Antibiotic resistance in bacterial pathogens or several indicator bacteria is commonly studied but the extent of antibiotic resistance in bacterial commensals colonising the intestinal tract is essentially unknown. In this study, we aimed to investigate the presence of horizontally acquired antibiotic resistance genes among chicken gut microbiota members in 259 isolates with known whole genomic sequences. Altogether 124 isolates contained at least one gene coding for antibiotic resistance. Genes coding for the resistance to tetracyclines (detected in 101 isolates), macrolide-lincosamide-streptogramin B antibiotics (28 isolates) and aminoglycosides (25 isolates) were the most common. The most frequent tetracycline resistance genes were tet(W), tet(32), tet(O) and tet(Q). Lachnospiraceae and Ruminococcaceae frequently encoded tet(W). Lachnospiraceae commonly coded also for tet(32) and tet(O). The tet(44) gene was associated with Erysipelotrichaceae and tet(Q) was detected in the genomes of Bacteroidaceae and Porphyromonadaceae. Without any bias we have shown that antibiotic resistance is quite common in gut commensals. However, a comparison of codon usage showed that the above-mentioned families represent the most common current reservoirs but probably not the original host of the detected resistances.

Department of Biomedical Engineering Brno University of Technology Brno Czech Republic

Veterinary Research Institute Brno Czech Republic

Zobrazit více v PubMed

Faldynova M, et al. Evolution of antibiotic resistance in Salmonella enterica serovar typhimurium strains isolated in the Czech Republic between 1984 and 2002. Antimicrob. Agents Chemother. 2003;47:2002–2005. doi: 10.1128/aac.47.6.2002-2005.2003. PubMed DOI PMC

De Oliveira DMP, et al. Antimicrobial resistance in ESKAPE pathogens. Clin. Microbiol. Rev. 2020 doi: 10.1128/CMR.00181-19. PubMed DOI PMC

Raimondi S, et al. Antibiotic resistance, virulence factors, phenotyping, and genotyping of E. coli isolated from the feces of healthy s ubjects. Microorganisms. 2019 doi: 10.3390/microorganisms7080251. PubMed DOI PMC

Dec M, Urban-Chmiel R, Stepien-Pysniak D, Wernicki A. Assessment of antibiotic susceptibility in Lactobacillus isolates from chickens. Gut Pathog. 2017;9:54. doi: 10.1186/s13099-017-0203-z. PubMed DOI PMC

Masco L, Van Hoorde K, De Brandt E, Swings J, Huys G. Antimicrobial susceptibility of Bifidobacterium strains from humans, animals and probiotic products. J. Antimicrob. Chemother. 2006;58:85–94. doi: 10.1093/jac/dkl197. PubMed DOI

Qu A, et al. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS ONE. 2008;3:e2945. doi: 10.1371/journal.pone.0002945. PubMed DOI PMC

Yeoman CJ, et al. The microbiome of the chicken gastrointestinal tract. Anim. Health Res. Rev. 2012;13:89–99. doi: 10.1017/S1466252312000138. PubMed DOI

Danzeisen JL, Kim HB, Isaacson RE, Tu ZJ, Johnson TJ. Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment. PLoS ONE. 2011;6:e27949. doi: 10.1371/journal.pone.0027949. PubMed DOI PMC

Kazimierczak KA, Flint HJ, Scott KP. Comparative analysis of sequences flanking tet(W) resistance genes in multiple species of gut bacteria. Antimicrob. Agents Chemother. 2006;50:2632–2639. doi: 10.1128/AAC.01587-05. PubMed DOI PMC

Whittle G, Shoemaker NB, Salyers AA. The role of Bacteroides conjugative transposons in the dissemination of antibiotic resistance genes. Cell Mol. Life Sci. 2002;59:2044–2054. doi: 10.1007/s000180200004. PubMed DOI PMC

Buckwold SL, Shoemaker NB, Sears CL, Franco AA. Identification and characterization of conjugative transposons CTn86 and CTn9343 in Bacteroides fragilis strains. Appl. Environ. Microbiol. 2007;73:53–63. doi: 10.1128/AEM.01669-06. PubMed DOI PMC

Lagier JC, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin. Microbiol. Infect. 2012;18:1185–1193. doi: 10.1111/1469-0691.12023. PubMed DOI

Rettedal EA, Gumpert H, Sommer MO. Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria. Nat. Commun. 2014;5:4714. doi: 10.1038/ncomms5714. PubMed DOI

Lau JT, et al. Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling. Genome Med. 2016;8:72. doi: 10.1186/s13073-016-0327-7. PubMed DOI PMC

Crhanova M, et al. Systematic culturomics shows that half of chicken caecal microbiota members can be grown in vitro except for two lineages of Clostridiales and a single lineage of Bacteroidetes. Microorganisms. 2019 doi: 10.3390/microorganisms7110496. PubMed DOI PMC

Medvecky M, et al. Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures. BMC Genom. 2018;19:561. doi: 10.1186/s12864-018-4959-4. PubMed DOI PMC

Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242–245. doi: 10.1093/nar/gkw290. PubMed DOI PMC

R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/. (2017).

