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Guo Y, McMullen C, Timsit E, Hallewell J, Orsel K, van der Meer F, Yan S, Alexander TW. Genetic relatedness and antimicrobial resistance in respiratory bacteria from beef calves sampled from spring processing to 40 days after feedlot entry. Vet Microbiol 2019; 240:108478. [PMID: 31902491 DOI: 10.1016/j.vetmic.2019.108478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 01/05/2023]
Abstract
Recent studies have shown an increase in antimicrobial-resistant bovine respiratory disease (BRD) pathogens. To investigate the origin of antimicrobial resistance in the respiratory microbiota of beef cattle, three groups (A, B, or C) of 40 calves sourced from different calf-ranches were sampled by deep nasopharyngeal swab (DNS) at the time of first on-ranch vaccination (Time point 1, T1), feedlot entry (Time point 2, T2), and 40 days after feedlot entry (Time point 3, T3; feedlots differed by group). Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni were isolated from DNS samples, tested for antimicrobial susceptibility, and subtyped by pulsed-field gel electrophoresis (PFGE). Antimicrobial resistance genes [tet(H), tet(W), and sul2] were also quantified in DNS metagenomic DNA using PCR. Prevalence of calves positive for BRD pathogens differed among groups and time-points but P. multocida was the most prevalent (61% of calves positive, at least, at one timepoint), followed by M. haemolytica (48%) and H. somni (26%). Most M. haemolytica were susceptible to all antimicrobials (88.6%; n = 70). For P. multocida, the dominant resistance phenotype was against oxytetracycline and neomycin (35.8%). Resistant P. multocida isolates were mainly detected in group C at T3 and had the same PFGE profile. For H. somni, the dominant resistance phenotype was against neomycin (63.3%) and was only observed at T3. The abundance of tet(W) did not change significantly over time (P > 0.05). Abundances of tet(H) and sul2 only increased for group C at T3 (P < 0.05). Overall, this study showed that resistance in the respiratory microbiota of beef calves can increase from calf-ranch to feedlot however, the results can vary by calf-ranch and feedlot.
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Affiliation(s)
- Yongmei Guo
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada; Inner Mongolia Key Laboratory of Animal Nutrition and Feed Science, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Christopher McMullen
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Edouard Timsit
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada; Simpson Ranch Chair in Beef Cattle Health and Wellness, University of Calgary, Calgary, AB, Canada
| | | | - Karin Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Frank van der Meer
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Sumei Yan
- Inner Mongolia Key Laboratory of Animal Nutrition and Feed Science, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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Klima CL, Cook SR, Zaheer R, Laing C, Gannon VP, Xu Y, Rasmussen J, Potter A, Hendrick S, Alexander TW, McAllister TA. Comparative Genomic Analysis of Mannheimia haemolytica from Bovine Sources. PLoS One 2016; 11:e0149520. [PMID: 26926339 PMCID: PMC4771134 DOI: 10.1371/journal.pone.0149520] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/02/2016] [Indexed: 11/18/2022] Open
Abstract
Bovine respiratory disease is a common health problem in beef production. The primary bacterial agent involved, Mannheimia haemolytica, is a target for antimicrobial therapy and at risk for associated antimicrobial resistance development. The role of M. haemolytica in pathogenesis is linked to serotype with serotypes 1 (S1) and 6 (S6) isolated from pneumonic lesions and serotype 2 (S2) found in the upper respiratory tract of healthy animals. Here, we sequenced the genomes of 11 strains of M. haemolytica, representing all three serotypes and performed comparative genomics analysis to identify genetic features that may contribute to pathogenesis. Possible virulence associated genes were identified within 14 distinct prophage, including a periplasmic chaperone, a lipoprotein, peptidoglycan glycosyltransferase and a stress response protein. Prophage content ranged from 2–8 per genome, but was higher in S1 and S6 strains. A type I-C CRISPR-Cas system was identified in each strain with spacer diversity and organization conserved among serotypes. The majority of spacers occur in S1 and S6 strains and originate from phage suggesting that serotypes 1 and 6 may be more resistant to phage predation. However, two spacers complementary to the host chromosome targeting a UDP-N-acetylglucosamine 2-epimerase and a glycosyl transferases group 1 gene are present in S1 and S6 strains only indicating these serotypes may employ CRISPR-Cas to regulate gene expression to avoid host immune responses or enhance adhesion during infection. Integrative conjugative elements are present in nine of the eleven genomes. Three of these harbor extensive multi-drug resistance cassettes encoding resistance against the majority of drugs used to combat infection in beef cattle, including macrolides and tetracyclines used in human medicine. The findings here identify key features that are likely contributing to serotype related pathogenesis and specific targets for vaccine design intended to reduce the dependency on antibiotics to treat respiratory infection in cattle.
