Emergence of two novel sequence types (3366 and 3367) NDM-1- and OXA-48-co-producing K. pneumoniae in Italy

• Published in: European journal of clinical microbiology & infectious diseases Vol. 38; no. 9; pp. 1687 - 1691
• Main Authors: Gona, Floriana, Bongiorno, Dafne, Aprile, Ausilia, Corazza, Erika, Pasqua, Betta, Scuderi, Maria Grazia, Chiacchiaretta, Matteo, Cirillo, Daniela Maria, Stefani, Stefania, Mezzatesta, Maria Lina
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.09.2019; Springer Nature B.V
• Subjects: ABC transporter; Anti-Bacterial Agents - pharmacology; Antibiotics; Bacterial Proteins - genetics; Bacterial Typing Techniques; beta-Lactamases - genetics; Biomedical and Life Sciences; Biomedicine; Biosynthesis; Carbapenems - pharmacology; Clinical isolates; Disease Outbreaks; Electrophoresis; Electrophoresis, Gel, Pulsed-Field; Gel electrophoresis; Gene sequencing; Genes; Genomes; Humans; Infant, Newborn; Intensive Care, Neonatal; Internal Medicine; Italy; Klebsiella; Klebsiella Infections - microbiology; Klebsiella pneumoniae; Klebsiella pneumoniae - drug effects; Klebsiella pneumoniae - enzymology; Klebsiella pneumoniae - genetics; Medical Microbiology; Microbial Sensitivity Tests; Multilocus Sequence Typing; Neonates; Nucleotide sequence; Original Article; Pili; Plasmids; Pulsed-field gel electrophoresis; Virulence; Virulence factors; Websites; Whole Genome Sequencing; Italy; ST3366; Carbapenemase; ST101; ST3367; OXA-48; NDM; K. pneumoniae
• ISSN: 0934-9723; 1435-4373
• DOI: 10.1007/s10096-019-03597-w

The aim of this study was to analyze the alarming spread of NDM-1- and OXA-48-co-producing Klebsiella pneumoniae clinical isolates, collected between October 2016 and January 2018 in a neonatal intensive care unit of the University Hospital, Catania, Italy, through whole genome sequencing. All confirmed carbapenem-resistant K. pneumoniae (CRKp) isolates were characterized pheno- and geno-typically, as well as by whole genome sequencing (WGS). A total of 13 CRKp isolates were identified from 13 patients. Pulsed-field gel electrophoresis (PFGE) was performed, and the multilocus sequence typing (MLST) scheme used was based on the gene sequence as published on the MLST Pasteur website. Core genome MLST (cgMLST) was also performed. All isolates co-carried bla oxa-48 and bla NDM-1 genes located on different plasmids belonging to the IncM/L and IncA/C2 groups, respectively. The 13 strains had identical PFGE profiles. MLST and cgMLST showed that K. pneumoniae was dominated by CRKp ST101 and two novel STs (ST3666 and ST3367), identified after submission to the MLST database for ST assignment. All isolates shared the same virulence factors such as type 3 fimbriae, genes for yersiniabactin biosynthesis, yersiniabactin receptor, and iron ABC transporter. They carried the wzi137 variant associated with the K17 serotype. To the best of our knowledge, this is the first report of two novel STs, 3366 and 3367, NDM-OXA-48-co-producing K. pneumoniae clinical isolates, in Italy.