Mobile Genetic Elements as Dissemination Drivers of Multidrug-Resistant Gram-Negative Bacteria

Editorial

17 March 2023

Editorial: Mobile genetic elements as dissemination drivers of multidrug-resistant Gram-negative bacteria

Carolina Silva Nodari

Andrés Opazo-Capurro

Santiago Castillo-Ramirez

and

Vittoria Mattioni Marchetti

2,299 views

1 citations

Editors

Carolina Silva Nodari

Institut Pasteur

Andres Felipe Opazo-Capurro

University of Concepcion

Thomas Jové

INSERM U1092 Anti-Infectieux supports moléculaires des résistances et innovations thérapeutiques

Santiago Castillo Ramírez

National Autonomous University of Mexico

Vittoria Mattioni Marchetti

University of Pavia

Impact

Original Research

28 November 2022

Diversity of resistant determinants, virulence factors, and mobile genetic elements in Acinetobacter baumannii from India: A comprehensive in silico genome analysis

Shital N. Kumkar

, 3 more and

Karishma R. Pardesi

Introduction: The frequency of infections associated with multidrug resistant A. baumannii has risen substantially in India. The use of next-generation sequencing (NGS) techniques combined with comparative genomics has great potential for tracking, monitoring, and ultimately controlling the spread of this troublesome pathogen. Here, we investigated the whole genome sequences of 47 A. baumannii from India.

Methods: In brief, A. baumannii genomes were analyzed for the presence of antibiotic resistance genes (ARGs), virulence factors genes (VFGs), and mobile genetic elements (MGEs) using various in silico tools. The AbaR-type resistance islands (AbaRIs) were detected by examining the genetic environment of the chromosomal comM gene. Multilocus sequence types were determined using the Pasteur scheme. The eBURST and whole genome SNPs-based phylogenetic analysis were performed to analyze genetic diversity between A. baumannii genomes.

Results and discussion: A larger number of A. baumannii isolates belonging to the ST2 genotype was observed. The SNPs-based phylogenetic analysis showed a diversity between compared genomes. The predicted resistome showed the presence of intrinsic and acquired ARGs. The presence of plasmids, insertion sequences, and resistance islands carrying putative ARGs conferring resistance to antibiotics, quaternary ammonium compounds, and heavy metals was predicted in 43 (91%) genomes. The presence of putative VFGs related to adherence, biofilm formation and iron uptake was observed in the study. Overall, the comprehensive genome analysis in this study provides an essential insight into the resistome, virulome and mobilome of A. baumannii isolates from India.

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11 citations

pneumoniae strains. cgMLST was conducted based on the 2358 alleles using Ridom SeqSphere+ server with cluster alert distance set at 15. Strains collected from China, Hungary, Spain and United Kingdom were shown as different colors. The blue pentagram indicated the position of KPTCM strain.

Original Research

29 September 2022

Whole genome sequencing of OXA-232-producing wzi93-KL112-O1 carbapenem-resistant Klebsiella pneumoniae in human bloodstream infection co-harboring chromosomal ISEcp1-based blaCTX-M-15 and one rmpA2-associated virulence plasmid

Chongmei Tian

, 5 more and

Siwei Wang

Objectives: To characterize one OXA-232-producing wzi93-KL112-O1 carbapenem-resistant Klebsiella pneumoniae (CRKP) co-harboring chromosomal bla_CTX-M-15 and one rmpA2-associated virulence plasmid.

Methods: Minimum inhibitory concentrations (MICs) were measured via broth microdilution method. Conjugation, chemical transformation, string test and Galleria mellonella infection model experiments were also conducted. Whole-genome sequencing (WGS) was performed on the Illumina and Nanopore platforms. Antimicrobial resistance determinants were identified using ABRicate program with ResFinder database. Insertion sequences (ISs) were identified using ISfinder. Bacterial virulence factors were identified using virulence factor database (VFDB). Wzi, capsular polysaccharide (KL) and lipoolygosaccharide (OCL) were analyzed using Kleborate with Kaptive. Phylogenetic analysis of 109 ST15 K. pneumoniae strains was performed using core genome multilocus sequence typing (cgMLST) on the Ridom SeqSphere+ server. MLST, replicons type, SNP strategies and another cgMLST analysis for 45 OXA-232-producing K. pneumoniae strains were further conducted using BacWGSTdb server.

