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Updated: Sep 23, 2025
Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes
Published on: March 3, 2023
Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic
Claire L Gorrie1, Anders Gonçalves Da Silva2, Danielle J Ingle3
1Microbiological Diagnostic Unit, Public Health Laboratory, University of Melbourne, Melbourne, VIC, Australia; Department of Microbiology & Immunology, Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, VIC, Australia.
Genomic surveillance for multidrug-resistant (MDR) organisms is improved by using closely related reference genomes and a sliding-window approach. This enhances accuracy and consistency in inferring transmission events in hospitals.
Area of Science:
- Genomics
- Infectious Disease Epidemiology
- Bioinformatics
Background:
- Genomic surveillance using pairwise single nucleotide polymorphisms (SNPs) is crucial for tracking multidrug-resistant (MDR) organisms in hospitals.
- Systematic assessment of analytical approaches impacting transmission inference is lacking.
Purpose of the Study:
- To systematically assess the impact of various analytical approaches on the inference of MDR organism transmission using whole genome sequencing data.
- To identify optimal methods for accurate and consistent genomic surveillance of MDR organisms.
Main Methods:
- Prospective 15-month study across eight hospitals in Melbourne, Australia.
- Whole genome sequencing of meticillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium, and extended-spectrum β-lactamase-producing E. coli and K. pneumoniae isolates.
- Systematic assessment of reference genome diversity, masking of genomic regions (prophage, recombination), and sample inclusion strategies (cumulative vs. sliding-window).
Main Results:
- Using a same-sequence-type reference genome improved pairwise SNP resolution compared to broader references.
- Omitting recombination regions variably affected SNP distances; omitting prophage regions had minimal impact.
- A sliding-window approach for sample inclusion provided more consistent SNP distance estimates over time than a cumulative approach.
Conclusions:
- A closely related reference genome, without masking of prophage or recombination regions, combined with a sliding-window approach, is recommended for accurate MDR organism transmission inference.
- Standardized genomic surveillance approaches are essential for reliable detection of MDR organism transmission in healthcare settings.
