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Aleri JW, Sahibzada S, Harb A, Fisher AD, Waichigo FK, Lee T, Robertson ID, Abraham S. Molecular epidemiology and antimicrobial resistance profiles of Salmonella isolates from dairy heifer calves and adult lactating cows in a Mediterranean pasture-based system of Australia. J Dairy Sci 2021; 105:1493-1503. [PMID: 34955273 DOI: 10.3168/jds.2021-21084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/23/2021] [Indexed: 12/31/2022]
Abstract
Dairy cows can be reservoirs of foodborne pathogens such as Salmonella that pose serious public health risks to humans. The study was designed to examine the molecular epidemiology and antimicrobial resistance profiles of Salmonella isolates from dairy heifer calves and adult lactating cows in the pasture-based system of Australia. A total of 838 animals (328 heifer calves and 510 lactating cows) from 22 farms were sampled. Overall, 54 Salmonella isolates were recovered (calves 28/328 and cows 26/510). A herd-level Salmonella prevalence of 50% (95% confidence interval: 31%-69%) was recorded. Within-herd prevalence for Salmonella ranged between 4%-29% and 4%-45% among the heifer calves and adult lactating cows, respectively. Three different serovars were identified with Salmonella Infantis being the most common serovar (n = 33, 61%) followed by Salmonella Kiambu (n = 20, 37.0%) and one isolate of Salmonella Cerro (2%). The highest antimicrobial resistance prevalence of Salmonella isolates was found against streptomycin (n = 31, 57%), followed by cefoxitin (n = 12, 22%), ceftriaxone (n = 2, 4%), and chloramphenicol (n = 1, 2%). Multiple class resistance was observed on 4 isolates against cefoxitin, chloramphenicol, and streptomycin. Multilocus sequence types ST32 (61%), ST309 (37%), and ST367 (2%) were strongly linked to the serovars Salmonella Infantis, Salmonella Kiambu, and Salmonella Cerro, respectively. Whole genome sequencing of Salmonella isolates detected only 2 resistance genes: aac(6') gene that confers resistance against aminoglycosides among 40.7% of the isolates, and a single isolate positive for the blaDHA-16 gene. Two distinct clusters among the serovars were observed suggesting 2 independent sources of spread. Despite the low prevalence of antimicrobial resistance among Salmonella from the dairy farms, our findings contribute to the regional and national understanding of antimicrobial resistance in dairy herds in Australia. There is need for continued antimicrobial resistance stewardship and surveillance programs to ensure the production of high-quality food products and the long-term protection of both animal and human health.
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Affiliation(s)
- J W Aleri
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia; Centre for Animal Production and Health, Future Foods Institute, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia; Antimicrobial Resistance and Infectious Diseases Research Laboratory, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia.
| | - S Sahibzada
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia; Antimicrobial Resistance and Infectious Diseases Research Laboratory, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia
| | - A Harb
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia; Antimicrobial Resistance and Infectious Diseases Research Laboratory, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia
| | - A D Fisher
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, 3030 VIC, Australia; Animal Welfare Science Centre, University of Melbourne, 3010 VIC, Australia
| | - F K Waichigo
- Brunswick Veterinary Services, 27 Ommaney Road, Brunswick Junction, 6224 WA, Australia
| | - T Lee
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia; Antimicrobial Resistance and Infectious Diseases Research Laboratory, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia
| | - I D Robertson
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia; College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
| | - S Abraham
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia; Antimicrobial Resistance and Infectious Diseases Research Laboratory, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, 6150 WA, Australia
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Antimicrobial resistance in fecal Escherichia coli isolated from poultry chicks in northern Iran. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abraham S, O’Dea M, Sahibzada S, Hewson K, Pavic A, Veltman T, Abraham R, Harris T, Trott DJ, Jordan D. Escherichia coli and Salmonella spp. isolated from Australian meat chickens remain susceptible to critically important antimicrobial agents. PLoS One 2019; 14:e0224281. [PMID: 31644602 PMCID: PMC6808415 DOI: 10.1371/journal.pone.0224281] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
