1
|
Clawson ML, Schuller G, Dickey AM, Bono JL, Murray RW, Sweeney MT, Apley MD, DeDonder KD, Capik SF, Larson RL, Lubbers BV, White BJ, Blom J, Chitko-McKown CG, Brichta-Harhay DM, Smith TPL. Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica. BMC Microbiol 2020; 20:250. [PMID: 32787780 PMCID: PMC7424683 DOI: 10.1186/s12866-020-01932-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Mannheimia haemolytica strains isolated from North American cattle have been classified into two genotypes (1 and 2). Although members of both genotypes have been isolated from the upper and lower respiratory tracts of cattle with or without bovine respiratory disease (BRD), genotype 2 strains are much more frequently isolated from diseased lungs than genotype 1 strains. The mechanisms behind the increased association of genotype 2 M. haemolytica with BRD are not fully understood. To address that, and to search for interventions against genotype 2 M. haemolytica, complete, closed chromosome assemblies for 35 genotype 1 and 34 genotype 2 strains were generated and compared. Searches were conducted for the pan genome, core genes shared between the genotypes, and for genes specific to either genotype. Additionally, genes encoding outer membrane proteins (OMPs) specific to genotype 2 M. haemolytica were identified, and the diversity of their protein isoforms was characterized with predominantly unassembled, short-read genomic sequences for up to 1075 additional strains. RESULTS The pan genome of the 69 sequenced M. haemolytica strains consisted of 3111 genes, of which 1880 comprised a shared core between the genotypes. A core of 112 and 179 genes or gene variants were specific to genotype 1 and 2, respectively. Seven genes encoding predicted OMPs; a peptidase S6, a ligand-gated channel, an autotransporter outer membrane beta-barrel domain-containing protein (AOMB-BD-CP), a porin, and three different trimeric autotransporter adhesins were specific to genotype 2 as their genotype 1 homologs were either pseudogenes, or not detected. The AOMB-BD-CP gene, however, appeared to be truncated across all examined genotype 2 strains and to likely encode dysfunctional protein. Homologous gene sequences from additional M. haemolytica strains confirmed the specificity of the remaining six genotype 2 OMP genes and revealed they encoded low isoform diversity at the population level. CONCLUSION Genotype 2 M. haemolytica possess genes encoding conserved OMPs not found intact in more commensally prone genotype 1 strains. Some of the genotype 2 specific genes identified in this study are likely to have important biological roles in the pathogenicity of genotype 2 M. haemolytica, which is the primary bacterial cause of BRD.
Collapse
Affiliation(s)
- Michael L Clawson
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA.
| | - Gennie Schuller
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Aaron M Dickey
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - James L Bono
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | | | | | - Keith D DeDonder
- Veterinary and Biomedical Research Center, Inc, Manhattan, KS, USA
| | - Sarah F Capik
- Texas A&M AgriLife Research, Texas A&M University System, Amarillo, TX, USA
- Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | | | | | | | - Jochen Blom
- Justus-Liebig-University Giessen, Giessen, Hesse, Germany
| | - Carol G Chitko-McKown
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Dayna M Brichta-Harhay
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Timothy P L Smith
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| |
Collapse
|
2
|
Lim A, Naidenov B, Bates H, Willyerd K, Snider T, Couger MB, Chen C, Ramachandran A. Nanopore ultra-long read sequencing technology for antimicrobial resistance detection in Mannheimia haemolytica. J Microbiol Methods 2019; 159:138-147. [PMID: 30849421 DOI: 10.1016/j.mimet.2019.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 03/02/2019] [Accepted: 03/04/2019] [Indexed: 02/02/2023]
Abstract
Disruptive innovations in long-range, cost-effective direct template nucleic acid sequencing are transforming clinical and diagnostic medicine. A multidrug resistant strain and a pan-susceptible strain of Mannheimia haemolytica, isolated from pneumonic bovine lung samples, were sequenced at 146× and 111× coverage, respectively with Oxford Nanopore Technologies MinION. De novo assembly produced a complete genome for the non-resistant strain and a nearly complete assembly for the drug resistant strain. Functional annotation using RAST (Rapid Annotations using Subsystems Technology), CARD (Comprehensive Antibiotic Resistance Database) and ResFinder databases identified genes conferring resistance to different classes of antibiotics including β-lactams, tetracyclines, lincosamides, phenicols, aminoglycosides, sulfonamides and macrolides. Resistance phenotypes of the M. haemolytica strains were determined by minimum inhibitory concentration (MIC) of the antibiotics. Sequencing with a highly portable MinION device corresponded to MIC assays with most of the antimicrobial resistant determinants being identified with as few as 5437 reads, except for the genes responsible for resistance to Fluoroquinolones. The resulting quality assemblies and AMR gene annotation highlight the efficiency of ultra-long read, whole-genome sequencing (WGS) as a valuable tool in diagnostic veterinary medicine.
