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Zaidi SEZ, Zaheer R, Zovoilis A, Fossen J, Van Domselaar G, Waldner C, McAllister TA. Genomic Characterization of Enterococcus casseliflavus Isolated from Beef Cows and Calves. Microorganisms 2025; 13:907. [PMID: 40284743 PMCID: PMC12029791 DOI: 10.3390/microorganisms13040907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Revised: 04/04/2025] [Accepted: 04/07/2025] [Indexed: 04/29/2025] Open
Abstract
Enterococcus species are used as One Health indicators of antimicrobial resistance (AMR) in humans, animals, and the environment. A surveillance study in beef cows and calves isolated Enterococcus casseliflavus along with E. faecium, E. faecalis, and E. hirae. Given the high prevalence of E. casseliflavus, we elected to characterize this species to better understand its role in the antimicrobial resistance of enterococci in cows and calves. Almost 12% of E. casseliflavus isolates exhibited multidrug resistance with the majority being resistant to lincomycin (99%), followed by quinupristin-dalfopristin (34%), ciprofloxacin (9.6%), tylosin (4.5%), erythromycin (2.7%), tetracycline (1.8%), tigecycline (1.5%), daptomycin (0.6%), streptomycin (0.3%), and kanamycin (0.3%). All E. casseliflavus were susceptible to chloramphenicol, penicillin, streptomycin, nitrofurantoin, gentamicin, and linezolid. Whole genome antimicrobial resistance gene profiling identified vanC-type intrinsic vancomycin resistance genes in all E. casseliflavus, with the vanC4XYT gene cluster being dominant (67%) followed by vanC2XYT (31%) and vanC3XYT (1.5%). Resistance genes for erythromycin (ermB) and tetracycline (tetM) were rarely identified (2.1% and 1.2%, respectively) within E. casseliflavus genomes. No resistance genes were identified to explain either the quinupristin-dalfopristin or ciprofloxacin resistance in these isolates. A core genome phylogenetic tree revealed two clades that exhibited no distinct association with the age of the host, time of sample collection, or the farm sampled. The open nature of the E. casseliflavus pan-genome highlighted its intraspecies diversity. These findings suggest that E. casseliflavus is likely a low-risk species in terms of contributing to antimicrobial resistance in the cow-calf sector.
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Affiliation(s)
- Sani-e-Zehra Zaidi
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 3P5, Canada; (S.-e.-Z.Z.); (A.Z.)
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada;
| | - Athanasios Zovoilis
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 3P5, Canada; (S.-e.-Z.Z.); (A.Z.)
| | - Jayce Fossen
- Large Animal Clinical Sciences, Western College of Veterinary Medicine, 52 Campus Dr., University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada; (J.F.); (C.W.)
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Government of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada;
| | - Cheryl Waldner
- Large Animal Clinical Sciences, Western College of Veterinary Medicine, 52 Campus Dr., University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada; (J.F.); (C.W.)
| | - Tim A. McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada;
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Calabro C, Sadhu R, Xu Y, Aprea M, Guarino C, Cazer CL. Longitudinal antimicrobial susceptibility trends of canine Staphylococcus pseudintermedius. Prev Vet Med 2024; 226:106170. [PMID: 38493570 DOI: 10.1016/j.prevetmed.2024.106170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024]
Abstract
Antimicrobial resistance within Staphylococcus pseudintermedius poses a significant risk for the treatment of canine pyoderma and as a reservoir for resistance and potential zoonoses, but few studies examine long-term temporal trends of resistance. This study assesses the antimicrobial resistance prevalence and minimum inhibitory concentration (MIC) trends in S. pseudintermedius (n=1804) isolated from canine skin samples at the Cornell University Animal Health Diagnostic Center (AHDC) between 2007 and 2020. Not susceptible (NS) prevalence, Cochran-Armitage tests, logrank tests, MIC50 and MIC90 quantiles, and survival analysis models were used to evaluate resistance prevalence and temporal trends to 23 antimicrobials. We use splines as predictors in accelerated failure time (AFT) models to model non-linear temporal trends in MICs. Multidrug resistance was common among isolates (47%), and isolates had moderate to high NS prevalence to the beta-lactams, chloramphenicol, the fluoroquinolones, gentamicin, the macrolides/lincosamides, the tetracyclines, and