Increasing Trends of Association of 16S rRNA Methylases and Carbapenemases in Enterobacterales Clinical Isolates from Switzerland, 2017–2020

Abstract

Aminoglycosides (AGs) in combination with β-lactams play an important role in antimicrobial therapy in severe infections. Pan-resistance to clinically relevant AGs increasingly arises from the production of 16S rRNA methylases (RMTases) that are mostly encoded by plasmids in Gram-negative bacteria. The recent emergence and spread of isolates encoding RMTases is worrisome, considering that they often co-produce extended-spectrum β-lactamases (ESBLs) or carbapenemases. Our study aimed to retrospectively analyze and characterize the association of carbapenem- and aminoglycoside-resistant clinical isolates in Switzerland during a 3.5-year period between January 2017 and June 2020. A total of 103 pan-aminoglycoside- and carbapenem-resistant clinical isolates were recovered at the NARA (Swiss National Reference Center for Emerging Antibiotic Resistance) during the 2017–2020 period. Carbapenemase and RMTase determinants were identified by PCR and sequencing. The characterization of plasmids bearing resistance determinants was performed by a mating-out assay followed by PCR-based replicon typing (PBRT). Clonality of the isolates was investigated by multilocus sequence typing (MLST). Over the 991 Enterobacterales collected at the NARA during this period, 103 (10.4%) of them were resistant to both carbapenems and all aminoglycosides. Among these 103 isolates, 35 isolates produced NDM-like carbapenemases, followed by OXA-48-like (n = 23), KPC-like (n = 21), or no carbapenemase (n = 13), OXA-48-like and NDM-like co-production (n = 7), and VIM-like enzymes (n = 4). The RMTases ArmA, RmtB, RmtC, RmtF, RmtG, and RmtB + RmtF were identified among 51.4%, 13.6%, 4.9%, 24.3%, 1%, and 1%, respectively. Plasmid co-localization of the carbapenemase and the RMTase encoding genes was found among ca. 20% of the isolates. A high diversity was identified in terms of the nature of associations between RMTase and carbapenemase-encoding genes, of incompatibility groups of the corresponding plasmids, and of strain genetic backgrounds, highlighting heterogeneous importations rather than clonal dissemination.

Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolates from Two Romanian Hospitals Co-Presenting Resistance and Heteroresistance to Colistin

“…Since the first description of the RMT gene aminoglycoside resistance methylase ( armA ) in K. pneumoniae in 2003 [ 44 ], eight other plasmid-mediated variants ( rmtA to rmtH ) and N1-A1408 methyltransferase (MTase) ( npmA ) have emerged in Gram-negative pathogens in various parts of the world [ 45 ]. In contrast to our findings, a study performed in Switzerland between 2017 and 2020, which analyzed 103 carbapenem- and aminoglycoside-resistant Enterobacterales strains, did not find any K. pneumoniae isolates harboring the rmtC gene; the most frequently identified was the armA gene [ 46 ]. Among the RMT genes, armA , rmtB , and rmtC genes are distributed worldwide and confer high-level, broad-range aminoglycoside resistance, including against plazomicin, a newly approved aminoglycoside compound that can evade virtually all clinically relevant AMEs, including acetyltransferase (aac), phosphotransferase (aph), and adenylyltransferase (aad or ant) [ 45 ].…”

High prevalence of ArmA-16S rRNA methyltransferase among aminoglycoside-resistant Klebsiella pneumoniae bloodstream isolates

“…A great majority (88%) of the aminoglycoside-resistant CPK isolates carried an RMT. RMT prevalence amongst carbapenem-resistant Enterobacterales isolates vary widely from low in Spain (5%) and Greece (8%) [15, 16]; to high in UK, Ireland (95%) and Switzerland (96%) [17, 18]. ArmA was the most prevalent RMT in our collection, similar to the UK and Swiss studies [17, 18].…”

“…We were unable to determine the plasmid-resistance gene association in this study. In the Swiss study, NDM and ArmA were mainly cocarried on an A/C type plasmid, whereas OXA-48 and ArmA were carried on two different plasmids, mainly L/M and A/C, respectively [17]. There were six OXA-232 and RmtF producers in the Swiss study, and those were carried on two different plasmids (FIB and colKp3, respectively) [17].…”

Research Updates of Plasmid-Mediated Aminoglycoside Resistance 16S rRNA Methyltransferase

“…An example of rmtG and its genetic context is shown in Figure 2 . In addition, it was important to emphasize that the RmtG-producing strains such as K. pneumoniae were predominantly clonal complex 258 (CC258), which included sequence types such as ST11, ST258, ST437, and ST340 [ 35 , 80 , 96 , 97 , 127 ]. The coproduction of RmtG, ESBLs of the CTX-M type (eg., CTX-M-2, CTX-M-15, CTX-M-59) and carbapenemases (e.g., KPC-2) could further limit the treatment options for multidrug-resistant bacteria [ 35 , 96 , 101 , 127 ].…”