Collapse
Affiliation(s)
- Alexander Lim
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Stillwater, OK 74078, United States
| | - Bryan Naidenov
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Stillwater, OK 74078, United States
| | - Haley Bates
- Oklahoma Animal Disease Diagnostic Laboratory, Center for Veterinary Health Sciences, 1950 W. Farm Road, Stillwater, OK 74078, United States
| | - Karyn Willyerd
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Stillwater, OK 74078, United States
| | - Timothy Snider
- Oklahoma Animal Disease Diagnostic Laboratory, Center for Veterinary Health Sciences, 1950 W. Farm Road, Stillwater, OK 74078, United States
| | - Matthew Brian Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, OK 74078, United States
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Stillwater, OK 74078, United States.
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, Center for Veterinary Health Sciences, 1950 W. Farm Road, Stillwater, OK 74078, United States.
| |
Collapse
|
3
|
Workman AM, Chitko-McKown CG, Smith TPL, Bennett GL, Kalbfleisch TS, Basnayake V, Heaton MP. A bovine CD18 signal peptide variant with increased binding activity to Mannheimia hemolytica leukotoxin. F1000Res 2018; 7:1985. [PMID: 30881690 PMCID: PMC6406179 DOI: 10.12688/f1000research.17187.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/13/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Mannheimia haemolytica is the major bacterial infectious agent of bovine respiratory disease complex and causes severe morbidity and mortality during lung infections.
M. haemolytica secretes a protein leukotoxin (Lkt) that binds to the CD18 receptor on leukocytes, initiates lysis, induces inflammation, and causes acute fibrinous bronchopneumonia. Lkt binds the 22-amino acid CD18 signal peptide domain, which remains uncleaved in ruminant species. Our aim was to identify missense variation in the bovine CD18 signal peptide and measure the effects on Lkt binding. Methods: Missense variants in the integrin beta 2 gene (
ITGB2) encoding CD18 were identified by whole genome sequencing of 96 cattle from 19 breeds, and targeted Sanger sequencing of 1238 cattle from 46 breeds. The ability of different CD18 signal peptide variants to bind Lkt was evaluated by preincubating the toxin with synthetic peptides and applying the mixture to susceptible bovine cell cultures in cytotoxicity-blocking assays. Results: We identified 14 missense variants encoded on 15 predicted haplotypes, including a rare signal peptide variant with a cysteine at position 5 (C
5) instead of arginine (R
5). Preincubating Lkt with synthetic signal peptides with C
5 blocked cytotoxicity significantly better than those with R
5. The most potent synthetic peptide (C
5PQLLLLAGLLA) had 30-fold more binding activity compared to that with R
5. Conclusions: The results suggest that missense variants in the CD18 signal peptide affect Lkt binding, and animals carrying the C
5 allele may be more susceptible to the effects of Lkt. The results also identify a potent class of non-antibiotic Lkt inhibitors that could potentially protect cattle from cytotoxic effects during acute lung infections.
