Services

Bioinformatics at MDU PHL is responsible for quality control, management and analysis of microbial whole genome sequence data. Bioinformatic develop and implement tools and pipelines which characterise of bacterial pathogens, detect of virulence and antimicrobial resistance determinants and contribute to outbreak investigations employing phylogenomic methods. Our team has expertise in computer science, clinical epidemiology, clinical infectious diseases, evolutionary biology, and microbiology.

The Enteric Reference Laboratory (ERL) provides national reference and surveillance laboratory services for human, animal, food and environmental enteric bacterial pathogens. Confirmation and characterisation is performed using a combination of traditional and molecular typing methods.

Typing results and analyses allow the ERL to detect clusters, identify outbreaks or exotic isolates, which inform public health authorities for targeted responses and interventions in food and waterborne investigations.

Epidemiology staff perform data analyses on surveillance typing and antimicrobial susceptibility data for special projects and multi-jurisdictional outbreaks, and co-ordinate the Victorian Carbapenemase-producing Enterobacterales Surveillance and Response Unit (VCRSU); the Victorian Hospital Pathogens Surveillance Scheme (VHPSS); the National Enteric Pathogens Surveillance Scheme (NEPSS) and MDU PHL activities as a WHO Regional Reference Laboratory for the Invasive Bacterial – Vaccine Preventable Diseases Program (IB-VPD).

Victorian Carbapenemase-producing Enterobacteriaceae Surveillance and Response Unit (VCRSU)

The Victorian Carbapenemase-producing Enterobacteriaceae (CPE) Surveillance and Response Unit was implemented in 2015 in response to increasing detection of CPE in Victoria. All Victorian CPE isolates are referred to MDU PHL for confirmation and genomic analysis. In conjunction with the Victorian Department of Health and Human Services and VICNISS, patients are interviewed and case records reviewed to ascertain possible transmission routes, with infection control intervention to prevent further spread.

Antibiograms of Victorian carbapenemase-producing organisms. This document outlines the observed antimicrobial resistance patterns in Victorian carbapenemase-producing Enterobacterales, Pseudomonas and Acinetobacter isolates received at MDU PHL from July 1 2020 by species and carbapenemase gene. This document outlines the observed antimicrobial resistance patterns specifically for NDM-1 producing Enterobacterales, Pseudomonas and Acinetobacter isolates received at MDU PHL from 1st January 2019. These documents may assist clinicians in guideline development and empirical therapy for the treatment of patients with suspected infection with a carbapenemase-producing organism.

The Victorian Hospital Pathogens Surveillance Scheme (VHPSS)

The Victorian Hospital Pathogens Surveillance Scheme is a laboratory-based surveillance program for bacterial and fungal isolates from bloodstream infections and meningitis. The scheme was established in 1988 with contributors including metropolitan and regional laboratories throughout.

National Enteric Pathogens Surveillance Scheme (NEPSS)

The National Enteric Pathogens Surveillance Scheme was established in 1978 to provide a repository of data on enteric pathogens isolated from human gastrointestinal and extraintestinal infections and from various non-human sources such as animals, animal feed, food, food ingredients, water and environmental samples. This supports the monitoring and control of endemic and epidemic human infection with enteric pathogens throughout Australia.

The WHO Invasive Bacterial-Vaccine Preventable Diseases Program

The WHO Invasive Bacterial-Vaccine Preventable Diseases Program aims to enhance laboratory diagnosis of patients with bacterial meningitis due to Haemophilus influenzae, Neisseria meningitidis or Streptococcus pneumoniae. MDU PHL is a Regional Reference Laboratory in the Western Pacific Region and assists with regional training and quality control of bacterial detection and typing assays, as well as providing sequencing of internationally referred samples.

The Food, Environment and Outbreak Response (FEOR) Section provides analytical microbiology services to support public health outbreak investigations and the Victorian Department of Health surveillance programs. The science knowledge includes the specific disciplines of food, water and environmental microbiology and associated processing, hygiene and public health safety.

The Molecular Diagnostics, Development and Informatics (MDDI) section provides a comprehensive range of genomic technologies for the molecular detection and characterisation of clinical, foodborne and environmental pathogens. Our services include:

• NAAT of microorganisms and primary specimens
• WHO regional reference laboratory for vaccine preventable, invasive bacterial diseases
• Fragment analysis for genotyping (MLVA for S. Typhimurium)
• Next Generation Sequencing/whole genome sequencing
• Sanger Sequencing

The core application of MDDI in conjunction with Bioinformatics is communicable diseases genomics. This is the application of whole genome sequencing (WGS) to the characterisation of pathogens for the purpose of informing public health surveillance and investigation of communicable diseases. Employing SBS chemistry on the Illumina NextSeq and MiSeq platforms, our robotic WGS sequencing pipeline can process up to 500 bacterial isolates per week using Illumina paired end sequencing with read lengths ranging from 75 to 300 bases. This is used for resistome detection, identification of unusual pathogens, genotyping and phylogenomics for outbreak detection and cluster analysis. Additionally, we support the research activities of DAMG with custom applications including metagenomics of clinical samples, population analysis and gene discovery.

We also offer tours of the facility are provided and training programs in Whole Genome Sequencing of Bacteria targeted to Clinicians, Medical Scientists and Epidemiologists. Please contact us  for details on future tour and course dates.

