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

Abstract

<i>K. pneumoniae</i> (KPN) is one of the widest spread bacteria in which combined resistance to several antimicrobial groups is frequent. The most common β-lactamases found in <i>K. pneumoniae</i> 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 β-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 <i>bla_KPC-</i>₂, <i>bla_KPC-</i>₃, <i>bla_KPC-</i>₉, <i>bla_SHV-</i>₁₁, <i>bla_SHV-</i>₂₈, <i>bla_CTX-M-</i>₁₅, <i>bla_OXA-</i>₁, <i>bla_OXA-</i>₉, <i>bla_OXA-</i>₂₃, <i>qnrS1</i>, <i>qnrB19</i>, <i>qnrB66</i>, <i>aac(6')-Ib-cr</i>, and <i>fosA</i> 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 β-lactamase.