Page SW, Gautier P. Use of antimicrobial agents in livestock. OIE Rev Sci Tech. 2012;31:145–88.
Article
CAS
Google Scholar
Mehdi Y, Létourneau-Montminy MP, Gaucher ML, Chorfi Y, Suresh G, Rouissi T, et al. Use of antibiotics in broiler production: global impacts and alternatives. Anim Nutr. 2018;4:170–8.
Article
PubMed
PubMed Central
Google Scholar
Costa MC, Bessegatto JA, Alfieri AA, Weese JS, Filho JAB, Oba A. Different antibiotic growth promoters induce specific changes in the cecal microbiota membership of broiler chicken. PLoS One. 2017;12:1–13.
Google Scholar
Rodrigue DC, Tauxe RV, Rowe B. International increase in Salmonella enteritidis: a new pandemic? Epidemiol Infect. 1990;105:21–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mead PS, Slutsker L, Dietz V, McCaig LF, Bresee JS, Shapiro C, et al. Food-related illness and death in the United States. Emerg Infect Dis. 1999;5:607–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Randall LP, Cooles SW, Coldham NC, Stapleton KS, Piddock LJV, Woodward MJ. Modification of enrofloxacin treatment regimens for poultry experimentally infected with Salmonella enterica serovar typhimurium DT104 to minimize selection of resistance. Antimicrob Agents Chemother. 2006;50:4030–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nelson JM, Chiller TM, Powers JH, Angulo FJ. Fluoroquinolone-resistant Campylobacter species and the withdrawal of fluoroquinolones from use in poultry: a public health success story. Clin Infect Dis. 2007;44:977–80.
Article
CAS
PubMed
Google Scholar
Roth N, Käsbohrer A, Mayrhofer S, Zitz U, Hofacre C, Domig KJ. The application of antibiotics in broiler production and the resulting antibiotic resistance in Escherichia coli: a global overview. Poult Sci. 2019;98:1791–804.
Article
CAS
PubMed
Google Scholar
Mellata M. Human and avian extraintestinal pathogenic escherichia coli: infections, zoonotic risks, and antibiotic resistance trends. Foodborne Pathog Dis. 2013;10:916–32.
Article
PubMed
PubMed Central
Google Scholar
Cox G, Wright GD. Intrinsic antibiotic resistance: mechanisms, origins, challenges and solutions. Int J Med Microbiol. 2013;303(6–7):287–92.
Article
CAS
PubMed
Google Scholar
Chen MY, Lira F, Liang HQ, Wu RT, Duan JH, Liao XP, et al. Multilevel selection of bcrABDR-mediated bacitracin resistance in Enterococcus faecalis from chicken farms. Sci Rep. 2016;6:1–7. https://doi.org/10.1038/srep34895. Nature Publishing Group.
Article
CAS
Google Scholar
Bager F, Madsen M, Christensen J, Aarestrup FM. Avoparcin used as a growth promoter is associated with the occurrence of vancomycin-resistant Enterococcus faecium on Danish poultry and pig farms. Prev Vet Med. 1997;31:95–112.
Article
CAS
PubMed
Google Scholar
Barbosa TM, Levy SB. The impact of antibiotic use on resistance development and persistence. Drug Resist Updat. 2000;3:303–11.
Article
PubMed
Google Scholar
Hegde NV, Kariyawasam S, DebRoy C. Comparison of antimicrobial resistant genes in chicken gut microbiome grown on organic and conventional diet. Vet Anim Sci. 2016;1–2:9–14. https://doi.org/10.1016/j.vas.2016.07.001. Elsevier.
Article
PubMed
PubMed Central
Google Scholar
Castanon JIR. History of the use of antibiotic as growth promoters in European poultry feeds. Poult Sci. 2007;86(11):2466–71.
Article
CAS
PubMed
Google Scholar
Casewell M, Friis C, Marco E, McMullin P, Phillips I. The European ban on growth-promoting antibiotics and emerging consequences for human and animal health. J Antimicrob Chemother. 2003;52(2):159–61.
