Genomic analysis of Citrobacter from Australian wastewater and silver gulls reveals novel sequence types carrying critically important antibiotic resistance genes

Sopheak Hem; Max L Cummins; Ethan R Wyrsch; Barbara Drigo; Bethany J Hoye; Kimberly Maute; Martina Sanderson-Smith; Jody Gorman; Daniel R Bogema; Cheryl Jenkins; Ania T Deutscher; Jerald Yam; Faisal Hai; Erica Donner; Veronica M Jarocki; Steven P Djordjevic

doi:10.1016/j.scitotenv.2023.168608

Genomic analysis of Citrobacter from Australian wastewater and silver gulls reveals novel sequence types carrying critically important antibiotic resistance genes

Sci Total Environ. 2024 Jan 20:909:168608. doi: 10.1016/j.scitotenv.2023.168608. Epub 2023 Nov 16.

Authors

Sopheak Hem¹, Max L Cummins¹, Ethan R Wyrsch¹, Barbara Drigo², Bethany J Hoye³, Kimberly Maute³, Martina Sanderson-Smith⁴, Jody Gorman⁴, Daniel R Bogema⁵, Cheryl Jenkins⁵, Ania T Deutscher⁵, Jerald Yam⁵, Faisal Hai⁶, Erica Donner⁷, Veronica M Jarocki⁸, Steven P Djordjevic⁹

Affiliations

¹ Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia.
² UniSA STEM, University of South Australia, Adelaide, SA, Australia.
³ School of Earth, Atmospheric and Life Sciences, University of Wollongong NSW, Australia; Environmental Futures Research Centre, University of Wollongong NSW, Australia.
⁴ School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, NSW, Australia.
⁵ Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia.
⁶ School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, NSW, Australia.
⁷ Cooperative Research Centre for Solving Antimicrobial resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia; Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia.
⁸ Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia. Electronic address: Veronica.Jarocki@uts.edu.au.
⁹ Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia. Electronic address: Steven.Djordjevic@uts.edu.au.

PMID: 37977387
DOI: 10.1016/j.scitotenv.2023.168608

Abstract

Antimicrobial resistance (AMR) is a major public health concern, and environmental bacteria have been recognized as important reservoirs of antimicrobial resistance genes (ARGs). Citrobacter, a common environmental bacterium and opportunistic pathogen in humans and other animals, has been largely understudied in terms of its diversity and AMR potential. Whole-genome (short-read) sequencing on a total of 77 Citrobacter isolates obtained from Australian silver gull (Chroicocephalus novaehollandiae) (n = 17) and influent wastewater samples (n = 60) was performed, revealing a diverse Citrobacter population, with seven different species and 33 sequence types, 17 of which were novel. From silver gull using non-selective media we isolated a broader range of species with little to no mobilised ARG carriage. Wastewater isolates (selected using Carbapenem- Resistant Enterobacterales (CRE) selective media) carried a heavy burden of ARGs (up to 21 ARGs, conferring resistance to nine classes of antibiotics), with several novel multidrug-resistant (MDR) lineages identified, including C. braakii ST1110, which carried ARGs conferring resistance to eight to nine classes of antibiotics, and C. freundii ST1105, which carried two carbapenemase genes, bla_IMP-4 in class 1 integron structure, and bla_KPC-2. Additionally, we identified an MDR C. portucalensis isolate carrying bla_NDM-1, bla_SHV-12, and mcr-9. We identified IncC, IncM2, and IncP6 plasmids as the likely vectors for many of the critically important mobilised ARGs. Phylogenetic analyses were performed to assess any epidemiological linkages between isolation sources, demonstrating low relatedness across sources beyond the ST level. However, these analyses did reveal some closer relationships between strains from disparate wastewater sources despite their collection some 13,000 km apart. These findings support the need for future surveillance of Citrobacter populations in wastewater and wildlife populations to monitor for potential opportunistic human pathogens.

Keywords: Antimicrobial resistance; Carbapenamases; Citrobacter; Gulls; Plasmids; Wastewater.

MeSH terms

Animals
Anti-Bacterial Agents / pharmacology
Anti-Infective Agents*
Australia
Charadriiformes* / genetics
Citrobacter / genetics
Drug Resistance, Multiple, Bacterial / genetics
Genomics
Humans
Microbial Sensitivity Tests
Phylogeny
Plasmids
Wastewater
beta-Lactamases / genetics

Substances

Anti-Bacterial Agents
Wastewater
beta-Lactamases
Anti-Infective Agents