Genomic Characterization of VIM and MCR Co-Producers: The First Two Clinical Cases, in Italy.

Vittoria Mattioni Marchetti,Erika Scaltriti,Elena Fogato,Chiara Bracchi,Roberta Migliavacca,Ibrahim Bitar,Stefano Pongolini,Mario Sarti,Jaroslav Hrabak

doi:10.3390/diagnostics11010079

Abstract

Background: the co-production of carbapenemases and mcr-genes represents a worrisome event in the treatment of Enterobacteriaceae infections. The aim of the study was to characterize the genomic features of two clinical Enterobacter cloacae complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. Methods: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the blaVIM- and mcr- type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio). Results: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The mcr-9.2 gene was harbored on a conjugative IncHI2 plasmid, while the blaVIM-1 determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: mcr-9 gene and its two component regulatory genes for increased expression on the chromosome, mcr-4.3 on non-conjugative (yet co-transferable) ColE plasmid, and blaVIM-1 on a non-conjugative IncA plasmid. Conclusions: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy.

Highlights

The ECC (Enterobacter cloacae complex) is composed of six species including E. cloacae and subspp, E. kobei, E. nimipressuralis, E. ludwigii, E. asburiae and E. hormaechei [1]
While colistin is considered as the last resort antibiotic for treating infections due to multi-drug resistant strains, increased reports of plasmid mediated mcr genes coding for colistin resistance in Enterobacterales represent a challenging and alarming situation [3]
The mcr-4.3 was reported for the first time in Singapore in 2014 on a ColE10 plasmid from a clinical E. cloacae isolate [5], and MCR-9 was initially described in 2010 in USA, in a clinical Salmonella enterica isolate [6]

Summary

Introduction

The ECC (Enterobacter cloacae complex) is composed of six species including E. cloacae and subspp, E. kobei, E. nimipressuralis, E. ludwigii, E. asburiae and E. hormaechei [1]. Carbapenem resistant E. cloacae complex (CREC) prevalence has increased significantly during recent years [2]. While colistin is considered as the last resort antibiotic for treating infections due to multi-drug resistant strains, increased reports of plasmid mediated mcr genes coding for colistin resistance in Enterobacterales represent a challenging and alarming situation [3]. Ten variants of the mcr gene, mcr-1-mcr-10, have been identified [4]. The mcr-4.3 was reported for the first time in Singapore in 2014 on a ColE10 plasmid from a clinical E. cloacae isolate [5], and MCR-9 was initially described in 2010 in USA, in a clinical Salmonella enterica isolate [6]. Up until 30 September 2020, 73 blaVIM variants were overall reported in the National Database of Antibiotic Resistant Organisms (https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/)

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