Background Enterobacter cloacae complex (ECC) bacteria, such as E. cloacae, E. sichuanensis, E. kobei, and E. roggenkampii, have been emerging as nosocomial pathogens. Many strains isolated from medical clinics were found to be resistant to antibiotics, and in the worst cases, acquired multidrug resistance. We present the whole genome sequence of SGAir0282, isolated from the outdoor air in Singapore, and its relevance to other ECC bacteria by in silico genomic analysis. Results Complete genome assembly of E. sichuanensis strain SGAir0282 was generated using PacBio RSII and Illumina MiSeq platforms, and the datasets were used for de novo assembly using Hierarchical Genome Assembly Process (HGAP) and error corrected with Pilon. The genome assembly consisted of a single contig of 4.71 Mb and with a G+C content of 55.5%. No plasmid was detected in the assembly. The genome contained 4371 coding genes, 83 tRNA and 25 rRNA genes, as predicted by NCBI's Prokaryotic Genome Annotation Pipeline (PGAP). Among the genes, the antibiotic resistance related genes were included: Streptothricin acetdyltransferase (SatA), fosfomycin resistance protein (FosA) and metal-dependent hydrolases of the beta-lactamase superfamily I (BLI). Conclusion Based on whole genome alignment and phylogenetic analysis, the strain SGAir0282 was identified to be Enterobacter sichuanensis. The strain possesses gene clusters for virulence, disease and defence, that can also be found in other multidrug resistant ECC type strains.

中文翻译：

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从新加坡空气中分离出的四川肠杆菌SGAir0282的全基因组。

背景 阴沟肠杆菌复合体 (ECC) 细菌，如阴沟肠杆菌、四川肠杆菌、科贝肠杆菌和罗根坎帕伊肠杆菌，已成为医院内的病原体。许多从医疗诊所中分离出来的菌株被发现对抗生素有抗药性，在最坏的情况下，还会获得多药耐药性。我们通过计算机基因组分析展示了从新加坡室外空气中分离出来的 SGAir0282 的全基因组序列，以及它与其他 ECC 细菌的相关性。结果 使用 PacBio RSII 和 Illumina MiSeq 平台生成了四川大肠杆菌菌株 SGAir0282 的完整基因组组装，并使用分层基因组组装过程 (HGAP) 将数据集用于从头组装，并使用 Pilon 进行错误校正。基因组组装由一个 4.71 Mb 的重叠群组成，G+C 含量为 55.5%。在组装中未检测到质粒。正如 NCBI 的原核基因组注释管道 (PGAP) 所预测的，基因组包含 4371 个编码基因、83 个 tRNA 和 25 个 rRNA 基因。在这些基因中，抗生素耐药相关基因包括：链丝菌素乙酰转移酶（SatA）、磷霉素耐药蛋白（FosA）和β-内酰胺酶超家族I（BLI）的金属依赖性水解酶。结论通过全基因组比对和系统发育分析，鉴定菌株SGAir0282为四川肠杆菌。该菌株具有毒力、疾病和防御基因簇，也可以在其他耐多药 ECC 型菌株中找到。抗生素耐药相关基因包括：链丝菌素乙酰转移酶（SatA）、磷霉素耐药蛋白（FosA）和β-内酰胺酶超家族I（BLI）的金属依赖性水解酶。结论通过全基因组比对和系统发育分析，鉴定菌株SGAir0282为四川肠杆菌。该菌株具有毒力、疾病和防御基因簇，也可以在其他耐多药 ECC 型菌株中找到。抗生素耐药相关基因包括：链丝菌素乙酰转移酶（SatA）、磷霉素耐药蛋白（FosA）和β-内酰胺酶超家族I（BLI）的金属依赖性水解酶。结论通过全基因组比对和系统发育分析，鉴定菌株SGAir0282为四川肠杆菌。该菌株具有毒力、疾病和防御基因簇，也可以在其他耐多药 ECC 型菌株中找到。