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Clin Infect Dis. 2019 Jan 7. doi: 10.1093/cid/ciz005. [Epub ahead of print]

Co-circulation of multidrug-resistant Shigella among men who have sex with men, Australia.

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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.
National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia.
Victorian Department of Health and Human Services, Melbourne, Australia.
Melbourne Bioinformatics Group, Victoria, Australia.
Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
Melbourne Sexual Health Centre, Alfred Health, Carlton, Victoria, Australia.
Central Clinical School, Monash University, Melbourne, Australia.



In urban Australia, the burden of shigellosis is either in returning travellers 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.


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


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, two major MSM-associated lineages were identified, a S. sonnei lineage (n=159) and a S. flexneri 2a lineage (n=105). Of concern, 147/159 (92.4%) of isolates within the S. sonnei MSM-associated lineage harboured 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 lineage, but predominantly associated with MSM isolates.


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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