Full Length Research Paper
References
|
Abebe R, Hatiya H, Abera M, Megersa B, Asmare K (2016). Bovine mastitis: prevalence, risk factors and isolation of Staphylococcus aureus in dairy herd at Hawassa milk shed, South Ethiopia. BMC Veterinary Research, 12(1):270. |
|
|
Abo-Shama UH (2014). Prevalence and antimicrobial susceptibility of Staphylococcus aureus isolated from cattle, buffalo, sheep, and goats raw milk in Sohag Governorate, Egypt Veterinary Medical Journal, 60:141. |
|
|
Agga GE, Arthur MT, Durso ML, Harhay MD, Schmidt WJ (2015). Antimicrobial-Resistant Bacterial Populations and Antimicrobial Resistance Genes obtained from Environments Impacted by Livestock and Municipal Waste. J. PLoS ONE 10(7):e0132586. |
|
|
Ahmed MA, Shimamoto T (2011). Molecular characterization of antimicrobial resistance in Gram-negative bacteria isolated from bovine mastitis in Egypt. Microbiology and Immunology, 55:318-327. |
|
|
Ahsani MR, Mohammadabadi MR, Shamsaddini MB (2010). Clostridium perfringens isolate typing multiplex PCR. Journal of Venomous Animals and Toxins including Tropical Diseases, 16(4):573-578. |
|
|
Akindolire AM, Babalola OO, Ateba NC (2015). Detection of Antibiotic Resistant Staphylococcus aureus from Milk: A Public Health Implication. International Journal of Environmental Research and Public Health, 12(9):10254-10275. |
|
|
Amadi AV, Avendano E, Onyegbule AO, Pearl Z, Graeme S, Sharma R, Hariharan H (2015). Antimicrobial drug resistance in Escherichia coli including an O157:H7 isolate from feces of healthy goats in Grenada. Annual Research & Review in Biology, 7(1):68-74. |
|
|
Aslam M, Stanford K, McAllister AT (2010). Characterization of antimicrobial resistance and seasonal prevalence of Escherichia coli O157:H7 recovered from commercial feedlots in Albeta, Letters in Applied Microbiology, 50(3):320-326. |
|
|
Association of Analytical Communities. (1998). Official methods of analysis of AOAC International. Maryland: AOAC International. |
|
|
Bae W, Kaya NK, Hancock DD, Call RD, Park HY, Besser ET (2005). Prevalence and antimicrobial resistance of thermophilic Campylobacter spp. from cattle farms in Washington State. Applied and Environmental Microbiology, 71(1):169-174. |
|
|
Bako E, Kagambege A, Traore AK, Bagre ST, Ibrahim BH, Bouda CS, Bonkoungou OJI, Kabore S, Zongo C, Traore SA, Barro N (2017). Characterization of Diarrheagenic Escherichia coli isolated in organic waste products (cattle fecal matter, manure, and slurry) from cattle's markets in Ougadougou, Burkina Faso. International Journal of Environmental Research and Public Health, 14:1100; |
|
|
Barzon L, Lavezzo E, Militello V, Toppo S, Palu G (2011). Applications of next-generation sequencing technologies to diagnostic virology. International Journal of Molecular Sciences (12):7861-7884. |
|
|
Bashir Y, Singh PS, Konwar KB (2014). Metagenomics:An Application Based Perspective. Chinese Journal of Biology, 2014:1-7. |
|
|
Beukers GA, Zaheer R, Goji N, Amoako KK, Chaves VA, Ward PM, McAllister AT (2017). Comparative genomics of Enterococcus spp. isolated from bovine feces. BMC Microbiology, 17:52. |
|
|
