ST405 NDM-5 producing Escherichia coli in Northern Italy: the first two clinical cases

Abstract

Fig. 1. Linear map of the plasmids. (a) Schematic representation of the genetic structures surrounding bla NDM-5 gene and (b) structure of bla CMY-42 genetic environment. Letter to the Editor / Clinical Microbiology and Infection 23 (2017) 489e490

Complete Nucleotide Sequence of Plasmids of Two Escherichia coli Strains Carrying blaNDM–5 and blaNDM–5 and blaOXA–181 From the Same Patient

“…The sequence comparison of the two NDM-5 producing plasmids (isolated from 5M and 5P) along with the first reported plasmid producing NDM-5 in Italy revealed that the backbones, and the ARIs, are in some way different. In fact, even though E. coli 5P belongs to the same ST405 of the first Italian NDM-5 producing E. coli strain (ECDT-2_GA) previously collected from the same hospital and the plasmid belongs to the incompatibility group IncFII (same as the plasmid pIBAC_IncFII_NDM5), the plasmid backbone (rep, tra and stability genes) were different as well as TA systems (Bitar et al, 2017). pVSI_IncFII_NDM-5 (carried by 5P) shared most of the regions found in pIBAC_IncFII_NDM5 with more acquired regions as shown in Figure 1.…”

“…pISV_IncI_CMY-42, that harbored the bla CMY-42 gene coding for beta-lactam resistance, exhibited high similarity to plasmid pCMY-42 (KY463221.1; 99.48% sequence similarity 93% query coverage) isolated in 2017 from an E. coli strain in Italy (Bitar et al, 2017). While pISV_IncX3_OXA181, which harbored genes coding for quinolone resistance (qnrS1) and betalactam resistance (bla OXA-181 ), showed 100% sequence similarity and coverage to several plasmids found in NCBI database (AP018837.1 (Sugawara et al, 2019); Myanmar, MG893567.1; China, CP024806; Denmark, MG570092; Lebanon (Bitar et al, 2018), KX894452.1; Germany, KX523903; Czechia).…”

“…On the other hand, the comparison of pISV_IncI_ CMY-42 with the plasmid pIBAC_IncI_CMY-42 isolated with pIBAC_IncFII_NDM-5 (Bitar et al, 2017), showed similar plasmid structure except for a small segment that harbored parM, parB, stbB and SOS protein, which was replaced by a segment harboring some hypothetical proteins with the insertion sequence ISCro (Figure 2). pISV_IncX3_OXA181 was the most conserved plasmid among reported IncX3 plasmids harboring the bla OXA-181 .…”

“…The two E. coli strains (5M and 5P) were carbapenem-resistant and resulted positive for NDM-like for 5P and NDM-like and OXA-48-like production for 5M by Xpert Carba-R test (GeneXpert, Cepheid). Then the isolates were sent to the University of Pavia, where carbapenemase production was confirmed by the KPC/MBL Confirm kit (Rosco Diagnostic) and polymerase chain reaction (PCR) (Balm et al, 2013;Bitar et al, 2017). Finally, the isolates were sent to Charles University in Prague for further genomic characterization.…”

“…Not long after, it has been reported in Japan (Nakano et al, 2014), China (Shen et al, 2018), United States (Mediavilla et al, 2016), South Korea (Park et al, 2016), Lebanon (Dagher et al, 2019). In Italy, NDM-5 was firstly reported in 2017 from an E. coli strain isolated from a patient with travel history to Thailand, who was hospitalized in Desenzano del Garda (Bitar et al, 2017). According to ECDC 2018-2019 regional report 1 , outbreaks with involvement of NDM-producers have been increasingly reported from Italy.…”