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Dissecting microbial communities and resistomes for interconnected people, soil, and livestock

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  • Ikhimiukor OO, Odih EE, Donado-Godoy P, Okeke IN. A bottom-up view of antimicrobial resistance transmission in growing international locations. Nat Microbiol. 2022;7:757–65.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Donado-Godoy P, Gardner I, Byrne BA, Leon M, Perez-Gutierrez E, Ovalle MV, et al. Prevalence, threat elements, and antimicrobial resistance profiles of Salmonella from business broiler farms in two necessary poultry-producing areas of Colombia. J Meals Prot. 2012;75:874–83.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Van Boeckel TP, Brower C, Gilbert M, Grenfell BT, Levin SA, Robinson TP, et al. World tendencies in antimicrobial use in meals animals. Proc Natl Acad Sci USA. 2015;112:5649–54.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Roth N, Käsbohrer A, Mayrhofer S, Zitz U, Hofacre C, Domig KJ. The appliance of antibiotics in broiler manufacturing and the ensuing antibiotic resistance in Escherichia coli: a worldwide overview. Poult Sci. 2019;98:1791–804.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Thorp B. The poultry trade. In: Poultry well being: a information for professionals. CABI, Nosworthy Manner, Wallingford, Oxfordshire OX10 8DE; 2021. p. 25.

  • Meals and Agriculture Group of the United Nations. FAOSTAT (Meals Stability sheets and Inhabitants knowledge) – Crops and livestock merchandise. 2021. https://www.fao.org/faostat/en/knowledge/QCL.

  • Ritchie H, Roser M. Meat and seafood manufacturing & consumption. 2019. https://ourworldindata.org/meat-and-seafood-production-consumption.

  • Bruinsma J. World agriculture: in the direction of 2015/2030: an FAO perspective. London: Earthscan; 2003.

  • Hedman HD, Vasco KA, Zhang L. A evaluate of antimicrobial resistance in poultry farming inside low-resource settings. Animals. 2020;10:1264.

    PubMed Central 
    Article 

    Google Scholar 

  • Manyi-Loh C, Mamphweli S, Meyer E, Okoh A. Antibiotic use in agriculture and its consequential resistance in environmental sources: potential public well being implications. Molecules. 2018;23:795.

    PubMed Central 
    Article 

    Google Scholar 

  • Hu Y, Cheng H, Tao S. Environmental and human well being challenges of commercial livestock and poultry farming in China and their mitigation. Environ Int. 2017;107:111–30.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Looft T, Johnson TA, Allen HK, Bayles DO, Alt DP, Stedtfeld RD, et al. In-feed antibiotic results on the swine intestinal microbiome. Proc Natl Acad Sci USA. 2012;109:1691–6.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zhou Y, Li Y, Zhang L, Wu Z, Huang Y, Yan H, et al. Antibiotic administration routes and oral publicity to antibiotic resistant micro organism as key drivers for intestine microbiota disruption and resistome in poultry. Entrance Microbiol. 2020;11:1319.

  • Xiong W, Wang Y, Solar Y, Ma L, Zeng Q, Jiang X, et al. Antibiotic-mediated modifications within the fecal microbiome of broiler chickens outline the incidence of antibiotic resistance genes. Microbiome. 2018;6:34.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Shreiner AB, Kao JY, Younger VB. The intestine microbiome in well being and in illness. Curr Opin Gastroenterol. 2015;31:69–75.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wang Y, Hu Y, Cao J, Bi Y, Lv N, Liu F, et al. Antibiotic resistance gene reservoir in reside poultry markets. J Infect. 2019;78:445–53.

    PubMed 
    Article 

    Google Scholar 

  • Hu Y, Yang X, Qin J, Lu N, Cheng G, Wu N, et al. Metagenome-wide evaluation of antibiotic resistance genes in a big cohort of human intestine microbiota. Nat Commun. 2013;4:1–7.

    CAS 
    Article 

    Google Scholar 

  • Hu Y, Gao GF, Zhu B. The antibiotic resistome: gene circulate in environments, animals and human beings. Entrance Med. 2017;11:161–8.