Beyene T, Hayishe H, Gizaw F, Beyi FA, Abunna F, Mammo B, Ayana D, Waktole H, Abdi DR (2017). Prevalence and antimicrobial resistance profile of Staphylococcus in dairy farms, abattoir and humans in Addis Ababa, Ethiopia. BMC Research Notes 10:171. |
|
|
Call RD, Davis AM, Sawant AA (2008). Antimicrobial Resistance in beef and dairy cattle production. Animal Health Research Reviews 9(2):159-167. |
|
|
Cameron A, McAllister AT (2016). Antimicrobial usage and resistance in beef production. Journal of Animal Science and Biotechnology 7(68). |
|
|
Castillo M, Martin-Orue MS, Manzanilla GE, Badiola I, Martin M, Gasa J (2006). Quantification of total bacteria, enterobacteria and lactobacilli populations in pig digesta by real-time PCR. Veterinary Microbiology, 114(1-2):165-170. |
|
|
Chambers L, Yang Y, Littier H, Ray P, Zhang T, Pruden A, Strickland M, Knowlton K (2015). Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces Following Therapeutic Administration of Third Generation Cephalosporin. PLoS ONE. 10(8):e0133764. |
|
|
Chandra PS, Diwan V, Tamhankar JA, Joseph VB, Rosales KS, Mundayoor M, Lundborg SC, Macaden R (2014). Detection of carbapenem resistance genes and cephalosporin, and quinolone resistance genes along with oqxAB gene in Escherichia coli in hospital wastewater: a matter of concern. Journal of Applied Microbiology, 117(4):984-995. |
|
|
Chikhi R, Medvedev P (2013). Informed and Automated K-mer Size Selection for Genome Assembly. Bioinformatics 1:31-37. |
|
|
Creevey JC, Kelly JW, Henderson G, Leahy CS (2014). Determining the culturability of the rumen bacterial microbiome. Journal of Microbiology and Biotechnology, 7(5):467-479. |
|
|
Diarra SM, Rempel H, Champagne J, Masson L, Pritchard J, Topp E (2010). Distribution of Antimicrobial Resistance and Virulence Genes in Enterococcus spp. and Characterization of isolates from broiler chickens. Journal of Applied and Environmental Microbiology, 76(24):8033-8043. |
|
|
Dowd ES, Callaway RT, Walcott DR, Sun Y, McKeehan T, Hagevoort GR, Edrington ST (2008). Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiology, 8:125. |
|
|
Englen DM, Hill EA, Dargatz AD, Ladely RS, Fedorka-cray JP (2006). Prevalence and antimicrobial resistance of Campylobacter in US dairy cattle. Journal of Applied Microbiology, 102(6):1570-1577. |
|
|
Fohler S, Klein G, Haedemaker M, Scheu T, Seyboldt C, Campe A, Jensen CK, Abdulmawjod A (2016). Diversity of Clostridium perfringens toxin-genotypes from dairy animals. BMC Microbiology Journal, 16:199. |
|
|
Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Sera DT, Graf HE, Tardif DK, Kapusta lA, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding VK, Blaschke A, Byington LC, Jain S, Pavia A, Eilbeck KAK, Marth G, Yandell M, Schlaberg R (2016). Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biology, 17(1):111. |
|
|
Gao L, Tan Y, Zhang X, Hu J, Miao Z, Wei L, Chai T (2015). Emissions of Escherichia coli Carrying Extended-Spectrum-Beta-Lactamase resistance from Pig Farms to the Surrounding Environment. International Journal of Environmental Research and Public Health, 12:4203-4213. |
|
|
Gerzova L, Babak V, Sedlar K, Faldynova M, Videnska P, Cejkova D, Jensen NA, Denis M, Kerouanton A, Ricci A, Cibin V, Osterberg J, Rychlik I (2015). Characterization of antibiotic resistance gene abundance and microbiota composition in feces of organic and conventional pigs from four EU countries. PLOS ONE 10(7). |