trimethoprim-sulfamethoxazole. However, low levels of NS to amikacin, rifampin, and vancomycin were observed. Around one third of isolates (38%) were found to be methicillin resistant S. pseudintermedius (MRSP), and these isolates had a higher prevalence of NS to all tested antimicrobials than methicillin susceptible isolates. Amongst the MRSP isolates, one phenotypically vancomycin resistant isolate (MIC >16 µg/mL) was identified, but genomic sequence data was unavailable. AFT models showed increasing MICs across time to the beta-lactams, chloramphenicol, the fluoroquinolones, gentamicin, and the macrolides/lincosamides, and decreasing temporal resistance (decreasing MICs) to doxycycline was observed amongst isolates. Notably, ATF modeling showed changes in MIC distributions that were not identified using Cochran-Armitage tests on prevalence, MIC quantiles, and logrank tests. Increasing resistance amongst these S. pseudintermedius isolates highlights the need for rational, empirical prescribing practices and increased antimicrobial resistance (AMR) surveillance to maintain the efficacy of current therapeutic agents. AFT models with non-linear predictors may be a useful, breakpoint-independent, surveillance tool alongside other modeling methods and antibiograms.
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Affiliation(s)
- Caroline Calabro
- Department of Public and Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY, USA; Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Ritwik Sadhu
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Yuchen Xu
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Melissa Aprea
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Cassandra Guarino
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Casey L Cazer
- Department of Public and Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY, USA; Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA.
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Moon BY, Ali MS, Choi JH, Heo YE, Lee YH, Kang HS, Kim TS, Yoon SS, Moon DC, Lim SK. Antimicrobial Resistance Profiles of Enterococcus faecium and Enterococcus faecalis Isolated from Healthy Dogs and Cats in South Korea. Microorganisms 2023; 11:2991. [PMID: 38138136 PMCID: PMC10745814 DOI: 10.3390/microorganisms11122991] [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: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Enterococcus spp. are typically found in the gastrointestinal tracts of humans and animals. However, they have the potential to produce opportunistic infections that can be transmitted to humans or other animals, along with acquired antibiotic resistance. In this study, we aimed to investigate the antimicrobial resistance profiles of Enterococcus faecium and Enterococcus faecalis isolates obtained from companion animal dogs and cats in Korea during 2020-2022. The resistance rates in E. faecalis towards most of the tested antimicrobials were relatively higher than those in E. faecium isolated from dogs and cats. We found relatively higher resistance rates to tetracycline (65.2% vs. 75.2%) and erythromycin (39.5% vs. 49.6%) in E. faecalis isolated from cats compared to those from dogs. However, in E. faecium, the resistance rates towards tetracycline (35.6% vs. 31.5%) and erythromycin (40.3% vs. 35.2%) were comparatively higher for dog isolates than cats. No or very few E. faecium and E. faecalis isolates were found to be resistant to daptomycin, florfenicol, tigecycline, and quinupristin/dalfopristin. Multidrug resistance (MDR) was higher in E. faecalis recovered from cats (44%) and dogs (33.9%) than in E. faecium isolated from cats (24.1%) and dogs (20.5%). Moreover, MDR patterns in E. faecalis isolates from dogs (27.2%) and cats (35.2%) were shown to encompass five or more antimicrobials. However, E. faecium isolates from dogs (at 13.4%) and cats (at 14.8%) were resistant to five or more antimicrobials. Taken together, the prevalence of antimicrobial-resistant enterococci in companion animals presents a potential public health concern.
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Affiliation(s)
- Bo-Youn Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si 39660, Republic of Korea; (B.-Y.M.); (M.S.A.); (J.-H.C.); (Y.-E.H.); (Y.-H.L.); (H.-S.K.); (S.-S.Y.)
| | - Md. Sekendar Ali
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si 39660, Republic of Korea; (B.-Y.M.); (M.S.A.); (J.-H.C.); (Y.-E.H.); (Y.-H.L.); (H.-S.K.); (S.-S.Y.)
| | - Ji-Hyun Choi
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si 39660, Republic of Korea; (B.-Y.M.); (M.S.A.); (J.-H.C.); (Y.-E.H.); (Y.-H.L.); (H.-S.K.); (S.-S.Y.)
