Publications by authors named "Marion Easton"

18 Publications

  • Page 1 of 1

Genomic epidemiology and antimicrobial resistance mechanisms of imported typhoid in Australia.

Antimicrob Agents Chemother 2021 Sep 20:AAC0120021. Epub 2021 Sep 20.

Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia.

Typhoid fever is an invasive bacterial disease of humans that disproportionately affects low- and middle-income countries. Antimicrobial resistance (AMR) has been increasingly prevalent in recent decades in serovar Typhi (), the causative agent of typhoid fever, limiting treatment options. In Australia most cases of typhoid fever are imported due to travel to regions where typhoid fever is endemic. Here, all 116 isolates of isolated in Victoria, Australia between 1 July 2018 and 30 June 2020, underwent whole genome sequencing and antimicrobial susceptibility testing. Genomic data were linked to international travel data collected from routine case interviews. Travel to South Asia accounted for most cases, with 92.2% imported from seven primary countries (the top two were India n = 87 and Pakistan n = 12). A total of 17 genotypes were detected in the two-year cohort, with 47.4% genotyped as part of global AMR lineages. Ciprofloxacin resistance was detected in two lineages, 3.3 and 4.3.1.2, all from cases with reported travel to India. Nearly all multidrug and extensively drug resistant isolates (90%) were from cases with reported travel to Pakistan in genotypes 4.3.1.1 and 4.3.1.1.P1. Extended spectrum beta-lactamases, CTX-M-15 and SHV-12, were detected in cases with travel to Pakistan and India, respectively. Linking epidemiological data with genomic studies of provides an opportunity to improve understanding of the emergence, spread and risk of drug-resistant infections and to better inform empiric treatment guidelines in returned travellers.
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http://dx.doi.org/10.1128/AAC.01200-21DOI Listing
September 2021

An implementation science approach to evaluating pathogen whole genome sequencing in public health.

Genome Med 2021 07 28;13(1):121. Epub 2021 Jul 28.

Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.

Background: Pathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control systems worldwide and has the potential to make significant contributions to infectious disease surveillance, outbreak investigation and infection prevention and control. However, to date, there are limited data regarding (i) the optimal models for integration of genomic data into epidemiological investigations and (ii) how to quantify and evaluate public health impacts resulting from genomic epidemiological investigations.

Methods: We developed the Pathogen Genomics in Public HeAlth Surveillance Evaluation (PG-PHASE) Framework to guide examination of the use of WGS in public health surveillance and disease control. We illustrate the use of this framework with three pathogens as case studies: Listeria monocytogenes, Mycobacterium tuberculosis and SARS-CoV-2.

Results: The framework utilises an adaptable whole-of-system approach towards understanding how interconnected elements in the public health application of pathogen genomics contribute to public health processes and outcomes. The three phases of the PG-PHASE Framework are designed to support understanding of WGS laboratory processes, analysis, reporting and data sharing, and how genomic data are utilised in public health practice across all stages, from the decision to send an isolate or sample for sequencing to the use of sequence data in public health surveillance, investigation and decision-making. Importantly, the phases can be used separately or in conjunction, depending on the need of the evaluator. Subsequent to conducting evaluation underpinned by the framework, avenues may be developed for strategic investment or interventions to improve utilisation of whole genome sequencing.

Conclusions: Comprehensive evaluation is critical to support health departments, public health laboratories and other stakeholders to successfully incorporate microbial genomics into public health practice. The PG-PHASE Framework aims to assist public health laboratories, health departments and authorities who are either considering transitioning to whole genome sequencing or intending to assess the integration of WGS in public health practice, including the capacity to detect and respond to outbreaks and associated costs, challenges and facilitators in the utilisation of microbial genomics and public health impacts.
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http://dx.doi.org/10.1186/s13073-021-00934-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317677PMC
July 2021

Prolonged Outbreak of Multidrug-Resistant Shigella sonnei Harboring in Victoria, Australia.

Antimicrob Agents Chemother 2020 11 17;64(12). Epub 2020 Nov 17.

Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia

In Australia, cases of shigellosis usually occur in returned travelers from regions of shigellosis endemicity or in men who have sex with men. Resistance to multiple antibiotics has significantly increased in isolates and represents a significant public health concern. We investigate an outbreak of multidrug-resistant in Victoria, Australia. We undertook whole-genome sequencing of 54 extended-spectrum-beta-lactamase (ESBL)-producing isolates received at the Microbiological Diagnostic Unit Public Health Laboratory between January 2019 and March 2020. The population structure and antimicrobial resistance profiles were identified by genomic analyses, with 73 previously characterized Australian isolates providing context. Epidemiological data, including age and sex of the shigellosis cases, were also collected. There was a significant increase in cases of ESBL from July 2019. Most of the ESBL isolates (65%) fell within a single cluster that was predominantly comprised of male cases that were characterized by the presence of the gene conferring resistance to extended-spectrum cephalosporins. These isolates were also multidrug resistant, including resistance to azithromycin and co-trimoxazole and reduced susceptibility to ciprofloxacin. Our data uncovered a prolonged clonal outbreak of ESBL infection that was likely first introduced by returned travelers and has subsequently been circulating locally in Australia. The emergence of a local outbreak of ESBL with a multidrug-resistant profile, including reduced susceptibility to ciprofloxacin, represents a significant public health threat.
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http://dx.doi.org/10.1128/AAC.01518-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7674062PMC
November 2020

Tracking the COVID-19 pandemic in Australia using genomics.

Nat Commun 2020 09 1;11(1):4376. Epub 2020 Sep 1.

Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.

Genomic sequencing has significant potential to inform public health management for SARS-CoV-2. Here we report high-throughput genomics for SARS-CoV-2, sequencing 80% of cases in Victoria, Australia (population 6.24 million) between 6 January and 14 April 2020 (total 1,333 COVID-19 cases). We integrate epidemiological, genomic and phylodynamic data to identify clusters and impact of interventions. The global diversity of SARS-CoV-2 is represented, consistent with multiple importations. Seventy-six distinct genomic clusters were identified, including large clusters associated with social venues, healthcare and cruise ships. Sequencing sequential samples from 98 patients reveals minimal intra-patient SARS-CoV-2 genomic diversity. Phylodynamic modelling indicates a significant reduction in the effective viral reproductive number (R) from 1.63 to 0.48 after implementing travel restrictions and physical distancing. Our data provide a concrete framework for the use of SARS-CoV-2 genomics in public health responses, including its use to rapidly identify SARS-CoV-2 transmission chains, increasingly important as social restrictions ease globally.
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http://dx.doi.org/10.1038/s41467-020-18314-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462846PMC
September 2020

Search and Contain: Impact of an integrated genomic and epidemiological surveillance and response program for control of carbapenemase-producing Enterobacterales.

Clin Infect Dis 2020 Jul 14. Epub 2020 Jul 14.

Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, Victoria, Australia.

Background: Multi-resistant organisms (MROs) pose a critical threat to public health. Population-based programs for control of MROs such as Carbapenemase-producing Enterobacterales (CPE) have emerged and evaluation is needed. We assess the feasibility and impact of a state-wide CPE surveillance and response program deployed in December 2015 across Victoria, Australia (population 6.5 million).

Methods: A prospective multi-modal intervention including active screening, carrier isolation, centralised case investigation and comparative pathogen genomics was implemented. We analyze trend in CPE incidence and clinical presentation, risk factors and local transmission over the program's first three years (January 2016 to December 2018).

Results: CPE case ascertainment increased over the study period to 1.42 cases/100,000 population, linked to increased screening without a concomitant rise in active clinical infections (0.45-0.60 infections/100,000 population, p=0.640). KPC-2 infection decreased from 0.29 infections/100,000 population prior to intervention to 0.03 infections/100,000 population in 2018 (p=0.003). Comprehensive case investigation identified putative overseas community acquisition. Median time between isolate referral and initial genomic and epidemiological assessment for local transmission was 11 days (IQR 9-14). Prospective surveillance identified numerous small transmission networks (median 2, range 1-19 cases), predominantly IMP and KPC, with median pairwise distance of 8 (IQR 4-13) single nucleotide polymorphisms; low diversity between clusters of the same sequence type suggested genomic cluster definitions alone are insufficient for targeted response.

Conclusions: We demonstrate the value of centralised CPE control programs to increase case ascertainment, resolve risk factors and identify putative local transmission through prospective genomic and epidemiological surveillance; methodologies are transferable to low-prevalence settings and MROs globally.
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http://dx.doi.org/10.1093/cid/ciaa972DOI Listing
July 2020

Incursions of Candida auris into Australia, 2018.

Emerg Infect Dis 2020 06 17;26(6):1326-1328. Epub 2020 Jun 17.

