Background Antimicrobial resistance (AMR) surveillance in low- and middle-income countries (LMICs) often relies on poorly resourced laboratory processes. Centralized sequencing was combined with cloud-based, open-source bioinformatics solutions for national AMR surveillance in Cambodia. Methods Blood cultures growing gram-negative bacteria were collected at 6 Cambodian hospitals (January 2021 to October 2022). Isolates were obtained from pure plate growth and shotgun DNA sequencing performed in country. Using public nucleotide and protein databases, reads were aligned for pathogen identification and AMR gene characterization. Multilocus sequence typing was performed on whole-genome assemblies and haplotype clusters compared against published genomes. Results Genes associated with acquired resistance to fluoroquinolones were identified in 59%, trimethoprim/sulfamethoxazole in 45%, and aminoglycosides in 52% of 715 isolates. Extended-spectrum β-lactamase encoding genes were identified in 34% isolates, most commonly blaCTX-M-15, blaCTX-M-27, and blaCTX-M-55 in Escherichia coli sequence types 131 and 1193. Carbapenemase genes were identified in 12% isolates, most commonly blaOXA-23, blaNDM-1, blaOXA-58, and blaOXA-66 in Acinetobacter species. Phylogenetic analysis revealed clonal strains of Acinetobacter baumannii, representing suspected nosocomial outbreaks, and genetic clusters of quinolone-resistant typhoidal Salmonella and extended-spectrum β-lactamase E. coli cases suggesting community transmission. Conclusions With accessible sequencing platforms and bioinformatics solutions, bacterial genomics can supplement AMR surveillance in LMICs.

中文翻译：

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用于柬埔寨国家抗菌素耐药性监测的细菌基因组学


背景 低收入和中等收入国家 （LMIC） 的抗菌素耐药性 （AMR） 监测通常依赖于资源不足的实验室流程。集中测序与基于云的开源生物信息学解决方案相结合，用于柬埔寨的国家 AMR 监测。方法 在 2021 年 1 月至 2022 年 10 月的 6 家柬埔寨医院收集生长革兰阴性菌的血培养物。分离株来自在该国进行的纯平板生长和鸟枪法 DNA 测序。使用公共核苷酸和蛋白质数据库，对读数进行病原体鉴定和 AMR 基因表征。对全基因组组装和单倍型簇进行多位点序列分型，与已发表的基因组进行比较。结果 在 715 株分离株中，59% 的分离株中鉴定出与氟喹诺酮类药物获得性耐药相关的基因，45% 的甲氧苄啶/磺胺甲噁唑，52% 的分离株中鉴定出氨基糖苷类药物。在 34% 的分离株中鉴定出超广谱 β-内酰胺酶编码基因，最常见的是大肠杆菌序列类型 131 和 1193 中的 blaCTX-M-15、blaCTX-M-27 和 blaCTX-M-55。在 12% 的分离株中鉴定出碳青霉烯酶基因，最常见的是不动杆菌属的 blaOXA-23 、 blaNDM-1 、 blaOXA-58 和 blaOXA-66。系统发育分析显示鲍曼不动杆菌克隆菌株，代表疑似院内暴发，以及喹诺酮类耐药伤寒沙门氏菌和广谱 β-内酰胺酶大肠杆菌病例的遗传集群，提示社区传播。结论 借助可访问的测序平台和生物信息学解决方案，细菌基因组学可以补充低收入和中等收入国家的 AMR 监测。