The World Health Organisation has defined "highest priority critically important antimicrobials" (CIAs) as those requiring the greatest control during food production. Evidence demonstrating that restricted antimicrobial usage prevents the emergence of resistance to CIA's amongst pathogenic and commensal organisms on a production system-wide scale would strengthen international efforts to control antimicrobial resistance (AMR). Therefore, in a designed survey of all major chicken-meat producers in Australia, we investigated the phenotypic AMR of E. coli (n = 206) and Salmonella (n = 53) from caecal samples of chickens at slaughter (n = 200). A large proportion of E. coli isolates (63.1%) were susceptible to all tested antimicrobials. With regards to CIA resistance, only two E.coli isolates demonstrated resistance to fluoroquinolones, attributed to mutations in the quinolone resistance-determining regions of gyrA. Antimicrobial resistance was observed for trimethoprim/sulfamethoxazole (8.7%), streptomycin (9.7%), ampicillin (14.1%), tetracycline (19.4%) and cefoxitin (0.5%). All Salmonella isolates were susceptible to ceftiofur, chloramphenicol, ciprofloxacin, colistin, florfenicol, gentamicin and tetracycline. A low frequency of Salmonella isolates exhibited resistance to streptomycin (1.9%), ampicillin (3.8%), and cefoxitin (11.3%). AMR was only observed among Salmonella Sofia serovars. None of the Salmonella isolates exhibited a multi-class-resistant phenotype. Whole genome sequencing did not identify any known resistance mechanisms for the Salmonella isolates demonstrating resistance to cefoxitin. The results provide strong evidence that resistance to highest priority CIA's is absent in commensal E. coli and Salmonella isolated from Australian meat chickens, and demonstrates low levels of resistance to compounds with less critical ratings such as cefoxitin, trimethoprim/sulfamethoxazole, and tetracycline. Apart from regulated exclusion of CIAs from most aspects of livestock production, vaccination against key bacterial pathogens and stringent biosecurity are likely to have contributed to the favorable AMR status of the Australian chicken meat industry. Nevertheless, industry and government need to proactively monitor AMR and antimicrobial stewardship practices to ensure the long-term protection of both animal and human health.
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Affiliation(s)
- Sam Abraham
- Antimicrobial Resistance and Infectious Disease Laboratory, Murdoch University, Murdoch, Western Australia, Australia
| | - Mark O’Dea
- Antimicrobial Resistance and Infectious Disease Laboratory, Murdoch University, Murdoch, Western Australia, Australia
| | - Shafi Sahibzada
- Antimicrobial Resistance and Infectious Disease Laboratory, Murdoch University, Murdoch, Western Australia, Australia
| | - Kylie Hewson
- Australian Chicken Meat Federation, Sydney, New South Wales, Australia
| | - Anthony Pavic
- Birling Avian Laboratories, Bringelly, New South Wales, Australia
| | - Tania Veltman
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Rebecca Abraham
- Antimicrobial Resistance and Infectious Disease Laboratory, Murdoch University, Murdoch, Western Australia, Australia
| | - Taha Harris
- Birling Avian Laboratories, Bringelly, New South Wales, Australia
| | - Darren J. Trott
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - David Jordan
- New South Wales Department of Primary Industries, Wollongbar, New South Wales, Australia
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Raidal SL. Antimicrobial stewardship in equine practice. Aust Vet J 2019; 97:238-242. [DOI: 10.1111/avj.12833] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/10/2019] [Indexed: 11/29/2022]
Affiliation(s)
- SL Raidal
- School of Animal and Veterinary SciencesCharles Sturt University Wagga Wagga New South Wales 2650 Australia
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Badger S, Abraham S, O'Dea M, Saputra S, Abraham RJ, Worthing KA, Norris JM, Trott DJ, Jordan D, Caraguel CGB. Diagnostic accuracy of phenotypic assays for determining antimicrobial resistance status in Staphylococcus pseudintermedius isolates from canine clinical cases. Vet Microbiol 2019; 234:101-109. [PMID: 31213265 DOI: 10.1016/j.vetmic.2019.05.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/27/2019] [Accepted: 05/29/2019] [Indexed: 01/20/2023]
Abstract
