Whole-Genome Sequencing (WGS) of Carbapenem-Resistant K. pneumoniae Isolated in Long-Term Care Facilities in the Northern Italian Region

K. pneumoniae (KPN) is one of the widest spread bacteria in which combined resistance to several antimicrobial groups is frequent. The most common beta-lactamases found in K. pneumoniae are class A carbapenemases, both chromosomal-encoded (i.e., NMCA, IMI-1) and plasmid-encoded (i.e., GES-enzymes, IMI-2), VIM, IMP, NDM, OXA-48, and extended-spectrum beta-lactamases (ESBLs) such as CTX-M enzymes. In the present study, a total of 68 carbapenem-resistant KPN were collected from twelve long-term care facilities (LTCFs) in the Northern Italian region. The whole-genome sequencing (WGS) of each KPN strain was determined using a MiSeq Illumina sequencing platform and analysed by a bacterial analysis pipeline (BAP) tool. The WGS analysis showed the prevalence of ST307, ST512, and ST37 as major lineages diffused among the twelve LTCFs. The other lineages found were: ST11, ST16, ST35, ST253, ST273, ST321, ST416, ST1519, ST2623, and ST3227. The bla(KPC-2), bla(KPC-3), bla(KPC-9), bla(SHV-11), bla(SHV-28), bla(CTX-M-15), bla(OXA-1), bla(OXA-9), bla(OXA-23), qnrS1, qnrB19, qnrB66, aac(6 ')-Ib-cr, and fosA were the resistance genes widespread in most LTCFs. In this study, we demonstrated the spreading of thirteen KPN lineages among the LTCFs. Additionally, KPC carbapenemases are the most widespread beta-lactamase.

Automated summary

This study identified thirteen K. pneumoniae lineages spreading among long-term care facilities in Northern Italy, with the prevalence of ST307, ST512, and ST37 as major lineages. The most widespread resistance genes in these facilities were bla(KPC-2), bla(KPC-3), bla(KPC-9), bla(SHV-11), bla(SHV-28), bla(CTX-M-15), bla(OXA-1), bla(OXA-9), bla(OXA-23), qnrS1, qnrB19, qnrB66, aac(6 ')-Ib-cr, and fosA. Additionally, KPC carbapenemases were found to be the most common beta-lactamases.