|
|
Goskel E, Ugur P, Suheyla T, Nese U, Mehmet O, Osman K (2016). Distribution of Antibiotic Resistance Genes in Enterococcus spp. Isolated from Mastitis Bovine Milk. Acta Veterinaria 66(3):336-346 |
|
|
Hinthong W, Pumipuntu N, Santajit S, Kulpeanprasit S, Buranasinsup S, Sookrung N, Chaicumpa W, Aiumurai P, Indrawattana N (2017). Detection and drug resistance profile of Escherichia coli from subclinical mastitis cows and water supply in dairy farms in Saraburi, Thailand. Peer Journal, 13(5):e3431. |
|
|
Hossain MK, Paul S, Hossain MM, Islam MR, Alam MGS (2017). Bovine Mastitis and Its Therapeutic Strategy Doing Antibiotic Sensitivity Test. Austin Journal of Veterinary Science and Animal Husbandry 4(1):1030. |
|
|
Idriss ES, Foltys V, Tancin V, Kirchnerova K, Tancinova D, Zaujec K (2014). Mastitis pathogens and their resistance against antimicrobial agents in dairy cows in Nitra, Slovakia Slovak. Journal of Animimal Science, 47(1):33-38. |
|
|
Iweriebor CB, Iwu JC, Obi CL, Nwodo UU, Okoh IA (2015). Multiple antibiotic resistance among Shiga toxin producing Escherichia Coli O157 in feces of dairy cattle farms in Eastern Cape of South Africa. BMC Microbiology Journal, 15(21). |
|
|
Jami E, Shterzer N, Mizrahi I (2014). Evaluation of Automated Ribosomal Intergenic Spacer Analysis for Bacterial Fingerprinting of Rumen Microbiome Compared to Pyrosequencing Technology. Pathogens, 3(1):109-120. |
|
|
Jiang Y, Zhang XY (2013). Resistance patterns and detection of resistance genes in Escherichia coli Isolated from Diarrheic calves in Northeastern China. African Journal of Microbiology Research, 7(5):389-397. |
|
|
Jovel J, Patterson J, Wang W, Hotte N, KeefeO' S, Mitchel T, Perry T, Kao D, Mason LA, Madsen LK, Wong SKG (2016). Characterization of the gut microbiome using 16S or shotgun metagenomics. Frontiers in Microbiology. 7:459. |
|
|
Karikari BA, Obiri-Danso K, Frimpong HE, Krogfelt AK (2017). Antibiotic Resistance of Campylobacter Recovered from Faeces and Carcasses of Healthy Livestock. BioMed Research International, 2017:9. |
|
|
Karwani MG, Lulandala LLL, Kimaro A, Msigawa ZP (2016). The role of shot rotation coppice technology in fuel wood supply in Rungwe district, Tanzania. International Journal of Agricultural Research, Innovation and Technology, 6(1):41-46. |
|
|
Kashoma IP, Kassem II, Kumar, Kessy MB, Gebreyes W, Kazwala RR, Rajashekara G (2015). Antimicrobial resistance and genotypic diversity of Campylobacter isolated from pigs, dairy, and beef cattle in Tanzania. Frontiers in Microbiology, 6(1240). |
|
|
Kim H, Jebrail JM, Sinha A, Bent WZ, Solberg DO, Williams PK, Langevin AS, Renzi FR, VandeVreugde LJ, Meagher JR, Schoeniger SJ, Lane WT, Branda SS, Michael SB, Patel DK (2013). A microfluidic DNA library preparation platforms for next-generation sequencing. PLoS ONE. 8(7). |
|
|
Klein-Jobstl D, Schornsteiner E, Mann E, Wagner M, Drillich M, Schmitz-Esser S (2014). Pyrosequencing reveals diverse fecal microbiota in Simmental calves during early development. Frontiers in Microbiology 5:1-8. |
|
|
