Plasmids and phage predicted.

Klebsiella pneumoniae and Klebsiella quasipneumoniae are closely related human pathogens of global concern. The more recently described K. quasipneumoniae shares similar morphological characteristics with K. pneumoniae and is commonly misidentified as this species using traditional laboratory techniques. The vast mobilome in these pathogenic bacteria influences the dissemination of virulence factors in high-risk environments and it is, therefore, critical to monitor strains for developing effective clinical management strategies. Herein, this study utilized Illumina sequencing to characterize the whole genomes of nine clinical K. pneumoniae and one K. quasipneumoniae isolate obtained from patients of 3 major hospitals in Trinidad, West Indies. Reconstruction of the assembled genomes and implementation of several bioinformatic tools revealed unique features such as high pathogenicity islands associated with the isolates. The K. pneumoniae isolates were categorized as classical (n = 3), uropathogenic (n = 5), or hypervirulent (n = 1) strains. In silico multilocus sequence typing, and phylogenetic analysis showed that isolates were related to several international high-risk genotypes, including sequence types ST11, ST15, ST86, and ST307. Analysis of the virulome and mobilome of these pathogens showed unique and clinically important features including the presence of genes associated with Type 1 and Type 3 fimbriae, the aerobactin and yersiniabactin siderophore systems, the K2 and O1/2, and the O3 and O5 serotypes. These genes were either on or in close proximity to insertion sequence elements, phage sequences, and plasmids. Several secretion systems including the Type VI system and relevant effector proteins were prevalent in the local isolates. This is the first comprehensive study investigating the genomes of clinical K. pneumoniae and K. quasipneumoniae isolates from Trinidad, West Indies. The data presented illustrate the diversity of Trinidadian clinical K. pneumoniae isolates as well as significant virulence biomarkers and mobile elements associated with these isolates. Additionally, the genomes of the local isolates will add to global databases and thus can be used in future surveillance or genomic studies in this country and the wider Caribbean region.肺炎克雷伯菌（Klebsiella pneumoniae）和类肺炎克雷伯菌（Klebsiella quasipneumoniae）是受全球关注的亲缘关系密切的人类致病菌。新近被描述的类肺炎克雷伯菌与肺炎克雷伯菌具有相似的形态学特征，传统实验室检测技术常将其误鉴定为肺炎克雷伯菌。这类致病菌中庞大的移动基因组（mobilome）可在高风险环境中促进毒力因子的传播，因此监测菌株特征对于制定高效临床管理策略至关重要。本研究采用Illumina测序技术，对从西印度群岛特立尼达岛3家大型医院患者体内分离得到的9株临床肺炎克雷伯菌及1株类肺炎克雷伯菌的全基因组进行解析。通过基因组组装重建及多种生物信息学工具分析，发现了分离株的独特特征，例如与其相关的高致病性岛（pathogenicity islands）。肺炎克雷伯菌分离株可分为经典型（n=3）、尿路致病型（n=5）及高致病型（n=1）三类。计算机辅助多位点序列分型（multilocus sequence typing）与系统发育分析结果显示，这些分离株与多种国际高风险基因型相关，包括序列型ST11、ST15、ST86及ST307。对这些致病菌的毒力组（virulome）和移动基因组进行分析后，揭示了多项独特且具有临床重要性的特征，例如存在与1型菌毛（Type 1 fimbriae）、3型菌毛（Type 3 fimbriae）、气杆菌素与耶尔森菌素铁载体系统、K2及O1/2血清型、O3与O5血清型相关的基因。这些基因要么位于插入序列元件、噬菌体序列及质粒上，要么与这些遗传元件紧密相邻。多种分泌系统（包括VI型分泌系统（Type VI secretion system））及相关效应蛋白在本次研究的本地分离株中普遍存在。本研究是首个针对西印度群岛特立尼达岛临床肺炎克雷伯菌和类肺炎克雷伯菌分离株基因组开展的综合性研究。本研究呈现的数据展示了特立尼达岛临床肺炎克雷伯菌分离株的多样性，以及与这些分离株相关的关键毒力生物标志物和可移动遗传元件。此外，这些本地分离株的基因组将被补充至全球数据库，可用于该国及更广泛加勒比地区未来的监测或基因组学研究。