Article
CAS
PubMed
Google Scholar
Roca I, Akova M, Baquero F, Carlet J, Cavaleri M, Coenen S, et al. The global threat of antimicrobial resistance: science for intervention. New Microbes New Infect. 2015;6:22–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maron DF, Smith TJS, Nachman KE. Restrictions on antimicrobial use in food animal production: an international regulatory and economic survey. Global Health. 2013;9:48.
Article
PubMed
PubMed Central
Google Scholar
Lin J, Hunkapiller AA, Layton AC, Chang YJ, Robbins KR. Response of intestinal microbiota to antibiotic growth promoters in chickens. Foodborne Pathog Dis. 2013;10:331–7.
Article
CAS
PubMed
Google Scholar
Xiong W, Wang Y, Sun Y, Ma L, Zeng Q, Jiang X, et al. Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes. Microbiome Microbiome. 2018;6:1–11.
Article
CAS
Google Scholar
Kumar S, Chen C, Indugu N, Werlang GO, Singh M, Kim WK, et al. Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens. PLoS One. 2018;13:1–23.
Google Scholar
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lan PTN, Binh LT, Benno Y. Impact of two probiotic Lactobacillus strains feeding on fecal lactobacilli and weight gains in chicken. J Gen Appl Microbiol. 2003;49(1):29–36.
Article
CAS
PubMed
Google Scholar
Zhang AN, Li LG, Yin X, Dai CL, Groussin M, Poyet M, Topp E, Gillings MR, Hanage WP, Tiedje JM, Alm EJ. Choosing your battles: which resistance genes warrant global action? bioRxiv. 2019:784322. https://doi.org/10.1101/784322.
Ranjitkar S, Reck F, Ke X, Zhu Q, McEnroe G, Lopez SL, et al. Identification of mutations in the mrdA gene encoding PBP2 that reduce carbapenem and diazabicyclooctane susceptibility of Escherichia coli clinical isolates with mutations in ftsI (PBP3) and which carry bla NDM-1. mSphere. 2019;4:1–6.
Article
Google Scholar
Griggs DJ, Peake L, Johnson MM, Ghori S, Mott A, Piddock LJV. β-Lactamase-mediated β-lactam resistance in Campylobacter species: prevalence of Cj0299 (blaOXA-61) and evidence for a novel β-lactamase in C. jejuni. Antimicrob Agents Chemother. 2009;53:3357–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Diarrassouba F, Diarra MS, Bach S, Delaquis P, Pritchard J, Topp E, et al. Antibiotic resistance and virulence genes in commensal Escherichia coli and Salmonella isolates from commercial broiler chicken farms. J Food Prot. 2007;70(6):1316–27.
Article
CAS
PubMed
Google Scholar
Juricova H, Matiasovicova J, Kubasova T, Cejkova D, Rychlik I. The distribution of antibiotic resistance genes in chicken gut microbiota commensals. Sci Rep. 2021;11:1–10. https://doi.org/10.1038/s41598-021-82640-3. Nature Publishing Group UK.
Article
CAS
Google Scholar
Arkali A, Çetinkaya B. Molecular identification and antibiotic resistance profiling of Salmonella species isolated from chickens in eastern Turkey. BMC Vet Res. 2020;16:1–8.
Article
CAS
Google Scholar
Subedi M, Bhattarai RK, Devkota B, Phuyal S, Luitel H. Correction: Antibiotic resistance pattern and virulence genes content in avian pathogenic escherichia coli (APEC) from broiler chickens in Chitwan, Nepal [BMC Vet Res., 14, (2018) (113)]. BMC Vet Res. 2018;14:4–9. https://doi.org/10.1186/s12917-018-1453-9.
Article
Google Scholar
Lal Gupta C, Kumar Tiwari R, Cytryn E. Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes. Environ Int. 2020;138:105667. https://doi.org/10.1016/j.envint.2020.105667. Elsevier.
