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Leimbach A, Poehlein A, Vollmers J, Görlich D, Daniel R, Dobrindt U. No evidence for a bovine mastitis Escherichia coli pathotype. BMC Genomics 2017; 18:359. [PMID: 28482799 PMCID: PMC5422975 DOI: 10.1186/s12864-017-3739-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 04/27/2017] [Indexed: 11/30/2022] Open
Abstract
Background Escherichia coli bovine mastitis is a disease of significant economic importance in the dairy industry. Molecular characterization of mastitis-associated E. coli (MAEC) did not result in the identification of common traits. Nevertheless, a mammary pathogenic E. coli (MPEC) pathotype has been proposed suggesting virulence traits that differentiate MAEC from commensal E. coli. The present study was designed to investigate the MPEC pathotype hypothesis by comparing the genomes of MAEC and commensal bovine E. coli. Results We sequenced the genomes of eight E. coli isolated from bovine mastitis cases and six fecal commensal isolates from udder-healthy cows. We analyzed the phylogenetic history of bovine E. coli genomes by supplementing this strain panel with eleven bovine-associated E. coli from public databases. The majority of the isolates originate from phylogroups A and B1, but neither MAEC nor commensal strains could be unambiguously distinguished by phylogenetic lineage. The gene content of both MAEC and commensal strains is highly diverse and dominated by their phylogenetic background. Although individual strains carry some typical E. coli virulence-associated genes, no traits important for pathogenicity could be specifically attributed to MAEC. Instead, both commensal strains and MAEC have very few gene families enriched in either pathotype. Only the aerobactin siderophore gene cluster was enriched in commensal E. coli within our strain panel. Conclusions This is the first characterization of a phylogenetically diverse strain panel including several MAEC and commensal isolates. With our comparative genomics approach we could not confirm previous studies that argue for a positive selection of specific traits enabling MAEC to elicit bovine mastitis. Instead, MAEC are facultative and opportunistic pathogens recruited from the highly diverse bovine gastrointestinal microbiota. Virulence-associated genes implicated in mastitis are a by-product of commensalism with the primary function to enhance fitness in the bovine gastrointestinal tract. Therefore, we put the definition of the MPEC pathotype into question and suggest to designate corresponding isolates as MAEC. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3739-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Leimbach
- Institute of Hygiene, University of Münster, Mendelstrasse 7, 48149, Münster, Germany. .,Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany. .,Institute for Molecular Infection Biology, Julius-Maximilians-University of Würzburg, Würzburg, Germany.
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - John Vollmers
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dennis Görlich
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Mendelstrasse 7, 48149, Münster, Germany. .,Institute for Molecular Infection Biology, Julius-Maximilians-University of Würzburg, Würzburg, Germany.
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102
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Rainard P. Mammary microbiota of dairy ruminants: fact or fiction? Vet Res 2017; 48:25. [PMID: 28412972 PMCID: PMC5392980 DOI: 10.1186/s13567-017-0429-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/21/2017] [Indexed: 02/07/2023] Open
Abstract
Explorations of how the complex microbial communities that inhabit different body sites might contribute to health and disease have prompted research on the ways the harmonious relationship between a host and its microbiota could be used to keep animals healthy in their production conditions. In particular, there is a growing interest in the bacterial signatures that can be found in the milk of healthy or mastitic dairy cows. The concept of sterility of the healthy mammary gland of dairy ruminants has been challenged by the results of studies using bacterial DNA-based methodology. The newly obtained data have led to the concept of the intramammary microbiota composed of a complex community of diverse bacteria. Accordingly, mammary gland infections are not mere infections by a bacterial pathogen, but the consequence of mammary dysbiosis. This article develops the logical implications of this paradigm shift and shows how this concept is incompatible with current knowledge concerning the innate and adaptive immune system of the mammary gland of dairy ruminants. It also highlights how the concept of mammary microbiota clashes with results of experimental infections induced under controlled conditions or large field experiments that demonstrated the efficacy of the current mastitis control measures.
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Affiliation(s)
- Pascal Rainard
- ISP, INRA, Université de Tours, UMR1282, 37380, Nouzilly, France.
