Emergence of multidrug resistance in locally-acquired human infections with Salmonella Typhimurium in Australia owing to a new clade harbouring blaCTX-M-9

Sarah J Sparham; Jason C Kwong; Mary Valcanis; Marion Easton; Darren J Trott; Torsten Seemann; Timothy P Stinear; Benjamin P Howden

doi:10.1016/j.ijantimicag.2017.02.014

Emergence of multidrug resistance in locally-acquired human infections with Salmonella Typhimurium in Australia owing to a new clade harbouring bla_CTX-M-9

Int J Antimicrob Agents. 2017 Jul;50(1):101-105. doi: 10.1016/j.ijantimicag.2017.02.014. Epub 2017 May 2.

Authors

Sarah J Sparham¹, Jason C Kwong², Mary Valcanis³, Marion Easton⁴, Darren J Trott⁵, Torsten Seemann⁶, Timothy P Stinear⁷, Benjamin P Howden⁸

Affiliations

¹ Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, VIC, Australia; Infectious Diseases Department, Austin Health, Heidelberg, VIC, Australia.
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.
³ Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, VIC, Australia.
⁴ Department of Health and Human Services, Victorian Government, Australia.
⁵ Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia.
⁶ Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, 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; Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, Australia.
⁷ 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.
⁸ 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: bhowden@unimelb.edu.au.

PMID: 28476613
DOI: 10.1016/j.ijantimicag.2017.02.014

Abstract

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_CTX-M-9. 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_CTX-M-9 were identified that appear to be of bovine origin, raising concerns regarding the human impact of off-label use of ceftiofur in cattle.

Keywords: Antimicrobial resistance; Extended-spectrum β-lactamase; One Health; Salmonella; Salmonellosis; Whole-genome sequencing.

MeSH terms

Animals
Anti-Bacterial Agents / pharmacology*
Australia
Cattle
Cephalosporins / pharmacology*
Computational Biology
Drug Resistance, Multiple, Bacterial*
Escherichia coli Proteins / metabolism*
Humans
Molecular Epidemiology
Phylogeny
Salmonella Infections / epidemiology
Salmonella Infections / microbiology*
Salmonella Infections, Animal / epidemiology
Salmonella Infections, Animal / microbiology*
Salmonella typhimurium / classification
Salmonella typhimurium / drug effects*
Salmonella typhimurium / enzymology
Salmonella typhimurium / genetics
Whole Genome Sequencing
beta-Lactamases / metabolism*

Substances

Anti-Bacterial Agents
Cephalosporins
Escherichia coli Proteins
CTX-M-9 protein, E coli
beta-Lactamases