    PubMed 
    Article 

    Google Scholar 

  • Van den Bogaard A, Willems R, London N, Prime J, Stobberingh E. Antibiotic resistance of faecal enterococci in poultry, poultry farmers and poultry slaughterers. J Antimicrob Chemother. 2002;49:497–505.

    PubMed 
    Article 

    Google Scholar 

  • Van den Bogaard AE, London N, Driessen C, Stobberingh EE. Antibiotic resistance of faecal Escherichia coli in poultry, poultry farmers and poultry slaughterers. J Antimicrob Chemother. 2001;47:763–71.

    PubMed 
    Article 

    Google Scholar 

  • Van Gompel L, Dohmen W, Luiken RE, Bouwknegt M, Heres L, Van Heijnsbergen E, et al. Occupational publicity and carriage of antimicrobial resistance genes (tetW, ermB) in pig slaughterhouse staff. Ann Work Expo Well being. 2020;64:125–37.

    PubMed 
    Article 

    Google Scholar 

  • Van Gompel L, Luiken RE, Hansen RB, Munk P, Bouwknegt M, Heres L, et al. Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse staff: a metagenome-wide cross-sectional examine. Environ Int. 2020;143:105939.

    PubMed 
    Article 

    Google Scholar 

  • Ding D, Zhu J, Gao Y, Yang F, Ma Y, Cheng X, et al. Impact of cattle farm publicity on oropharyngeal and intestine microbial communities and antibiotic resistance genes in staff. Sci Whole Environ. 2022;806:150685.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Peng Z, Maciel-Guerra A, Baker M, Zhang X, Hu Y, Wang W, et al. Entire-genome sequencing and gene sharing community evaluation powered by machine studying identifies antibiotic resistance sharing between animals, people and atmosphere in livestock farming. PLoS Comput Biol. 2022;18:e1010018.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Solar J, Liao X-P, D’Souza AW, Boolchandani M, Li S-H, Cheng Ok, et al. Environmental reworking of human intestine microbiota and antibiotic resistome in livestock farms. Nat Commun. 2020;11:1427.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Kluytmans JAJW, Overdevest ITMA, Willemsen I, Kluytmans-van den Bergh MFQ, van der Zwaluw Ok, Heck M, et al. Prolonged-spectrum β-lactamase–producing Escherichia coli From retail rooster meat and people: comparability of strains, plasmids, resistance genes, and virulence elements. Clin Infect Dis. 2012;56:478–87.

    PubMed 
    Article 

    Google Scholar 

  • Voets GM, Fluit AC, Scharringa J, Schapendonk C, van den Munckhof T. Leverstein-van Corridor MA, et al. Equivalent plasmid AmpC beta-lactamase genes and plasmid varieties in E. coli isolates from sufferers and poultry meat within the Netherlands. Int J Meals Microbiol. 2013;167:359–62.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular organic examine. Lancet Infect Dis. 2016;16:161–8.

    PubMed 
    Article 

    Google Scholar 

  • Ludden C, Raven KE, Jamrozy D, Gouliouris T, Blane B, Coll F, et al. One well being genomic surveillance of Escherichia coli demonstrates distinct lineages and cellular genetic components in isolates from people versus livestock. mBio. 2019;10:e02693–18.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Thorpe H, Booton R, Kallonen T, Gibbon MJ, Couto N, Passet V, et al. One well being or three? Transmission modelling of Klebsiella isolates reveals ecological boundaries to transmission between people, animals and the atmosphere. 2021. https://www.biorxiv.org/content material/10.1101/2021.08.05.455249v1.

  • O’Neill J. Tackling drug-resistant infections globally: remaining report and proposals. The evaluate on antimicrobial resistance. 2016. http://amr-review.org/websites/default/information/160525_Finalpercent20paper_withpercent20cover.pdf (accessed Sept, 2022).

