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Westhoff TA, Borchardt S, Mann S. Invited review: Nutritional and management factors that influence colostrum production and composition in dairy cows. J Dairy Sci 2024; 107:4109-4128. [PMID: 38246551 DOI: 10.3168/jds.2023-24349] [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: 10/25/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024]
Abstract
Colostrum is a rich source of nutritional and non-nutritional components and is recognized as essential to transfer passive immunity to newborn calves. Because of the individual and seasonal variability in colostrum yield and composition, maintaining an adequate supply of high-quality colostrum year-round remains a challenge for commercial dairy producers. In this narrative review, we described the individual, seasonal, and herd-level variability of colostrum production and summarized the association between individual animal factors such as parity, sex of the calf, calf birth weight, as well as indicators of the cow's metabolic status and the yield and composition of colostrum. Further, we reviewed the current knowledge on the influence of prepartum nutrition and management strategies on colostrum production. Research on the metabolizable energy and protein supplied in the prepartum diet as well as on the inclusion and source of vitamins, minerals, and feed additives suggests prepartum nutrition influences the yield, quality, and composition of colostrum. Furthermore, the prepartum environment and dry period length remain influential factors in the production of colostrum. However, additional research is needed to understand the mechanisms by which prepartum nutrition and management affect colostrum production. Finally, time from calving to colostrum harvest and oxytocin administration as well as the current knowledge on the effect of heat treatment and colostrum storage strategies on colostral components were discussed. To conclude, we identify critical gaps in knowledge for future focus of investigation in colostrum research.
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Affiliation(s)
- T A Westhoff
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - S Borchardt
- Clinic for Animal Reproduction, Faculty of Veterinary Medicine, Freie Universitaet Berlin, 14163 Berlin, Germany
| | - S Mann
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
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2
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Yasir M, Al-Zahrani IA, Khan R, Soliman SA, Turkistani SA, Alawi M, Azhar EI. Microbiological risk assessment and resistome analysis from shotgun metagenomics of bovine colostrum microbiome. Saudi J Biol Sci 2024; 31:103957. [PMID: 38404539 PMCID: PMC10891335 DOI: 10.1016/j.sjbs.2024.103957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
Colostrum is known for its nutraceutical qualities, probiotic attributes, and health benefits. The aim of this study was to profile colostrum microbiome from bovine in rural sites of a developing country. The focus was on microbiological safety assessments and antimicrobial resistance, taking into account the risks linked with the consumption of raw colostrum. Shotgun sequencing was employed to analyze microbiome in raw buffalo and cow colostrum. Alpha and beta diversity analyses revealed increased inter and intra-variability within colostrum samples' microbiome from both livestock species. The colostrum microbiome was mainly comprised of bacteria, with over 90% abundance, whereas fungi and viruses were found in minor abundance. Known probiotic species, such as Leuconostoc mesenteroides, Lactococcus lactis, Streptococcus thermophilus, and Lactobacillus paracasei, were found in the colostrum samples. A relatively higher number of pathogenic and opportunistic pathogenic bacteria were identified in colostrum from both animals, including clinically significant bacteria like Clostridium botulinum, Pseudomonas aeruginosa, Escherichia coli, and Listeria monocytogenes. Binning retrieved 11 high-quality metagenome-assembled genomes (MAGs), with three MAGs potentially representing novel species from the genera Psychrobacter and Pantoea. Notably, 175 antimicrobial resistance genes (ARGs) and variants were detected, with 55 of them common to both buffalo and cow colostrum metagenomes. These ARGs confer resistance against aminoglycoside, fluoroquinolone, tetracycline, sulfonamide, and peptide antibiotics. In conclusion, this study describes a thorough overview of microbial communities in buffalo and cow colostrum samples. It emphasizes the importance of hygienic processing and pasteurization in minimizing the potential transmission of harmful microorganisms linked to the consumption of colostrum.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ibrahim A. Al-Zahrani
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | | | - Safaa A. Turkistani
- Medical Laboratory Sciences, Fakeeh College for Medical Sciences, Jeddah 21134, Saudi Arabia
| | - Maha Alawi
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Infection Control & Environmental Health Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Starkute V, Zokaityte E, Klupsaite D, Mockus E, Zokaityte G, Tusas S, Miseikiene R, Stankevicius R, Rocha JM, Bartkiene E. Influence of lactic acid fermentation on the microbiological parameters, biogenic amines, and volatile compounds of bovine colostrum. J Dairy Sci 2023; 106:8389-8403. [PMID: 37641360 DOI: 10.3168/jds.2023-23435] [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: 03/01/2023] [Accepted: 06/12/2023] [Indexed: 08/31/2023]
Abstract
