McDonagh Francesca, Singh Nitin Kumar, Venkateswaran Kasthuri, Lonappan Aneesa Mangalam, Hallahan Brian, Tuohy Alma, Burke Liam, Kovarova Aneta, Miliotis Georgios
Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland.
Biotechnology and Planetary Protection Group, NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California.
J Glob Antimicrob Resist. 2023 Mar;32:31-34. doi: 10.1016/j.jgar.2022.12.003. Epub 2022 Dec 28.
Kalamiella piersonii is a newly identified bacterial species, first isolated from surfaces of the International Space Station (ISS). It also appears as a novel human pathogen reported to be implicated in bacteremia and kidney stone disease. Here, we report the first complete genome of a multidrug-resistant strain of K. piersonii (GABEKP28), isolated from the saliva of a patient with treatment-resistant schizophrenia (TRS), to determine the mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and virulence factors (VFs) harboured by such a strain of this novel species.
Whole-genome sequencing was performed using DNABSEQ (PE150) and Nanopore MinION platforms. Hybrid assembly was conducted using Unicycler v0.5.0. Genome assembly quality was verified using QUAST v5.0.2. The assembly was annotated using PROKKA v1.14.5. ARGs and VFs were identified using Abricate v1.0.0.
K. piersonii strain GABEKP28 was classified as multidrug-resistant while also carrying plasmidic genetic determinants associated with a hypervirulent phenotype. The complete genome size is 3 881 479 bp and has a guanine-cytosine content of 57.76% while it encodes for 3 525 chromosome coding sequences. The strain was also identified to carry three plasmids of 513 647 bp, 261 771 bp, and 106 029 bp, respectively.
K.piersonii GABEKP28 is the first complete genome of this species to be submitted to GenBank and only the second to be sequenced from a human host. The whole-genome sequencing data with multiple plasmids, ARGs, and VFs will aid in understanding the pathogenicity, evolution, and phylogeny of this novel opportunistic pathogen.
皮尔逊卡拉米菌是一种新鉴定出的细菌物种，首次从国际空间站（ISS）表面分离得到。它还被报道为一种新型人类病原体，与菌血症和肾结石疾病有关。在此，我们报告了从一名难治性精神分裂症（TRS）患者唾液中分离出的一株多重耐药皮尔逊卡拉米菌（GABEKP28）的首个完整基因组，以确定该新物种的此类菌株所携带的可移动遗传元件（MGEs）、抗生素抗性基因（ARGs）和毒力因子（VFs）。
使用DNABSEQ（PE150）和纳米孔MinION平台进行全基因组测序。使用Unicycler v0.5.0进行混合组装。使用QUAST v5.0.2验证基因组组装质量。使用PROKKA v1.14.5对组装结果进行注释。使用Abricate v1.0.0鉴定ARGs和VFs。
皮尔逊卡拉米菌菌株GABEKP28被归类为多重耐药，同时还携带与高毒力表型相关的质粒遗传决定因素。完整基因组大小为3 881 479 bp，鸟嘌呤 - 胞嘧啶含量为57.76%，编码3 525个染色体编码序列。该菌株还被鉴定分别携带三个大小为513 647 bp、261 771 bp和106 029 bp的质粒。
皮尔逊卡拉米菌GABEKP28是该物种首个提交至GenBank的完整基因组，也是第二个从人类宿主中测序得到的基因组。具有多个质粒、ARGs和VFs的全基因组测序数据将有助于理解这种新型机会致病菌的致病性、进化和系统发育。
