Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments

Zeng, Jiaxiong; Pan, Yu; Yang, Jingwen; Hou, Mengtian; Zeng, Zhenling; Xiong, Wenguang

doi:10.1016/j.envint.2019.02.052

Cited by 85 publications

(61 citation statements)

References 68 publications

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“…Similar results were described for fish where ARGs were enriched at least 4.5 times in the gut during florfenicol exposure [33]. More than that, the previous study had found that the total coverage of ARGs of chicken samples was significantly higher than that of human, ocean, pig and soil samples [34]. A small dosage of in-feed antimicrobials could not only increase the level of ARGs, but also pose a risk by selecting bacteria able to perform chemotaxis mechanism [35,36].…”

Section: Discussionsupporting

confidence: 80%

Effects of pulsed in-feed antimicrobials on chicken fecal resistome

Chen¹,

Yang²,

Zeng³

et al. 2019

Preprint

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Background: Antimicrobial resistance has become a global problem that poses great threats to human health. Antimicrobials are widely used in broiler chicken production and consequently affect the fecal resistome. Here we used metagenomic approach to investigate the effects of pulsed antimicrobial administration on chicken fecal resistome. Chickens received three 5-day-course of alone/combined antimicrobials at therapeutic dose, including amoxicillin, chlortetracycline and florfenicol. Chicken feces was collected on T0 (before treatment), T5 (after first treatment), T10 (after second treatment), T15 (after third treatment) at the chicken age of 40 days that are ready for slaughter. Results: Tetracycline resistance gene and polymyxin resistance gene only responded to chlortetracycline and amoxicillin, respectively. The tetracycline resistance gene tetC significantly increased from T0 to T15 in chlortetracycline group. The multidrug resistance gene acrB, acrF, mdtA, mdtK and CRP only occurred significant increase in amoxicillin group (P<0.05). Klebsiella significantly decreased from T0 to T10 in florfenicol group, while significantly increased from T0 to T15 in chlortetracycline group (P<0.05). Amoxicillin did not lead significant change to Klebsiella. Escherichia was always the major host for multidrug resistance genes. ARG-harboring Escherichia increased mainly due to the antimicrobial selection for β-lactam, tetracycline, chloramphenicol resistance genes they harbored. Conclusions: The results indicated that the effects induced by amoxicillin, chlortetracycline and florfenicol significantly shaped the fecal microbiome and resistome. We provided a comprehensive insight into antimicrobial-mediated alteration of chicken fecal microbiome and resistome. These findings will give suggests to veterinarian for combating antimicrobial resistance in broiler chicken production.

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Section: Discussionsupporting

confidence: 80%

Effects of pulsed in-feed antimicrobials on chicken fecal resistome

Chen¹,

Yang²,

Zeng³

et al. 2019

Preprint

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“…The rapid emergence of multidrug resistance combined with the limited number of novel antibacterial agents has caused a public health crisis. 1,2 The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) were known for their ability to escape the inhibitory action of and develop high levels of resistance to traditional antibiotic drugs. These pathogens have recently been identified as the leading global cause of multidrug-resistant bacterial infections.…”

Section: Introductionmentioning

confidence: 99%

<p>In vitro Antibacterial Activity of Isopropoxy Benzene Guanidine Against Multidrug-Resistant <em>Enterococci</em></p>

Zhang¹,

Han²,

Pei³

et al. 2019

IDR

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“…The remaining seven studies were re-analysis of publicly available datasets. 5,8,13,21,25,31,32 With reference to the number of population by countries reported by the United Nations, 33 the number of recruited subjects ranged from 0.72 in China to 765 in the Netherlands per 10 million population (median = 19.07, interquartile range 4.56-37.10) ( Figure 2). Except for a Dutch study for which a general population-based cohort involving 1,135 individuals derived from 167,000 subjects across three provinces, 18 the remaining studies were either based on convenient samples or did not describe how the cohorts were derived.…”

Section: Resultsmentioning

confidence: 99%

“… Given sequence reads did not span the whole ARG length, its frequency could not be identified. 31 USA 29 SeqMeta 21 Prodigal, BLASTP DeepARG Sixty four ARGs were shared amongst the gut resistomes from chickens, pigs and humans. The genetic contexts of the ARGs were unclear.…”

Section: Resultsmentioning

confidence: 99%

Systematic review of human gut resistome studies revealed variable definitions and approaches

Yeoh

Barua

et al. 2020

Gut Microbes

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In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.

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Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments

Cited by 85 publications

References 68 publications

Effects of pulsed in-feed antimicrobials on chicken fecal resistome

Effects of pulsed in-feed antimicrobials on chicken fecal resistome

<p>In vitro Antibacterial Activity of Isopropoxy Benzene Guanidine Against Multidrug-Resistant <em>Enterococci</em></p>

Systematic review of human gut resistome studies revealed variable definitions and approaches

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