This is the first reported HEV outbreak in Australia. HEV should be considered in patients presenting with a compatible illness, even without a history of overseas travel. Pork products should be thoroughly cooked before consumption.

BackgroundSalmonella Typhimurium (STM) is an important cause of foodborne outbreaks worldwide. Subtyping of STM remains critical to outbreak investigation, yet current techniques (e.g. multilocus variable number tandem repeat analysis, MLVA) may provide insufficient discrimination. Whole genome sequencing (WGS) offers potentially greater discriminatory power to support infectious disease surveillance.MethodsWe performed WGS on 62 STM isolates of a single, endemic MLVA type associated with two epidemiologically independent, food-borne outbreaks along with sporadic cases in New South Wales, Australia, during 2014. Genomes of case and environmental isolates were sequenced using HiSeq (Illumina) and the genetic distance between them was assessed by single nucleotide polymorphism (SNP) analysis. SNP analysis was compared to the epidemiological context.ResultsThe WGS analysis supported epidemiological evidence and genomes of within-outbreak isolates were nearly identical. Sporadic cases differed from outbreak cases by a small number of SNPs, although their close relationship to outbreak cases may represent an unidentified common food source that may warrant further public health follow up. Previously unrecognised mini-clusters were detected.ConclusionsWGS of STM can discriminate foodborne community outbreaks within a single endemic MLVA clone. Our findings support the translation of WGS into public health laboratory surveillance of salmonellosis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0831-3) contains supplementary material, which is available to authorized users.

Routine whole genome sequencing (WGS) of pathogens is becoming more feasible as sequencing costs decrease and access to benchtop sequencing equipment and bioinformatics pipelines increases. This study examined the added value gained from implementing routine WGS of all Mycobacterium tuberculosis isolates in New South Wales, Australia.Drug resistance markers inferred from WGS data were compared to commercial genotypic drug susceptibility testing (DST) assays and conventional phenotypic DST in all isolates sequenced between 2016 and 2019. Of the 1107 clinical M. tuberculosis isolates sequenced, 29 (2.6%) were multi-drug resistant (MDR); most belonged to Beijing (336; 30.4%) or East-African Indian (332; 30%) lineages. Compared with conventional phenotypic DST, WGS identified an additional 1% of isolates which were likely drug resistant, explained by mutations previously associated with treatment failure and mixed bacterial populations. However, WGS provided a 20% increase in drug resistance detection in comparison with commercial genotypic assays by identifying mutations outside of the classic resistance determining regions in rpoB, inhA, katG, pncA and embB genes. Gains in drug resistance detection were significant (p = 0.0137, paired t-test), but varied substantially for different phylogenetic lineages.In low incidence settings, routine WGS of M. tuberculosis provides better guidance for person-centered management of drug resistant tuberculosis than commercial genotypic assays.

SUMMARYTwenty-two confirmed cases ofSalmonellaInfantis were identified in 70 residents of high-level care areas of a residential aged care facility in Sydney in April 2010 during an outbreak of gastroenteritis. A retrospective cohort study was conducted to identify a possible cause. Consuming a soft diet, puréed diet, or thickened fluid were each independently associated with illness. A logistic regression showed consumption of thickened fluid to be the only significant exposure associated with illness (adjusted odds ratio 11·8, 95% confidence interval 1·9–75·9). It was postulated that the thickened fluid had been contaminated by chicken mince, a sample of which also culturedS. Infantis. This finding reinforces the need to educate food-handlers on the risk of potential cross-contamination; it also highlights the need to consider all dietary components, such as thickened fluids, as potential vehicles for transmission in an outbreak.