Collapse
Affiliation(s)
- Aspen M Workman
- USDA, US Meat Animal Research Center (USMARC), Clay Center, Nebraska, 68933, USA
| | | | - Timothy P L Smith
- USDA, US Meat Animal Research Center (USMARC), Clay Center, Nebraska, 68933, USA
| | - Gary L Bennett
- USDA, US Meat Animal Research Center (USMARC), Clay Center, Nebraska, 68933, USA
| | - Theodore S Kalbfleisch
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, Kentucky, 40292, USA
| | | | - Michael P Heaton
- USDA, US Meat Animal Research Center (USMARC), Clay Center, Nebraska, 68933, USA
| |
Collapse
|
4
|
Legesse A, Abayneh T, Mamo G, Gelaye E, Tesfaw L, Yami M, Belay A. Molecular characterization of Mannheimia haemolytica isolates associated with pneumonic cases of sheep in selected areas of Central Ethiopia. BMC Microbiol 2018; 18:205. [PMID: 30518323 PMCID: PMC6280500 DOI: 10.1186/s12866-018-1338-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 11/14/2018] [Indexed: 11/24/2022] Open
Abstract
Background Mannheimia haemolytica has been recognized as the principal cause of pneumonic pasteurellosis in sheep and goats. It is one of the important diseases of small ruminants in Ethiopia. While annual vaccination using a monovalent vaccine (inactivated Pasteurella multocida biotype A) is common, respiratory diseases are still reported in various parts of Ethiopia. This suggests the need for further investigation into the species and strains responsible for the disease, which is vital information for development of a multivalent vaccine. The objective of the current study was to isolate M. heamolytica associated with pneumonic cases of sheep in selected areas of Central Ethiopia, determine its role and the strains/genotypes of the bacterium circulating in the study area. Results Bacteriological analysis of nasal swab samples collected from a total of 76 pneumonic cases of sheep showed that M. haemolytica was isolated from 26 of them while B.trehalosi from two cases. Further molecular analyses of the isolates using M. haemolytica species-specific and M.haemolytica serotype-1 antigen specific PCR assays revealed, 26 of the isolates were identified as M. haemolytica of which 21 of them were M. haemolytica serotype-1. Both M. haemolytica and B.trehalosi isolates were not detected in a PCR assay targeting capsular biosynthesis gene (capA) of P.multocida despite the non-specific products observed in M. haemolytica isolates. Phylogenetic analysis of M. haemolytica isolates included in this study in comparison with the reference strains with respect to PHSSA and Rpt2 genes revealed that the Ethiopian M. haemolytica isolates constituted three distinct genotypes consistent with site of origin. Conclusion The study indicated that M.haemolytica is commonly associated with cases of pneumonia in sheep in the study areas of central Ethiopia although the remaining other pathogens responsible for majority of the cases are yet to be determined. Molecular characterization revealed the existence of three genotypes of M. haemolytica circulating in the study areas consistent to the site of isolation. The findings suggest further extensive work to determine all pathogens associated with sheep pneumonia and the strain distribution of M. heamolytica to understand its molecular epidemiology at national level and design cost effective prevention and control methods.
Collapse
Affiliation(s)
- Abinet Legesse
- National Veterinary Institute, P.O. Box 19, Bishoftu, Ethiopia
| | - Takele Abayneh
- National Veterinary Institute, P.O. Box 19, Bishoftu, Ethiopia.
| | - Gezahegne Mamo
- College of Veterinary Medicine and Agriculture, Addis Ababa University, P.O. Box 34, Bishoftu, Ethiopia
| | - Esayas Gelaye
- National Veterinary Institute, P.O. Box 19, Bishoftu, Ethiopia
| | - Liyuwork Tesfaw
- National Veterinary Institute, P.O. Box 19, Bishoftu, Ethiopia
| | - Martha Yami
- National Veterinary Institute, P.O. Box 19, Bishoftu, Ethiopia
| | - Alebachew Belay
- National Veterinary Institute, P.O. Box 19, Bishoftu, Ethiopia
| |
Collapse
|
5
|
Closed Genome Sequences of Seven Histophilus somni Isolates from Beef Calves with Bovine Respiratory Disease Complex. GENOME ANNOUNCEMENTS 2017; 5:5/40/e01099-17. [PMID: 28983006 PMCID: PMC5629063 DOI: 10.1128/genomea.01099-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Histophilus somni is a fastidious Gram-negative opportunistic pathogenic Pasteurellaceae that affects multiple organ systems and is one of the principal bacterial species contributing to bovine respiratory disease complex (BRDC) in feed yard cattle. Here, we present seven closed genome sequences isolated from three beef calves showing sign of BRDC.
