Whole genome sequencing of Multi-drug resistant gram-negative bacteria isolated from poultry in the Noakhali region of Bangladesh

Antimicrobial resistance (AMR) poses a significant threat to global public health, with critical implications for both human and veterinary medicine. In veterinary settings, antibiotics are utilized therapeutically to treat infections and prophylactically to prevent disease, and are often added to animal feed at sub-therapeutic levels to enhance growth. The growing consumption of poultry as a primary protein source has led to rapid expansion in the agro-based poultry sector. However, improper use of antibiotics at both therapeutic and non-therapeutic levels can lead to severe public health issues.This study focuses on the presence of Escherichia coli and Providencia stuartii in poultry chickens, emphasizing their potential impact on animal health, food safety, and public health, particularly when these bacteria exhibit pathogenic and multi-drug resistant (MDR) characteristics. E. coli is a common inhabitant of the poultry gastrointestinal tract; however, MDR strains are increasingly concerning due to their resistance to multiple antibiotic classes, complicating treatment and posing risks of transmission to humans through contaminated meat or direct contact.Providencia stuartii, although less frequently encountered in poultry compared to E. coli, is an opportunistic pathogen with the potential to cause infections in both animals and humans, particularly among immunocompromised individuals. This bacterium is often resistant to several antibiotics, including beta-lactams and aminoglycosides. The presence of MDR Providencia stuartii in poultry indicates significant risks due to its ability to spread resistance genes to other bacteria.In this study, we conducted whole genome sequencing (WGS) of four novel strains of Escherichia coli and Providencia stuartii isolated from poultry in the Noakhali region of Bangladesh. These strains were identified as MDR gram-negative bacteria. The isolates were collected during routine antimicrobial resistance screenings in poultry farms and displayed resistance to multiple antibiotic classes, including beta-lactams, aminoglycosides, and fluoroquinolones.WGS was performed using the Illumina platform to elucidate the genetic mechanisms underlying antimicrobial resistance and to gain insights into the phylogeny and virulence factors of these strains. The draft genomes were assembled and annotated, uncovering key resistance genes such as blaCTX-M, qnrS, and aminoglycoside-modifying enzymes. Comparative genomic analysis and phylogenetic studies revealed that these strains are distinct from previously reported isolates, suggesting they may represent new variants of concern within the poultry sector.The data from this study will enhance the existing database of MDR pathogens in Bangladesh and will be instrumental in guiding future research on containment strategies and risk management for mitigating animal-to-human transmission of antibiotic resistance.

抗菌药物耐药性（Antimicrobial resistance, AMR）对全球公共卫生构成重大威胁，对人类与兽医医学均具有关键影响。在兽医领域，抗生素被用于治疗感染的治疗性给药，以及预防疾病的预防性给药，还常以亚治疗剂量添加至动物饲料中以促进动物生长。随着禽肉作为主要蛋白质来源的消费需求持续增长，农业家禽养殖业得以快速扩张。然而，无论治疗性还是非治疗性使用抗生素不当，均可能引发严重的公共卫生问题。

本研究聚焦家禽体内的大肠杆菌（Escherichia coli）与斯图普罗维登斯菌（Providencia stuartii）的存在情况，重点探讨其对动物健康、食品安全及公共卫生的潜在影响，尤其是当这些细菌呈现致病性与多重耐药（multi-drug resistant, MDR）特性时。大肠杆菌是家禽胃肠道的常见定植菌群，但多重耐药菌株因对多种抗生素类别产生耐药性而日益受到关注，这不仅使治疗难度大幅增加，还可通过受污染的肉类或直接接触传播给人类，构成公共健康风险。

斯图普罗维登斯菌虽相较于大肠杆菌在家禽中的检出率更低，却是一种机会致病菌，可引发动物与人类的感染，尤其对免疫功能低下人群风险更高。该细菌通常对β-内酰胺类（beta-lactams）、氨基糖苷类（aminoglycosides）等多种抗生素具有耐药性。家禽体内若存在多重耐药斯图普罗维登斯菌，将带来显著公共健康风险，因其可将耐药基因传播至其他细菌。

本研究对从孟加拉国诺阿卡利地区家禽中分离得到的4株大肠杆菌与斯图普罗维登斯菌新菌株开展了全基因组测序（whole genome sequencing, WGS）。这些菌株被鉴定为多重耐药革兰氏阴性菌。这些分离株采集自家禽养殖场的常规抗菌药物耐药性筛查工作，且对β-内酰胺类（beta-lactams）、氨基糖苷类（aminoglycosides）及氟喹诺酮类（fluoroquinolones）等多种抗生素类别表现出耐药性。

研究采用Illumina测序平台完成全基因组测序，以阐明抗菌药物耐药性的遗传机制，并深入解析这些菌株的系统发育特征与毒力因子。研究人员对草图基因组进行了组装与注释，揭示了blaCTX-M、qnrS以及氨基糖苷类修饰酶（aminoglycoside-modifying enzymes）等关键耐药基因。比较基因组学分析与系统发育研究结果显示，这些菌株与此前已报道的分离株存在显著差异，表明它们可能代表家禽养殖业中值得关注的新型变异株。

本研究产生的数据将丰富孟加拉国现有的多重耐药病原体数据库，并可为未来制定遏制策略与风险管理方案提供重要指导，以减轻抗生素耐药性从动物向人类的传播风险。