  • Ko KKK, Chng KR, Nagarajan N. Metagenomics-enabled microbial surveillance. Nat Microbiol. 2022;7:486–96.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Hyun JC, Kavvas ES, Monk JM, Palsson BO. Machine studying with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. PLoS Comput Biol. 2020;16:e1007608.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Kavvas ES, Catoiu E, Mih N, Yurkovich JT, Seif Y, Dillon N, et al. Machine studying and structural evaluation of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nat Commun. 2018;9:4306.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Pearcy N, Hu Y, Baker M, Maciel-Guerra A, Xue N, Wang W, et al. Genome-scale metabolic fashions and machine Studying reveal genetic determinants of antibiotic resistance in Escherichia coli and unravel the underlying metabolic adaptation mechanisms. mSystems. 2021;6:e00913–20.

    CAS 
    PubMed Central 
    Article 

    Google Scholar 

  • Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, et al. Prediction of antimicrobial resistance based mostly on whole-genome sequencing and machine studying. Bioinformatics. 2021;38:325–34.

    PubMed Central 
    Article 

    Google Scholar 

  • Wang W, Baker M, Hu Y, Xu J, Yang D, Maciel-Guerra A, et al. Entire-genome sequencing and machine studying evaluation of Staphylococcus aureus from a number of heterogeneous sources in China reveals widespread genetic traits of antimicrobial resistance. mSystems. 2021;6:e01185–20.

    PubMed Central 
    Article 

    Google Scholar 

  • Hendriksen RS, Bortolaia V, Tate H, Tyson GH, Aarestrup FM, McDermott PF. Utilizing genomics to trace world antimicrobial resistance. Public Well being Entrance. 2019;7:242.

  • Schürch AC, van Schaik W. Challenges and alternatives for whole-genome sequencing–based mostly surveillance of antibiotic resistance. Ann N Y Acad Sci. 2017;1388:108–20.

    PubMed 
    Article 

    Google Scholar 

  • Kim D-W, Cha C-J. Antibiotic resistome from the One-Well being perspective: understanding and controlling antimicrobial resistance transmission. Exp Mol Med. 2021;53:301–9.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hickman RA, Leangapichart T, Lunha Ok, Jiwakanon J, Angkititrakul S, Magnusson U, et al. Exploring the antibiotic resistance burden in livestock, livestock handlers and their non-livestock dealing with contacts: a One Well being perspective. Entrance Microbiol. 2021;12:651461.

  • Perry JA, Westman EL, Wright GD. The antibiotic resistome: what’s new? Curr Opin Microbiol. 2014;21:45–50.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Hu Y, Yang X, Li J, Lv N, Liu F, Wu J, et al. The bacterial cellular resistome switch community connecting the animal and human microbiomes. Appl Environ Microbiol. 2016;82:6672–81.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zhang A-N, Gaston JM, Dai CL, Zhao S, Poyet M, Groussin M, et al. An omics-based framework for assessing the well being threat of antimicrobial resistance genes. Nat Commun. 2021;12:4765.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Arevalillo JM, Sztein MB, Kotloff KL, Levine MM, Simon JK. Identification of immune correlates of safety in Shigella an infection by utility of machine studying. J Biomed Inf. 2017;74:1–9.

    Article 

    Google Scholar 

  • Katagiri M, Kuroda M, Sekizuka T, Nakada N, Ito Y, Otsuka M, et al. Complete genomic survey of antimicrobial-resistance micro organism within the sewage tank alternative with hospital relocation. Infect Drug Resist. 2021;14:5563–74.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Kutilova I, Medvecky M, Leekitcharoenphon P, Munk P, Masarikova M, Davidova-Gerzova L, et al. Prolonged-spectrum beta-lactamase-producing Escherichia coli and antimicrobial resistance in municipal and hospital wastewaters in Czech Republic: Tradition-based and metagenomic approaches. Environ Res. 2021;193:110487.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Cheng J, Hu H, Kang Y, Chen W, Fang W, Wang Ok, et al. Identification of pathogens in culture-negative infective endocarditis circumstances by metagenomic evaluation. Ann Clin Microbiol Antimicrob. 2018;17:43.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Sanabria AM, Janice J, Hjerde E, Simonsen GS, Hanssen A-M. Shotgun-metagenomics based mostly prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood tradition bottles. Sci Rep. 2021;11:20848.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Anjum MF, Schmitt H, Börjesson S, Berendonk TU, Donner E, Stehling EG, et al. The potential of utilizing E. coli as an indicator for the surveillance of antimicrobial resistance (AMR) within the atmosphere. Curr Opin Microbiol. 2021;64:152–8.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • European Meals Security Authority, European Centre for Illness Prevention Management. The European Union Abstract Report on Antimicrobial Resistance in zoonotic and indicator micro organism from people, animals and meals in 2018/2019. EFSA J. 2021;19:e06490.

