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基于下一代测序技术的感染多重耐药菌的肉鸡肠道耐药基因图谱分析

Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant .

作者信息

Afridi Ome Kalsoom, Ali Johar, Chang Jeong Ho

机构信息

Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea.

Center for Genome Sciences, Rehman Medical College, Hayatabad, Peshawar, Khyber Pakhtunkhwa 25000, Pakistan.

出版信息

Animals (Basel). 2020 Dec 9;10(12):2350. doi: 10.3390/ani10122350.

DOI:10.3390/ani10122350
PMID:33317082
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7764233/
Abstract

The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) (). Fecal samples ( = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR . Upon initial screening, thirteen (13) MDR isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were N, A, , and A. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as , , , and belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR of Khyber Pakhtunkhwa for the first time using NGS.

摘要

本研究旨在调查感染多重耐药（MDR）（）的肉鸡的粪便微生物组和耐药组。从开伯尔-普赫图赫瓦省随机选择的13个地点采集了肉鸡的粪便样本（n = 410），并筛选了MDR的存在情况。初步筛选后，对13株MDR分离株进行了鸟枪法宏基因组下一代测序（NGS）。基于NGS的耐药组分析确定，多药外排泵系统相关基因的流行率最高（36%），其次是氨基糖苷类（26.1%）、四环素类（15.9%）、大环内酯-林可酰胺-链阳霉素类（9.6%）、β-内酰胺类（6.6%）、利福平（2%）、磺胺类（1.3%）、氯霉素类（0.91%）、万古霉素（0.62%）、甲氧苄啶（0.34%）、黏菌素（0.30%）和喹诺酮类（0.33%）。鉴定出的最丰富的毒力相关基因（VAGs）是N、A、和A。基于NGS的门水平分类分析显示，变形菌门占主导地位（38.9%），其次是厚壁菌门（36.4%）、拟杆菌门（15.8%）和柔膜菌门（8.9%）。此外，主要发现了属于肠杆菌科的致病共生菌，如、、和。本研究首次使用NGS揭示了开伯尔-普赫图赫瓦省感染MDR的肉鸡中MDR基因的广泛存在、多样的VAGs以及肠道生态失调。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/adee/7764233/61b21d993a79/animals-10-02350-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/adee/7764233/e743bdab57e0/animals-10-02350-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/adee/7764233/ffd46b603206/animals-10-02350-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/adee/7764233/98b9a5be5154/animals-10-02350-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/adee/7764233/61b21d993a79/animals-10-02350-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/adee/7764233/e743bdab57e0/animals-10-02350-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/adee/7764233/ffd46b603206/animals-10-02350-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/adee/7764233/98b9a5be5154/animals-10-02350-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/adee/7764233/61b21d993a79/animals-10-02350-g004.jpg

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