Collapse
|
6
|
Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease. G3-GENES GENOMES GENETICS 2017; 7:3059-3071. [PMID: 28739600 PMCID: PMC5592931 DOI: 10.1534/g3.117.1137] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole-genome sequencing offers a culture-independent alternative to current bacterial identification methods, but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic diversity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease–associated bacterial isolates (Histophilus somni, Mycoplasma bovis, Mannheimia haemolytica, and Pasteurella multocida) from dairy and beef cattle. One hundred genomically distinct assemblies were added to the NCBI database, doubling the available genomic sequences for these four species. Computer-based methods identified 11 predicted antimicrobial resistance genes in three species, with none being detected in M. bovis. While computer-based analysis can identify antibiotic resistance genes within whole-genome sequences (genotype), it may not predict the actual antimicrobial resistance observed in a living organism (phenotype). Antimicrobial susceptibility testing on 64 H. somni, M. haemolytica, and P. multocida isolates had an overall concordance rate between genotype and phenotypic resistance to the associated class of antimicrobials of 72.7% (P < 0.001), showing substantial discordance. Concordance rates varied greatly among different antimicrobial, antibiotic resistance gene, and bacterial species combinations. This suggests that antimicrobial susceptibility phenotypes are needed to complement genomically predicted antibiotic resistance gene genotypes to better understand how the presence of antibiotic resistance genes within a given bacterial species could potentially impact optimal bovine respiratory disease treatment and morbidity/mortality outcomes.
Collapse
|
7
|
Oppermann T, Busse N, Czermak P. Mannheimia haemolytica growth and leukotoxin production for vaccine manufacturing — A bioprocess review. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
|
8
|
Clawson ML, Murray RW, Sweeney MT, Apley MD, DeDonder KD, Capik SF, Larson RL, Lubbers BV, White BJ, Kalbfleisch TS, Schuller G, Dickey AM, Harhay GP, Heaton MP, Chitko-McKown CG, Brichta-Harhay DM, Bono JL, Smith TPL. Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes. BMC Genomics 2016; 17:982. [PMID: 27894259 PMCID: PMC5127058 DOI: 10.1186/s12864-016-3316-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Mannheimia haemolytica typically resides in cattle as a commensal member of the upper respiratory tract microbiome. However, some strains can invade their lungs and cause respiratory disease and death, including those with multi-drug resistance. A nucleotide polymorphism typing system was developed for M. haemolytica from the genome sequences of 1133 North American isolates, and used to identify genetic differences between isolates from the lungs and upper respiratory tract of cattle with and without clinical signs of respiratory disease. RESULTS A total of 26,081 nucleotide polymorphisms were characterized after quality control filtering of 48,403 putative polymorphisms. Phylogenetic analyses of nucleotide polymorphism genotypes split M. haemolytica into two major genotypes (1 and 2) that each were further divided into multiple subtypes. Multiple polymorphisms were identified with alleles that tagged genotypes 1 or 2, and their respective subtypes. Only genotype 2 M. haemolytica associated with the lungs of diseased cattle and the sequence of a particular integrative and conjugative element (ICE). Additionally, isolates belonging to one subtype of genotype 2 (2b), had the majority of antibiotic resistance genes detected in this study, which were assorted into seven combinations that ranged from 1 to 12 resistance genes. CONCLUSIONS Typing of diverse M. haemolytica by nucleotide polymorphism genotypes successfully identified associations with diseased cattle lungs, ICE sequence, and antibiotic resistance genes. Management of cattle by their carriage of M. haemolytica could be an effective intervention strategy to reduce the prevalence of respiratory disease and supplemental needs for antibiotic treatments in North American herds.
Collapse
Affiliation(s)
- Michael L. Clawson
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | | | | | | | - Keith D. DeDonder
- Kansas State University, Manhattan, KS USA
- Veterinary and Biomedical Research Center, Inc, Manhattan, KS USA
| | | | | | | | | | | | - Gennie Schuller
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Aaron M. Dickey
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Gregory P. Harhay
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Michael P. Heaton
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Carol G. Chitko-McKown
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Dayna M. Brichta-Harhay
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - James L. Bono
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Timothy P. L. Smith
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE USA
| |
Collapse
|
9
|
Tucci P, Estevez V, Becco L, Cabrera-Cabrera F, Grotiuz G, Reolon E, Marín M. Identification of Leukotoxin and other vaccine candidate proteins in a Mannheimia haemolytica commercial antigen. Heliyon 2016; 2:e00158. [PMID: 27699279 PMCID: PMC5035357 DOI: 10.1016/j.heliyon.2016.e00158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 09/07/2016] [Indexed: 12/25/2022] Open
Abstract
Bovine Respiratory Disease is the most costly disease that affects beef and dairy cattle industry. Its etiology is multifactorial, arising from predisposing environmental stress conditions as well as the action of several different respiratory pathogens. This situation has hindered the development of effective control strategies. Although different type of vaccines are available, many currently marketed vaccines are based on inactivated cultures of the main viral and bacterial agents involved in this pathology. The molecular composition of commercial veterinary vaccines is a critical issue. The present work aims to define at the proteomic level the most relevant valence of a line of commercial respiratory vaccines widely used in Central and South America. Since Mannheimia haemolytica is responsible for most of the disease associated morbid-mortality, we focused on the main proteins secreted by this pathogen, in particular Leukotoxin A, its main virulence factor. By Western blot analysis and mass spectrometry, Leukotoxin A was identified as a major component of M. haemolytica culture supernatants. We also identified other ten M. haemolytica proteins, including outer membrane proteins, periplasmic transmembrane solute transporters and iron binding proteins, which are relevant to achieve protective immunity against the pathogen. This work allowed a detailed molecular characterization of this vaccine component, providing evidence of its quality and efficacy. Furthermore, our results contributed to the identification of several proteins of interest as subunit vaccine candidates.