Kruger M, Grobe-Herrenthey A, Schrodl W, Gerlach A, Rodloff A (2011). Visceral botulism at dairy farms in Schleswig Holstein, Germany-Prevalence of Clostridium botulinum in feces of cows, in animal feeds, in feces of the farmers, and in the house dust. Anaerobe 18(2):221- 223. |
|
|
Kyselkova M, Jirout J, Vrchotova N, Schmitt H, Elhottova D (2015). Spread of tetracycline resistance genes at a conventional dairy farm. Frontiers in Microbiology, 6(536). |
|
|
Loor JJ, Elolimy AA, McCann CJ (2016). Dietary impacts on rumen microbiota in beef and dairy production. Animal Frontiers, 6(3):22-29. |
|
|
Madoshi PB, Kudirkiene E, Mtambo AMM, Muhairwa PA, Lupindu MA, Olsen EJ (2016). Characterisation of commensal Escherichia coli Isolated from Apparently Healthy Cattle and Their Attendants in Tanzania. PLoS One 11(12). |
|
|
Mansour AMA, Zaki MH, Hassan AN, Al-Humiany AA (2014). Molecular characterization and immunoprotective activity of capsular polysaccharide of Klebsiella pneumonia isolated from farm animals at taif governorate. American Journal of Infectious Diseases, 10(1):1-14. |
|
|
Manyi-Loh EC, Mamphweli NS, Meyer LE, Makaka G, Simon M, Okoh IA (2016). An overview of the control of bacterial pathogens in cattle manure. International Journal of Environmental Research and Public Health, 13(9):843. |
|
|
Mekibib B, Furgasa M, Abunna F, Megersa B, Regassa A (2010). Bovine mastitis: Prevalence, risk factors and major pathogens in dairy farms in Holeta Town, Central Ethiopia. Veterinary World 3(9):397-403. |
|
|
Mersha G, Asrat D, Zewde MB, Kyule M (2009). Occurrence of Escherichia coli O157:H7 in faeces, skin, and carcasses from sheep and goats in Ethiopia. Letters in Applied Microbiology, 50(1):71-76. |
|
|
Messele EY, Abdi DR, Yalew TS, Tegegne TD, Emeru AB, Werid MG (2017). Molecular determination of antimicrobial resistance in Escherichia Coli Isolated from raw meat in Addis Ababa and Bishoftu, Ethiopia. Annals of Clinical Microbiology and Antimicrobials, 16(55). |
|
|
Mfune RL (2015). Epidemiological study of bovine brucellosis in smallholder dairy cattle in Lushoto and Rungwe districts, Tanzania. MSc. thesis. Sokoine University of Agriculture, Morogoro, Tanzania. pp. 38-39. |
|
|
Mir RA, Weppelmann TA, Johnson JA., Archer D, Morris JG, Jr, Jeong KC. (2016). Identification and characterization of cefotaxime resistant bacteria in beef cattle. PLoS One 11(9). |
|
|
Munoz AM, Welcome LF, Schukken HY, Zadoks NR (2007). Molecular epidemiology of two Klebsiella pneumonia mastitis outbreaks on a dairy farm in New york state. Journal of Clinical Microbiology, 45(12).3964-3971. |
|
|
Nakamura S, Maeda N, Miron MI, Yoh M, Izutsu K, Kataoka, C, Honda T, Yasunaga T, Nakay T, Kawai J, Hayashizaki Y, Horii T, lida T (2008). Metagenomic diagnosis of bacterial infections. Emerging Infectious Diseases, 14(11):1784-1786. |
|
|
Nathani MN, Patel KA, Dhamannpatil SP, Kothari KR, Singh MK, Joshi GC (2013). Comparative evaluation of rumen metagenome community using qPCR and MG-RAST. AMB Express.3:55. |
|
|
Neuhaus J, Schrodl W, Shehata AA, Kruger M (2015). Detection of Clostridium botulinum in liquid manure and plant wastes. Folia Microbiologica, 60(5):451-456. |
|
|
Nguyen MNT, Hotzel H, Njeru J, Mwituria J, El-Adawy H, Tomaso H, Neubauerand H, Hafez MH (2016). Antimicrobial resistance of Campylobacter isolates from small scale and backyard chicken in Kenya. Gut Pathogens, 8(1):39 |