| | - Ye-Eun Heo
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si 39660, Republic of Korea; (B.-Y.M.); (M.S.A.); (J.-H.C.); (Y.-E.H.); (Y.-H.L.); (H.-S.K.); (S.-S.Y.)
| | - Yeon-Hee Lee
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si 39660, Republic of Korea; (B.-Y.M.); (M.S.A.); (J.-H.C.); (Y.-E.H.); (Y.-H.L.); (H.-S.K.); (S.-S.Y.)
| | - Hee-Seung Kang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si 39660, Republic of Korea; (B.-Y.M.); (M.S.A.); (J.-H.C.); (Y.-E.H.); (Y.-H.L.); (H.-S.K.); (S.-S.Y.)
| | - Tae-Sun Kim
- Public Health and Environment Institute of Gwangju, Gwangju 14502, Republic of Korea;
| | - Soon-Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si 39660, Republic of Korea; (B.-Y.M.); (M.S.A.); (J.-H.C.); (Y.-E.H.); (Y.-H.L.); (H.-S.K.); (S.-S.Y.)
| | - Dong-Chan Moon
- Division of Antimicrobial Resistance Research, Centre for Infectious Diseases Research, Korea Disease Control and Prevention Agency, Cheongju 28159, Republic of Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si 39660, Republic of Korea; (B.-Y.M.); (M.S.A.); (J.-H.C.); (Y.-E.H.); (Y.-H.L.); (H.-S.K.); (S.-S.Y.)
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Jariyapamornkoon N, Boonkam P, Suanpairintr N. Assessment of the gradient diffusion method for fosfomycin susceptibility testing in Staphylococcus spp. and Enterococcus spp. isolated from the urine of companion dogs in Thailand. Vet World 2023; 16:2497-2503. [PMID: 38328370 PMCID: PMC10844777 DOI: 10.14202/vetworld.2023.2497-2503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/28/2023] [Indexed: 02/09/2024] Open
Abstract
Background and Aim The agar dilution method is the approved method for determining the minimum inhibitory concentration (MIC) in fosfomycin susceptibility testing, whereas the broth dilution method is not recommended. This study aimed to investigate the potential of the gradient diffusion method as a more convenient alternative to agar dilution method for MIC evaluation, particularly for the susceptibility testing of Staphylococcus spp. and Enterococcus spp. to fosfomycin. Materials and Methods A total of 194 isolates of Staphylococcus spp. and Enterococcus spp. were collected from urine samples of dogs diagnosed with bacterial cystitis. Bacterial identification and susceptibility to multiple antibiotics were tested using the Vitek 2 automated system. The susceptibility to fosfomycin was compared between agar dilution (reference method) and the gradient diffusion method. We assessed the agreement rates and errors between the two approaches by analyzing the MIC data. Results Staphylococcus pseudintermedius (98.7%) and Enterococcus faecalis (80.0%) exhibited high fosfomycin susceptibility rates, whereas Enterococcus faecium exhibited a lower susceptibility rate (38.5%). The gradient diffusion method demonstrated unacceptably low essential agreement (EA) rates (>90%) but acceptable categorical agreement (CA) rates (≥ 90%) for S. pseudintermedius (83.54% EA and 97.47% CA) and coagulase-negative staphylococci (CoNS) such as Staphylococcus chromogenes, Staphylococcus hominis, and Staphylococcus simulans (85.00% EA and 95.00% CA). Enterococcus spp. had an acceptable EA of 93.75%, but an unacceptably low CA rate of 82.81%, with a minor error rate of 17.19%. No significant errors were observed for Staphylococcus and Enterococcus spp. Conclusion The gradient diffusion method reliably determines MICs and interpretative breakpoints (S, I, R) for S. pseudintermedius. However, its applicability to CoNS and enterococci may be limited due to unacceptable errors.
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Affiliation(s)
- Nattha Jariyapamornkoon
- Department of Agricultural Technology, Faculty of Science and Technology, Thammasat University, Pathum Thani, Thailand
| | - Pongthai Boonkam
- Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Nipattra Suanpairintr
- Department of Pharmacology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Food and Water Risk Analysis (FAWRA), Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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