Candida auris is an emerging global healthcare-associated pathogen. During July-December 2018, four patients with C. auris were identified in Victoria, Australia, all with previous overseas hospitalization. Phylogenetic analysis revealed putative transmission between 2 patients and suspected overseas acquisition in the others. Vigilant screening of at-risk patients is required.
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http://dx.doi.org/10.3201/eid2606.190936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7258446PMC
June 2020

Incursions of Candida auris into Australia, 2018.

Emerg Infect Dis 2020 06 17;26(6):1326-1328. Epub 2020 Jun 17.

Candida auris is an emerging global healthcare-associated pathogen. During July-December 2018, four patients with C. auris were identified in Victoria, Australia, all with previous overseas hospitalization. Phylogenetic analysis revealed putative transmission between 2 patients and suspected overseas acquisition in the others. Vigilant screening of at-risk patients is required.
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http://dx.doi.org/10.3201/eid2606.190936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7258446PMC
June 2020

Bridging of Neisseria gonorrhoeae lineages across sexual networks in the HIV pre-exposure prophylaxis era.

Nat Commun 2019 09 5;10(1):3988. Epub 2019 Sep 5.

Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.

Whole genome sequencing (WGS) has been used to investigate transmission of Neisseria gonorrhoeae, but to date, most studies have not combined genomic data with detailed information on sexual behaviour to define the extent of transmission across population risk groups (bridging). Here, through combined epidemiological and genomic analysis of 2,186N. gonorrhoeae isolates from Australia, we show widespread transmission of N. gonorrhoeae within and between population groups. We describe distinct transmission clusters associated with men who have sex with men (MSM) and heterosexuals, and men who have sex with men and women (MSMW) are identified as a possible bridging population between these groups. Further, the study identifies transmission of N. gonorrhoeae between HIV-positive and HIV-negative individuals receiving pre-exposure prophylaxis (PrEP). Our data highlight several groups that can be targeted for interventions aimed at improving gonorrhoea control, including returning travellers, sex workers, and PrEP users.
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http://dx.doi.org/10.1038/s41467-019-12053-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728426PMC
September 2019

Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing in Victoria, Australia, 2012 to 2016.

J Clin Microbiol 2019 09 26;57(9). Epub 2019 Aug 26.

Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia

Carbapenemase-producing (CPE) are being increasingly reported in Australia, and integrated clinical and genomic surveillance is critical to effectively manage this threat. We sought to systematically characterize CPE in Victoria, Australia, from 2012 to 2016. Suspected CPE were referred to the state public health laboratory in Victoria, Australia, from 2012 to 2016 and examined using phenotypic, multiplex PCR and whole-genome sequencing (WGS) methods and compared with epidemiological metadata. Carbapenemase genes were detected in 361 isolates from 291 patients (30.8% of suspected CPE isolates), mostly from urine (42.1%) or screening samples (34.8%). IMP-4 (28.0% of patients), KPC-2 (25.3%), NDM (24.1%), and OXA carbapenemases (22.0%) were most common. (48.8% of patients) and (26.1%) were the dominant species. Carbapenemase-inactivation method (CIM) testing reliably detected carbapenemase-positive isolates (100% sensitivity, 96.9% specificity), identifying an additional five CPE among 159 PCR-negative isolates (IMI and SME carbapenemases). When epidemiologic investigations were performed, all pairs of patients designated "highly likely" or "possible" local transmission had ≤23 pairwise single-nucleotide polymorphisms (SNPs) by genomic transmission analysis; conversely, all patient pairs designated "highly unlikely" local transmission had ≥26 pairwise SNPs. Using this proposed threshold, possible local transmission was identified involving a further 16 patients for whom epidemiologic data were unavailable. Systematic application of genomics has uncovered the emergence of polyclonal CPE as a significant threat in Australia, providing important insights to inform local public health guidelines and interventions. Using our workflow, pairwise SNP distances between CPE isolates of ≤23 SNPs suggest local transmission.
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http://dx.doi.org/10.1128/JCM.00573-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711911PMC
September 2019

Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia.

Clin Infect Dis 2019 10;69(9):1535-1544

Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.

Background: In urban Australia, the burden of shigellosis is either in returning travelers from shigellosis-endemic regions or in men who have sex with men (MSM). Here, we combine genomic data with comprehensive epidemiological data on sexual exposure and travel to describe the spread of multidrug-resistant Shigella lineages.