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103
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Oultram JWH, Ganda EK, Boulding SC, Bicalho RC, Oikonomou G. A Metataxonomic Approach Could Be Considered for Cattle Clinical Mastitis Diagnostics. Front Vet Sci 2017; 4:36. [PMID: 28344976 PMCID: PMC5344926 DOI: 10.3389/fvets.2017.00036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/24/2017] [Indexed: 12/19/2022] Open
Abstract
Mastitis is one of the most costly diseases affecting the dairy industry, and identification of the causative microorganism(s) is essential. Here, we report the use of next-generation sequencing of bacterial 16S rRNA genes for clinical mastitis diagnosis. We used 65 paired milk samples, collected from the mastitic and a contralateral healthy quarter of mastitic dairy cattle to evaluate the technique as a potential alternative to bacterial culture or targeted PCR. One large commercial dairy farm was used, with one trained veterinarian collecting the milk samples. The 16S rRNA genes were individually amplified and sequenced using the MiSeq platform. The MiSeq Reporter was used in order to analyze the obtained sequences. Cattle were categorized according to whether or not 1 of the 10 most abundant bacterial genera in the mastitic quarter exhibited an increase in relative abundance between the healthy and mastitic quarters equal to, or exceeding, twofold. We suggest that this increase in relative abundance is indicative of the genus being a causative mastitis pathogen. Well-known mastitis-causing pathogens such as Streptococcus uberis and Staphylococcus spp. were identified in most cattle. We were able to diagnose 53 out of the 65 studied cases and identify potential new mastitis pathogens such as Sneathia sanguinegens and Listeria innocua, which are difficult to identify by bacterial culture because of their fastidious nature.
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Affiliation(s)
- Joanne W. H. Oultram
- Department of Livestock Health and Welfare, Institute of Veterinary Science, University of Liverpool, Neston, UK
| | - Erika K. Ganda
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sarah C. Boulding
- Department of Livestock Health and Welfare, Institute of Veterinary Science, University of Liverpool, Neston, UK
| | - Rodrigo C. Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Georgios Oikonomou
- Department of Livestock Health and Welfare, Institute of Veterinary Science, University of Liverpool, Neston, UK
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, UK
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104
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Lima SF, Teixeira AGV, Lima FS, Ganda EK, Higgins CH, Oikonomou G, Bicalho RC. The bovine colostrum microbiome and its association with clinical mastitis. J Dairy Sci 2017; 100:3031-3042. [PMID: 28161185 DOI: 10.3168/jds.2016-11604] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/13/2016] [Indexed: 11/19/2022]
Abstract
In an effort to characterize colostrum microbial diversity and its potential associations with early-lactation clinical mastitis, we used high-throughput sequencing of the 16S rRNA gene to investigate the bovine colostrum microbiome. A prospective observational study was conducted that included 70 Holstein cows; colostrum samples were collected from all 4 mammary gland quarters. Colostrum samples were categorized according to whether the quarter was diagnosed (CMC) or not diagnosed (NCMC) with clinical mastitis during the first 30 d postpartum. Colostrum samples were dominated by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Fusobacteria, and Tenericutes phyla, with the 6 most common taxa [order (o), family (f), and genus (g)] being g_Staphylococcus, g_Prevotella, f_Ruminococcaceae, o_Bacteroidales, o_Clostridiales, and g_Pseudomonas. The colostrum microbiota of primiparous cows was significantly richer (higher number of bacterial species) than that of multiparous cows, and differences in colostrum taxonomic structure between parities were also observed. The microbial community of NCMC samples of primiparous cows was significantly more diverse than that of CMC samples, and the relative abundances of the Tenericutes and Fusobacteria phyla as well as the Mycoplasma and Fusobacterium genera were significantly higher in NCMC than in CMC samples of primiparous cows. The colostrum core microbiome, defined as the bacterial taxa common to all colostrum samples examined, was composed of 20 taxa and included bacterial genera already known to be associated with mastitis (e.g., Staphylococcus, Mycoplasma, and Streptococcus spp.). Our results indicate that the colostrum microbiome of primiparous cows differs from that of multiparous cows, and it harbors some diversity and taxonomic markers of mammary gland health specific to primiparous cows only.
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Affiliation(s)
- Svetlana F Lima
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, New York
| | - Andre G V Teixeira
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, New York
| | - Fabio S Lima
- Department of Veterinary Medical Science, College of Veterinary Medicine, University of Illinois, Urbana 61802
| | - Erika K Ganda
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, New York
| | - Catherine H Higgins
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, New York
| | - Georgios Oikonomou
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, New York; Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston CH64 7TE, United Kingdom
| | - Rodrigo C Bicalho
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, New York.