Article
CAS
PubMed
Google Scholar
Huang P, Zhang Y, Xiao K, Jiang F, Wang H, Tang D, et al. The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids 06 Biological Sciences 0605 Microbiology. Microbiome. 2018;6(1):1–7.
Article
CAS
Google Scholar
Vouga M, Greub G. Emerging bacterial pathogens: the past and beyond. Clin Microbiol Infect. 2016;22(1):12–21.
Article
PubMed
Google Scholar
Bassetti M, Merelli M, Temperoni C, Astilean A. New antibiotics for bad bugs: where are we? Ann Clin Microbiol Antimicrob. 2013;12(1):1–5.
Article
CAS
Google Scholar
Newell DG, Fearnley C. Sources of Campylobacter colonization in broiler chickens. Appl Environ Microbiol. 2003;69(8):4343–5.
Engberg J, Aarestrup FM, Gerner-Smidt P, Nachamkin I. Quinolone and macrolide resistance in Campylobacter jejuni and C. coli: resistance mechanisms and trends in human isolates. Emerg Infect Dis. 2001;7(1):24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wielders CLC, Fluit AC, Brisse S, Verhoef J, Schmitz FJ. mecA gene is widely disseminated in Staphylococcus aureus population. J Clin Microbiol. 2002;40(11):3970–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lakhundi S, Zhang K. Methicillin-resistant Staphylococcus aureus: molecular characterization, evolution, and epidemiology. Clin Microbiol Rev. 2018;31(4):e00020-18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Courvalin P. Vancomycin resistance in gram-positive cocci. Clin Infect Dis. 2006;42(Supplement_1):S25-34.
Article
CAS
PubMed
Google Scholar
Abrar S, Ain NU, Liaqat H, Hussain S, Rasheed F, Riaz S. Distribution of blaCTX − M, blaTEM, blaSHV and blaOXA genes in extended-spectrum-β-lactamase-producing clinical isolates: a three-year multi-center study from Lahore, Pakistan. Antimicrob Resist Infect Control. 2019;8:80.
Article
PubMed
PubMed Central
Google Scholar
Castro JC, Rodriguez LM, Harvey WT, Weigand MR, Hatt JK, Carter MQ, et al. ImGLAD: accurate detection and quantification of target organisms in metagenomes. PeerJ. 2018;6:e5882.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shaaly A, Kalamorz F, Gebhard S, Cook GM. Undecaprenyl pyrophosphate phosphatase confers low-level resistance to bacitracin in Enterococcus faecalis. J Antimicrob Chemother. 2013;68:1583–93.
Article
CAS
PubMed
Google Scholar
Kubasova T, Kollarcikova M, Crhanova M, Karasova D, Cejkova D, Sebkova A, et al. Contact with adult hen affects development of caecal microbiota in newly hatched chicks. PLoS One. 2019;14(3):e0212446.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yin Y, He X, Szewczyk P, Nguyen T, Chang G. Structure of the multidrug transporter EmrD from Escherichia coli. Science (80-). 2006;312(5774):741–4.
Article
CAS
Google Scholar
Slipski CJ, Zhanel GG, Bay DC. Biocide selective TolC-independent efflux pumps in Enterobacteriaceae. J Membr Biol. 2018;251(1):15–33.
Article
CAS
PubMed
Google Scholar
Yu L, Li W, Xue M, Li J, Chen X, Ni J, et al. Regulatory role of the two-component system BasSR in the expression of the EmrD multidrug efflux in Escherichia coli. Microb Drug Resist. 2020;26(10):1163–73.
Article
CAS
PubMed
Google Scholar
He LY, Liu YS, Su HC, Zhao JL, Liu SS, Chen J, et al. Dissemination of antibiotic resistance genes in representative broiler feedlots environments: identification of indicator ARGs and correlations with environmental variables. Environ Sci Technol. 2014;48(22):13120–9.