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Affiliation(s)
- Cassidy L. Klima
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB T1J 4B1, Canada
- Department of Large Animal Clinial Science, Western Colledge of Verterinary Medicine, University of Saskatoon, Saskatoon, Canada
| | - Shaun R. Cook
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB T1J 4B1, Canada
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB T1J 4B1, Canada
| | - Chad Laing
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | - Vick P. Gannon
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | - Yong Xu
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Jay Rasmussen
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB T1J 4B1, Canada
| | - Andrew Potter
- Vaccine and Infectious Disease Organization, Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Steve Hendrick
- Department of Large Animal Clinial Science, Western Colledge of Verterinary Medicine, University of Saskatoon, Saskatoon, Canada
| | - Trevor W. Alexander
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB T1J 4B1, Canada
- * E-mail: (TAM); (TWA)
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB T1J 4B1, Canada
- * E-mail: (TAM); (TWA)
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Rai AN, Epperson WB, Nanduri B. Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. Bioinform Biol Insights 2015; 9:13-23. [PMID: 26526746 PMCID: PMC4620937 DOI: 10.4137/bbi.s30525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/24/2015] [Accepted: 08/26/2015] [Indexed: 12/27/2022] Open
Abstract
Bovine respiratory disease (BRD) is the most common economically important disease affecting cattle. For developing accurate diagnostics that can predict disease susceptibility/resistance and stratification, it is necessary to identify the molecular mechanisms that underlie BRD. To study the complex interactions among the bovine host and the multitude of viral and bacterial pathogens, as well as the environmental factors associated with BRD etiology, genome-scale high-throughput functional genomics methods such as microarrays, RNA-seq, and proteomics are helpful. In this review, we summarize the progress made in our understanding of BRD using functional genomics approaches. We also discuss some of the available bioinformatics resources for analyzing high-throughput data, in the context of biological pathways and molecular interactions. Although resources for studying host response to infection are avail-able, the corresponding information is lacking for majority of BRD pathogens, impeding progress in identifying diagnostic signatures for BRD using functional genomics approaches.
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Affiliation(s)
- Aswathy N Rai
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, MS, USA
| | - William B Epperson
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, MS, USA
| | - Bindu Nanduri
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, MS, USA. ; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, MS, USA
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Niu YD, Cook SR, Wang J, Klima CL, Hsu YH, Kropinski AM, Turner D, McAllister TA. Comparative analysis of multiple inducible phages from Mannheimia haemolytica. BMC Microbiol 2015; 15:175. [PMID: 26318735 PMCID: PMC4553209 DOI: 10.1186/s12866-015-0494-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 07/24/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Mannheimia haemolytica is a commensal bacterium that resides in the upper respiratory tract of cattle that can play a role in bovine respiratory disease. Prophages are common in the M. haemolytica genome and contribute significantly to host diversity. The objective of this research was to undertake comparative genomic analysis of phages induced from strains of M. haemolytica serotype A1 (535A and 2256A), A2 (587A and 1127A) and A6 (1152A and 3927A). RESULTS Overall, four P2-like (535AP1, 587AP1, 1127AP1 and 2256AP1; genomes: 34.9-35.7 kb; G+C content: 41.5-42.1 %; genes: 51-53 coding sequences, CDSs), four λ-like (535AP2, 587AP2, 1152AP2 and 3927AP1; genomes: 48.6-52.1 kb; 41.1-41.4 % mol G+C; genes: 77-83 CDSs and 2 tRNAs) and one Mu-like (3927AP2; genome: 33.8 kb; 43.1 % mol G+C; encoding 50 CDSs) phages were identified. All P2-like phages are collinear with the temperate phage φMhaA1-PHL101 with 535AP1, 2256AP1 and 1152AP1 being most closely related, followed by 587AP1 and 1127AP1. Lambdoid phages are not collinear with any other known λ-type phages, with 587AP2 being distinct from 535AP2, 3927AP1 and 1152AP2. All λ-like phages contain genes encoding a toxin-antitoxin (TA) system and cell-associated haemolysin XhlA. The Mu-like phage induced from 3927A is closely related to the phage remnant φMhaMu2 from M. haemolytica PHL21, with similar Mu-like phages existing in the genomes of M. haemolytica 535A and 587A. CONCLUSIONS This is among the first reports of both λ- and Mu-type phages being induced from M. haemolytica. Compared to phages induced from commensal strains of M. haemolytica serotype A2, those induced from the more virulent A1 and A6 serotypes are more closely related. Moreover, when P2-, λ- and Mu-like phages co-existed in the M. haemolytica genome, only P2- and λ-like phages were detected upon induction, suggesting that Mu-type phages may be more resistant to induction. Toxin-antitoxin gene cassettes in λ-like phages may contribute to their genomic persistence or the establishment of persister subpopulations of M. haemolytica. Further work is required to determine if the cell-associated haemolysin XhlA encoded by λ-like phages contributes to the pathogenicity and ecological fitness of M. haemolytica.
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Affiliation(s)
- Yan D Niu
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1, Canada. .,Alberta Agriculture and Rural Development, Agriculture Centre, Lethbridge, AB, T1J 4V6, Canada.
| | - Shaun R Cook
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1, Canada.
| | - Jiaying Wang
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1, Canada. .,College of Veterinary Medicine, South China Agricultural University, Guangdong, 510642, People's Republic of China.
| | - Cassidy L Klima
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1, Canada.
| | - Yu-hung Hsu
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1, Canada. .,Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada.
| | - Andrew M Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, ON, N1G 3W4, Canada. .,Department of Molecular Biology, Cellular Biology and Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Dann Turner
- Centre for Research in Biosciences, Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
| | - Tim A McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1, Canada.
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