Value of routine whole genome sequencing for Mycobacterium tuberculosis drug resistance detection.

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.

Hepatitis E virus infections in travellers: assessing the threat to the Australian blood supply.

BACKGROUND: In many developed countries hepatitis E virus (HEV) infections have occurred predominantly in travellers to countries endemic for HEV. HEV is a potential threat to blood safety as the virus is transfusion-transmissible. To minimise this risk in Australia, individuals diagnosed with HEV are deferred. Malarialdeferrals, when donors are restricted from donating fresh blood components following travel toanareain which malaria is endemic, probably also decrease the HEV risk, by deferring donors who travel to many countries also endemic for HEV. The aim of this study is to describe overseas-acquired HEV cases in Australia, in order to determine whether infection in travellers poses a risk to Australian blood safety. MATERIALS AND METHODS: Details of all notified HEV cases in Australia from 2002 to 2014 were accessed, and importation rates estimated. Countries in which HEV was acquired were compared to those for which donations are restricted following travel because of a malaria risk. RESULTS: Three hundred and thirty-two cases of HEV were acquired overseas. Travel to India accounted for most of these infections, although the importation rate was highest for Nepal and Bangladesh. Countries for which donations are restricted following travel due to malaria risk accounted for 94% of overseas-acquired HEV cases. DISCUSSION: The vast majority of overseas-acquired HEV infections were in travellers returning from South Asian countries, which are subject to donation-related travel restrictions for malaria. This minimises the risk HEV poses to the Australian blood supply.

Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014.

BACKGROUND: Salmonella 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. METHODS: We 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. RESULTS: The 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. CONCLUSIONS: WGS 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.

First reported outbreak of locally acquired hepatitis E virus infection in Australia.

OBJECTIVE: To determine the source and extent of a locally acquired hepatitis E virus (HEV) infection outbreak. DESIGN, SETTING AND PARTICIPANTS: A cluster of notified cases of HEV infection linked to a single restaurant (X) was identified in May 2014. People with laboratory-confirmed HEV infection in New South Wales between January 2013 and December 2014 were interviewed about potential risk factors for HEV infection. Co-diners at restaurant X and patients with suspected but unexplained viral hepatitis were retrospectively tested. Foods eaten by the infected persons were compared with those of seronegative co-diners. HEV RNA detected in sera from infected persons was sequenced and genotyped. Implicated foods were traced back to their sources. MAIN OUTCOME MEASURES: Potential sources of infection, including overseas travel and foods eaten, and origin of implicated food products. RESULTS: In 55 serologically confirmed cases of HEV infection, 24 people had not travelled overseas during their incubation periods. Of the 24, 17 reported having eaten at restaurant X, 15 of whom could be interviewed. All reported consuming pork liver pâté, compared with only four of seven uninfected co-diners (P < 0.05). The other seven people with locally acquired infections each reported consuming a pork product during their incubation periods. HEV RNA was detected in 16 of the 24 cases; all were of genotype 3. Sequencing indicated greater than 99% homology among restaurant X isolates. HEV RNA was isolated from pork sausages from a batch implicated in one of the locally acquired infections not linked with restaurant X. The pork livers used for pâté preparation by restaurant X were traced to a single Australian farm. CONCLUSIONS: 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.

Use of a prohibition order after a large outbreak of gastroenteritis caused by norovirus among function attendees.

INTRODUCTION: In May 2011, an outbreak of acute gastroenteritis occurred among guests attending two functions (Function A and B) at a local function centre in Sydney, Australia. The Sydney South West Public Health Unit and the New South Wales (NSW) Food Authority sought to determine the cause of the outbreak and implement control measures. METHODS: A retrospective cohort study was planned. A complete guest list was unavailable, so guests who could be contacted were asked to provide details of other guests. Attendee demographics, symptom profile and food histories were obtained using a standard response questionnaire. Stool samples were requested from symptomatic guests. The NSW Food Authority conducted a site inspection. RESULTS: Of those interviewed, 73% of Function A guests and 62% of Function B guests were ill, with mean incubation times of 27 and 23 hours respectively. Diarrhoea was the most common symptom. Three stool samples and four environmental swabs were positive for norovirus. One food handler reported feeling ill before and during the functions. A prohibition order was used to stop food handlers implicated in the outbreak from preparing food. DISCUSSION: This outbreak strongly suggests transmission of norovirus, possibly caused by an infected food handler. Regulatory measures such as prohibition orders can be effective in enforcing infection control standards and minimising ongoing public health risk.