    Google Scholar 

  • Card RM, Cawthraw SA, Nunez-Garcia J, Ellis RJ, Kay G, Pallen MJ, et al. An in vitro rooster intestine mannequin demonstrates switch of a multidrug resistance plasmid from Salmonella to Commensal Escherichia coli. mBio 2017;8:e00777–17.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Gargiullo L, Del Chierico F, D’Argenio P, Putignani L. Intestine microbiota modulation for multidrug-resistant organism decolonization: current and future views. Entrance Microbiol. 2019;10:1704.

  • Wallace MJ, Fishbein SRS, Dantas G. Antimicrobial resistance in enteric micro organism: present state and next-generation options. Intestine Microbes. 2020;12:1799654.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • European Meals Security Authority, European Centre for Illness Prevention Management. The European Union Abstract Report on Antimicrobial Resistance in zoonotic and indicator micro organism from people, animals and meals in 2017/2018. EFSA J. 2020;18:e06007.

    Google Scholar 

  • Allen GC, Flores-Vergara MA, Krasynanski S, Kumar S, Thompson WF. A modified protocol for fast DNA isolation from plant tissues utilizing cetyltrimethylammonium bromide. Nat Protoc. 2006;1:2320–5.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Glendinning L, Stewart RD, Pallen MJ, Watson KA, Watson M. Meeting of a whole lot of novel bacterial genomes from the rooster caecum. Genome Biol. 2020;21:1–16.

    Article 

    Google Scholar 

  • Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial group profiling utilizing distinctive clade-specific marker genes. Nat Strategies. 2012;9:811–4.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Langmead B, Salzberg SL. Quick gapped-read alignment with Bowtie 2. Nat Strategies. 2012;9:357–9.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Dixon P. VEGAN, A bundle of R capabilities for group ecology. J Veg Sci. 2003;14:927–30.

    Article 

    Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Primary native alignment search device. J Mol Biol. 1990;215:403–10.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Lee Ok, Kim DW, Lee DH, Kim YS, Bu JH, Cha JH, et al. Cellular resistome of human intestine and pathogen drives anthropogenic bloom of antibiotic resistance. Microbiome. 2020;8:2.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Li D, Liu CM, Luo R, Sadakane Ok, Lam TW. MEGAHIT: an ultra-fast single-node answer for giant and sophisticated metagenomics meeting by way of succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Che Y, Yang Y, Xu X, Břinda Ok, Polz MF, Hanage WP, et al. Conjugative plasmids work together with insertion sequences to form the horizontal switch of antimicrobial resistance genes. Proc Natl Acad Sci USA. 2021;118:e2008731118.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hua X, Liang Q, Deng M, He J, Wang M, Hong W, et al. BacAnt: a mixture annotation server for bacterial DNA sequences to establish antibiotic resistance genes, integrons, and transposable components. Entrance Microbiol. 2021;12:649969.

  • Ellabaan MMH, Munck C, Porse A, Imamovic L, Sommer MOA. Forecasting the dissemination of antibiotic resistance genes throughout bacterial genomes. Nat Commun. 2021;12:2435.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. Microbial strain-level inhabitants construction and genetic range from metagenomes. Genome Res. 2017;27:626–38.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, Von Haeseler A, et al. IQ-TREE 2: New fashions and environment friendly strategies for phylogenetic inference within the genomic period. Mol Biol Evol. 2020;37:1530–4.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Seemann T. Prokka: fast prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Web page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. Roary: fast large-scale prokaryote pan genome evaluation. Bioinformatics. 2015;31:3691–3.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: a web-based device for phylogenetic tree show and annotation. Nucleic Acids Res. 2021;49:W293–W296.

  • Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, et al. Scikit-learn: machine studying in Python. J Mach Be taught Res. 2011;12:2825–30.

    Google Scholar 

  • Chawla NV, Bowyer KW, Corridor LO, Kegelmeyer WP. SMOTE: artificial minority over-sampling approach. J Artif Intell Res. 2002;16:321–57.

    Article 

    Google Scholar 

  • Perneger TV. What’s fallacious with Bonferroni changes. BMJ. 1998;316:1236–8.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hagberg A, Swart P, Chult DS. Exploring community construction, dynamics, and performance utilizing NetworkX. Los Alamos, NM, United States: Los Alamos Nationwide Lab. (LANL); 2008.

  • Cawley GC, Talbot NL. On over-fitting in mannequin choice and subsequent choice bias in efficiency analysis. J Mach Be taught Res. 2010;11:2079–107.

    Google Scholar 

  • Wainer J, Cawley G. Empirical analysis of resampling procedures for optimising SVM hyperparameters. J Mach Be taught Res. 2017;18:1–35.

    Google Scholar 

  • Munk P, Knudsen BE, Lukjancenko O, Duarte ASR, Van Gompel L, Luiken RE, et al. Abundance and variety of the faecal resistome in slaughter pigs and broilers in 9 European international locations. Nat Microbiol. 2018;3:898–908.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Chen C, Zhou Y, Fu H, Xiong X, Fang S, Jiang H, et al. Expanded catalog of microbial genes and metagenome-assembled genomes from the pig intestine microbiome. Nat Commun. 2021;12:1106.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Stewart RD, Auffret MD, Warr A, Walker AW, Roehe R, Watson M. Compendium of 4941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. Nat Biotechnol. 2019;37:953–61.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA, Beatson SA, et al. Antimicrobial resistance in ESKAPE pathogens. Clin Microbiol Rev. 2020;33:e00181–19.

  • Beleites C, Neugebauer U, Bocklitz T, Krafft C, Popp J. Pattern dimension planning for classification fashions. Anal Chim Acta. 2013;760:25–33.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Mosites E, Sammons M, Otiang E, Eng A, Noecker C, Manor O, et al. Microbiome sharing between kids, livestock and family surfaces in western Kenya. PLoS ONE. 2017;12:e0171017.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Bubier JA, Chesler EJ, Weinstock GM. Host genetic management of intestine microbiome composition. Mamm Genome. 2021;32:263–81.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Rinninella E, Raoul P, Cintoni M, Franceschi F, Miggiano GAD, Gasbarrini A, et al. What’s the wholesome intestine microbiota composition? A altering ecosystem throughout age, atmosphere, weight loss plan, and illnesses. Microorganisms. 2019;7:14.

    CAS 
    PubMed Central 
    Article 

    Google Scholar 

  • Rychlik I. Composition and performance of rooster intestine microbiota. Animals. 2020;10:103.

    PubMed Central 
    Article 

    Google Scholar 

  • Moor J, Wüthrich T, Aebi S, Mostacci N, Overesch G, Oppliger A, et al. Affect of pig farming on human intestine microbiota: function of airborne microbial communities. Intestine Microbes. 2021;13:1–13.

    PubMed 
    Article 

    Google Scholar 

  • Wang Y, Lyu N, Liu F, Liu WJ, Bi Y, Zhang Z, et al. Extra diversified antibiotic resistance genes in chickens and staff of the reside poultry markets. Environ Int. 2021;153:106534.

    PubMed 
    Article 

    Google Scholar 

  • Mazhar SH, Li X, Rashid A, Su J, Xu J, Brejnrod AD, et al. Co-selection of antibiotic resistance genes, and cellular genetic components within the presence of heavy metals in poultry farm environments. Sci Whole Environ. 2021;755:142702.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Yang J, Tong C, Xiao D, Xie L, Zhao R, Huo Z, et al. Metagenomic insights into rooster intestine antibiotic resistomes and microbiomes. Microbiol Spectr. 2022;10:e01907–21.

