Plasmid carrying mcr-9 from an extensively drug-resistant NDM-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae clinical isolate

Abstract

The extensively drug-resistant NDM-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae M17277 (Kqsq-M17277) was only susceptible to colistin and fosfomycin. Whole genome sequencing of Kqsq-M17277 was performed through Illumina (short reads) and Oxford Nanopore Technologies (long reads). Hybrid assembly of short and long reads rendered circular contigs of the Kqsq-M17277 chromosome and three plasmids of 477,340 (p17277A_477), 138,998 (p17277C_138, which harbored blaNDM-1) and 123,307 bp (p17277B_123). In silico analysis showed that p17277A_477 was not previously described, belonged to the IncHI2 incompatibility group and contained 51 complete or partial (≥300 bp) insertion sequences and Tn3 family transposons, which encompassed, as a whole, 14% of the p17277A_477 sequence. In silico search for antimicrobial resistance genes revealed that p17277A_477 harbored the recently described plasmid-encoded mcr-9 gene (colistin resistance), besides other resistance genes. This is the first worldwide report of a K. quasipneumoniae harboring mcr-9 and blaNDM-1 and the first report of mcr-9 in Latin America. This gene was embedded in a genetic structure, i.e., IS903B-like/mcr-9/wbuC/IS26, that was found in 71% of the mcr-9-harboring sequences of the NCBI Nucleotide Collection database. The qseC and qseB genes involved in mcr-9 expression were not found in Kqsq-M17277, which could explain its colistin susceptibility. Fifteen additional resistance genes were detected in p17277A_477. Ten of them [aac(6′)-IIc, aadA2, aph(3′)-Ia, blaDHA-1, dfrA12, ereA2, mphA, qnrB4, sul1 and tet(D)] were found clustered within a 44,907-bp-long array of IS26-bounded resistance genes. The plasmid-mediated quinolone resistance gene qnrB4 was located in a complex class 1 integron within this IS26-bounded resistance gene cluster. p17277A_477 was self-transferable by conjugation to Escherichia coli J53, azide-resistant. The Tra1 and Tra2 conjugative transfer regions of the IncHI2 plasmid R478 were found by in silico search. p17277A_477 is a complex plasmid that provides a large baggage of both resistance genes and genetic resources for plasmid rearrangements and additional resistance gene acquisition.