{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T21:07:04Z","timestamp":1763500024969,"version":"build-2065373602"},"reference-count":43,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2025,3,14]],"date-time":"2025-03-14T00:00:00Z","timestamp":1741910400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Bintuan Science and Technology Program Corps","award":["2020AB015","RCZK201902","2022YFD1800702","CARS36"],"award-info":[{"award-number":["2020AB015","RCZK201902","2022YFD1800702","CARS36"]}]},{"name":"Research Initiation Program for High-level Talents at Shihezi University","award":["2020AB015","RCZK201902","2022YFD1800702","CARS36"],"award-info":[{"award-number":["2020AB015","RCZK201902","2022YFD1800702","CARS36"]}]},{"name":"National Key Research and Development Program of China","award":["2020AB015","RCZK201902","2022YFD1800702","CARS36"],"award-info":[{"award-number":["2020AB015","RCZK201902","2022YFD1800702","CARS36"]}]},{"name":"earmarked fund for CARS","award":["2020AB015","RCZK201902","2022YFD1800702","CARS36"],"award-info":[{"award-number":["2020AB015","RCZK201902","2022YFD1800702","CARS36"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Veterinary Sciences"],"abstract":"<jats:p>Nontuberculous mycobacteria (NTM) are environmental organisms that can cause opportunistic infections in humans and animals. Mycobacterium abscessus (Mab) is a rapidly growing Mycobacterium known for its resistance to multiple antibiotics and ability to cause respiratory, skin, and mucosal infections. Understanding the distribution and prevalence of NTM, particularly Mab, in cattle farms and slaughterhouses is crucial for developing effective prevention and control measures. We collected environmental swabs from various surfaces (e.g., feed troughs, sinks, walls, floors, feces, and padding) in cattle farms and slaughterhouses across multiple provinces. High-throughput sequencing technology was utilized to analyze the 16S rDNA V3\u2013V4 region of bacterial DNA extracted from the samples, and qPCR methods were employed to detect and quantify Mycobacterium abscessus in the collected samples. Bioinformatics analysis was performed to identify and classify the NTM species present in the samples. This study compared the abundance and diversity of NTM in different environments and assessed the potential zoonotic risk. A total of 1648 environmental swabs were collected from cattle farms and slaughterhouses in 12 provinces of China in 2023, of which 12 samples tested positive for Mab qPCR detection, yielding a detection rate of 0.73% (12\/1648). Among them, the detection rate of environmental samples from cattle farms and slaughterhouses was 0.42% (3\/720) and 0.87% (9\/928), respectively. This study provides valuable information on the epidemiology of NTM in cattle farms and slaughterhouses, contributing to developing effective strategies for preventing and controlling NTM infections. It also enhances our understanding of the zoonotic potential of Mycobacterium abscessus and other NTM species.<\/jats:p>","DOI":"10.3390\/vetsci12030275","type":"journal-article","created":{"date-parts":[[2025,3,14]],"date-time":"2025-03-14T13:07:51Z","timestamp":1741957671000},"page":"275","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["High-Throughput Sequencing of Nontuberculous Mycobacterial Flora and Mycobacterium abscessus in Cattle"],"prefix":"10.3390","volume":"12","author":[{"given":"Siqi","family":"Chen","sequence":"first","affiliation":[{"name":"College of Animal Science and Technology, Shihezi University, Shihezi 832003, China"},{"name":"Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4039-9143","authenticated-orcid":false,"given":"Mengda","family":"Liu","sequence":"additional","affiliation":[{"name":"Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Li","sequence":"additional","affiliation":[{"name":"Xinjiang Production and Construction Corps Animal Husbandry and Veterinary Station, Urumqi 830063, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiarui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Xinjiang Production and Construction Corps Animal Husbandry and Veterinary Station, Urumqi 830063, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanfang","family":"Li","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Shihezi University, Shihezi 832003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Liang","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Shihezi University, Shihezi 