Abstract
BackgroundKlebsiella pneumoniae ST101 is an emerging high-risk clone which exhibits extensive drug resistance. Bacterial strains residing in multiple hosts show unique signatures related to host adaptation. In this study, we assess the genetic relationship of K. pneumoniae ST101 isolated from hospital samples, the environment, community, and livestock using whole genome sequencing (WGS).Materials and MethodsWe selected ten K. pneumoniae ST101 strains from hospitalized patients in Italy (n = 3) (2014) and Spain (n = 5) (2015–2016) as well as Belgian livestock animals (n = 2) (2017–2018). WGS was performed with 2 × 250 bp paired-end sequencing (Nextera XT) sample preparation kit and MiSeq (Illumina Inc.). Long-read sequencing (Pacbio Sequel I) was used to sequence the two livestock strains and three Italian hospital-associated strains. Furthermore, a public ST101 sequence collection of 586 strains (566 hospital-associated strains, 12 environmental strains, six strains from healthy individuals, one food-associated strain and one pig strain) was obtained. BacPipe and Kleborate were used to conduct genome analysis. ISFinder was used to find IS elements, and PHASTER was utilized to identify prophages. A phylogenetic tree was constructed to illustrate genetic relatedness.ResultsHospital-associated K. pneumoniae ST101 showed higher resistance scores than non-clinical isolates from healthy individuals, the environment, food and livestock (1.85 ± 0.72 in hospital-associated isolates vs. 1.14 ± 1.13 in non-clinical isolates, p < 0.01). Importantly, the lack of integrative conjugative elements ICEKp bearing iron-scavenging yersiniabactin siderophores (ybt) in livestock-associated strains suggests a lower pathogenicity potential than hospital-associated strains. Mobile genetic elements (MGE) appear to be an important source of diversity in K. pneumoniae ST101 strains from different origins, with a highly stable genome and few recombination events outside the prophage-containing regions. Core genome MLST based analysis revealed a distinct genetic clustering between human and livestock-associated isolates.ConclusionThe study of K. pneumoniae ST101 hospital-associated and strains from healthy individuals and animals revealed a genetic diversity between these two groups, allowing us to identify the presence of yersiniabactin siderophores in hospital-associated isolates. Resistance and virulence levels in livestock-associated strains were considerably lower than hospital-associated strains, implying that the public health risk remains low. The introduction of an ICEKp into animal strains, on the other hand, might pose a public threat over time.
Highlights
Klebsiella pneumoniae is part of the Enterobacteriaceae family and is widely present in the gastrointestinal tract of humans and animals as well as in the environment
All K. pneumoniae ST101 sequences originating from different sources [human including sequences from hospital-associated infections (n = 566) and healthy, asymptomatic carriers in the community (n = 6), animal (n = 1), food (n = 1) and the environment including river water (n = 1), hospital sewage (n = 7) and a surface at a NICU ward (n = 4)] available on NCBI and A Global Platform for Genomic Surveillance: Pathogenwatch on 27 September 2021 (n = 586) were added for comparison analysis (Supplementary Table 1)
Higher Minimum inhibitory concentrations (MIC) values for third generation cephalosporins, imipenem, fluoroquinolones and aminoglycoside antibiotics were consistently observed among hospital-associated strains compared to the animal strains (Table 1)
Summary
Klebsiella pneumoniae is part of the Enterobacteriaceae family and is widely present in the gastrointestinal tract of humans and animals as well as in the environment. Opportunistic, hypervirulent and multidrug-resistant (MDR) K. pneumoniae strains have emerged across the world (Martin and Bachman, 2018). K. pneumoniae causes a range of extraintestinal infections in humans, including pneumonia, urinary tract infections and bloodstream infections, usually in the context of opportunistic health-care-associated infections in vulnerable patient groups (Martin and Bachman, 2018). Hypervirulent strains of K. pneumoniae can cause severe infections including pneumonia, pyogenic liver abscess, endophtalmitis, necrotizing fasciitis and meningitis in otherwise healthy persons (Wyres et al, 2020). The global success of the pathogen lies in its accessory genome, which plays an essential role in the emergence of high-risk isolates that are antibiotic-resistant and/or hypervirulent, and are associated with increased pathogenesis, invasive infections and fast adaptation to a specific niche or host (Hamza et al, 2016; Roe et al, 2019). We assess the genetic relationship of K. pneumoniae ST101 isolated from hospital samples, the environment, community, and livestock using whole genome sequencing (WGS)
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