|
|
National Research Council (NRC) (2001). Nutrient requirements of dairy cattle. 7th Revised Edition, Subcommittee on Dairy Cattle Nutrition, Committee on Animal Nutrition, Board on Agriculture and Natural Resources, National Research Council, National Academy Press, Washington, D.C. |
|
|
Nyabundi D, Onkoba N, Kimathi R, Nyachieo A, Juma G, Kinyanjui P, Kamau J (2017). Molecular characterization and antibiotic resistance profiles of Salmonella isolated from fecal matter of domestic animals and animal products in Nairobi. Tropical Diseases, Travel Medicine and Vaccines, 3(2). |
|
|
Olowe AO, Adewumi O, Odewale G, Ojurongbe O, Adefioye JO (2015). Phenotypic and Molecular Characterisation of Extended-Spectrum-Beta-Lactamase Producing Escherichia coli Obtained from Animal Fecal Samples in Ado Ekiti, Nigeria. J. Environ. Pub. Health Dx.doi.org/10.1155/2015/497980. |
|
|
Omojowo SF, Omojasola PF (2013). Antibiotic resistance pattern of bacterial pathogens isolated from cow dung used to fertilize Nigerian Fish Ponds. Notulae Scientia Biologicae 5(1):15-19. |
|
|
Onate PF, Batto JM, Juste C, Fadlallah J, Fougeroux C, Gouas D, Pons N, Kennedy S, Levenez F, Dore J, Ehrlich DS, Gorochov G, Larsen M (2015). Quality control of microbiota metagenomics by K-mer analysis. BMC Genomics 16:183. |
|
|
Osman MK, El-Enbaawy IM, Ezzeldeen AN, Hussein GMH (2009). Mastitis in dairy buffalo and cattle in Egypt due to clostridium perfringens: prevalence, incidence, risk factors and costs. Revue Scientifique et Technique, 28 (3):975-986. |
|
|
Osman MK, Hassan MH, Orabi A, Abdelhafez TSA (2014). Phenotypic, antimicrobial susceptibility profile and virulence factors of Klebsiella pneumonia isolated from buffalo and cow mastitic milk. Pathogens and Global Health, 108(4):191-199. |
|
|
Pandey A, Joshi N, Joshi KR, Prajapati R, Singh A (2015). Virulence attributes and antibiotic resistance pattern of E. coli isolated from human and animals. Asian Journal of Animal and Veterinary Advances, 11:67-72. |
|
|
Peng S, Yin J, Liu X, Jia b, Chang Z, Lu, H, Jiang N, Chen Q (2015). First insights into the microbial diversity in the omasum and reticulum of bovine using illumina sequencing. Journal of Applied Genetics, 56(3):393-401. |
|
|
Petri RM, Schwaiger T, Penner GB, Beauchemin KA, Forster RJ, McKinnon JJ, McAllister TA (2013). Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge. PLoS One. 8(12). |
|
|
Pitta DW, Pinchak EW, Indugu N, Vicchiarelli B, Sinha R, Fulford DJ (2016). Metagenomic analysis of the rumen microbiome of steers with wheat-induced frothy bloat. Frontiers in Microbiology, 7(68). |
|
|
Roehe R, Dewhurst JR, Duthie CA, Rooke AJ, McKain, N, Ross WD, Hyslop JJ, Waterhouse A, Freeman CT, Watson M, Wallace JR (2016). Bovine host genetic variation influences rumen microbial methane production with best selection criterion for low methane emitting and efficiently feed converting hosts based on metagenomic gene abundance. PLoS Genetics 12(2). |
|
|
Ross EM, Moate PJ, Davidson SE, Sawbridge TI, Guthridge KM, Cocks BG, Hayes BJ (2012). High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing. BMC Genomics, 13(1):53. |
|
|
