Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China View Full Text


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Article Info

DATE

2017-07-19

AUTHORS

Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael R. Gillings, Hong Chen, Tong Zhang, Yong-Guan Zhu

ABSTRACT

BackgroundAntibiotic-resistant pathogens are challenging treatment of infections worldwide. Urban sewage is potentially a major conduit for dissemination of antibiotic resistance genes into various environmental compartments. However, the diversity and abundance of such genes in wastewater are not well known.MethodsHere, seasonal and geographical distributions of antibiotic resistance genes and their host bacterial communities from Chinese urban sewage were characterized, using metagenomic analyses and 16S rRNA gene-based Illumina sequencing, respectively.ResultsIn total, 381 different resistance genes were detected, and these genes were extensively shared across China, with no geographical clustering. Seasonal variation in abundance of resistance genes was observed, with average concentrations of 3.27 × 1011 and 1.79 × 1012 copies/L in summer and winter, respectively. Bacterial communities did not exhibit geographical clusters, but did show a significant distance-decay relationship (P < 0.01). The core, shared resistome accounted for 57.7% of the total resistance genes, and was significantly associated with the core microbial community (P < 0.01). The core human gut microbiota was also strongly associated with the shared resistome, demonstrating the potential contribution of human gut microbiota to the dissemination of resistance elements via sewage disposal.ConclusionsThis study provides a baseline for investigating environmental dissemination of resistance elements and raises the possibility of using the abundance of resistance genes in sewage as a tool for antibiotic stewardship. More... »

PAGES

84

References to SciGraph publications

  • 2010-04-11. QIIME allows analysis of high-throughput community sequencing data in NATURE METHODS
  • 2009-06-09. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age in BMC MICROBIOLOGY
  • 2011-10-30. Ecology drives a global network of gene exchange connecting the human microbiome in NATURE
  • 2015-03-06. The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2012-09-26. A metagenome-wide association study of gut microbiota in type 2 diabetes in NATURE
  • 2011-09-08. Using network analysis to explore co-occurrence patterns in soil microbial communities in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2016-05-11. Interconnected microbiomes and resistomes in low-income human habitats in NATURE
  • 2015-04-28. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2015-09-30. Limited dissemination of the wastewater treatment plant core resistome in NATURE COMMUNICATIONS
  • 2015-02-08. Increased levels of antibiotic resistance in urban stream of Jiulongjiang River, China in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
  • 2002-12. Temporal changes in the bacterioplankton of a Northeast Ohio [2pt] (USA) River in HYDROBIOLOGIA
  • 2016-04-14. Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation in MICROBIAL ECOLOGY
  • 2013-07-23. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota in NATURE COMMUNICATIONS
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    32 schema:description BackgroundAntibiotic-resistant pathogens are challenging treatment of infections worldwide. Urban sewage is potentially a major conduit for dissemination of antibiotic resistance genes into various environmental compartments. However, the diversity and abundance of such genes in wastewater are not well known.MethodsHere, seasonal and geographical distributions of antibiotic resistance genes and their host bacterial communities from Chinese urban sewage were characterized, using metagenomic analyses and 16S rRNA gene-based Illumina sequencing, respectively.ResultsIn total, 381 different resistance genes were detected, and these genes were extensively shared across China, with no geographical clustering. Seasonal variation in abundance of resistance genes was observed, with average concentrations of 3.27 × 1011 and 1.79 × 1012 copies/L in summer and winter, respectively. Bacterial communities did not exhibit geographical clusters, but did show a significant distance-decay relationship (P < 0.01). The core, shared resistome accounted for 57.7% of the total resistance genes, and was significantly associated with the core microbial community (P < 0.01). The core human gut microbiota was also strongly associated with the shared resistome, demonstrating the potential contribution of human gut microbiota to the dissemination of resistance elements via sewage disposal.ConclusionsThis study provides a baseline for investigating environmental dissemination of resistance elements and raises the possibility of using the abundance of resistance genes in sewage as a tool for antibiotic stewardship.
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    39 ConclusionsThis study
    40 Illumina sequencing
    41 MethodsHere
    42 ResultsIn total
    43 abundance
    44 analysis
    45 antibiotic resistance genes
    46 antibiotic resistome
    47 antibiotic stewardship
    48 average concentration
    49 bacterial communities
    50 baseline
    51 clustering
    52 clusters
    53 community
    54 compartments
    55 concentration
    56 conduit
    57 contribution
    58 copies/L
    59 core
    60 core microbial community
    61 different resistance genes
    62 disposal
    63 dissemination
    64 distance-decay relationship
    65 distribution
    66 diversity
    67 elements
    68 environmental compartments
    69 environmental dissemination
    70 genes
    71 geographical clustering
    72 geographical clusters
    73 geographical distribution
    74 gut microbiota
    75 host bacterial communities
    76 human gut microbiota
    77 infection
    78 major conduit
    79 metagenomic analysis
    80 metagenomics
    81 microbial communities
    82 microbiota
    83 pathogens
    84 possibility
    85 potential contribution
    86 rRNA gene-based Illumina sequencing
    87 relationship
    88 resistance elements
    89 resistance genes
    90 resistome
    91 seasonal variation
    92 sequencing
    93 sewage
    94 sewage disposal
    95 significant distance-decay relationship
    96 stewardship
    97 study
    98 such genes
    99 summer
    100 tool
    101 total
    102 treatment
    103 treatment of infections
    104 urban sewage
    105 variation
    106 wastewater
    107 winter
    108 schema:name Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China
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