To use our molecular diagnostic service or to submit samples for whole genome sequencing please download the relevant Sample Submission Form, complete and return to MDU PHL with your sample as per the delivery address. Further details can be found in our Sample Submission Guidelines. For further information on WGS, sample processing and analysis and for a quote on Next Generation Sequencing services please contact us.

The Melbourne Sexual Health Centre (MSHC) specialises in sexual health, specifically through testing, treatment and management of Sexually Transmissible Infections (STIs). The onsite laboratory, operated by the Microbiological Diagnostic Unit, provides the laboratory focus for the primary testing and analysis of microbiological samples for sexual healthinfections, received from patients attending the MSHC.  Being on site, the laboratory can provide on the spot diagnosis of some infections. Tests include detection of:

• Chlamydia trachomatis (including LGV)
• Neisseria gonorrhoeae
• Trichomonas vaginalis
• Mycoplasma genitalium
• Treponema pallidum
• Candida albicans
• Bacterial vaginosis

The Reference, Unusual Pathogens and Resistance Section (RUPR) undertakes phenotypic and genotypic analysis to enable the detection and characterisation of bacterial pathogens associated with notifiable diseases and uncommon or difficult to identify bacteria from human or veterinary origin.

Laboratory based surveillance of Neisseria gonorrhoeae and Neisseria meningitidis is conducted as part of the Australian Gonococcal and Meningococcal Surveillance programs.

Antimicrobial susceptibility testing of Enterobacterales, Enterococci and Staphylococci is also undertaken to support the national Critical Antimicrobial Resistance Alert (CARAlert) program and the Victorian Carbapenemase-producing Enterobacteriaceae Surveillance and Response Unit (VCRSU).

MDU PHL has an active research programme program covering areas such as the clinical and molecular epidemiology of enteric infections, antimicrobial resistance, vaccine-preventable bacterial diseases and sexually-transmitted infections.  In addition, Doherty Applied Microbial Genomics is a recently established research initiative working in the area of public health and clinical microbiology, and is situated within MDU PHL.

All request forms sent electronically must comply with the Privacy Act 1988, Health Records Act (Victoria) 2001 and the Information Privacy Act (Victoria) .

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FM Number	Request Form Name
FM108	VHPSS Request Form Download
FM110	Human NEPSS Request Form Download
FM111	Non-Human NEPSS Request Form Download
FM116	HS Public Health Investigations Specimens Download
FM117	WT Water Samples Download
FM118	FD Food, Food Ingredient and Packaging Specimens Download
FM119	HC Human Clinical Download
FM123	General Specimens Request Form Download
FM377	MDU PHL CBR Chain of Custody Form Download
FM935	MDU Internal Chain of Custody Form Download
FM979	MDU PHL General Chain of Custody Form Download
FM1045	Legionella Chain of Custody Form Download
FM1062	NS Neisseria cultures Request Form Download
FM1541	Food and Water Chain of Custody Form Download
FM1698	Request Form - Cryptosporidium typing Download
FM1716	VIFM Request and Chain of Custody Form Download
FM1718	Sealed Primary Container Description form Download
FM1851	Culture Referral from Meat and Meat products Download
FM1856	Food Act s23 Form Download
FM1885	EV Environmental Samples, Swabs and Equipment Download
FM2085	L monocytogenes Molecular Subtyping Download
FM2159	VPFS Request and Chain of Custody Form Download
FM2458	Carbapenemase detection, Human isolates Request Form Download
FM2609	Enviromental Surveillance Sampling for CT and NG rRNA Download
FM2634	Request Form – WGS Download
FM2634	WGS-electronic download 2-COVID Download
FM2673	DNA Bacterial Isolates for sequencing  Download
FM2680	Pathology Request Form  Download
FM2699	Carbapenemase detection Environmental samples Request Form Download
FM2713	Superbugs Project Request Form  Download
FM2728	Traveller's Diarrhoea Metagenomics Study PR2017-004 Download
FM2739	Research samples Request Form Download
FM2753	Multiple Human Clinical Isolates Request Form Download
FM2784	iGas_Eastern Study Request Form Download
FM2787	Phylogeny and Analysis of Whole Genome Sequence data Download
FM2794	CDGNA Interjurisdictional AMR Genomic Surveillance Poject Download
FM2810	Pathology Request_Mgen Download
FM2845	Clinical Samples-Covid19 Download
FM2871	Spit Study PR2020_014 CIRQIT Download
FM2871	Spit Study PR2020_014 cohealth Download
FM2875	Innovative Testing Project - Abbott ID NOW COVID-19 Download
FM2876	Innovative Testing Project - Credo VitaPCR SARS-CoV-2 Download
FM2877	Innovative Testing Project - SARS-CoV-2 Antigen Test Download
FM2915	Request form-WGS International Covid Samples Download
FM2921	Request Form - BARISTA Study Download
FM2923	MSD Gram negative ICU study PR2021_010 Download
FM2929	Staphylococcal Snap Trial PR2021_014 Download
FM2935	COVID-19 WGS request form - minimal data Download
FM2936	Request form - COVID Healthcare worker genome sequencing and phylogenetic analysis Download
FM2941	Vancomycin Resistant Enterococcus (vanA) referral - single isolate Download
FM2942	Vancomycin Resistant Enterococcus (vanA) referral - multiple isolates Download