Putative mobilized colistin resistance genes in the human gut microbiome

被引:5
作者
Andrade, Bruno G. N. [1 ]
Goris, Tobias [2 ]
Afli, Haithem [1 ]
Coutinho, Felipe H. [3 ]
Davila, Alberto M. R. [4 ,5 ]
Cuadrat, Rafael R. C. [6 ,7 ]
机构
[1] Munster Technol Univ, Dept Comp Sci, MTU ADAPT, Cork, Ireland
[2] German Inst Human Nutr Potsdam Rehbruecke DIfE, Dept Mol Toxicol, Res Grp Intestinal Microbiol, Arthur Scheunert Allee 114-116, D-14558 Nuthetal, Germany
[3] Univ Miguel Hernandez, Dept Prod Vegetal & Microbiol, Alicante, Spain
[4] Fiocruz MS, Oswaldo Cruz Inst, Computat & Syst Biol Lab, Rio De Janeiro, RJ, Brazil
[5] Fiocruz MS, Oswaldo Cruz Inst, Grad Program Biodivers & Hlth, Rio De Janeiro, RJ, Brazil
[6] Max Delbruck Ctr MDC, Berlin Inst Med Syst Biol BIMSB, Bioinformat & Omics Data Sci, Berlin, Germany
[7] German Inst Human Nutr Potsdam Rehbrucke, Dept Mol Epidemiol, Arthur Scheunert Allee 114-116, D-14558 Nuthetal, Germany
基金
欧盟地平线“2020”; 爱尔兰科学基金会;
关键词
Colistin; Human microbiome; MCR; Metagenomics; Antibiotic resistance genes; MULTIPLE SEQUENCE ALIGNMENT; ANTIBIOTIC-RESISTANCE; IDENTIFICATION; INFECTIONS; EPIDEMIOLOGY; PERFORMANCE; BACTERIA;
D O I
10.1186/s12866-021-02281-4
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Background The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes. Results A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings. Conclusion This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.
引用
收藏
页数:10
相关论文
共 71 条
  • [1] mcr-1 and mcr-2 variant genes identified in Moraxella species isolated from pigs in Great Britain from 2014 to 2015
    AbuOun, Manal
    Stubberfield, Emma J.
    Duggett, Nick A.
    Kirchner, Miranda
    Dormer, Luisa
    Nunez-Garcia, Javier
    Randall, Luke P.
    Lemma, Fabrizio
    Crook, Derrick W.
    Teale, Christopher
    Smith, Richard P.
    Anjum, Muna F.
    [J]. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 2017, 72 (10) : 2745 - 2749
  • [2] Aberrant intestinal microbiota in individuals with prediabetes
    Allin, Kristine H.
    Tremaroli, Valentina
    Caesar, Robert
    Jensen, Benjamin A. H.
    Damgaard, Mads T. F.
    Bahl, Martin I.
    Licht, Tine R.
    Hansen, Tue H.
    Nielsen, Trine
    Dantoft, Thomas M.
    Linneberg, Allan
    Jorgensen, Torben
    Vestergaard, Henrik
    Kristiansen, Karsten
    Franks, Paul W.
    Hansen, Torben
    Backhed, Fredrik
    Pedersen, Oluf
    [J]. DIABETOLOGIA, 2018, 61 (04) : 810 - 820
  • [3] A unified catalog of 204,938 reference genomes from the human gut microbiome
    Almeida, Alexandre
    Nayfach, Stephen
    Boland, Miguel
    Strozzi, Francesco
    Beracochea, Martin
    Shi, Zhou Jason
    Pollard, Katherine S.
    Sakharova, Ekaterina
    Parks, Donovan H.
    Hugenholtz, Philip
    Segata, Nicola
    Kyrpides, Nikos C.
    Finn, Robert D.
    [J]. NATURE BIOTECHNOLOGY, 2021, 39 (01) : 105 - 114
  • [4] A new genomic blueprint of the human gut microbiota
    Almeida, Alexandre
    Mitchell, Alex L.
    Boland, Miguel
    Forster, Samuel C.
    Gloor, Gregory B.
    Tarkowska, Aleksandra
    Lawley, Trevor D.
    Finn, Robert D.
    [J]. NATURE, 2019, 568 (7753) : 499 - +
  • [5] DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data
    Arango-Argoty, Gustavo
    Garner, Emily
    Prudent, Amy
    Heath, Lenwood S.
    Vikesland, Peter
    Zhang, Liqing
    [J]. MICROBIOME, 2018, 6
  • [6] Baron SA., 2018, Human Microbiome J, V10, P43, DOI DOI 10.1016/J.HUMIC.2018.08.005
  • [7] The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents
    Bengtsson-Palme, Johan
    Angelin, Martin
    Huss, Mikael
    Kjellqvist, Sanela
    Kristiansson, Erik
    Palmgren, Helena
    Larsson, D. G. Joakim
    Johanssone, Anders
    [J]. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2015, 59 (10) : 6551 - 6560
  • [8] Acquired Resistance to Colistin via Chromosomal And Plasmid-Mediated Mechanisms in Klebsiella pneumoniae
    Berglund, Bjorn
    [J]. INFECTIOUS MICROBES & DISEASES, 2019, 1 (01): : 10 - 19
  • [9] High Prevalence of Multidrug-Resistant and Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae: A Cross-Sectional Study at Arsho Advanced Medical Laboratory, Addis Ababa, Ethiopia
    Bitew, Adane
    Tsige, Estifanos
    [J]. JOURNAL OF TROPICAL MEDICINE, 2020, 2020
  • [10] Growing group of extended-spectrum β-lactamases:: The CTX-M enzymes
    Bonnet, R
    [J]. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2004, 48 (01) : 1 - 14