This study evaluated the diagnostic test accuracy of disc diffusion relative to broth-microdilution for clinical Staphylococcus pseudintermedius isolated from dogs in Australia (n = 614). Accuracy of disc diffusion and broth-microdilution for oxacillin relative to mecA real-time PCR was also assessed. Each isolate had paired minimum inhibitory concentration and zone diameter values for ten antimicrobial agents. Data was dichotomised using Clinical and Laboratory Standards Institute susceptible and resistant clinical breakpoints. Test accuracy was reported using relative diagnostic sensitivity (RSe), specificity (RSp), likelihood ratio pairs, diagnostic odds ratio, and area-under-the receiver-operating characteristic (ROC AUC) analysis. Disc diffusion was found to have high test accuracy for most antimicrobials (ROC AUC range: 0.96 - 0.99) except rifampicin (ROC AUC = 0.80). The RSp of disc diffusion was high for all antimicrobials (range, 97.1%-100%). However, RSe was considerably variable (range, 35.7%-98.8%), particularly for amoxicillin-clavulanic acid (51.5%, 95% CI, 38.9%, 64.0%), cefoxitin (35.7%, 95% CI, 12.8%, 64.9%), and cephalothin (43.6%, 95% CI, 27.8%, 60.4%). When disc diffusion and broth-microdilution were compared to mecA real-time PCR, the overall accuracy of both assays was similar (ROC AUC, 0.99 respectively). However, the RSe for broth-microdilution (96.1%, 95% CI, 88.9%, 99.2%) was significantly higher than for disc diffusion (86.8%, 95% CI, 77.1%, 93.5%) (McNemars mid-p value 0.01). Overall, these findings demonstrate that for most antimicrobials, disc diffusion performed according to CLSI guidelines can be used to differentiate clinical S. pseudintermedius isolates that might otherwise be assessed by broth-microdilution, provided consideration is given to the performance estimates reported here.
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Affiliation(s)
- Skye Badger
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, 5371, Australia; School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, Western Australia, 6150, Australia.
| | - Sam Abraham
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, 5371, Australia.
| | - Mark O'Dea
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, Western Australia, 6150, Australia. M.O'
| | - Sugiyono Saputra
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, 5371, Australia.
| | - Rebecca J Abraham
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, 5371, Australia.
| | - Kate A Worthing
- University of Sydney, Sydney School of Veterinary Science, NSW, Australia; Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia.
| | | | - Darren J Trott
- Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, 5371, Australia.
| | - David Jordan
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, Western Australia, 6150, Australia; Wollongbar Primary Industries Institute, NSW Department of Primary Industries, 1243 Bruxner Highway, Wollongbar, New South Wales, 2477, Australia.
| | - Charles G B Caraguel
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, 5371, Australia.
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Characterisation of Staphylococcus felis isolated from cats using whole genome sequencing. Vet Microbiol 2018; 222:98-104. [PMID: 30080680 DOI: 10.1016/j.vetmic.2018.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/05/2018] [Accepted: 07/05/2018] [Indexed: 11/20/2022]
Abstract
This study used phenotypic tests and whole genome sequencing to characterise a collection of 37 clinical Staphylococcus felis isolates from cats. Samples were isolated from a range of diseases including feline lower urinary tract disease (n = 15), otitis externa (n = 13), and ocular disease (n = 2). Isolates were identified using MALDI-TOF MS and by BLASTn analysis of S. felis-specific 16S rRNA, rpoB and nuc genes in whole genome sequence-based contigs. Phenotypic antimicrobial resistance was determined using disk diffusion and broth microdilution. Coagulase activity was assessed using feline and rabbit plasma. Genomes were screened for putative virulence and antimicrobial resistance genes using the sequences of known genes from other staphylococci as homologous references. Phylogenetic relationships were inferred using single nucleotide polymorphisms. One isolate was coagulase-positive when tested with feline plasma but all isolates were rabbit plasma coagulase-negative. No genetic determinant of coagulase activity was identified in this isolate. A range of putative virulence genes were found amongst isolates including genes associated with adhesion, toxin production and immune evasion. Ninety two percent of isolates were fully susceptible to all antimicrobials tested, which was reflected by a general absence of resistance genes. Clustering within the phylogenetic tree suggested a multiclonal population structure; this clustering did not correlate with disease syndrome or geographic origin of the isolate. Future studies of veterinary staphylococci will benefit from the publicly available S. felis draft genomes that were generated in this study.
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