Genomic epidemiology of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) strains from three university hospitals in Northern-Italy and investigation of intra- and inter- hospitals genetic diversity

Objectives Genomic surveillance of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) is crucial for virulence and drug-resistance monitoring and outbreak containment. Methods Genomic analysis on 87 KPC-Kp strains isolated from 3 Northern-Italy hospitals in 2019-2021 was performed by whole genome sequencing, to determine genotype and characterize resistome, virulome and mobilome. Maximum Likelihood method and Minimum Spanning Tree were used to determine strains correlations and identify putative transmission chains. Results Predominant STs included ST307 (35, 40.2%), ST512/1519 (sharing 1 allele difference, 15, 17.2%), ST20 (12, 13.8%), and ST101 (7, 8.1%). All strains carried carbapenemase genes, always on a Tn4401a transposon, comprising KPC-3 (48, 55.2%), KPC-2 (38, 43.7%) and KPC-33 (1, 1.2%), the latter conferring ceftazidime/avibactam (CZA) resistance. Seven (8.1%) KPC-Kp strains carried multiple Tn4401a copies and displayed higher meropenem (MEM) and CZA resistance compared to those carrying 1 copy (median[IQR] MIC of 32[32-32] vs 10[8-32] mg/ml p=0.035, and 7[6.5-7.5] vs 1.5[1-2] mg/ml, p=0.002, respectively). Virulence factors identified were siderophores enterobactin (87, 100%), yersiniabactin (53, 60.9%) and aerobactin (11, 12.6%), and truncated rmpA2 hypermucoidy gene (5, 5.8%). Only 10/12 ST20 strains and 5/7 ST101 strains belonged to single clusters characterized by a lower median[IQR] n° of SNPs (7[5-11] vs 414[413-417], p<0.001 and 7.5[5-10] vs 176[123-177], p=0.028, respectively), while strains belonging to other STs did not show evidence of transmission chains or clustering based on hospital. Conclusions Our findings provide in-depth insights into circulating KPC-Kp in Northern-Italy, characterizing STs against resistome and virulome, and addressing new perspectives on intra- and inter- hospital circulation dynamics.