In this study we hypothesized that the relations between the bovine colostrum (BC) microbiota, biogenic amine (BA) as well as volatile compound (VC) profiles can lead to new deeper insights concerning the BC changes during the biological preservation. To implement such an aim, BC samples were collected from 5 farms located in Lithuania and fermented with Lactiplantibacillus plantarum and Lacticaseibacillus paracasei strains. Nonfermented and fermented BC were subjected to microbiological [lactic acid bacteria (LAB), Escherichia coli, and total bacteria (TBC), total Enterobacteriaceae (TEC) and total mold and yeast (M-Y) viable counts] and physicochemical (pH, color coordinates, BA content and VC profile) parameters evaluation, and the relationship between the tested parameters were also further analyzed. In comparison pH and dry matter (DM) of nonfermented samples, significant differences were not found, and pH of BC was, on average, 6.30, and DM, on average, 27.5%. The pH of fermented samples decreased, on average, until 4.40 in Lp. plantarum fermented group, and, on average, until 4.37 in Lc. paracasei fermented group. Comparing color characteristics among nonfermented BC groups, significant differences between lightness (L*) and yellowness (b*) were not detected, however, the origin (i.e., agricultural company), LAB strain used for fermentation and the interaction between these factors were statistically significant on BC redness (a*) coordinate. The microbial contamination among all the tested BC groups was similar. However, different LAB strains used for BC fermentation showed different effects toward the microbial contamination reduction, and specifically Lc. paracasei was more effective than Lp. plantarum strain. Predominant BA in BC were putrescine and cadaverine. The main VC in nonfermented and fermented BC were decane, 2-ethyl-1-hexanol, dodecane, 1,3-di-tert-butylbenzene, 3,6-dimethyldecane and tetradecane. Moreover, this study showed worrying trends with respect to the frozen colostrum storage, because most of the dominant VC in BC were contaminants from the packaging material. Additionally, significant correlations between separate VC and microbial contamination were obtained. Finally, these experimental results showed that the separate VC in BC can be an important marker for biological as well as chemical contamination of BC. Also, it should be pointed out that despite the fermentation with LAB is usually described as a safe and natural process with many advantages, control of BA in the end product is necessary.
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Affiliation(s)
- Vytaute Starkute
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania; Department of Food Safety and Quality, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - Egle Zokaityte
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - Dovile Klupsaite
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - Ernestas Mockus
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - Gintare Zokaityte
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - Saulius Tusas
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - Ramute Miseikiene
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - Rolandas Stankevicius
- Department of Animal Nutrition, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - João Miguel Rocha
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal; Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal; Centro de Biotecnologia e Química Fina (CBQF), Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa Centro, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Elena Bartkiene
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania; Department of Food Safety and Quality, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania.
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4
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Miranda C, Igrejas G, Poeta P. Bovine Colostrum: Human and Animal Health Benefits or Route Transmission of Antibiotic Resistance-One Health Perspective. Antibiotics (Basel) 2023; 12:1156. [PMID: 37508251 PMCID: PMC10376235 DOI: 10.3390/antibiotics12071156] [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: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
After calving, bovine colostrum is obtained from the mammary gland of the dam in the first days and fed to newborn ruminant to prevent microbial infections. Each bovine colostrum has a unique biochemical composition with high nutraceutical value compared to milk. However, bovine colostrum is influenced by various factors, such as environmental, individual, and genetic factors, as well as processing methods. Proper colostrum management is crucial for obtaining high-quality colostrum and mitigating bacterial contamination. This is important not only for the health and survival of calves but also for the health of humans who consume colostrum and its co-products. It is essential to ensure that the consumed colostrum is free of pathogens to reap its benefits. Health-promoting products based on colostrum have gained significant interest. However, colostrum can contain pathogens that, if not eliminated, can contribute to their transmission and spread, as well as antibiotic resistance. The aim of this review was to promote the animal and human health benefits of bovine colostrum by improving its microbial quality and highlighting potential routes of dissemination of antibiotic-resistant pathogens. Implementing hygienic measures is one of the key factors in mitigating colostrum bacterial contamination and obtaining safe and high-quality colostrum. This helps reduce the exposure of pathogens to newborn calves, other animals, and humans, in a One Health analysis.
