melbourne’s Janet Strachan and Dr. Anders Goncalves da Silva, also from the Doherty Institute, reported on the findings of the Victorian Vancomycin Resistant Enterococcus (VRE) Snapshot Study conducted in November 2015. The study looked at all vancomycin-resistant Enterococcus faecium from all specimens from all Victorian laboratories for one month, plus any vancomycin-susceptible E. faecium from blood cultures. Whole genome sequencing was performed on the isolates to define resistance determinants and phylogenetic relatedness. Overall, there were 323 VREfm: vanA (59); vanB (262) and vanA+B (2). There were 10 vancomycin-susceptible E. faecium from bacteraemia. The predominant VREfm strain type was a highly clonal ST796 vanB VREfm (202/323, 63% of all VRE isolates).

Associate Professor Aeron Hurt, Acting Deputy Director of the WHO Collaborating Centre for Reference and Research on Influenza at the Doherty Institute, conveyed antiviral resistance in influenza viruses. Currently, circulating influenza viruses are virtually all resistant to the M2 ion channel inhibitors, an old class of influenza antivirals, thereby creating a reliance on the neuraminidase inhibitors (NAIs) for the treatment of influenza virus infections. The frequency of resistance amongst circulating viruses to the most commonly used NAI, oseltamivir (Tamiflu), is currently low (<2%), but local clusters of cases in the last few years involving oseltamivir-resistant viruses both in Australia and Japan have demonstrated the potential for these viruses to spread amongst the community. Understanding why some antiviral-resistant viruses are able to readily transmit and spread is important to help reduce the chances of this occurring in the future.

Finally, I covered trends in AMR in enteric pathogens. Antimicrobial susceptibility testing of enteric organisms was introduced in the 1970s at MDU PHL for epidemiological purposes to monitor antimicrobial resistance (AMR) trends and detect emerging resistances. In Victoria, the level of resistance in Salmonella (2000-2013) and Shigella (2000-2016) isolates was moderate and high, respectively. In Salmonella, MDR (≥3 antimicrobials) and resistance to ampicillin and ciprofloxacin are of concern; the latter because it may result in treatment failure. Resistance in non-human Salmonella isolates was highest in animal sources.

Emergence of a third generation cephalosporin ESBL was first noted in a S. Typhimurium strain isolated from dairy cattle and humans in 2012, which highlights the importance of a One Health approach to the AMR problem. Almost all Shigella isolates were resistant to at least one antimicrobial and most were MDR. Resistance in Shigella to ciprofloxacin and azithromycin emerged around 2003 and late 2014, respectively. Ongoing testing is vital to identify critical AMR in these organisms and to inform treatment.