832003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoxu","family":"Fan","sequence":"additional","affiliation":[{"name":"Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao 266032, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2649-4144","authenticated-orcid":false,"given":"Yonggang","family":"Qu","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Shihezi University, Shihezi 832003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Fedrizzi, T., Meehan, C.J., Grottola, A., Giacobazzi, E., Serpini, G.F., Tagliazucchi, S., Fabio, A., Bettua, C., Bertorelli, R., and Sanctis, V.D. (2017). Genomic characterization of nontuberculous Mycobacteria. Sci. Rep., 7.","DOI":"10.1038\/srep45258"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1038\/s41579-020-0331-1","article-title":"Non-tuberculous mycobacteria and the rise of Mycobacterium abscessus","volume":"18","author":"Johansen","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2000792","DOI":"10.1002\/smtd.202000792","article-title":"High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings","volume":"5","author":"Li","year":"2020","journal-title":"Small Methods"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.ccm.2014.10.002","article-title":"Epidemiology of Human Pulmonary Infection with Nontuberculous Mycobacteria","volume":"36","author":"Prevots","year":"2015","journal-title":"Clin. Chest Med."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Degiacomi, G., Sammartino, J.C., Chiarelli, L.R., Riabova, O., Makarov, V., and Pasca, M.R. (2019). Mycobacterium abscessus, an emerging and worrisome pathogen among cystic fibrosis patients. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20235868"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Lopeman, R.C., Harrison, J., Desai, M., and Cox, J.A.G. (2019). Mycobacterium abscessus: Environmental bacterium turned clinical nightmare. Microorganisms, 7.","DOI":"10.20944\/preprints201901.0273.v1"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1638","DOI":"10.3201\/2109.141634","article-title":"Mycobacterium abscessus complex infections in humans","volume":"21","author":"Lee","year":"2015","journal-title":"Emerg. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4471","DOI":"10.1099\/ijsem.0.001376","article-title":"Emended description of Mycobacterium abscessus, Mycobacterium abscessus subsp. abscessus and Mycobacterium abscessus subsp. bolletii and designation of Mycobacterium abscessus subsp. massiliense comb. nov","volume":"66","author":"Tortoli","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Degiacomi, G., Chiarelli, L.R., Recchia, D., Petricci, E., Gianibbi, B., Fiscarelli, E.V., Fattorini, L., Manetti, F., and Pasca, M.R. (2021). The Antimalarial Mefloquine Shows Activity against Mycobacterium abscessus, Inhibiting Mycolic Acid Metabolism. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22168533"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1111\/jpc.14427","article-title":"Pulmonary Mycobacterium abscessus complex in children with cystic fibrosis: A practical management guideline","volume":"55","author":"Andrew","year":"2019","journal-title":"J. Paediatr. Child Health"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1080\/14787210.2016.1238304","article-title":"Infections caused by Mycobacterium abscessus: Epidemiology, diagnostic tools and treatment","volume":"14","author":"Mougari","year":"2016","journal-title":"Expert. Rev. Anti-Infect. Ther."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/S2213-2600(16)30444-1","article-title":"Multidrug-resistant Mycobacterium abscessus threatens patients with cystic fibrosis","volume":"5","author":"Dorn","year":"2017","journal-title":"Lancet Respir. Med."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Honda, J.R., Virdi, R., and Chan, E.D. (2018). Global environmental nontuberculous Mycobacteria and their contemporaneous man-made and natural niches. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.02029"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Gcebe, N., and Hlokwe, T.M. (2017). Non-tuberculous mycobacteria in South African wildlife: Neglected pathogens and potential impediments for bovine tuberculosis diagnosis. Front. Cell. Infect. Microbiol., 7.","DOI":"10.3389\/fcimb.2017.00015"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/s10096-024-04981-x","article-title":"Comparison of molecular testing methods for diagnosing non-tuberculous mycobacterial infections","volume":"44","author":"Wang","year":"2024","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_16","unstructured":"International Office of Epizootics Biological Standards Commission (2023). Manual of Diagnostic Tests and Vaccines for Terrestrial Animals, Office International des \u00c9pizooties. [12th ed.]