Laboratorio de Biología Molecular y Genómica de Microorganismos de Interés Clínico y Económico, Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, Sonora, 83621, H. Caborca, Mexico.
Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, 72570, Puebla, Mexico.
Genes Genomics. 2023 May;45(5):569-579. doi: 10.1007/s13258-022-01348-4. Epub 2023 Jan 12.
Leclercia adecarboxylata is a bacteria closely related to Escherichia coli according to its biochemical characteristics and is commonly considered non-pathogenic although a growing number of publications classify it as an emerging pathogen. Fosfomycin resistance is a common trait for L. adecarboxylata encoded by fosA gene.
To analyze genomic traits of sixteen L. adecarboxylata strains isolated from blood culture and a bottle of total parenteral nutrition.
Twenty-eight L. adecarboxylata strains isolated from blood culture and a bottle of total parenteral nutrition were identified biochemically with a Vitek ® automated system. The strains were phenotyped by their growth on Eosin Methylene Blue agar or MacConkey agar plates. Additionally, Pulsed field gel electrophoresis (PFGE) was performed to establish the clonal relationship. The genomic DNA of sixteen strains was obtained using a Qubit ® dsDNA HS Assay Kit and sequenced on an Illumina ® MiSeq instrument. Draft genomes were assembled using PROKKA and Rast. Assemblies were submitted to Resfinder and PathogenFinder from the Center for Genomic Epidemiology in order to find resistance genes and pathogenic potential. IslandViewer4 was also used to find Pathogenicity and Phage Islands. For identification of the fosA gene, manual curation and Clustal analysis was performed. A novel FosA variant was identified. Finally, phylogenetic analysis was performed using VAMPhyRE software and Mega X.
In this paper, we report the genomes of sixteen strains of Leclercia adecarboxylata causing an outbreak associated with parenteral nutrition in public hospitals in Mexico. The genomes were analyzed for genetic determinants of virulence and resistance. A high pathogenic potential (pathogenicity index 0.82) as well as multiple resistance genes including carbapenemics, colistin and efflux pumps were determined. Based on sequence analysis, a new variant of the fosA gene was described. Finally, the outbreak was confirmed by establishing the clonal relationship among the sixteen genomes obtained.
Commensal strains of L. adecarboxylata may acquire genetic determinants that provide mechanisms of host damage and go unnoticed in clinical diagnosis. L. adecarboxylata can evolve in a variety of ways including the acquisition of resistance and virulence genes representing a therapeutic challenge in patient care.
根据生化特性，拉氏不动杆菌与大肠杆菌关系密切，通常被认为是非致病性的，但越来越多的出版物将其归类为新兴病原体。福沙霉素耐药是拉氏不动杆菌由 fosA 基因编码的常见特征。
分析从血培养和一瓶全胃肠外营养中分离出的 16 株拉氏不动杆菌的基因组特征。
采用 Vitek ® 自动化系统对从血培养和一瓶全胃肠外营养中分离出的 28 株拉氏不动杆菌进行生化鉴定。通过在曙红亚甲基蓝琼脂或麦康凯琼脂平板上的生长情况对菌株进行表型分析。此外，还进行脉冲场凝胶电泳（PFGE）以建立克隆关系。使用 Qubit ® dsDNA HS 测定试剂盒从 16 株菌中提取基因组 DNA，并在 Illumina ® MiSeq 仪器上进行测序。使用 PROKKA 和 Rast 对草图基因组进行组装。将组装体提交给基因组流行病学中心的 Resfinder 和 PathogenFinder，以查找耐药基因和致病潜力。还使用 IslandViewer4 查找致病性和噬菌体岛。为了鉴定 fosA 基因，进行了手动注释和 Clustal 分析。鉴定出一种新型的 FosA 变体。最后，使用 VAMPhyRE 软件和 Mega X 进行系统发育分析。
本研究报告了十六株引起与墨西哥公立医院肠外营养相关的暴发的拉氏不动杆菌的基因组。对这些基因组进行了分析，以确定其毒力和耐药性的遗传决定因素。确定了较高的致病性（致病性指数 0.82）和多种耐药基因，包括碳青霉烯类、粘菌素和外排泵。基于序列分析，描述了 fosA 基因的一个新变体。最后，通过建立从 16 个获得的基因组之间的克隆关系来确认暴发。
共生的拉氏不动杆菌菌株可能获得遗传决定因素，从而提供对宿主造成损害的机制，而在临床诊断中却未被发现。拉氏不动杆菌可以通过多种方式进化，包括获得耐药性和毒力基因，这对患者治疗构成了治疗挑战。