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Affiliation(s)
- Carla Miranda
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
- Toxicology Research Unit (TOXRUN), Advanced Polytechnic and University Cooperative (IUCS-CESPU), University Institute of Health Sciences, 4585-116 Gandra, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 1099-085 Caparica, Portugal
| | - Gilberto Igrejas
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 1099-085 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 1099-085 Caparica, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
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Bartkiene E, Starkute V, Jomantaite I, Zokaityte E, Mockus E, Tolpeznikaite E, Zokaityte G, Petrova P, Santini A, Rocha JM, Özogul F, Klupsaite D. Multifunctional Nutraceutical Composition Based on Fermented Spirulina, Apple Cider Vinegar, Jerusalem Artichoke, and Bovine Colostrum. Foods 2023; 12:foods12081690. [PMID: 37107485 PMCID: PMC10138001 DOI: 10.3390/foods12081690] [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: 03/18/2023] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
The main purpose of this experiment was to develop a multifunctional nutraceutical composition based on ingredients of different origins (Spirulina powder (SP), bovine colostrum (BC), Jerusalem artichoke powder (JAP), and apple cider vinegar (ACV)) which possess different health benefits through their different mechanisms of action. In order to improve the functional properties of Spirulina and bovine colostrum, fermentation with the Pediococcus acidilactici No. 29 and Lacticaseibacillus paracasei LUHS244 strains, respectively, was carried out. These LAB strains were chosen due to their good antimicrobial properties. The following parameters were analysed: for Spirulina (non-treated and fermented)-pH, colour coordinates, fatty acid profile, and contents of L-glutamic and GABA acids; for bovine colostrum (non-treated and fermented)-pH, colour coordinates, dry matter, and microbiological parameters (total LAB, total bacteria, total enterobacteria, Escherichia coli, and mould/yeast counts); for the produced nutraceuticals-hardness, colour coordinates, and overall acceptability. It was established that fermentation reduced the pH of the SP and BC and affected their colour coordinates. Fermented SP contained a greater concentration of gamma-aminobutyric and L-glutamic acids (by 5.2 times and 31.4% more, respectively), compared to the non-treated SP and BC. In addition, the presence of gamma-linolenic and omega-3 fatty acids was observed in fermented SP. Fermentation of BC reduces Escherichia coli, total bacteria, total enterobacteria, and total mould/yeast counts in samples. The obtained three-layer nutraceutical (I layer-fermented SP; II-fermented BC and JAP; III-ACV) demonstrated a high overall acceptability. Finally, our finding suggest that the selected nutraceutical combination has immense potential in the production of a multifunctional product with improved functionality and a high acceptability.
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Affiliation(s)
- Elena Bartkiene
- Department of Food Safety and Quality, Veterinary Academy, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania
- Institute of Animal Rearing Technologies, Faculty of Animal Sciences, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania
| | - Vytaute Starkute
- Department of Food Safety and Quality, Veterinary Academy, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania
- Institute of Animal Rearing Technologies, Faculty of Animal Sciences, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania
| | - Ieva Jomantaite
- Department of Food Safety and Quality, Veterinary Academy, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania
| | - Egle Zokaityte
- Institute of Animal Rearing Technologies, Faculty of Animal Sciences, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania
| | - Ernestas Mockus
- Institute of Animal Rearing Technologies, Faculty of Animal Sciences, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania
| | - Ernesta Tolpeznikaite
- Institute of Animal Rearing Technologies, Faculty of Animal Sciences, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania
| | - Gintare Zokaityte
- Institute of Animal Rearing Technologies, Faculty of Animal Sciences, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania
| | - Penka Petrova
- Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G. Bontchev Str. bl. 26, 1113 Sofia, Bulgaria
| | - Antonello Santini
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - João Miguel Rocha
- CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal
- ALiCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal
| | - Fatih Özogul
- Department of Seafood Processing Technology, Faculty of Fisheries, Cukurova University, Balcali, Adana 01330, Turkey