."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Marras, S.A.E., Chen, L., Shashkina, E., Davidson, R.M., Strong, M., Daley, C.L., and Kreiswirth, B.N. (2021). A molecular-beacon-based multiplex real-Time PCR assay to distinguish Mycobacterium abscessus subspecies and determine macrolide susceptibility. J. Clin. Microbiol., 59.","DOI":"10.1128\/JCM.00455-21"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1017\/S0950268812003020","article-title":"Occurrence of non-tuberculous mycobacteria species in livestock from northern China and first isolation of Mycobacterium caprae","volume":"141","author":"Zeng","year":"2013","journal-title":"Epidemiol. Infect."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.prevetmed.2018.02.003","article-title":"Cross reactive immune responses in cattle arising from exposure to Mycobacterium bovis and non-tuberculous mycobacteria","volume":"152","author":"Jenkins","year":"2018","journal-title":"Prev. Vet. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1128\/CVI.00116-07","article-title":"Assessment of cross-reactivity between Mycobacterium bovis and M. kansasii ESAT-6 and CFP-10 at the T-Cell epitope level","volume":"14","author":"Vordermeier","year":"2007","journal-title":"Clin. Vaccine Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Bisognin, F., Ferraro, V., Sorella, F., Lombardi, G., Lazzarotto, T., and Monte, P.D. (2023). First isolation of Mycobacterium saskatchewanense from medical devices. Sci. Rep., 13.","DOI":"10.1038\/s41598-023-48974-w"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"926","DOI":"10.7589\/JWD-D-21-00156","article-title":"Systemic infection of Mycobacterium abscessus in a free-ranging wild Eurasian Eagle Owl (Bubo bubo)","volume":"58","author":"Kim","year":"2022","journal-title":"J. Wildl. Dis."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Rodr\u00edguez-Cerdeira, C., Hern\u00e1ndez-Castro, R., S\u00e1nchez-C\u00e1rdenas, C.D., Arenas, R., Meza-Robles, A., Toussaint-Caire, S., Atoche-Di\u00e9guez, C., and Mart\u00ednez-Herrera, E. (2022). Atypical Mycobacteriosis due to Mycobacterium abscessus subsp. massiliense: Our experince. Pathogens, 11.","DOI":"10.3390\/pathogens11121399"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"211","DOI":"10.3168\/jds.2020-18214","article-title":"Genotypic analysis of nontuberculous mycobacteria isolated from raw milk and human cases in Wisconsin","volume":"104","author":"Ali","year":"2021","journal-title":"J. Dairy Sci."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Soliman, N.S., Soliman, M.S., Khairat, S.M., Gad, M.A., Shawky, S., and Elkholy, A.A. (2024). Genetic diversities and drug resistance in Mycobacterium bovis isolates from zoonotic tuberculosis using whole genome sequencing. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10909-8"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1080\/23744235.2023.2276785","article-title":"The application of nanopore targeted sequencing for pathogen diagnosis in bronchoalveolar lavage fluid of patients with pneumonia: A prospective multicenter study","volume":"56","author":"Lin","year":"2024","journal-title":"Infect. Dis."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Huang, C., Huang, Y., Wang, Z., Lin, Y., Li, Y., Chen, Y., Chen, X., Zhang, C., Li, W., and Zhang, W. (2023). Multiplex PCR-based next generation sequencing as a novel, targeted and accurate molecular approach for periprosthetic joint infection diagnosis. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1181348"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"S231","DOI":"10.1093\/cid\/ciy693","article-title":"Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice","volume":"67","author":"Miao","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Choi, H., Kim, S.-Y., Lee, H., Jhun, B.W., Park, H.Y., Jeon, K., Kim, D.H., Huh, H.J., Ki, C.-S., and Lee, N.Y. (2017). Clinical Characteristics and Treatment Outcomes of Patients with Macrolide-Resistant Mycobacterium massiliense Lung Disease. Antimicrob. Agents Chemother., 61.","DOI":"10.1128\/AAC.02189-16"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2000535","DOI":"10.1183\/13993003.00535-2020","article-title":"Treatment of nontuberculous mycobacterial pulmonary disease: An official ATS\/ERS\/ESCMID\/IDSA clinical practice guideline","volume":"56","author":"Daley","year":"2020","journal-title":"Eur. Respir. J."