    PubMed Central 

    Google Scholar 

  • Andersen H, Connolly N, Bangar H, Staat M, Mortensen J, Deburger B, et al. Use of shotgun metagenome sequencing to detect fecal colonization with multidrug-resistant micro organism in kids. J Clin Microbiol. 2016;54:1804–13.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Fitzpatrick D, Walsh F. Antibiotic resistance genes throughout all kinds of metagenomes. FEMS Microbiol Ecol. 2016;92:1–8.

  • Zhou Y, Wylie KM, El Feghaly RE, Mihindukulasuriya KA, Elward A, Haslam DB, et al. Metagenomic method for identification of the pathogens related to diarrhea in stool specimens. J Clin Microbiol. 2016;54:368–75.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Pasolli E, Truong DT, Malik F, Waldron L, Segata N. Machine studying meta-analysis of enormous metagenomic datasets: instruments and organic insights. PLoS Comput Biol. 2016;12:e1004977.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Khanna S, Montassier E, Schmidt B, Patel R, Knights D, Pardi DS, et al. Intestine microbiome predictors of therapy response and recurrence in major Clostridium difficile an infection. Aliment Pharmacol Ther. 2016;44:715–27.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, et al. Attribute male urine microbiomes affiliate with asymptomatic sexually transmitted an infection. PLoS ONE. 2010;5:e14116.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Van Rensburg JJ, Lin H, Gao X, Toh E, Fortney KR, Ellinger S, et al. The human pores and skin microbiome associates with the end result of and is influenced by bacterial an infection. mBio. 2015;6:e01315–15.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Penders J, Stobberingh E, Savelkoul P, Wolffs P. The human microbiome as a reservoir of antimicrobial resistance. Entrance Microbiol. 2013;4:87.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Li X, Stokholm J, Brejnrod A, Vestergaard GA, Russel J, Trivedi U, et al. The toddler intestine resistome associates with E. coli, environmental exposures, intestine microbiome maturity, and asthma-associated bacterial composition. Cell Host Microbe. 2021;29:975–87.e4.

  • Stanley D, Geier MS, Hughes RJ, Denman SE, Moore RJ. Extremely variable microbiota improvement within the rooster gastrointestinal tract. PLoS ONE. 2014;8:e84290.

    Article 

    Google Scholar 

  • Gautam R, Bani-Yaghoub M, Neill WH, Döpfer D, Kaspar C, Ivanek R. Modeling the impact of seasonal variation in ambient temperature on the transmission dynamics of a pathogen with a free-living stage: instance of Escherichia coli O157:H7 in a dairy herd. Prev Vet Med. 2011;102:10–21.

    PubMed 
    Article 

    Google Scholar 

  • Oakley BB, Vasconcelos EJR, Diniz P, Calloway KN, Richardson E, Meinersmann RJ, et al. The cecal microbiome of economic broiler chickens varies considerably by season. Poult Sci. 2018;97:3635–44.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Wang X, Feng J, Zhang M, Li X, Ma D, Chang S. Results of excessive ambient temperature on the group construction and composition of ileal microbiome of broilers. Poult Sci. 2018;97:2153–8.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Yang Y, Liu G, Ye C, Liu W. Bacterial group and local weather change implication affected the range and abundance of antibiotic resistance genes in wetlands on the Qinghai-Tibetan Plateau. J Hazard Mater. 2019;361:283–93.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • MacFadden DR, McGough SF, Fisman D, Santillana M, Brownstein JS. Antibiotic resistance will increase with native temperature. Nat Clim Change. 2018;8:510–4.

    CAS 
    Article 

    Google Scholar 

  • Fuchsman CA, Collins RE, Rocap G, Brazelton WJ. Impact of the atmosphere on horizontal gene switch between micro organism and archaea. PeerJ. 2017;5:e3865.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Islam MM, Hofstra N, Islam MA. The influence of environmental variables on faecal indicator micro organism within the Betna river basin, Bangladesh. Environ. Environ Course of. 2017;4:319–32.