Collapse
Affiliation(s)
- Paula Tucci
- Biotechnology Division, Laboratorios Celsius, S.A. Avenida Italia 6201, Montevideo, Uruguay; Biochemistry-Molecular Biology Section, Faculty of Sciences, Universidad de la República, Iguá 4225, Montevideo, Uruguay
| | - Verónica Estevez
- Biotechnology Division, Laboratorios Celsius, S.A. Avenida Italia 6201, Montevideo, Uruguay
| | - Lorena Becco
- Biotechnology Division, Laboratorios Celsius, S.A. Avenida Italia 6201, Montevideo, Uruguay
| | - Florencia Cabrera-Cabrera
- Biochemistry-Molecular Biology Section, Faculty of Sciences, Universidad de la República, Iguá 4225, Montevideo, Uruguay
| | - Germán Grotiuz
- Virbac Uruguay, S.A. Avda. Millán 4175, Montevideo, Uruguay
| | - Eduardo Reolon
- Virbac Uruguay, S.A. Avda. Millán 4175, Montevideo, Uruguay
| | - Mónica Marín
- Biochemistry-Molecular Biology Section, Faculty of Sciences, Universidad de la República, Iguá 4225, Montevideo, Uruguay
| |
Collapse
|
10
|
Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi. PLoS One 2016; 11:e0161499. [PMID: 27556252 PMCID: PMC4996451 DOI: 10.1371/journal.pone.0161499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/05/2016] [Indexed: 01/31/2023] Open
Abstract
We examined and compared both the methylomes and the modification-related gene content of four sequenced strains of Bibersteinia trehalosi isolated from the nasopharyngeal tracts of Nebraska cattle with symptoms of bovine respiratory disease complex. The methylation patterns and the encoded DNA methyltransferase (MTase) gene sets were different between each strain, with the only common pattern being that of Dam (GATC). Among the observed patterns were three novel motifs attributable to Type I restriction-modification systems. In some cases the differences in methylation patterns corresponded to the gain or loss of MTase genes, or to recombination at target recognition domains that resulted in changes of enzyme specificity. However, in other cases the differences could be attributed to differential expression of the same MTase gene across strains. The most obvious regulatory mechanism responsible for these differences was slipped strand mispairing within short sequence repeat regions. The combined action of these evolutionary forces allows for alteration of different parts of the methylome at different time scales. We hypothesize that pleiotropic transcriptional modulation resulting from the observed methylomic changes may be involved with the switch between the commensal and pathogenic states of this common member of ruminant microflora.
Collapse
|
11
|
DeDonder KD, Harhay DM, Apley MD, Lubbers BV, Clawson ML, Schuller G, Harhay GP, White BJ, Larson RL, Capik SF, Riviere JE, Kalbfleisch T, Tessman RK. Observations on macrolide resistance and susceptibility testing performance in field isolates collected from clinical bovine respiratory disease cases. Vet Microbiol 2016; 192:186-193. [PMID: 27527782 DOI: 10.1016/j.vetmic.2016.07.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/12/2016] [Accepted: 07/25/2016] [Indexed: 12/21/2022]
Abstract
The objectives of this study were; first, to describe gamithromycin susceptibility of Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni isolated from cattle diagnosed with bovine respiratory disease (BRD) and previously treated with either gamithromycin for control of BRD (mass medication=MM) or sham-saline injected (control=CON); second, to describe the macrolide resistance genes present in genetically typed M. haemolytica isolates; third, use whole-genome sequencing (WGS) to correlate the phenotypic resistance and genetic determinants for resistance among M. haemolytica isolates. M. haemolytica (n=276), P. multocida (n=253), and H. somni (n=78) were isolated from feedlot cattle diagnosed with BRD. Gamithromycin susceptibility was determined by broth microdilution. Whole-genome sequencing was utilized to determine the presence/absence of macrolide resistance genes and to genetically type M. haemolytica. Generalized linear mixed models were built for analysis. There was not a significant difference between MM and CON groups in regards to the likelihood of culturing a resistant isolate of M. haemolytica or P. multocida. The likelihood of culturing a resistant isolate of M. haemolytica differed significantly by state of origin in this study. A single M. haemolytica genetic subtype was associated with an over whelming majority of the observed resistance. H. somni isolation counts were low and statistical models would not converge. Phenotypic resistance was predicted with high sensitivity and specificity by WGS. Additional studies to elucidate the relationships between phenotypic expression of resistance/genetic determinants for resistance and clinical response to antimicrobials are necessary to inform judicious use of antimicrobials in the context of relieving animal disease and suffering.