Methods: A population-level study of all cultured Shigella isolates in the state of Victoria, Australia, was undertaken from 1 January 2016 through 31 March 2018. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analyses of 545 Shigella isolates were performed at the Microbiological Diagnostic Unit Public Health Laboratory. Risk factor data on travel and sexual exposure were collected through enhanced surveillance forms or by interviews.

Results: Rates of antimicrobial resistance were high, with 17.6% (95/541) and 50.6% (274/541) resistance to ciprofloxacin and azithromycin, respectively. There were strong associations between antimicrobial resistance, phylogeny, and epidemiology. Specifically, 2 major MSM-associated lineages were identified: a Shigellasonnei lineage (n = 159) and a Shigella flexneri 2a lineage (n = 105). Of concern, 147/159 (92.4%) of isolates within the S. sonnei MSM-associated lineage harbored mutations associated with reduced susceptibility to recommended oral antimicrobials: namely, azithromycin, trimethoprim-sulfamethoxazole, and ciprofloxacin. Long-read sequencing demonstrated global dissemination of multidrug-resistant plasmids across Shigella species and lineages, but predominantly associated with MSM isolates.

Conclusions: Our contemporary data highlight the ongoing public health threat posed by resistant Shigella, both in Australia and globally. Urgent multidisciplinary public health measures are required to interrupt transmission and prevent infection.
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http://dx.doi.org/10.1093/cid/ciz005DOI Listing
October 2019

Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak.

PeerJ 2018 3;6:e4210. Epub 2018 Jan 3.

Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.

Background: Until recently, carbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks.

Methods: All KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids.

Results: Initial investigations indicated that the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates ( 92%) identified from 35 different locations across metropolitan and rural Victoria between 2012 and 2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation.

Conclusion: A real-time combined epidemiological and genomic investigation proved critical to identifying and defining multiple transmission networks of KPC Enterobacteriaceae, while data from either investigation alone were inconclusive. The investigation was fundamental to informing infection control measures in real-time and the development of state-wide public health guidelines on carbapenemase-producing Enterobacteriaceae surveillance and management.
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http://dx.doi.org/10.7717/peerj.4210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5756455PMC
January 2018

Increasing Antimicrobial Resistance in Nontyphoidal Salmonella Isolates in Australia from 1979 to 2015.

Antimicrob Agents Chemother 2018 02 25;62(2). Epub 2018 Jan 25.

Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.

Australia has high and increasing rates of salmonellosis. To date, the serovar distribution and associated antimicrobial resistance (AMR) patterns of nontyphoidal (NTS) in Australia have not been assessed. Such information provides critical knowledge about AMR in the food chain and informs decisions about public health. We reviewed longitudinal data on NTS in two Australian states over a 37-year period, between 1979 and 2015, and antimicrobial resistance since 1984. Overall, 17% of isolates were nonsusceptible to at least one antimicrobial, 4.9% were nonsusceptible to ciprofloxacin, and 0.6% were nonsusceptible to cefotaxime. In total, 2.5% of isolates were from invasive infections, with no significant difference in AMR profiles between invasive and noninvasive isolates. Most isolates with clinically relevant AMR profiles were associated with travel, particularly to Southeast Asia, with multiple "incursions" of virulent and resistant clones into Australia. Our findings represent the largest longitudinal surveillance system for NTS in Australia and provide valuable public health knowledge on the trends and distribution of AMR in NTS. Ongoing surveillance is critical to identify local emergence of resistant isolates.
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http://dx.doi.org/10.1128/AAC.02012-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786757PMC
February 2018

Waterparks are high risk for cryptosporidiosis: A case-control study in Victoria, 2015.

Commun Dis Intell Q Rep 2017 Jun 30;41(2):E142-E149. Epub 2017 Jun 30.

Convener, Master of Philosophy in Applied Epidemiology, National Centre for Epidemiology and Population Health, Australian National University, Acton, Australian Capital Territory.

Background: An increase in notifications of cryptosporidiosis was observed in Victoria between March and April 2015. Cases mostly resided in one metropolitan region and hypothesis-generating interviews identified common exposures to aquatic facilities. We conducted a case-control study to determine exposure source(s) and facilitate control measures.

Methods: Laboratory-confirmed cases of cryptosporidiosis from the region of interest notified between 1 March and 23 April 2015 were included. Controls residing in the same region were recruited from participants in a population health survey and frequency matched (2 per case) by age group. Details of exposure to potential risk factors were collected using a standardised telephone questionnaire for the 14-days prior to illness for cases, and an analogous exposure period for controls. Univariable and multivariable logistic regression were used to determine risk factors associated with illness using STATA SE 13.1.

