Outbreak caused by a multi-resistant Klebsiella pneumoniae strain of new sequence type ST341 carrying new genetic environments of aac(6′)-Ib-cr and qnrS1 genes in a neonatal intensive care unit in Spain

An outbreak due to a Klebsiella pneumoniae clone occurred in a neonatal intensive care unit of a Spanish Hospital in which three newborns were infected (all with gestational age ≤29 weeks; two of them died) and seven were colonized (gestational age >32 weeks; none died). One K. pneumoniae strain per patient was further characterized. The 10 strains showed an indistinguishable pulsed-field-gel-electrophoresis pattern, were typed in the phylogenetic group KpI and were ascribed into a new sequence type registered as ST341. All 10 strains presented the same multiple-antibiotic-resistant phenotype, showed extended-spectrum-beta-lactamase production, and harbored the bla_CTX-M-15, bla_SHV-11, bla_OXA-1,aac(6′)-Ib-cr, qnrS1, aac(3)-II, aph(3′)-Ia and aadA5 resistance genes. No class 1 or class 2 integrons were detected. The bla_CTX-M-15 gene presented the following genetic environment: ISEcp1-bla_CTX-M-15-orf477. These strains contained two copies of the aac(6′)-Ib-cr gene included in the following new genetic environments: aac(3)-II-IS26-aac(6′)-Ib-cr-bla_OXA-1 and aac(3)-II-IS26-ΔcatB3-bla_OXA-1-aac(6′)-Ib-cr (registered at GenBank with accession numbers GQ438247 and GQ438248, respectively). The genetic environment of the qnrS1 gene (IS26-ΔISEcl2-qnrS1) (GenBank accession number GQ438249) was also not described previously. The aac(6′)-Ib-cr, qnrS1, bla_CTX-M-15, aac(3)-II, and bla_OXA-1 genes, located in a plasmid of 33.5 kb, could be transferred to Escherichia coli by transformation.