Results: K. pneumoniae KPTCM strain belongs to ST15 with wzi93, KL112 and O1. It possessed a multidrug-resistant (MDR) profile and was resistant to carbapenems (meropenem and ertapenem), ciprofloxacin and amikacin. Virulence assays demonstrated KPTCM strain possesses a low virulence phenotype. WGS revealed it contained one circular chromosome and nine plasmids. The carbapenemase-encoding gene bla_OXA-232 was located in a 6141-bp ColKP3-type non-conjugative plasmid and flanked by ΔISEcp1 and ΔlysR-ΔereA. Interestingly, bla_CTX-M-15 was located in the chromosome mediated by ISEcp1-based transposon Tn2012. Importantly, it harbored a rmpA2-associated pLVPK-like virulence plasmid with iutA-iucABCD gene cluster and one IS26-mediated MDR fusion plasmid according to 8-bp (AGCTGCAC or GGCCTTTG) target site duplications (TSD). Based on the cgMLST and SNP analysis, data showed OXA-232-producing ST15 K. pneumoniae isolates were mainly isolated from China and have evolved in recent years.

Conclusions: Early detection of CRKP strains carrying chromosomal bla_CTX-M-15, OXA-232 carbapenemase and pLVPK-like virulence plasmid is recommended to avoid the extensive spread of this high-risk clone.

4,806 views

10 citations

The 66 blaOXA-181-harboring IncX3 plasmids were highlighted in light green. The outermost grey bars denote the lengths of the blaOXA-181-harboring plasmids. The bars in light blue denote the GC content of the 81 blaOXA-181-harboring plasmids.

Original Research

08 September 2022

In silico characterization of IncX3 plasmids carrying blaOXA-181 in Enterobacterales

Zhijian Yu

, 8 more and

Xiaobin Li

3,504 views

11 citations

Original Research

02 September 2022

Acquisition of resistance to ceftazidime-avibactam during infection treatment in Pseudomonas aeruginosa through D179Y mutation in one of two blaKPC-2 gene copies without losing carbapenem resistance

Patricia García

, 6 more and

Aniela Wozniak

Ceftazidime/Avibactam (CAZ/AVI) is frequently used to treat KPC-producing Pseudomonas aeruginosa (KPC-PA) and Enterobacterales. CAZ/AVI resistance is driven by several mechanisms. In P. aeruginosa this mainly occurs through alteration of AmpC, porins, and/or efflux pump overexpression, whereas in Enterobacterales it frequently occurs through D179Y substitution in the active site of KPC enzyme. This aminoacid change abolishes AVI binding to the KPC active site, hence inhibition is impaired. However, this substitution also decreases KPC-mediated resistance to carbapenems (“see-saw” effect). The goal of this work was to characterize the in vivo acquisition of CAZ/AVI resistance through D179Y substitution in a KPC-PA isolated from a hospitalized patient after CAZ/AVI treatment. Two KPC-PA isolates were obtained. The first isolate, PA-1, was obtained before CAZ/AVI treatment and was susceptible to CAZ/AVI. The second isolate, PA-2, was obtained after CAZ/AVI treatment and exhibited high-level CAZ/AVI resistance. Characterization of isolates PA-1 and PA-2 was performed through short and long-read whole genome sequencing analysis. The hybrid assembly showed that PA-1 and PA-2A had a single plasmid of 54,030 bp, named pPA-1 and pPA-2 respectively. Each plasmid harbored two copies of the bla_KPC-containing Tn4401b transposon. However, while pPA-1 carried two copies of bla_KPC-2, pPA-2 had one copy of bla_KPC-2 and one copy of bla_KPC-33, the allele with the D179Y substitution. Interestingly, isolate PA-2 did not exhibit the “see-saw” effect. The bla_KPC-33 allele was detected only through hybrid assembly using a long-read-first approach. The present work describes a KPC-PA isolate harboring a plasmid-borne CAZ/AVI resistance mechanism based on two copies of bla_KPC-2-Tn4401b and D179Y mutation in one of them, that is not associated with loss of resistance to carbapenems. These findings highlight the usefulness of a fine-tuned combined analysis of short and long-read data to detect similar emerging resistance mechanisms.