Jacob Jobin John, Aravind V, Beresford-Jones Benjamin S, Lal Y Binesh, Shankar Chaitra, Yesudoss M, Abdullah Fiza, Priya T Monisha, Kulkarni Sanika, Baker Stephen, Veeraraghavan Balaji, Walia Kamini
Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.
J Epidemiol Glob Health. 2024 Dec;14(4):1668-1677. doi: 10.1007/s44197-024-00323-4. Epub 2024 Nov 12.
Klebsiella pneumoniae is a common opportunistic pathogen in humans, often associated with both virulence and antimicrobial resistance (AMR) phenotypes. K. pneumoniae have a highly plastic genome and can act as a vehicle for disseminating genetic information. Aiming to assess the impact of the human-animal-environment interface on AMR dissemination in K. pneumoniae we sampled and genome sequenced organisms from a range of environments and compared their genetic composition.
Representative K. pneumoniae isolated from clinical specimens (n = 59), livestock samples (n = 71), and hospital sewage samples (n = 16) during a two-year surveillance study were subjected to whole genome sequencing. We compared the taxonomic and genomic distribution of K. pneumoniae, AMR gene abundance, virulence gene composition, and mobile genetic elements between the three sources.
The K. pneumoniae isolates originating from livestock were clonally distinct from those derived from clinical/hospital effluent samples. Notably, the clinical and hospital sewage isolates typically possessed a greater number of resistance/virulence genes than those from animals. Overall, we observed a limited overlap of K. pneumoniae clones, AMR genes, virulence determinants, and plasmids between the different settings.
In this setting, the spread of XDR and hypervirulent clones of K. pneumoniae appears to be restricted to humans with no obvious association with non-clinical sources. Emergent clones of K. pneumoniae carrying both resistance and virulence determinants are likely to have emerged in hospital settings rather than in animal or natural environments. These data challenge the current view of AMR transmission in K. pneumoniae in a One-Health context.
肺炎克雷伯菌是人类常见的机会致病菌，常与毒力和抗菌药物耐药性（AMR）表型相关。肺炎克雷伯菌基因组具有高度可塑性，可作为传播遗传信息的载体。为评估人类-动物-环境界面在肺炎克雷伯菌AMR传播中的影响，我们从一系列环境中采集样本并对菌株进行全基因组测序，比较它们的基因组成。
在一项为期两年的监测研究中，对从临床标本（n = 59）、家畜样本（n = 71）和医院污水样本（n = 16）中分离出的代表性肺炎克雷伯菌进行全基因组测序。我们比较了三种来源的肺炎克雷伯菌的分类学和基因组分布、AMR基因丰度、毒力基因组成以及可移动遗传元件。
源自家畜的肺炎克雷伯菌分离株在克隆上与源自临床/医院污水样本的分离株不同。值得注意的是，临床和医院污水分离株通常比动物来源的分离株拥有更多的耐药/毒力基因。总体而言，我们观察到不同环境中肺炎克雷伯菌克隆、AMR基因、毒力决定因素和质粒的重叠有限。
在这种情况下，肺炎克雷伯菌的广泛耐药（XDR）和高毒力克隆的传播似乎仅限于人类，与非临床来源无明显关联。携带耐药和毒力决定因素的肺炎克雷伯菌新出现的克隆可能是在医院环境中而非动物或自然环境中出现的。这些数据挑战了“同一健康”背景下当前关于肺炎克雷伯菌AMR传播的观点。
