Genomic characterization of 16S rRNA methyltransferase-producing Escherichia coli isolates from the Parisian area, France

Abstract

Background The resistance to all aminoglycosides (AGs) conferred by 16S rRNA methyltransferase enzymes (16S-RMTases) is a major public health concern. Objectives To characterize the resistance genotype, its genetic environment and plasmid support, and the phylogenetic relatedness of 16S-RMTase-producing Escherichia coli from France. Methods We screened 137 E. coli isolates resistant to all clinically relevant AGs from nine Parisian hospitals for 16S-RMTases. WGS was performed on clinical isolates with high-level AG resistance (MIC ≥256 mg/L) and their transformants. Results Thirty of the 137 AG-resistant E. coli produced 16S-RMTases: 11 ArmA, 18 RmtB and 1 RmtC. The 16S-RMTase producers were also resistant to third-generation cephalosporins (90% due to a blaCTX-M gene), co-trimoxazole, fluoroquinolones and carbapenems (blaNDM and blaVIM genes) in 97%, 83%, 70% and 10% of cases, respectively. Phylogenomic diversity was high in ArmA producers, with 10 different STs, but a similar genetic environment, with the Tn1548 transposon carried by a plasmid closely related to pCTX-M-3 in 6/11 isolates. Conversely, RmtB producers belonged to 12 STs, the most frequent being ST405 and ST complex (STc) 10 (four and four isolates, respectively). The rmtB gene was carried by IncF plasmids in 10 isolates and was found in different genetic environments. The rmtC gene was carried by the pNDM-US plasmid. Conclusions ArmA and RmtB are the predominant 16S-RMTases in France, but their spread follows two different patterns: (i) dissemination of a conserved genetic support carrying armA in E. coli with high levels of genomic diversity; and (ii) various genetic environments surrounding rmtB in clonally related E. coli.

Co-Occurrence of Rare ArmA-, RmtB-, and KPC-2–Encoding Multidrug-Resistant Plasmids and Hypervirulence iuc Operon in ST11-KL47 Klebsiella pneumoniae

“…Although the genetic identity of p1632-2 ( armA -positive plasmid in K. pneumoniae 1632) and p1864-1 ( armA -positive plasmid in K. pneumoniae 1864) was low, the genetic regions surrounding the armA gene were conserved in two plasmids, which were carried by complete Tn 1548 transposon closely relating to pCTX-M-3 ( 11 ). The complete Tn 1548 sequence was flanked by two IS 26 elements, together with several other mobile elements, such as intI , IS CR1 , IS Ec35 (IS 903 group), and ISEc29 (IS 10 group).…”

“…Until now, we have found ten 16S RMTase-encoding genes ( armA , rmtA to rmtH , npmA , and npmB ), which confer high-level resistance to all clinically relevant aminoglycosides (minimal inhibitory concentration [MIC], >256 mg/L) ( 8 , 9 ). Among these genes, rmtB and armA present the most widespread 16S rRNA methylase genes ( 10 , 11 ). Notably, genes encoding methylases can be carried in integrons or transposons located in a variety of plasmids and sometimes along with those for extended spectrum β-lactamases (ESBLs), carbapenemases, and fluoroquinolone resistance determinants, which may not only facilitate the rapid spread of 16S-RMTase genes but also could render ineffective multiple classes of antimicrobials used to treat multidrug-resistant Gram-negative infections ( 12 ).…”

Whole Genome Sequence Analysis of Multidrug Resistant Escherichia coli and Klebsiella pneumoniae Strains in Kuwait

“…If we had such information, this asymptomatic patient could have been subjected to further strict surveillance cultures to detect potential sources of colonization and/or might be placed on contact isolation to cease any probable silent transmission chain that may occur in the hospital. Aminoglycoside resistance rates in E. coli and K. pneumoniae have been described in many countries, leading to global concerns [ 31 , 32 ]. The mechanism of resistance to aminoglycosides mainly occurs due to the presence of aminoglycoside-modifying enzymes (AMEs) and their different ability to modify aminoglycosides.…”

Rapid Detection and Characterization of Carbapenemases in Enterobacterales with a New Modified Carbapenem Inactivation Method, mCIMplus

“…The whole genomes of 123 isolates from Saint-Louis Hospital were sequenced with Illumina technology. The resistome was evaluated for these isolates with ResFinder (15). For the others, the resistance genotype had already been characterized (14).…”