- Biotechnology Research and Application Center, Cukurova University, Balcali, Adana 01330, Turkey
| | - Dovile Klupsaite
- Institute of Animal Rearing Technologies, Faculty of Animal Sciences, Lithuanian University of Health Sciences, Tilzes Str. 18, LT-47181 Kaunas, Lithuania
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Li C, Li S, Yang C, Ding Y, Zhang Y, Wang X, Zhou X, Su Z, Ming W, Zeng L, Ma Y, Shi Y, Kang X. Blood transcriptome reveals immune and metabolic-related genes involved in growth of pasteurized colostrum-fed calves. Front Genet 2023; 14:1075950. [PMID: 36814903 PMCID: PMC9939824 DOI: 10.3389/fgene.2023.1075950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
The quality of colostrum is a key factor contributing to healthy calf growth, and pasteurization of colostrum can effectively reduce the counts of pathogenic microorganisms present in the colostrum. Physiological changes in calves fed with pasteurized colostrum have been well characterized, but little is known about the underlying molecular mechanisms. In this study, key genes and functional pathways through which pasteurized colostrum affects calf growth were identified through whole blood RNA sequencing. Our results showed that calves in the pasteurized group (n = 16) had higher body height and daily weight gain than those in the unpasteurized group (n = 16) in all months tested. Importantly, significant differences in body height were observed at 3 and 4 months of age (p < 0.05), and in daily weight gain at 2, 3, and 6 months of age (p < 0.05) between the two groups. Based on whole blood transcriptome data from 6-months old calves, 630 differentially expressed genes (DEGs), of which 235 were upregulated and 395 downregulated, were identified in the pasteurized compared to the unpasteurized colostrum groups. Most of the DEGs have functions in the immune response (e.g., CCL3, CXCL3, and IL1A) and metabolism (e.g., PTX3 and EXTL1). Protein-protein interaction analyses of DEGs revealed three key subnetworks and fifteen core genes, including UBA52 and RPS28, that have roles in protein synthesis, oxidative phosphorylation, and inflammatory responses. Twelve co-expression modules were identified through weighted gene co-expression network analysis. Among them, 17 genes in the two modules that significantly associated with pasteurization were mainly involved in the tricarboxylic acid cycle, NF-kappa B signaling, and NOD-like receptor signaling pathways. Finally, DEGs that underwent alternative splicing in calves fed pasteurized colostrum have roles in the immune response (SLCO4A1, AKR1C4, and MED13L), indicative of potential roles in immune regulation. Results from multiple analytical methods used suggest that differences in calf growth between the pasteurized and unpasteurized groups may be due to differential immune activity. Our data provide new insights into the impact of pasteurization on calf immune and metabolic-related pathways through its effects on gene expression.
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Gordonia species as a rare pathogen isolated from milk of dairy cows with mastitis. Sci Rep 2022; 12:6028. [PMID: 35411009 PMCID: PMC9001696 DOI: 10.1038/s41598-022-09340-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 03/21/2022] [Indexed: 11/24/2022] Open
Abstract
While Gordonia species have long been known to cause severe inflammation in humans, the pathogenic effects of Gordonia species in veterinary medicine have rarely been described. Between 2010 and 2019, we collected microorganisms of the genus Gordonia isolated from milk samples from dairy cows with mastitis. We describe the growth properties of these microorganisms and their prevalence, virulence factors and susceptibility to antimicrobial agents. From 31,534 quarter milk samples processed by standard culture methods, 27 isolates of Gordonia species (0.086% prevalence) were identified by a molecular phenotyping method. The isolates originated from 17 farms in 12 districts of the Czech Republic. Twenty-one isolates were tested for susceptibility to 7 antimicrobials by the disc diffusion method. Notably, 100% of these isolates were susceptible to streptomycin and neomycin, 85.7% to cefovecin and tetracycline, 76.2% to penicillin G, 47.6% to trimethoprim/sulfamethoxazole and 0% to clindamycin. The species was determined to be Gordonia paraffinivorans by whole genome sequencing for 9 isolates (from 8 farms in 7 districts). These isolates showed the highest similarity to two reference strains from the environment. In all these isolates, we identified genes encoding virulence factors that are very similar to genes encoding virulence factors expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis. However, genome analysis revealed 61 unique genes in all 9 sequenced isolates.
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