Emergence of blaNDM-5-Carrying Klebsiella aerogenes in Japan.

LETTER

An increase in carbapenemase-producing Enterobacterales is the most serious risk to public health among drug-resistant bacteria. Since 2018, Klebsiella aerogenes has been ranked among the top 35 to 40% of carbapenem-resistant Enterobacteriaceae (CRE) isolated in Japan (1, 2), but few carbapenemase-positive isolates have been reported (3, 4). In the Japan Antimicrobial Resistant Bacterial Surveillance conducted in 2019 to 2020, 1,725 Enterobacterales isolates showing meropenem (MEM) MICs of ≥0.25 μg/mL were collected from 175 medical institutions throughout Japan. In this surveillance, there were 142 K. aerogenes isolates collected with low susceptibility to carbapenem, which was similar to the number of Escherichia coli isolates collected (146 isolates). Among the K. aerogenes isolates, 97.2% of them did not have carbapenemases. Two blaNDM-5-carrying K. aerogenes strains were isolated in 2 regions that are 800 km apart (Fukuoka and Aichi Prefectures). The Aichi and Fukuoka isolates were isolated from vaginal discharge and spontaneous urination, respectively. Both isolates were resistant to imipenem (IPM)/MEM (MIC of >8 μg/mL).

Complete sequences of the Fukuoka and Aichi plasmids obtained by short-read sequencing with Illumina and long-read sequencing with MinION revealed that blaNDM-5 was present on the IncX3 plasmid of 46,161 bp and 44,811 bp, respectively. A linear comparison of blaNDM-5 plasmid sequences revealed that these plasmids are similar to those from China: pNDM-Z244, pP855-NDM5, and pNDM-CR33 (accession numbers MK450346, MF547508, and MK450349, respectively). No other resistance genes were detected in these plasmids using ResFinder 3.2. In both the Fukuoka and Aichi plasmids, Tn2 inserted upstream of blaNDM-5 was inactivated by an insertion of IS3000 (Fig. 1). In the Fukuoka plasmid, ISAba125 just upstream of blaNDM-5 was disrupted by insertion of IS5, while in the Aichi plasmid IS5 was inserted at the 3′ portion of IS3000. Although IS5 is present in both plasmids in similar positions, the different insertion order appears to suggest different origins of the plasmids (Fig. 1).

FIG 1

Detailed comparison of the 5′ ends of blaNDM-5 sequences of the K. aerogenes NDM-5 plasmid of the Fukuoka isolate (accession number DRA011229) and of the Aichi isolate (accession number DRA011229) from Japan. Red arrows and white arrows in blue and green boxes indicate blaNDM-5, IS5, and IS3000, respectively.

Analysis by MLST-2.0 showed different chromosomal backgrounds, with ST209 in the Fukuoka isolate, and the new sequence type ST224 (nearest STs: 10, 117, and 12) in the Aichi isolate. In addition to the blaNDM-5 plasmid, the Aichi strain also carried 3 other plasmids. One of them is 116,630 bp and contained aadA16, aac(3)-IId, aph(6)-Id, aph(3″)-Ib, aac(6′)-Ib-cr, mph(A), sul1, sul2, qnrB52, qnrB2, qnrS1, blaTEM-1B, blaCTX-M-3, ARR-3, tet(A), floR, and dfrA27. The other two plasmids were small and did not carry drug resistance genes. In the Fukuoka isolate, the blaNDM-5 plasmid was the only completed one, and the sequence reads converged to 6 contigs. These nucleotide fragments together with the plasmid indicated that the Fukuoka isolate had no resistance genes other than the blaNDM-5 in the plasmid and fosA7 in the chromosome.

A BLAST search revealed 23 previous reports of blaNDM-carrying K. aerogenes isolates around the world, with a blaNDM-5-carrying isolate reported in China in 2020 (5). Japanese cases had no history of traveling abroad, thereby suggesting that there is no epidemiological link with China.

The emergence of K. aerogenes isolates carrying the blaNDM-5 plasmid should henceforth call for more careful attention to carbapenemase-producing K. aerogenes.

Data availability.

The nucleotide sequence of the NDM-5-carrying K. aerogenes isolate described in this study was deposited in the DDBJ Sequence Read Archive (DRA) under accession number DRA011229 (BioSample SAMD00261449 for Fukuoka isolate JARBS-GNR_440044-19-0003 and SAMD00261448 for Aichi isolate JARBS-GNR_23029-19-0094).