Sandra B (2013). Clinical and subclinical mastitis in dairy cattle in Kampala, Uganda. Ph.D. thesis. Swedish University of Agriculture Sciences. |
|
|
Sawant AA, Hegde VN, Straley AB, Donaldson CS, Love CB, Knabel JS, Jayarao MB (2007). Antimicrobial-Resistant Enteric Bacteria from Dairy Cattle. J. App. Envir. Microbiol. 73(1): 156-163. |
|
|
Schmid A, Hormansdorfer S, Messelhausser S, Kasbohrer A, Sauter-Louis A, Mansfeld R (2013). Prevalence of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli on Bavarian Dairy and Beef Cattle Farms. Applied and Environmental Microbiology 79(9):3027. |
|
|
Seemann T (2014). Prokka: Rappid prokaryotic genome annotation. Bioinformatics 30(14):2068-2069. |
|
|
Sharif A, Muhammad G (2009). Mastitis control in dairy animals. Pakistan Veterinary Journal, 29(3):145-148. |
|
|
Sievers A, Bosiek K, Bisch M, Dreessen C, Riedel J, FroB P, Haussmann M, Hildenbrand G (2017). Function and Evolutionary Features. Journal of Genetics, 8(122):1-18. |
|
|
Srinivasan V, Nam HM, Sawant AA, Headrick IS, Nguyen TL, Oliver PS (2007). Distribution of tetracyclin and streptomycin resistance genes and class 1 integrons in Enterobacteriaceae isolated from dairy and nondairy farm soils. Microbial Ecology, 55:184-193. |
|
|
Sudda MM, Mtenga BA, Kusiluka JL, Kassim N (2016). Prevalence and Antibiotic Susceptibility of Escherichia coli and Salmonella spp. isolated from Milk of Zero grazed cows in Arusha city. African Journal of Microbiology Research, 10(46):1944-1951. |
|
|
Thames HC, Pruden A, James ER, Ray PP, Knowlton FK (2012). Excretion of antibiotic resistance genes by dairy calves fed milk replacers with varying doses of antibiotics. Frontiers in Microbiology, 3(139). |
|
|
Thompson-crispi K, Atalla H, Miglior F, Mallard AB (2014). Bovine mastitis: frontier in immunogenetics. Frontiers in Immunology 5(493). |
|
|
Van Soest PJ, Robertson JB, Lewis BA (1991). Methods for dietary fiber, neutral detergent fiber, and nonstarch polysaccharides in relation to animal nutrition. Journal of Dairy Science, 74(10):3583-3597. |
|
|
Wang Y, Ametaj NB, Ambrose JD, Ganzle GM (2013). Characterization of the bacterial microbiota of the vagina of dairy cows and isolation of pediocin-producing Pedococcus acidi lactici. BMC Microbiology, 13(19):1-11. |
|
|
Wittun ET, Mollenkopf FD, Daniels BJ, Parkinson EA, Mathews LJ, Fry RP, Abley JM, Gebreyes AW (2010). CTX-M-type-extended-spectrum-beta-lactamases present in Escherichia coli from the feces of cattle in Ohio, United States. Foodborne Pathogens and Disease, 7(12). |
|
|
Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aerustrup MF, Larsen VM (2012). Identification of acquired antimicrobial resistance genes. Journal of Antimicrobial Chemotherapy, 67:2640-2644. |
|
|
Zhang S, Gu J, Wang C, Wang P, Jiao S, He Z, Han B (2015). Characterization of antibiotics and antibiotic resistance genes on an ecological farm system. Journal of Chemistry, Article ID 526143, 8 p. |
|
|
Zhu Z (2016). Dynamics of rumen bacterial and archaeal communities in dairy cows over different lactation cycle stages. Ph.D. thesis. Aarhus University. |
|
Copyright © 2024 Author(s) retain the copyright of this article.
This article is published under the terms of the Creative Commons Attribution License 4.0