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1016\/j.jiac.2018.07.021","article-title":"Efficacy and safety of intermittent maintenance therapy after successful treatment of Mycobacterium avium complex lung disease","volume":"25","author":"Asakura","year":"2019","journal-title":"J. Infect. Chemother."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Moon, S.M., Yoo, I.Y., Huh, H.J., Lee, N.Y., and Jhun, B.W. (2019). Intermittent Treatment with Azithromycin and Ethambutol for Noncavitary Mycobacterium avium Complex Pulmonary Disease. Antimicrob. Agents Chemother., 64.","DOI":"10.1128\/AAC.01787-19"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1007\/s11748-018-1029-4","article-title":"Outcomes and risk factors after adjuvant surgical treatments for Mycobacterium avium complex lung disease","volume":"67","author":"Yamada","year":"2019","journal-title":"Gen. Thorac. Cardiovasc. Surg."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.thorsurg.2018.09.011","article-title":"Surgical Treatment of Pulmonary Nontuberculous Mycobacterial Infections","volume":"29","author":"Mitchell","year":"2019","journal-title":"Thorac. Surg. Clin."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Lombard, J.E., Patton, E.A., Gibbons-Burgener, S.N., Klos, R.F., Tans-Kersten, J.L., Carlson, B.W., Keller, S.J., Pritschet, D.J., Rollo, S., and Dutcher, T.V. (2021). Human-to-Cattle Mycobacterium tuberculosis Complex Transmission in the United States. Front. Vet. Sci., 8.","DOI":"10.3389\/fvets.2021.691192"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e129","DOI":"10.1016\/j.ijid.2009.11.037","article-title":"Tracing the origins of Mycobacterium bovis tuberculosis in humans in the USA to cattle in Mexico using spoligotyping","volume":"14","author":"Rodwell","year":"2010","journal-title":"Int. J. Infect. Dis."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2393","DOI":"10.3201\/eid1712.101476","article-title":"Humans as source of Mycobacterium tuberculosis infection in cattle, Spain","volume":"17","author":"Romero","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1007\/s10393-012-0754-x","article-title":"Zoonotic transmission of tuberculosis between pastoralists and their livestock in South-East Ethiopia","volume":"9","author":"Gumi","year":"2012","journal-title":"EcoHealth"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Malama, S., Munyeme, M., Mwanza, S., and Muma, J.B. (2014). Isolation and characterization of non tuberculous mycobacteria from humans and animals in Namwala District of Zambia. BMC Res. Notes, 7.","DOI":"10.1186\/1756-0500-7-622"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1016\/j.tube.2005.08.005","article-title":"Bovine tuberculosis in India: Potential basis for zoonosis","volume":"85","author":"Prasad","year":"2005","journal-title":"Tuberculosis"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Adesokan, H.K., Akinseye, V.O., Streicher, E.M., Van Helden, P., Warren, R.M., and Cadmus, S.I. (2019). Reverse zoonotic tuberculosis transmission from an emerging Uganda I strain between pastoralists and cattle in South-Eastern Nigeria. BMC Vet. Res., 15.","DOI":"10.1186\/s12917-019-2185-1"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1016\/j.rvsc.2011.03.026","article-title":"Detection of Mycobacterium tuberculosis infection in dogs in a high-risk setting","volume":"92","author":"Parsons","year":"2012","journal-title":"Res. Vet. Sci."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1111\/j.1749-6632.2002.tb04388.x","article-title":"Mycobacterial isolations in captive elephants in the United States","volume":"969","author":"Payeur","year":"2002","journal-title":"Ann. N. Y. Acad. Sci."}],"container-title":["Veterinary Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-7381\/12\/3\/275\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:54:00Z","timestamp":1760028840000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-7381\/12\/3\/275"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,14]]},"references-count":43,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2025,3]]}},"alternative-id":["vetsci12030275"],"URL":"https:\/\/doi.org\/10.3390\/vetsci12030275","relation":{},"ISSN":["2306-7381"],"issn-type":[{"type":"electronic","value":"2306-7381"}],"subject":[],"published":{"date-parts":[[2025,3,14]]}}}