1
|
Hem S, Cummins ML, Wyrsch ER, Drigo B, Hoye BJ, Maute K, Sanderson-Smith M, Gorman J, Bogema DR, Jenkins C, Deutscher AT, Yam J, Hai F, Donner E, Jarocki VM, Djordjevic SP. Genomic analysis of Citrobacter from Australian wastewater and silver gulls reveals novel sequence types carrying critically important antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168608. [PMID: 37977387 DOI: 10.1016/j.scitotenv.2023.168608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
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, blaIMP-4 in class 1 integron structure, and blaKPC-2. Additionally, we identified an MDR C. portucalensis isolate carrying blaNDM-1, blaSHV-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.
Collapse
Affiliation(s)
- Sopheak Hem
- 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
| | - Max L Cummins
- 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
| | - Ethan R Wyrsch
- 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
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, SA, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, University of Wollongong NSW, Australia; Environmental Futures Research Centre, University of Wollongong NSW, Australia
| | - Kimberly Maute
- School of Earth, Atmospheric and Life Sciences, University of Wollongong NSW, Australia; Environmental Futures Research Centre, University of Wollongong NSW, Australia
| | - Martina Sanderson-Smith
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, NSW, Australia
| | - Jody Gorman
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, NSW, Australia
| | - Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Cheryl Jenkins
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Ania T Deutscher
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Jerald Yam
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Faisal Hai
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, NSW, Australia
| | - Erica Donner
- 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
| | - Veronica M Jarocki
- 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.
| | - Steven P Djordjevic
- 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.
| |
Collapse
|
2
|
Guitart-Matas J, Espunyes J, Illera L, Gonzalez-Escalona N, Ribas MP, Marco I, Migura-Garcia L. High-risk lineages of extended spectrum cephalosporinase producing Escherichia coli from Eurasian griffon vultures (Gyps fulvus) foraging in landfills in north-eastern Spain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168625. [PMID: 37977396 DOI: 10.1016/j.scitotenv.2023.168625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Extended-spectrum cephalosporinase producing (ESC) E. coli are regarded as key indicator microorganisms of antimicrobial resistance (AMR), calling for a One Health integrated global surveillance strategy. Wildlife is exposed to antibiotic contaminants and/or resistant bacteria that have been released into the environment, potentially acting as reservoirs and spreaders of resistance genes as well as sentinels of anthropogenic pressure. Monitoring AMR in wildlife has become crucial in determining anthropogenic environmental impacts as well as transmission routes. In this study, we determined the occurrence and potential sources of ESC E. coli in 218 Eurasian griffon vultures (Gyps fulvus) foraging regularly on human waste disposed at a dumpsite in north-eastern Spain. Minimal inhibitory concentration for 14 different antimicrobials was performed to evaluate the phenotype of the isolates, and whole genome sequencing was carried out to investigate lineages and plasmids harbouring ESC genes. Our sequences were compared to previously published Spanish sequences of human, animal, and wildlife origin. We report a high prevalence of CTX-M-15, as well as the presence of other resistance genes such as OXA-10, CTX-M-27, and CTX-M-65 which are rarely described in European livestock, suggesting a human origin. The isolates also carried a diverse range of additional AMR genes for a broad spectrum of drug families, with the majority being multi-drug resistant. The phylogenomic analyses suggests the transmission of high-risk lineages from humans to vultures, with 49 % of our isolates matching the most common extraintestinal pathogenic E. coli (ExPEC) lineages described in humans worldwide, including ST131, ST10 and ST58. We conclude that anthropogenically altered habitats, such as landfills, are hotspots for the acquisition and spread of high-risk ESC E. coli lineages associated with hospital infections. Measures must be implemented to limit their spread into natural environments.
