First Report of New Delhi Metallo-β-Lactamase-6 (NDM-6) in a Clinical Acinetobacter baumannii Isolate From Northern Spain.

Kyriaki Xanthopoulou,Sandra Sánchez-Urtaza,Lucía Gallego,Paul G Higgins,Julia Wille,Mikel Urrutikoetxea-Gutiérrez,Matxalen Vidal-Garcia,Harald Seifert,José-Luis Diaz De Tuesta Del Arco

doi:10.3389/fmicb.2020.589253

Abstract

The objective of this study was the phenotypic and genotypic characterization of a carbapenem resistant Acinetobacter baumannii (CRAB) isolate. The isolate, recovered in Northern Spain in 2019, was identified by MALDI-TOF to the species level. Antimicrobial susceptibility testing was performed using the Phoenix BD NMIC-502 Panel, E-test, and broth microdilution methods. The presence of a metallo-β-lactamase (MBL) was verified by PCR and immunochromatographic assays. The genetic location of the MBL was confirmed using S1-pulsed-field gel electrophoresis (S1-PFGE) followed by Southern blot hybridization. Whole genome sequencing (WGS) was completed using the Miseq and MinION platforms, followed by core-genome MLST (cgMLST) and seven-locus MLST analysis. The CRAB was assigned ST85 (Pasteur scheme) and ST957 (Oxford scheme) representing international clone (IC) 9 and harbored the intrinsic β-lactamase OXA-94 with ISAba1 upstream of it, and the MBL blaNDM-6. Hybridization experiments revealed that the blaNDM-6 was encoded on the chromosome. Using WGS the blaNDM-6 environment could be identified arranged in the following order: ISAba14, aphA6, ISAba125, blaNDM-6, bleMBL, trpF, dsbC, cutA, and ISAba14. Downstream, a 10,462 bp duplication was identified, including a second copy of blaNDM-6 in the following genetic composition: ISAba125, blaNDM-6, bleMBL, trpF, dsbC, cutA, and ISAba14. To our knowledge, this is the first description of blaNDM-6 in A. baumannii. The MBL was present in two copies in the chromosome in a new genetic environment associated with IS elements highlighting the contribution of mobile genetic elements in the dissemination of this gene.

Highlights

Infections caused by multidrug-resistant Acinetobacter baumannii have become a health care challenge worldwide (Peleg et al, 2008; Higgins et al, 2010)
The bacterial isolate AbBAS-1 was identified by MALDI-TOF and Whole genome sequencing (WGS) as A. baumannii
Antimicrobial susceptibility testing revealed that the isolate was resistant to all tested antimicrobial

Summary

Introduction

Infections caused by multidrug-resistant Acinetobacter baumannii have become a health care challenge worldwide (Peleg et al, 2008; Higgins et al, 2010). In 2019, the World Health Organization (WHO) classified carbapenem resistant A. baumannii (CRAB) as one of the “Priority 1: Critical group” organisms for which new NDM-6 in an Acinetobacter Baumannii Isolate From Spain antimicrobials are urgently needed.. Carbapenem resistance in A. baumannii is mainly mediated through acquired carbapenem-hydrolyzing class D ß-lactamases (oxacillinases), encoded by blaOXA-23-like, blaOXA-40-like, blaOXA-58-like, blaOXA-143-like, and blaOXA-235-like (Higgins et al, 2013; Evans and Amyes, 2014). Class B metalloβ-lactamases (MBLs), such as IMP, VIM, SIM, and NDM are less frequently reported in CRAB isolates (Müller et al, 2019). MBL-positive A. baumannii are increasingly reported worldwide (Kaase et al, 2011; Pfeifer et al, 2011; Berrazeg et al, 2014; Karampatakis et al, 2017; Adams et al, 2020; Ramirez et al, 2020)

Objectives

Methods

Results