Collapse
Affiliation(s)
- Keith D DeDonder
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, KS, United States.
| | - Dayna M Harhay
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
| | - Michael D Apley
- Clinical Sciences, Kansas State University College of Veterinary Medicine, Manhattan, KS, United States
| | - Brian V Lubbers
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University College of Veterinary Medicine, Manhattan, KS, United States
| | - Michael L Clawson
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
| | - Gennie Schuller
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
| | - Gregory P Harhay
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
| | - Brad J White
- Clinical Sciences, Kansas State University College of Veterinary Medicine, Manhattan, KS, United States
| | - Robert L Larson
- Clinical Sciences, Kansas State University College of Veterinary Medicine, Manhattan, KS, United States
| | - Sarah F Capik
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, KS, United States
| | - Jim E Riviere
- Institute of Computational Comparative Medicine, Kansas State University College of Veterinary Medicine, Manhattan, KS, United States
| | - Ted Kalbfleisch
- Biochemistry and Molecular Genetics Department, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Ronald K Tessman
- Pharmaceutical Research and Development, Merial, Duluth, GA, United States
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Complete Closed Genome Sequences of a Mannheimia haemolytica Serotype A1 Leukotoxin Deletion Mutant and Its Wild-Type Parent Strain. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00417-15. [PMID: 25953160 PMCID: PMC4424311 DOI: 10.1128/genomea.00417-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Mannheimia haemolytica is a bacterial pathogen that secretes leukotoxin (LktA) which binds to leukocyte membranes via CD18, causing bacterial pneumonia in ruminants. We report the complete closed genome sequences of a leukotoxin mutant and its parent strain that are frequently used in respiratory disease studies.
Collapse
|
15
|
Complete Genome Sequence of Mannheimia haemolytica Strain Mh10517, Isolated from Sheep in South Africa. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00129-15. [PMID: 25858825 PMCID: PMC4392137 DOI: 10.1128/genomea.00129-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Respiratory disease caused by Mannheimia haemolytica is a major concern in the cattle and small stock industry worldwide. This problem arises due to the interaction of numerous contributing factors, including physical stresses associated with weaning, shipment, inclement weather, and overcrowding coupled with viral and bacterial infections. The whole genome of M. haemolytica strain Mh10517 was analyzed using an Illumina MiSeq high-throughput sequencing platform. The genome size is 2.67 Mb with 2,879 predicted gene sequences. The availability of this genome sequence will advance studies on various aspects of the biology of M. haemolytica in Africa and the world at large.
Collapse
|
16
|
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol 2014; 23:110-20. [PMID: 25461581 DOI: 10.1016/j.mib.2014.11.014] [Citation(s) in RCA: 265] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 11/20/2022]
Abstract
Like a jigsaw puzzle with large pieces, a genome sequenced with long reads is easier to assemble. However, recent sequencing technologies have favored lowering per-base cost at the expense of read length. This has dramatically reduced sequencing cost, but resulted in fragmented assemblies, which negatively affect downstream analyses and hinder the creation of finished (gapless, high-quality) genomes. In contrast, emerging long-read sequencing technologies can now produce reads tens of kilobases in length, enabling the automated finishing of microbial genomes for under $1000. This promises to improve the quality of reference databases and facilitate new studies of chromosomal structure and variation. We present an overview of these new technologies and the methods used to assemble long reads into complete genomes.
Collapse
|