Collapse
Affiliation(s)
- Judith Guitart-Matas
- Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Autonomous University of Barcelona (UAB), Catalonia, Spain; Institute of Agrifood Research and Technology (IRTA), Animal Health Program (CReSA), WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe, Autonomous University of Barcelona (UAB), Catalonia, Spain
| | - Johan Espunyes
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | - Lucia Illera
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | | | - Maria Puig Ribas
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | - Ignasi Marco
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | - Lourdes Migura-Garcia
- Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Autonomous University of Barcelona (UAB), Catalonia, Spain; Institute of Agrifood Research and Technology (IRTA), Animal Health Program (CReSA), WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe, Autonomous University of Barcelona (UAB), Catalonia, Spain.
| |
Collapse
|
3
|
Rodrigues IC, Cristal AP, Ribeiro-Almeida M, Silveira L, Prata JC, Simões R, Vaz-Pires P, Pista Â, Martins da Costa P. Gulls in Porto Coastline as Reservoirs for Salmonella spp.: Findings from 2008 and 2023. Microorganisms 2023; 12:59. [PMID: 38257887 PMCID: PMC10819206 DOI: 10.3390/microorganisms12010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Gulls act as intermediaries in the exchange of microorganisms between the environment and human settlements, including Salmonella spp. This study assessed the antimicrobial resistance and molecular profiles of Salmonella spp. isolates obtained from fecal samples of gulls in the city of Porto, Portugal, in 2008 and 2023 and from water samples in 2023. Antimicrobial susceptibility profiling revealed an improvement in the prevalence (71% to 17%) and antimicrobial resistance between the two collection dates. Two isolate collections from both 2008 and 2023 underwent serotyping and whole-genome sequencing, revealing genotypic changes, including an increased frequency in the monophasic variant of S. Typhimurium. qacE was identified in 2008 and 2023 in both water and fecal samples, with most isolates exhibiting an MDR profile. The most frequently observed plasmid types were IncF in 2008 (23%), while IncQ1 predominated in 2023 (43%). Findings suggest that Salmonella spp. circulate between humans, animals, and the environment. However, the genetic heterogeneity among the isolates from the gulls' feces and the surface water may indicate a complex ecological and evolutionary dynamic shaped by changing conditions. The observed improvements are likely due to measures to reduce biological contamination and antimicrobial resistance. Nevertheless, additional strategies must be implemented to reduce the public health risk modeled by the dissemination of pathogens by gulls.
Collapse
Affiliation(s)
- Inês C. Rodrigues
- ICBAS-UP—School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (A.P.C.); (M.R.-A.); (J.C.P.); (R.S.); (P.V.-P.)
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Ana Paula Cristal
- ICBAS-UP—School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (A.P.C.); (M.R.-A.); (J.C.P.); (R.S.); (P.V.-P.)
| | - Marisa Ribeiro-Almeida
- ICBAS-UP—School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (A.P.C.); (M.R.-A.); (J.C.P.); (R.S.); (P.V.-P.)
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Leonor Silveira
- INSA—National Institute of Health, Department of Infectious Diseases, Av. Padre Cruz, 1649-016 Lisbon, Portugal; (L.S.); (Â.P.)
| | - Joana C. Prata
- ICBAS-UP—School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (A.P.C.); (M.R.-A.); (J.C.P.); (R.S.); (P.V.-P.)
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
| | - Roméo Simões
- ICBAS-UP—School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (A.P.C.); (M.R.-A.); (J.C.P.); (R.S.); (P.V.-P.)
| | - Paulo Vaz-Pires
- ICBAS-UP—School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (A.P.C.); (M.R.-A.); (J.C.P.); (R.S.); (P.V.-P.)
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Ângela Pista
- INSA—National Institute of Health, Department of Infectious Diseases, Av. Padre Cruz, 1649-016 Lisbon, Portugal; (L.S.); (Â.P.)
| | - Paulo Martins da Costa
- ICBAS-UP—School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (A.P.C.); (M.R.-A.); (J.C.P.); (R.S.); (P.V.-P.)
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| |
Collapse
|