Whole Genome Sequencing of Pediatric Klebsiella pneumoniae Strains Reveals Important Insights Into Their Virulence-Associated Traits

Abstract

Klebsiella pneumoniae is recognized as a common cause of nosocomial infections and outbreaks causing pneumonia, septicemia, and urinary tract infections. This opportunistic bacterium shows an increasing acquisition of antibiotic-resistance genes, which complicates treatment of infections. Hence, fast reliable strain typing methods are paramount for the study of this opportunistic pathogen’s multi-drug resistance genetic profiles. In this study, thirty-eight strains of K. pneumoniae isolated from the blood of pediatric patients were characterized by whole-genome sequencing and genomic clustering methods. Genes encoding β-lactamase were found in all the bacterial isolates, among which the blaSHV variant was the most prevalent (53%). Moreover, genes encoding virulence factors such as fimbriae, capsule, outer membrane proteins, T4SS and siderophores were investigated. Additionally, a multi-locus sequence typing (MLST) analysis revealed 24 distinct sequence types identified within the isolates, among which the most frequently represented were ST76 (16%) and ST70 (11%). Based on LPS structure, serotypes O1 and O3 were the most prevalent, accounting for approximately 63% of all infections. The virulence capsular types K10, K136, and K2 were present in 16, 13, and 8% of the isolates, respectively. Phylogenomic analysis based on virtual genome fingerprints correlated with the MLST data. The phylogenomic reconstruction also denoted association between strains with a higher abundance of virulence genes and virulent serotypes compared to strains that do not possess these traits. This study highlights the value of whole-genomic sequencing in the surveillance of virulence attributes among clinical K. pneumoniae strains.

Genomic insights into virulence factors affecting tissue-invasive Klebsiella pneumoniae infection

“…We expect that prompt, simple, and accurate diagnostic tests will be developed to identify these factors and will be made available in clinical laboratories. Second, this study dose not closely emphasize on the phenotypic features of the strains, such as the biofilm formation, quantification of the capsular glucuronic acid for examining hypermucoviscous phenomenon [ 23 , 34 , 35 ], and resistance to macrophage-mediated phagocytosis. Nevertheless, it is noteworthy that our findings signify the huge impact of the genomic traits on the clinical virulence for tissue-invasive K. pneumoniae infection.…”

Resistance Phenotype and Molecular Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolated from Nanjing Children’s Hospital in Jiangsu Province, China

“…Although the two strains carrying the bla NDM-5 gene were all of the same ST (ST76), the PFGE map showed different clusters, reflecting the diversity of the ST76-type pedigree. It was reported that Klebsiella pneumoniae ST76 caused an infection outbreak in neonatal wards in Mexico, 39 suggesting that ST76 is a potential high-risk clone that needs more attention. NDM-5-producing Klebsiella pneumoniae has been reported in some countries, such as China: ST4, 40 ST65, 41 ST290, 42 ST337, 13 and ST485; 43 Italy: ST383; 44 Nigeria: ST476; 45 Singapore: ST231; 46 and USA: ST147.…”

The Spread of NDM-1 and NDM-7-Producing Klebsiella pneumoniae Is Driven by Multiclonal Expansion of High-Risk Clones in Healthcare Institutions in the State of Pará, Brazilian Amazon Region

“…Despite the non-HRCs being found related with the minority of NDM-producing K. pneumoniae isolates in our study, they were interestingly detected carrying the bla NDM-7 variant. ST1401 was first described in a human blood sample from Kuwait and has been reported in the USA and Mexico [ 68 , 69 , 70 ]. ST138/CC138 has been associated with KPC-2-producing and NDM-7-producing isolates in Brazil and Canada, respectively [ 14 , 71 ].…”