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105
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Longitudinal metagenomic profiling of bovine milk to assess the impact of intramammary treatment using a third-generation cephalosporin. Sci Rep 2016; 6:37565. [PMID: 27874095 PMCID: PMC5118806 DOI: 10.1038/srep37565] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/01/2016] [Indexed: 01/09/2023] Open
Abstract
Antimicrobial usage in food animals has a direct impact on human health, and approximately 80% of the antibiotics prescribed in the dairy industry are used to treat bovine mastitis. Here we provide a longitudinal description of the changes in the microbiome of milk that are associated with mastitis and antimicrobial therapy. Next-generation sequencing, 16 S rRNA gene quantitative real-time PCR, and aerobic culturing were applied to assess the effect of disease and antibiotic therapy on the milk microbiome. Cows diagnosed with clinical mastitis associated with Gram-negative pathogens or negative aerobic culture were randomly allocated into 5 days of Ceftiofur intramammary treatment or remained as untreated controls. Serial milk samples were collected from the affected quarter and the ipsilateral healthy quarter of the same animal. Milk from the mastitic quarter had a higher bacterial load and reduced microbial diversity compared to healthy milk. Resolution of the disease was accompanied by increases in diversity indexes and a decrease in pathogen relative abundance. Escherichia coli-associated mastitic milk samples had a remarkably distinct bacterial profile, dominated by Enterobacteriaceae, when compared to healthy milk. However, no differences were observed in culture-negative mastitis samples when compared to healthy milk. Antimicrobial treatment had no significant effect on clinical cure, bacteriological cure, pathogen clearance rate or bacterial load.
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106
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Jeon SJ, Cunha F, Ma X, Martinez N, Vieira-Neto A, Daetz R, Bicalho RC, Lima S, Santos JEP, Jeong KC, Galvão KN. Uterine Microbiota and Immune Parameters Associated with Fever in Dairy Cows with Metritis. PLoS One 2016; 11:e0165740. [PMID: 27802303 PMCID: PMC5089738 DOI: 10.1371/journal.pone.0165740] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/17/2016] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE This study aimed to evaluate bacterial and host factors causing a fever in cows with metritis. For that, we investigated uterine microbiota using a metagenomic sequencing of the 16S rRNA gene (Study 1), and immune response parameters (Study 2) in metritic cows with and without a fever. PRINCIPAL FINDINGS (STUDY1) Bacterial communities were similar between the MNoFever and MFever groups based on distance metrics of relative abundance of bacteria. Metritic cows showed a greater prevalence of Bacteroidetes, and Bacteroides and Porphyromonas were the largest contributors to that difference. A comparison of relative abundance at the species level pointed to Bacteroides pyogenes as a fever-related species which was significantly abundant in the MFever than the MNoFever and Healthy groups; however, absolute abundance of Bacteroides pyogenes determined by droplet digital PCR (ddPCR) was similar between MFever and MNoFever groups, but higher than the Healthy group. The same trend was observed in the total number of bacteria. PRINCIPAL FINDINGS (STUDY2) The activity of polymorphonuclear leukocyte (PMN) and the production of TNFα, PGE2 metabolite, and PGE2 were evaluated in serum, before disease onset, at 0 and 3 DPP. Cows in the MNoFever had decreased proportion of PMN undergoing phagocytosis and oxidative burst compared with the MFever. The low PMN activity in the MNoFever was coupled with the low production of TNFα, but similar PGE2 metabolite and circulating PGE2. CONCLUSION/SIGNIFICANCE Our study is the first to show a similar microbiome between metritic cows with and without a fever, which indicates that the host response may be more important for fever development than the microbiome. Bacteroides pyogenes was identified as an important pathogen for the development of metritis but not fever. The decreased inflammatory response may explain the lack of a febrile response in the MNoFever group.
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Affiliation(s)
- Soo Jin Jeon
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Federico Cunha
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Xiaojie Ma
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Natalia Martinez
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Achilles Vieira-Neto
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Rodolfo Daetz
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Rodrigo C. Bicalho
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, United States of America
| | - Svetlana Lima
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, United States of America
| | - Jose E. P. Santos
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - K. Casey Jeong
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Klibs N. Galvão
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, Florida, United States of America
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107
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Addis MF, Tanca A, Uzzau S, Oikonomou G, Bicalho RC, Moroni P. The bovine milk microbiota: insights and perspectives from -omics studies. MOLECULAR BIOSYSTEMS 2016; 12:2359-72. [DOI: 10.1039/c6mb00217j] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent findings and future perspectives of -omics studies on the bovine milk microbiota, focusing on its impact on animal health.
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Affiliation(s)
- M. F. Addis
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
| | - A. Tanca
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
| | - S. Uzzau
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
- Università degli Studi di Sassari
| | - G. Oikonomou
- Epidemiology and Population Health
- Institute of Infection and Global Health
- University of Liverpool
- Liverpool
- UK
| | - R. C. Bicalho
- Cornell University
- Department of Population Medicine and Diagnostic Sciences
- College of Veterinary Medicine
- Ithaca
- USA
| | - P. Moroni
- Cornell University
- Department of Population Medicine and Diagnostic Sciences
- College of Veterinary Medicine
- Ithaca
- USA
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