Genomic characterization of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) strains circulating in three university hospitals in Northern Italy over three years.

OBJECTIVES: Genomic surveillance of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) is crucial for virulence, 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 (WGS), to characterize resistome, virulome, and mobilome, and to assess potential associations with phenotype resistance and clinical presentation. Maximum Likelihood and Minimum Spanning Trees were used to determine strain correlations and identify potential transmission clusters. RESULTS: Overall, 15 different STs were found; the predominant ones included ST307 (35, 40.2%), ST512/1519 (15, 17.2%), ST20 (12, 13.8%), and ST101 (7, 8.1%). 33 (37.9%) KPC-Kp strains were noticed to be in five transmission clusters (median number of isolates in each cluster: 5 [3-10]), four of them characterized by intra-hospital transmission. All 87 strains harbored Tn4401a transposon, carrying blaKPC-3 (48, 55.2%), blaKPC-2 (38, 43.7%), and in one case (1.2%) blaKPC-33, the latter gene conferred resistance to ceftazidime/avibactam (CZA). Thirty strains (34.5%) harbored porin mutations; of them, 7 (8.1%) carried multiple Tn4401a copies. These strains were characterized by significantly higher CZA minimum inhibitory concentration compared with strains with no porin mutations or single Tn4401a copy, respectively, even if they did not overcome the resistance breakpoint of 8 ug/mL. Median 2 (IQR:1-2) virulence factors per strain were detected. The lowest number was observed in ST20 compared to the other STs (p<0.001). While ST307 was associated with infection events, a trend associated with colonization events could be observed for ST20. CONCLUSIONS: Integration of genomic, resistance score, and clinical data allowed us to define a relative diversification of KPC-Kp in Northern Italy between 2019 and 2021, characterized by few large transmission chains and rare inter-hospital transmission. Our results also provided initial evidence of correlation between KPC-Kp genomic signatures and higher MIC levels to some antimicrobial agents or colonization/infection status, once again underlining WGS's importance in bacterial surveillance.

Isolation of a Colistin-Susceptible MDR Pantoea calida Harboring the mcr-9 Gene Suggests the Silent Spread of the Resistance Factor.

Pantoea spp. are bacteria that are often detected in the environment and as symbionts of arthropods. They sporadically cause infections in humans and recently extended spectrum beta-lactamases (ESBL)- and carbapenemase-producing strains have started to emerge. In this study, we report the isolation and the complete genome sequence of a strain of Pantoea calida encoding the colistin-resistance gene mcr-9. The strain was isolated from a preterm newborn in a neonatal pathology ward. On clinical examination, his vital signs were normal and blood culture was negative. Rectal swab screening for ESBL-producing Enterobacterales allowed to isolate the bacterium, and a complete genome was obtained using both short and long read sequencing. The mcr-9 gene was found to be encoded on a IncHI2 superplasmid, which confers resistance to six classes of antibiotics, including beta lactams (ESBL). Despite the presence of mcr-9, the isolate retains susceptibility to colistin, which could be explained by the absence of compatible regulatory genes (qseBC) from the genome. The presence of the resistance gene is undetectable with the routine clinical procedures, that is, phenotypic tests. This suggests that a silent spread might be ongoing in the ward. To our knowledge, this is the first description of an MDR P. calida and of a Pantoea spp. encoding any mobile colistin resistance gene.