{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T15:46:07Z","timestamp":1772466367575,"version":"3.50.1"},"reference-count":50,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2020,12,9]],"date-time":"2020-12-09T00:00:00Z","timestamp":1607472000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Basic Science Research Program of the National Research Foundation of Korea and the Ministry of Science and ICT","award":["grand No. NRF-2019R1A2C4069796"],"award-info":[{"award-number":["grand No. NRF-2019R1A2C4069796"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli 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 iroN, iutA, iss, and iucA. 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 E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri 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 E. coli of Khyber Pakhtunkhwa for the first time using NGS.<\/jats:p>","DOI":"10.3390\/ani10122350","type":"journal-article","created":{"date-parts":[[2020,12,9]],"date-time":"2020-12-09T09:17:58Z","timestamp":1607505478000},"page":"2350","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli"],"prefix":"10.3390","volume":"10","author":[{"given":"Ome Kalsoom","family":"Afridi","sequence":"first","affiliation":[{"name":"Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johar","family":"Ali","sequence":"additional","affiliation":[{"name":"Center for Genome Sciences, Rehman Medical College, Hayatabad, Peshawar, Khyber Pakhtunkhwa 25000, Pakistan"},{"name":"Executive Development Center, Sukkur Institute of Business Administration University, Sindh 65200, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2126-0317","authenticated-orcid":false,"given":"Jeong Ho","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,12,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"106809","DOI":"10.1016\/j.foodcont.2019.106809","article-title":"Addressing the antibiotic resistance and improving the food safety in food supply chain (farm-to-fork) in Southeast Asia","volume":"108","author":"Thapa","year":"2020","journal-title":"Food Control"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"De Kraker, M.E., Stewardson, A.J., and Harbarth, S. 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