Results: Thirty cases and 66 controls were included in the study. Half the cases were less than 12 years of age and 62% were female. Illness was most strongly associated with recreational water exposure at any waterpark (adjusted odds ratio (aOR)=73.5; 95% confidence interval (CI):6.74-802), and specifically at Victorian waterparks (aOR=45.6; 95% CI:5.20-399). Cases were linked with attendance at either a waterpark in the region or an adjacent region. As a result of this investigation, hyperchlorination was completed at identified facilities and swim hygiene information distributed.

Conclusion: This study reinforces the potential for recreational water facilities, particularly waterparks, to act as a transmission source of Cryptosporidium infections. Continued communication to patrons is required to ensure healthy swimming practice in Victorian aquatic facilities.
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June 2017

An outbreak of foodborne norovirus gastroenteritis linked to a restaurant in Melbourne, Australia, 2014.

Western Pac Surveill Response J 2017 Apr-Jun;8(2):12-16. Epub 2017 May 5.

Victorian Department of Health and Human Services, Melbourne, Australia.

Introduction: In May 2014 an outbreak of norovirus occurred among patrons of a restaurant in Melbourne, Australia. Investigations were conducted to identify the infectious agent, mode of transmission and source of illness, and to implement controls to prevent further transmission.

Methods: A retrospective case-control study was conducted to test the hypothesis that food served at the restaurant between 9 and 15 May 2014 was the vehicle for infection. A structured questionnaire was used to collect demographic, illness and food exposure data from study participants. To ascertain whether any food handlers had experienced gastroenteritis symptoms and were a possible source of infection, investigators contacted and interviewed staff who had worked at the restaurant between 9 and 16 May 2014.

Results: Forty-six cases (including 16 laboratory-confirmed cases of norovirus) and 49 controls were interviewed and enrolled in the study. Results of the analysis revealed a statistically significant association with illness and consumption of grain salad (OR: 21.6, 95% CI: 1.8-252.7,  = 0.015) and beetroot dip (OR: 22.4, 95% CI: 1.9-267.0,  = 0.014). An interviewed staff member who reported an onset of acute gastrointestinal illness on 12 May 2014 had prepared salads on the day of onset and the previous two days.

Discussion: The outbreak was likely caused by person-to-food-to-person transmission. The outbreak emphasizes the importance of the exclusion of symptomatic food handlers and strict hand hygiene practices in the food service industry to prevent contamination of ready-to-eat foods and the kitchen environment.
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http://dx.doi.org/10.5365/WPSAR.2017.8.1.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516399PMC
May 2018

Emergence of multidrug resistance in locally-acquired human infections with Salmonella Typhimurium in Australia owing to a new clade harbouring bla.

Int J Antimicrob Agents 2017 Jul 2;50(1):101-105. Epub 2017 May 2.

Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, VIC, Australia; Infectious Diseases Department, Austin Health, Heidelberg, VIC, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia. Electronic address:

Antimicrobial resistance in non-typhoidal Salmonella is a critical problem globally, with the emergence of resistance to third-generation cephalosporins (3GCs) a particular concern. The aim of this study was to use whole-genome sequencing (WGS) to characterise recently identified human and non-human isolates of 3GC-resistant Salmonella enterica subsp. enterica serovar Typhimurium from Australia. The Illumina NextSeq sequencing platform was used to determine the genome sequences of 78 S. Typhimurium definitive type 44 isolated in Australia between 1992 and 2016, including 31 3GC-resistant isolates. Phylogenetic and bioinformatics analyses were subsequently performed using a number of in silico tools. We report the emergence of 3GC resistance in locally-acquired Australian S. Typhimurium for the first time. Phenotypically resistant isolates of human and animal origin were geographically restricted and were found by WGS all to be closely related and to carry bla. Dairy cattle were the suspected source based on geographical clustering of animal isolates, which were predominantly bovine in origin. In conclusion, locally-acquired human cases of S. Typhimurium carrying bla were identified that appear to be of bovine origin, raising concerns regarding the human impact of off-label use of ceftiofur in cattle.
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http://dx.doi.org/10.1016/j.ijantimicag.2017.02.014DOI Listing
July 2017

A review of the public health management of shigellosis in Australia in the era of culture-independent diagnostic testing.

Aust N Z J Public Health 2016 Dec 23;40(6):588-591. Epub 2016 Oct 23.

Communicable Diseases Epidemiology & Surveillance and OzFoodNet, Department of Health & Human Services, Victoria.