Article
CAS
PubMed
Google Scholar
Ozgumus OB, Sandalli C, Sevim A, Celik-Sevim E, Sivri N. Class 1 and class 2 integrons and plasmid-mediated antibiotic resistance in coliforms isolated from ten rivers in northern Turkey. J Microbiol. 2009;47(1):19–27.
Article
CAS
PubMed
Google Scholar
Jones-Dias D, Manageiro V, Martins AP, Ferreira E, Caniça M. New class 2 integron In2-4 among IncI1-positive Escherichia coli isolates carrying ESBL and PMAβ genes from food animals in Portugal. Foodborne Pathog Dis. 2016;13:36–9.
Article
CAS
PubMed
Google Scholar
Andrews S. FASTQC: a quality control tool for high throughput sequence data. 2015. Available at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
PubMed
PubMed Central
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(16):2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. MetaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27(5):824–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95(6):315–27.
Article
CAS
PubMed
Google Scholar
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11(1):1.
Article
CAS
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, et al. MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol. 2016;12(6):e1004957.
Article
PubMed
PubMed Central
CAS
Google Scholar
Arango-Argoty G, Garner E, Pruden A, Heath LS, Vikesland P, Zhang L. DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome Microbiome. 2018;6:1–15.
Article
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014;12(1):59–60.
Hu Y, Yang X, Qin J, Lu N, Cheng G, Wu N, et al. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat Commun. 2013;4(1):1–7.
CAS
Google Scholar
Ma L, Li B, Jiang XT, Wang YL, Xia Y, Li AD, et al. Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey. Microbiome. 2017;5(1):1–2.
Article
CAS
Google Scholar
Chen H, Chen R, Jing L, Bai X, Teng Y. A metagenomic analysis framework for characterization of antibiotic resistomes in river environment: application to an urban river in Beijing. Environ Pollut. 2019;245:398–407.
Article
CAS
PubMed
Google Scholar
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;2019:1–13.
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Article
CAS
PubMed
Google Scholar
Olm MR, Brown CT, Brooks B, Banfield JF. DRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8. https://doi.org/10.1038/ismej.2017.126. Nature Publishing Group.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics. 2020;36:1925–7.
CAS
Google Scholar
Green SJ, Venkatramanan R, Naqib A. Deconstructing the polymerase chain reaction: understanding and correcting bias associated with primer degeneracies and primer-template mismatches. PLoS One. 2015;10(5):e0128122.
Article
PubMed
PubMed Central
CAS
Google Scholar
Naqib A, Poggi S, Wang W, Hyde M, Kunstman K, Green SJ. Making and sequencing heavily multiplexed, high-throughput 16S ribosomal RNA gene amplicon libraries using a flexible, two-stage PCR protocol. Methods Mol Biol. 2018;1783:149–69.
Article
PubMed
Google Scholar
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10–2.
Article
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590–6.
CAS
PubMed
Google Scholar
Zhu G, Wang X, Yang T, Su J, Qin Y, Wang S, et al. Air pollution could drive global dissemination of antibiotic resistance genes. ISME J. 2020;15(1):270–81.
Article
PubMed
CAS
PubMed Central
Google Scholar
Liu J, Taft DH, Maldonado-Gomez MX, Johnson D, Treiber ML, Lemay DG, et al. The fecal resistome of dairy cattle is associated with diet during nursing. Nat Commun. 2019;10(1):1–5.
Article
CAS
Google Scholar
Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. ICWSM Conf. 2009;8:361–2.
Li X, Xing J, Li B, Wang P, Liu J. Use of tuf as a target for sequence-based identification of Gram-positive cocci of the genus Enterococcus, Streptococcus, coagulase-negative Staphylococcus, and Lactococcus. Ann Clin Microbiol Antimicrob. 2012;11(1):1–6.
Article
CAS
Google Scholar
The Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing CLSI supplement M100S 26th ed. Wayne: Clinical & Laboratory Standards Institute; 2016.
Google Scholar
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. R package version 2.5–2. 2019. https://cran.r-project.org/web/packages/vegan/.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):1–21.
Article
CAS
Google Scholar