Genomic features of Argentinean KPC-2 producing Klebsiella pneumoniae ST25 and comparative genomics with carbapenem susceptible ST25 isolates.

DANIELA CEJAS; VINCENZO DI PILATO; LUCIA HENRICI DE ANGELIS; SABRINA DI GREGORIO; LUCIA PALLECCHI; FABIO ARENA; GIAN MARIA ROSSOLINI; GABRIEL GUTKIND; MARCELA RADICE

Paris

Congreso; 30th ECCMID (European Congress in Clinical Microbiology and Infectious Diseases); 2020

ESCMID (European Society in Clinical Microbiology and Infectious Diseases)

https://www.eccmidlive.org/#!contentsessions/44582Category: 3b. Resistance surveillance & epidemiology: Gram-negatives8303 Genomic features of Argentinean KPC-2 producing Klebsiellapneumoniae ST25 and comparative genomics with carbapenem susceptibleST25 isolates.Background: The hypervirulent-K.pneumoniae (hvKp) strains display higher virulence potential, suchas, an increased capsular production, giving a hypermucoviscous phenotype. Carbapenem resistancein hvKP has rarely been reported, and KPC-2 positive isolates are concentrated in four clonal lineages, ST11, 15, 101, 258/512. However, we have described the emergence KPC-2-hvKp strains,belonging to ST25, in Argentina. Objective: to explore the genomic features of these isolates and to establish the phylogenetic relationship with other worldwide ST25 strains, which did not displayed carbapenem resistance.Materials/methods: KPC-2 producing isolates, hvKp2015 and hvKp2017, recovered in different hospitals in Buenos Aires, in 2015 and 2017, were included. These isolates displayed resistance to allbeta-lactams, gentamycin and trimethoprime-sulphametoxazole, susceptibility to amikacin and colistin,and intermediate to fluroquinolones. WGS was performed on total DNA using Illumina MiSeq andreads were assembled using SPAdes. BLASTn, Plasmid Finder, Rest Finder, Kleborate, PROKKA, Roary, SniPPy and GUBBINS, were used for sequence analysis. Phylogenetic studies were performed using IQ-Tree and RAxML. Nineteen samples were analyzed, including hvKp2015 and hvKp2017, and all publicly available genomes of ST25 isolates from Australia(1), Belgium(1), Croatia(2), Denmark(1), Germany(2), Italy(2),Poland(1), Romania(2), Turkey(1), UK(3) and USA(1). All these genomes corresponded to clinical human samples. Results: Genomes presented an approximate size of 5.0 Mb (6391 and 6088 CDS for Kp2015 andKp2017). blaKPC-2 plasmids belonged to IncL/M in both isolates. A capsular locus KL2-wzi72 resembling KN2 capsular type was detected, however the loci were not identical and genetic rearrangements were identified. Among resistance genes blaKPC-2, blaOXA-1, aac(6´)-Ib cr, aac(3)-IIa,aph(3´´)-Ib, aph(6)-Id, dfrA14, qnrB1, oqxA in both isolates andblaCTX-M-15 inhvKp2015. Whole and core genome phylogenetic analysis showed strong relationship and two main clusters could be recognized. Argentinean samples grouped together with Italy, Belgium and USA isolates. The same group setting was observed when a closely related ST (ST65) was used to route the phylogenetic tree. Conclusions: Phylogenetic analysis of ST25 isolates including KPC-2-producing isolates is not available in indexed literature. Carbapenem-resistant K.pneumoniae-ST25 appear to have evolved from susceptible strains, indicating a confluence of virulence and carbapenem resistance, which might poses major problems in the management of K. pneumoniae infections.