Objective: To review the national case definition for shigellosis following the introduction of culture independent diagnostic testing by clinical laboratories and provide evidence to reform jurisdictional public health practices for the management shigellosis., .

Methods: A review of all Australian jurisdictional public health guidelines for shigellosis was conducted. Victorian 2014 shigellosis data were analysed: demographics and risk factors for cases identified by conventional culture or culture-independent diagnostic methods were described.

Results: There was considerable variation in reporting of cases to the National Notifiable Disease Surveillance System (NNDSS) by the eight Australian jurisdictions, with an array of classifications based on diagnostic testing methodologies. Analysis of Victorian 2014 shigellosis data found that culture positive cases were more likely to have reported men who have sex with men (MSM) as a risk factor than PCR positive only cases (p<0.0001) and less likely to have reported overseas travel during their incubation period (p<0.0001). Over a 10-year period (2005 to 2014), only two of 86 cases who were employed in high-risk occupations had ongoing positive faecal cultures after appropriate treatment.

Conclusions: The national surveillance case definition for shigellosis should be reviewed to facilitate standardised reporting across Australia. All jurisdictions must consider the public health significance of PCR positive only results in their surveillance risk assessments to inform management of shigellosis cases.
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http://dx.doi.org/10.1111/1753-6405.12590DOI Listing
December 2016

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes.

J Clin Microbiol 2016 Feb 25;54(2):333-42. Epub 2015 Nov 25.

Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia Infectious Diseases Department, Austin Health, Heidelberg, Victoria, Australia

Whole-genome sequencing (WGS) has emerged as a powerful tool for comparing bacterial isolates in outbreak detection and investigation. Here we demonstrate that WGS performed prospectively for national epidemiologic surveillance of Listeria monocytogenes has the capacity to be superior to our current approaches using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA), binary typing, and serotyping. Initially 423 L. monocytogenes isolates underwent WGS, and comparisons uncovered a diverse genetic population structure derived from three distinct lineages. MLST, binary typing, and serotyping results inferred in silico from the WGS data were highly concordant (>99%) with laboratory typing performed in parallel. However, WGS was able to identify distinct nested clusters within groups of isolates that were otherwise indistinguishable using our current typing methods. Routine WGS was then used for prospective epidemiologic surveillance on a further 97 L. monocytogenes isolates over a 12-month period, which provided a greater level of discrimination than that of conventional typing for inferring linkage to point source outbreaks. A risk-based alert system based on WGS similarity was used to inform epidemiologists required to act on the data. Our experience shows that WGS can be adopted for prospective L. monocytogenes surveillance and investigated for other pathogens relevant to public health.
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http://dx.doi.org/10.1128/JCM.02344-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733179PMC
February 2016

Emergence of a ribotype 244 strain of Clostridium difficile associated with severe disease and related to the epidemic ribotype 027 strain.

Clin Infect Dis 2014 Jun 4;58(12):1723-30. Epub 2014 Apr 4.

Monash Infectious Diseases, Monash Health Department of Microbiology, Monash University Department of Microbiology, Monash Health, Clayton Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia.

Background: We identified 12 patients with Clostridium difficile infection between July 2011 and March 2012 from whom an unusual C. difficile strain was isolated. This strain had a single-nucleotide deletion of the tcdC gene at position 117 and binary toxin genes, which are characteristic of the hypervirulent ribotype (RT) 027 strain.

Methods: A retrospective cohort study of 12 patients infected with C. difficile RT244 and 24 patients infected with non-RT244/non-RT027 strains matched for place of diagnosis and time of collection of specimen was performed. We performed whole-genome sequencing to understand the relationship of the RT244 strain to other C. difficile strains and further understand its virulence potential.

Results: Clostridium difficile RT244 was associated with more severe disease and a higher mortality rate. Phylogenomic analysis using core genome single-nucleotide polymorphisms showed that RT244 is in the same genetic clade (clade 2) as RT027 but is distinct from all RT027 strains. The pathogenicity locus of the RT244 strain encodes a variant toxin B, and this was confirmed by demonstration of Clostridium sordellii-like cytopathic effect on Vero cells. Toxin B production in culture supernatants was lower than that seen with a RT027 strain.

Conclusions: Our findings demonstrate the pathogenic potential of this RT244 C. difficile strain and emphasize the importance of ongoing surveillance for emergent strains.
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http://dx.doi.org/10.1093/cid/ciu203DOI Listing
June 2014
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