Genomics of Klebsiella pneumoniae Species Complex Reveals the Circulation of High-Risk Multidrug-Resistant Pandemic Clones in Human, Animal, and Environmental Sources

Abstract

The Klebsiella species present a remarkable genetic and ecological diversity, being ubiquitous in nature. In particular, the Klebsiella pneumoniae species complex (KpSC) has emerged as a major public health threat in the world, being an interesting model to assess the risk posed by strains recovered from animals and the environment to humans. We therefore performed a genomic surveillance analysis of the KpSC using every public genome in Brazil, aiming to show their local and global relationships, and the connectivity of antibiotic resistance and virulence considering human, animal, and environmental sources. The 390 genomes from distinct sources encompassed the K. pneumoniae, Klebsiella quasipneumoniae subsp. quasipneumoniae, Klebsiella quasipneumoniae subsp. similipneumoniae, Klebsiella variicola subsp. variicola, Klebsiella variicola subsp. tropica, and Klebsiella grimontii species and subspecies. K. pneumoniae harbored dozens of antibiotic resistance genes, while most of the genomes belong to the high-risk pandemic CC258 occurring in humans, animals, and the environment. In K. pneumoniae ST11, a high prevalence of the virulence determinants yersiniabactin, colibactin, and T6SS was revealed in association with multi-drug resistance (MDR), including carbapenem resistance. A diversity of resistance genes is carried by plasmids, some shared between strains from different STs, regions, and sources. Therefore, here were revealed some factors driving the success of KpSC as a pathogen.

Genomic characterization of a pandrug-resistantKlebsiella pneumoniaebelonging to the high-risk ST11 in the Brazilian Amazon region

“…The in vitro analyses revealed that Kp196 corresponded to a PDR strain (Table 1), and the cgMLST assigned it to the ST11 pandemic lineage. In spite of the high prevalence of this lineage in Brazil [13], this is the first report of a PDR ST11 in the country. In fact, PDR K. pneumoniae remains rare in Brazil, having only been reported in ST437 and ST258 restricted to the South/Southeast regions [4][5][6].…”

Occurrence of Multidrug-Resistant Bacteria Resulting from the Selective Pressure of Antibiotics: A Comprehensive Analysis of ESBL K. pneumoniae and MRSP Isolated in a Dog with Rhinorrhea

“…The two strains of K. pneumoniae recovered in this study presented the capsular-type KL105 and Sequence Type 11, previously associated with MDR and virulence determinants (yersiniabactin and colibactin) [ 42 ]. The ST11 KL105 clade has been successfully disseminated in Europe, even circulating in Portuguese hospitals for years [ 43 , 44 ].…”

Lignin-Degrading Bacteria in Paper Mill Sludge

“…species are widely distributed in natural environments, such as soils, waters, plants, etc. [ 62 ]; then, they can be found in samples involving the use of cellulose-based raw materials, such as black liquor. In this way, these species of bacteria may produce enzymes capable of degrading lignin as Klebsiella pneumoniae NX-1 [ 63 ].…”