We report first complete genomic investigation of extensive drug resistance (XDR) in a nosocomial Stenotrophomonas maltophilia complex strain that is resistant to mainstream drugs (trimethoprim/sulfamethoxazole and levofloxacin). Comprehensive genomic investigation revealed its exclusive fourteen dynamic regions and highly enriched resistome comprising of two sulfonamide resistance genes on two diverse super-integrons of chromosomal origin. In addition, both these integrons harbour array of antibiotic resistance and commonly used disinfectant's resistace genes linked to ISCR elements. Isolation of a novel XDR strain from Indian tertiary care unit belonging to novel ST with diverse array of resistance genes on ISCR linked super-integrons indicates extent and nature of selection pressure in hospitals. Since, repetitive elements have major role in their spread and due to limitations of draft genomes, there is an urgent need to employ complete genome-based investigation for tracking the emergence of XDR at global level and designing strategies of antimicrobial stewardship and disinfection.

Importance

Hospital settings in India have one of the highest usages of antimicrobials and a heavy patient load. We hereby report a novel clinical isolate of S. maltophilia complex with two super-integrons that harbour array of antimicrobial resistance genes along with biocide and heavy metal resistance genes. Further, the presence of ISCR type of transposable elements on both the integrons indicates their propensity to transfer resistome while their chromosomal origin suggests possibilities for further genomic/phenotypic complexities according to selection pressure. Such complex mobile cassettes in a novel strain is a potential threat to global health care. Hence, to understand the evolution of opportunistic nosocomial pathogen, there is an urgent need to employ cost-effective long read technologies to keep vigilance on novel and XDR pathogens in populous countries. There is also need for surveillance of the usage of disinfectants and other antimicrobials for environmental hygiene and linked/rapid co-evolution of XDR in nosocomial pathogens.

Repositories: Complete genome sequence of Stenotrophomonas maltophilia SM866: CP031058.

中文翻译：

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对嗜麦芽窄食单胞菌复合体广泛耐药性进化的基因组学见解。

我们报告了对医院内嗜麦芽窄食单胞菌广泛耐药性 (XDR) 的首次完整基因组研究对主流药物（甲氧苄啶/磺胺甲恶唑和左氧氟沙星）耐药的复杂菌株。全面的基因组研究揭示了其独有的 14 个动态区域和高度富集的抗性组，该抗性组由两个不同的染色体来源的超级整合子上的两个磺胺类抗性基因组成。此外，这两个整合子都具有一系列抗生素抗性和与 ISCR 元件相关的常用消毒剂抗性基因。来自印度三级保健单位的新型 XDR 菌株的分离属于新型 ST，在 ISCR 连接的超级整合子上具有多种抗性基因，表明医院选择压力的程度和性质。由于重复元件在其传播中起主要作用，并且由于基因组草图的限制，

重要性

印度的医院环境是抗菌药物使用率最高的地区之一，患者负担也很重。我们在此报告一种新的嗜麦芽窄食单胞菌临床分离株与两个超级整合子复合，其中包含一系列抗菌素抗性基因以及杀生物剂和重金属抗性基因。此外，两个整合子上 ISCR 类型的转座元件的存在表明它们倾向于转移抗性组，而它们的染色体起源表明根据选择压力进一步基因组/表型复杂性的可能性。这种新型菌株的复杂移动盒对全球医疗保健构成潜在威胁。因此，为了了解机会性医院病原体的演变，迫切需要采用具有成本效益的长读长技术来保持对人口稠密国家的新型病原体和 XDR 病原体的警惕。

存储库：嗜麦芽窄食单胞菌SM866 的完整基因组序列：CP031058。