Metsalu T, Vilo J. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res. 2015;43:W566–570. doi: 10.1093/nar/gkv468. PubMed DOI PMC

Granados-Chinchilla F, Rodriguez C. Tetracyclines in food and feedingstuffs: From regulation to analytical methods, bacterial resistance, and environmental and health implications. J. Anal. Methods Chem. 2017;2017:1315497. doi: 10.1155/2017/1315497. PubMed DOI PMC

Zhu YG, et al. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc. Natl. Acad. Sci. U S A. 2013;110:3435–3440. doi: 10.1073/pnas.1222743110. PubMed DOI PMC

Hu Y, et al. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat. Commun. 2013;4:2151. doi: 10.1038/ncomms3151. PubMed DOI

Kollarcikova M, et al. Use of 16S rRNA gene sequencing for prediction of new opportunistic pathogens in chicken ileal and cecal microbiota. Poult. Sci. 2019;98:2347–2353. doi: 10.3382/ps/pey594. PubMed DOI

Rychlik I. Composition and function of chicken gut microbiota. Animals (Basel) 2020 doi: 10.3390/ani10010103. PubMed DOI PMC

Roberts MC. Update on acquired tetracycline resistance genes. FEMS Microbiol. Lett. 2005;245:195–203. doi: 10.1016/j.femsle.2005.02.034. PubMed DOI

Lorenzo M, et al. Antimicrobial resistance determinants among anaerobic bacteria isolated from footrot. Vet. Microbiol. 2012;157:112–118. doi: 10.1016/j.vetmic.2011.11.029. PubMed DOI

Veloo ACM, Baas WH, Haan FJ, Coco J, Rossen JW. Prevalence of antimicrobial resistance genes in Bacteroides spp. and Prevotella spp. Dutch clinical isolates. Clin. Microbiol. Infect. 2019;25(1156):e1159–e1156. doi: 10.1016/j.cmi.2019.02.017. PubMed DOI

Videnska P, et al. Succession and replacement of bacterial populations in the caecum of egg laying hens over their whole life. PLoS ONE. 2014;9:e115142. doi: 10.1371/journal.pone.0115142. PubMed DOI PMC

Ammor MS, Florez AB, Alvarez-Martin P, Margolles A, Mayo B. Analysis of tetracycline resistance tet(W) genes and their flanking sequences in intestinal Bifidobacterium species. J. Antimicrob. Chemother. 2008;62:688–693. doi: 10.1093/jac/dkn280. PubMed DOI

Yutin N, Galperin MY. A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia. Environ. Microbiol. 2013;15:2631–2641. doi: 10.1111/1462-2920.12173. PubMed DOI PMC

Warburton P, et al. Characterization of tet(32) genes from the oral metagenome. Antimicrob. Agents Chemother. 2009;53:273–276. doi: 10.1128/AAC.00788-08. PubMed DOI PMC

Poly F, Threadgill D, Stintzi A. Identification of Campylobacter jejuni ATCC 43431-specific genes by whole microbial genome comparisons. J. Bacteriol. 2004;186:4781–4795. doi: 10.1128/JB.186.14.4781-4795.2004. PubMed DOI PMC

Elhadidy M, et al. Antimicrobial resistance patterns and molecular resistance markers of Campylobacter jejuni isolates from human diarrheal cases. PLoS ONE. 2020;15:e0227833. doi: 10.1371/journal.pone.0227833. PubMed DOI PMC

Blau K, et al. Manure and doxycycline affect the bacterial community and its resistome in lettuce rhizosphere and bulk soil. Front. Microbiol. 2019;10:725. doi: 10.3389/fmicb.2019.00725. PubMed DOI PMC

Kecerova Z, Cizek A, Nyc O, Krutova M. Clostridium difficile isolates derived from Czech horses are resistant to enrofloxacin; cluster to clades 1 and 5 and ribotype 033 predominates. Anaerobe. 2019;56:17–21. doi: 10.1016/j.anaerobe.2019.01.005. PubMed DOI

Zankari E, et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 2012;67:2640–2644. doi: 10.1093/jac/dks261. PubMed DOI PMC

Cock PJ, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25:1422–1423. doi: 10.1093/bioinformatics/btp163. PubMed DOI PMC

Gerzova L, et al. Characterization of antibiotic resistance gene abundance and microbiota composition in feces of organic and conventional pigs from four EU countries. PLoS ONE. 2015;10:e0132892. doi: 10.1371/journal.pone.0132892. PubMed DOI PMC

Aminov RI, Garrigues-Jeanjean N, Mackie RI. Molecular ecology of tetracycline resistance: development and validation of primers for detection of tetracycline resistance genes encoding ribosomal protection proteins. Appl. Environ. Microbiol. 2001;67:22–32. doi: 10.1128/AEM.67.1.22-32.2001. PubMed DOI PMC

Madeira F, et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 2019;47:W636–W641. doi: 10.1093/nar/gkz268. PubMed DOI PMC

Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis

Antibiotic Susceptibility, Resistance Gene Determinants and Corresponding Genomic Regions in Lactobacillus amylovorus Isolates Derived from Wild Boars and Domestic Pigs

Succession, Replacement, and Modification of Chicken Litter Microbiota