1646 – Whole genome sequencing of antimicrobial-resistant pathogens

Page last updated: 22 June 2022

Application Detail

Description of Medical Service

The applicant has described the proposed medical service as 'Sequencing and analysis of the complete nucleotide sequence of the microbial genome (bacterial, mycobacterial, or viral) of an isolate or to characterise an organism from a patient for the purpose of determining the antibiotic resistance markers (resistome) of the isolate to guide the patient’s treatment and/or chemoprophylaxis of close contacts. WGS usually involves ‘shotgun’ sequencing of short reads that are either assembled de novo or mapped onto a high-quality reference genome. Genome-wide analysis can identify changes conferring resistance to standard of care antibiotics as well as newer antimicrobials for which established phenotypic susceptibility testing guidelines or protocols are not available.'

Description of Medical Condition

The applicant’s response is: ‘Antimicrobial resistance, also referred to as antibiotic resistance, is defined as the ability of a microorganism to reproduce in the presence of a specific antimicrobial compound. Of particular concern is the emergence of multiple drug resistant pathogens associated with the widespread use of antibiotics and high-density clinical care that are capable of causing outbreaks and epidemics. Whole genome sequencing (WGS) provides rapid and simultaneous screening of all clinically-relevant mutations in close to real-time to predict a pathogen’s full resistance profile to multiple drugs (the ‘resistome’) in order to guide a patient’s treatment and/or the chemoprophylaxis of close contacts. The literature describes the use of WGS to determine and characterise resistance in numerous clinically relevant pathogens including, but not limited to: Campylobacter; Escherichia coli; Klebsiella pneumoniae; Enterobacter cloacae; Pseudomonas aeruginosa; Bacteroides; Salmonella; Staphylococcus aureus; Streptococcus pneumoniae; Neisseria gonorrhoeae; Acinetobacter baumannii; Clostridium difficile and Plasmodium falciparum. The most common reported use of WGS for the determination of resistance; however, is for the pathogen Mycobacterium tuberculosis. Given the extensive list of potential pathogens and their associated clinical conditions, this application will focus on Mycobacterium tuberculosis as an exemplar of how WGS provides rapid and accurate characterisation of antimicrobial resistance.’

Reason for Application

New MBS item

Medical Service Type


Previous Application Number/s

Not Applicable

Associated Documentation

Application Form

Application Form (PDF 1397 KB)
Application Form (Word 338 KB)

Consultation Survey

Consultation Survey (PDF 559 KB)
Consultation Survey (Word 70 KB)

PASC Consultation
Not applicable

MSAC Consultation
MSAC consultation closed 11 February 2022.

For further information please refer to PASC, ESC, MSAC Key Dates
For further information on the consultation process please refer to MSAC Consultation Process

PICO Confirmation

PICO Confirmation (PDF 1579 KB)
PICO Confirmation (Word 394 KB)

Assessment Report


Public Summary Document

Public Summary Document (PDF 551 KB)
Public Summary Document (Word 172 KB)

Meetings for this Application


15-16 April 2021


10-11 February 2022


31 March-1 April 2022