Genomic Insights into Pangenome and Antimicrobial Resistance in Campylobacter spp. Isolated from Chickens at Specific Growth Stages

被引:0
|
作者
Zang, Xiaoqi [1 ]
Lv, Hongyue [2 ]
Huang, Pingyu [1 ]
Sun, Zhichu [1 ]
Gu, Chen [1 ]
Ding, Wei [1 ]
Jiao, Xinan [1 ,2 ,3 ]
Huang, Jinlin [1 ,2 ,3 ]
机构
[1] Yangzhou Univ, Jiangsu Coinnovat Ctr Prevent & Control Important, Jiangsu Key Lab Zoonosis, Yangzhou 225009, Peoples R China
[2] Yangzhou Univ, Joint Int Res Lab Agr & Agriprod Safety, Minist Educ China, Yangzhou, Peoples R China
[3] Yangzhou Univ, Key Lab Prevent & Control Biol Hazard Factors Anim, Minist Agr China, Yangzhou, Peoples R China
基金
中国国家自然科学基金;
关键词
Campylobacter colonization; Chicken specific growth stage; whole genome sequencing; sequence types; Pangenome-wide association analysis; Antimicrobial resistance; JEJUNI;
D O I
10.1089/fpd.2023.0008
中图分类号
TS2 [食品工业];
学科分类号
0832 ;
摘要
Improved understanding of the genetic basis of Campylobacter spp. colonization of poultry at specific growth stage is the key to developing a farm-based strategy to prevent flock colonization. In this study, 39 Campylobacter spp. strains (chicken isolates, n = 29; environmental isolates, n = 10) were collected from six marked chickens at the growth stage from week 7 to week 13. Then, we use comparative genomics techniques to analyze the temporal genomic characteristics of Campylobacter spp. in individual chickens across a production cycle. Genotype, average nucleotide identity (ANI), and phylogenetic trees all indicated the evolutionary relationships between the strains from different sampling weeks. The clustering of isolates was not dependent on sampling time and sample source, indicating that strains could persist over several weeks in a flock. Notably, 10 antimicrobial resistance (AMR) genes were identified in the genome of Campylobacter coli isolates, and the genomes of isolates sampled at week 11 harbored fewer AMR genes and insertion sequences (IS) than the isolates from other weeks. Consistent with this, pangenome-wide association analysis demonstrated that gene acquisition and loss could happen at week 11 and week 13. These genes were mainly associated with cell membrane biogenesis, ion metabolism, and DNA replication, suggesting that genomic change may be related to Campylobacter adaptive response. This is a novel study focused on the genetic changes occurring in Campylobacter spp. isolates in a particular space and time; it highlights that accessory genes and AMR genes were overall stable at chicken farm, which will help us understand the survival and the transmission route of Campylobacter spp. better, and have the potential to inform the strategy on the safety control of market-ready chickens.
引用
收藏
页码:303 / 312
页数:10
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