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

Area of Science:

• Veterinary Microbiology
• Genomics
• Antimicrobial Resistance

Background:

• Multidrug-resistant (MDR) Escherichia coli (E. coli) poses a significant threat to poultry health and food safety.
• Understanding the fecal microbiome and resistome of broiler chickens infected with MDR E. coli is crucial for developing effective control strategies.

Purpose of the Study:

• To investigate the fecal microbiome and resistome of broiler chickens infected with MDR E. coli.
• To identify prevalent antimicrobial resistance genes and virulence-associated genes (VAGs) in E. coli isolates.
• To characterize the gut microbial community structure in infected chickens.

Main Methods:

• Collection and screening of 410 fecal samples from broiler chickens in Khyber Pakhtunkhwa.
• Isolation and identification of MDR E. coli.
• Shotgun metagenome next-generation sequencing (NGS) for resistome and taxonomic profiling.

Main Results:

• NGS identified multidrug efflux pump genes (36%) as the most prevalent resistance genes, followed by aminoglycoside (26.1%) and tetracycline (15.9%).
• Abundant virulence-associated genes (VAGs) included iroN, iutA, iss, and iucA.
• The dominant phyla in the gut microbiome were Proteobacteria (38.9%) and Firmicutes (36.4%), with the presence of pathobionts like E. coli, Salmonella enterica, and Klebsiella pneumoniae.

Conclusions:

• The study reveals a widespread presence of MDR genes and diverse VAGs in broiler chickens infected with MDR E. coli in Khyber Pakhtunkhwa.
• NGS analysis demonstrated a dysbiotic gut microbiome in infected chickens.
• These findings underscore the critical need for surveillance and control of antimicrobial resistance in poultry production.