Genomic Characterization of <i>Enterococcus casseliflavus</i> Isolated from Beef Cows and Calves
<i>Enterococcus</i> 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 <i>Enterococcus casseliflavus</i> along with <i>E. faecium</i>, <i>...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-04-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/13/4/907 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849714176981729280 |
|---|---|
| author | Sani-e-Zehra Zaidi Rahat Zaheer Athanasios Zovoilis Jayce Fossen Gary Van Domselaar Cheryl Waldner Tim A. McAllister |
| author_facet | Sani-e-Zehra Zaidi Rahat Zaheer Athanasios Zovoilis Jayce Fossen Gary Van Domselaar Cheryl Waldner Tim A. McAllister |
| author_sort | Sani-e-Zehra Zaidi |
| collection | DOAJ |
| description | <i>Enterococcus</i> 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 <i>Enterococcus casseliflavus</i> along with <i>E. faecium</i>, <i>E. faecalis</i>, and <i>E. hirae</i>. Given the high prevalence of <i>E. casseliflavus</i>, we elected to characterize this species to better understand its role in the antimicrobial resistance of enterococci in cows and calves. Almost 12% of <i>E. casseliflavus</i> 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 <i>E. casseliflavus</i> were susceptible to chloramphenicol, penicillin, streptomycin, nitrofurantoin, gentamicin, and linezolid. Whole genome antimicrobial resistance gene profiling identified <i>vanC</i>-type intrinsic vancomycin resistance genes in all <i>E. casseliflavus</i>, with the <i>vanC4XYT</i> gene cluster being dominant (67%) followed by <i>vanC2XYT</i> (31%) and <i>vanC3XYT</i> (1.5%). Resistance genes for erythromycin (<i>ermB</i>) and tetracycline (<i>tetM</i>) were rarely identified (2.1% and 1.2%, respectively) within <i>E. casseliflavus</i> 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 <i>E. casseliflavus</i> pan-genome highlighted its intraspecies diversity. These findings suggest that <i>E. casseliflavus</i> is likely a low-risk species in terms of contributing to antimicrobial resistance in the cow–calf sector. |
| format | Article |
| id | doaj-art-c9f0d24103e94e22b2d4b040088a3c0e |
| institution | DOAJ |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj-art-c9f0d24103e94e22b2d4b040088a3c0e2025-08-20T03:13:45ZengMDPI AGMicroorganisms2076-26072025-04-0113490710.3390/microorganisms13040907Genomic Characterization of <i>Enterococcus casseliflavus</i> Isolated from Beef Cows and CalvesSani-e-Zehra Zaidi0Rahat Zaheer1Athanasios Zovoilis2Jayce Fossen3Gary Van Domselaar4Cheryl Waldner5Tim A. McAllister6Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 3P5, CanadaLethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, CanadaDepartment of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 3P5, CanadaLarge Animal Clinical Sciences, Western College of Veterinary Medicine, 52 Campus Dr., University of Saskatchewan, Saskatoon, SK S7N 5B4, CanadaNational Microbiology Laboratory, Public Health Agency of Canada, Government of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, CanadaLarge Animal Clinical Sciences, Western College of Veterinary Medicine, 52 Campus Dr., University of Saskatchewan, Saskatoon, SK S7N 5B4, CanadaLethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada<i>Enterococcus</i> 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 <i>Enterococcus casseliflavus</i> along with <i>E. faecium</i>, <i>E. faecalis</i>, and <i>E. hirae</i>. Given the high prevalence of <i>E. casseliflavus</i>, we elected to characterize this species to better understand its role in the antimicrobial resistance of enterococci in cows and calves. Almost 12% of <i>E. casseliflavus</i> 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 <i>E. casseliflavus</i> were susceptible to chloramphenicol, penicillin, streptomycin, nitrofurantoin, gentamicin, and linezolid. Whole genome antimicrobial resistance gene profiling identified <i>vanC</i>-type intrinsic vancomycin resistance genes in all <i>E. casseliflavus</i>, with the <i>vanC4XYT</i> gene cluster being dominant (67%) followed by <i>vanC2XYT</i> (31%) and <i>vanC3XYT</i> (1.5%). Resistance genes for erythromycin (<i>ermB</i>) and tetracycline (<i>tetM</i>) were rarely identified (2.1% and 1.2%, respectively) within <i>E. casseliflavus</i> 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 <i>E. casseliflavus</i> pan-genome highlighted its intraspecies diversity. These findings suggest that <i>E. casseliflavus</i> is likely a low-risk species in terms of contributing to antimicrobial resistance in the cow–calf sector.https://www.mdpi.com/2076-2607/13/4/907antimicrobial resistance<i>Enterococcus casseliflavus</i>whole genome sequencingpan-genomecow–calf system |
| spellingShingle | Sani-e-Zehra Zaidi Rahat Zaheer Athanasios Zovoilis Jayce Fossen Gary Van Domselaar Cheryl Waldner Tim A. McAllister Genomic Characterization of <i>Enterococcus casseliflavus</i> Isolated from Beef Cows and Calves Microorganisms antimicrobial resistance <i>Enterococcus casseliflavus</i> whole genome sequencing pan-genome cow–calf system |
| title | Genomic Characterization of <i>Enterococcus casseliflavus</i> Isolated from Beef Cows and Calves |
| title_full | Genomic Characterization of <i>Enterococcus casseliflavus</i> Isolated from Beef Cows and Calves |
| title_fullStr | Genomic Characterization of <i>Enterococcus casseliflavus</i> Isolated from Beef Cows and Calves |
| title_full_unstemmed | Genomic Characterization of <i>Enterococcus casseliflavus</i> Isolated from Beef Cows and Calves |
| title_short | Genomic Characterization of <i>Enterococcus casseliflavus</i> Isolated from Beef Cows and Calves |
| title_sort | genomic characterization of i enterococcus casseliflavus i isolated from beef cows and calves |
| topic | antimicrobial resistance <i>Enterococcus casseliflavus</i> whole genome sequencing pan-genome cow–calf system |
| url | https://www.mdpi.com/2076-2607/13/4/907 |
| work_keys_str_mv | AT saniezehrazaidi genomiccharacterizationofienterococcuscasseliflavusiisolatedfrombeefcowsandcalves AT rahatzaheer genomiccharacterizationofienterococcuscasseliflavusiisolatedfrombeefcowsandcalves AT athanasioszovoilis genomiccharacterizationofienterococcuscasseliflavusiisolatedfrombeefcowsandcalves AT jaycefossen genomiccharacterizationofienterococcuscasseliflavusiisolatedfrombeefcowsandcalves AT garyvandomselaar genomiccharacterizationofienterococcuscasseliflavusiisolatedfrombeefcowsandcalves AT cherylwaldner genomiccharacterizationofienterococcuscasseliflavusiisolatedfrombeefcowsandcalves AT timamcallister genomiccharacterizationofienterococcuscasseliflavusiisolatedfrombeefcowsandcalves |