    Article 

    Google Scholar 

  • Hanon J-B, Jaspers S, Butaye P, Wattiau P, Méroc E, Aerts M, et al. A pattern evaluation of antimicrobial resistance in commensal Escherichia coli from a number of livestock species in Belgium (2011–2014). Prev Vet Med. 2015;122:443–52.

    PubMed 
    Article 

    Google Scholar 

  • Hesp A, Veldman Ok, van der Goot J, Mevius D, van Schaik G. Monitoring antimicrobial resistance tendencies in commensal Escherichia coli from livestock, the Netherlands, 1998 to 2016. Eur Surveill. 2019;24:1800438.

    Article 

    Google Scholar 

  • Mathai E, Chandy S, Thomas Ok, Antoniswamy B, Joseph I, Mathai M, et al. Antimicrobial resistance surveillance amongst commensal Escherichia coli in rural and concrete areas in Southern India. Trop Med Int Well being. 2008;13:41–5.

    PubMed 
    Article 

    Google Scholar 

  • Teshager T, Herrero IA, Porrero MC, Garde J, Moreno MA, Domı́nguez L. Surveillance of antimicrobial resistance in Escherichia coli strains remoted from pigs at Spanish slaughterhouses. Int J Antimicrob Brokers. 2000;15:137–42.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Laird TJ, Jordan D, Lee ZZ, O’Dea M, Stegger M, Truswell A, et al. Variety detected in commensals at host and farm stage reveals implications for nationwide antimicrobial resistance surveillance programmes. J Antimicrob Chemother. 2022;77:400–8.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Munk P, Andersen VD, de Knegt L, Jensen MS, Knudsen BE, Lukjancenko O, et al. A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds. J Antimicrob Chemother. 2017;72:385–92.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • EFSA Panel on Organic Hazards, Koutsoumanis Ok, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, et al. Entire genome sequencing and metagenomics for outbreak investigation, supply attribution and threat evaluation of meals‐borne microorganisms. EFSA J. 2019;17:e05898.

    Google Scholar 

  • Duarte ASR, Stärk KDC, Munk P, Leekitcharoenphon P, Bossers A, Luiken R, et al. Addressing studying wants on using metagenomics in antimicrobial resistance surveillance. Public Well being Entrance. 2020;8:38.

  • Rice EW, Wang P, Smith AL, Stadler LB. Figuring out hosts of antibiotic resistance genes: a evaluate of methodological advances. Environ Sci Technol Lett. 2020;7:282–91.

    CAS 
    Article 

    Google Scholar 

  • Gil-Gil T, Ochoa-Sánchez LE, Baquero F, Martínez JL. Antibiotic resistance: time of synthesis in a post-genomic age. Comput Struct. Comput Struct Biotechnol J. 2021;19:3110–24.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Rowe E, Dawkins MS, Gebhardt-Henrich SG. A scientific evaluate of precision livestock farming within the poultry sector: Is expertise focussed on enhancing chicken welfare? Animals. 2019;9:614.

    PubMed Central 
    Article 

    Google Scholar 

  • Li N, Ren Z, Li D, Zeng L. Evaluate: automated methods for monitoring the behaviour and welfare of broilers and laying hens: in the direction of the objective of precision livestock farming. Animal. 2020;14:617–25.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Okinda C, Nyalala I, Korohou T, Okinda C, Wang J, Achieng T, et al. A evaluate on pc imaginative and prescient methods in monitoring of poultry: a welfare perspective. Artif Intell Agric. 2020;4:184–208.

    Google Scholar 

  • Astill J, Dara RA, Fraser EDG, Sharif S Detecting and predicting rising illness in poultry with the implementation of latest applied sciences and large knowledge: a deal with avian influenza virus. Entrance Vet Sci. 2018;5:263.

  • Ahmed G, Malick RAS, Akhunzada A, Zahid S, Sagri MR, Gani A. An method in the direction of IoT-based predictive service for early detection of illnesses in poultry chickens. Sustainability. 2021;13:13396.

    Article 

    Google Scholar 

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