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

Abstract

K. pneumoniae (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 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 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 blaKPC-2, blaKPC-3, blaKPC-9, blaSHV-11, blaSHV-28, blaCTX-M-15, blaOXA-1, blaOXA-9, blaOXA-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 β-lactamase.

Resistome and Virulome of Multi-Drug Resistant E. coli ST131 Isolated from Residents of Long-Term Care Facilities in the Northern Italian Region

“…Similarly, the KPC-3 carbapenemase was found only in three E. coli strains (ST131 and ST1193) collected in CDS_RO, IPABRT_VI and PCS_VR LTCFs. In a previous paper where we characterized the resistome of K. pneumoniae isolates, we found, in the same LTCFs, KPC-3 producing K. pneumoniae [ 26 ]. The E. coli and K. pneumoniae strains harbored the same IncFIB(pQil) plasmid.…”

Molecular Characterization by Whole-Genome Sequencing of Clinical and Environmental Serratia marcescens Strains Isolated during an Outbreak in a Neonatal Intensive Care Unit (NICU)

“…Total nucleic acid was extracted from S. marcescens liquid cultures using a modified protocol of MagMAX Microbiome Ultra Nucleic Acid Isolation kit (Applied Biosystems, ThermoFisher Scientific, Monza, Italy) [ 30 ]. Genomic libraries were prepared using Swift 2S Turbo DNA Library kit (Swift Biosciences, Ann Arbor, MI, USA) as previously reported [ 31 ]. The WGS was performed on an Illumina MiSeq platform using v3 reagent kits generating 2 × 300 bp paired-end reads (Illumina, San Diego, CA, USA) [ 32 , 33 ].…”

Determination of multidrug-resistant populations and molecular characterization of complex Klebsiella spp. in wild animals by multilocus sequence typing

“…One ST35 isolate was from a blue and yellow Macaw, and the other ST1948 was from a puma. K. pneumoniae ST35 is an MDR clone and has been identified in humans from several countries [33,36,37]. It is also found in feces, milk from [id: 3084, id: 13421), broiler and turkey in Norway [38], urban rodents in China [39], and wastewater in Romania [40].…”