LETTER
Acinetobacter spp. are emerging pathogens causing opportunistic and health care-associated infections. The increasing rate of drug-resistant Acinetobacter spp. is one of the most serious concerns in the world. Carbapenem-resistant Acinetobacter spp. isolates are especially critical in clinical settings because carbapenem serves as a last resort antibiotic that is used in cases of severe infections (1, 2). Recently, Acinetobacter colistiniresistens was renamed from Acinetobacter genomic species 13BJ/14TU in 2017 by Nemec et al. because of intrinsic resistance to colistin (3). In this study, we investigated the molecular characteristics of a novel carbapenem-resistant Acinetobacter colistiniresistens isolate.
Carbapenem-resistant Acinetobacter sp. strain NR1165 was isolated from the sputum of an inpatient at Tohoku University Hospital, Japan, in 2015. The isolate was identified as A. colistiniresistens by DNA sequencing of the RNA polymerase β-subunit gene (4). The draft genome of this isolate (GenBank accession no. BGNT00000000.1) was obtained by MiSeq (Illumina), and average nucleotide identity (ANI) analysis using A. colistiniresistens NIPH1860 (GenBank accession no. APRT00000000.1), NIPH2036 (GenBank accession no. ATGK00000000.1), and NIPH1859 (GenBank accession no. APRZ00000000.1) as reference genomes showed ANI values of 98.40%, 95.13%, and 95.2%, respectively (https://www.ezbiocloud.net/tools/ani) (5). Antibiotic susceptibilities of the isolate, excluding colistin, were determined using the agar dilution method, and colistin susceptibility was determined by the broth microdilution method following CLSI guidelines (6). The isolate was resistant to all β-lactams including carbapenems (Table 1), and the MIC of meropenem was higher than that of imipenem. PCR and DNA sequencing (MiSeq) were performed to identify the carbapenemase genes (OXA-51-, OXA-23-, OXA-24/40-, and OXA-58-like carbapenemase genes and IMP-, VIM-, SIM-, and NDM-type metallo-β-lactamase genes) and the genetic environments of the isolate (7, 8). Molecular analysis showed that the isolate possessed blaIMP-34, which was located in a class 1 integron with the following structure: blaIMP-34-fosX/fosE/fosI family-gcuD-like gene-aac(6ʹ)-Ib-blaOXA-1 (GenBank accession no. LC276939). The unique structure of the IMP-34-harboring integron identified in this study differs from that in previously described strains (9–11). blaOXA-58 was also detected and was found to be linked to ISAba3. Therefore, it is possible that the carbapenem-resistance mechanism of this isolate involves a gene encoding both IMP-34 and OXA-58 (12). Based on genome sequence analysis, IMP-34 and OXA-58 were located on different contigs. Because this draft genome had short contigs, it was difficult to assess whether these resistance genes were carried on the plasmid. Analysis of antimicrobial resistance genes by ResFinder 2.1 (13) showed the presence of non-β-lactamase genes encoding resistance to aminoglycosides [aph(3’)-Vla, aac(6’)-Ib, and aac(6’)-Ij], macrolide-lincosamide-streptogramin [msr(E) and mph(E)], and sulfonamide (sul1).
TABLE 1.
Susceptibility profile of Acinetobacter colistiniresistens NR1165 harboring IMP-34 and OXA-58 β-lactamases
| Antibiotic agent | MIC (μg/ml) |
|---|---|
| Ampicillin | 32 |
| Cefotaxime | 32 |
| Ceftazidime | 64 |
| Cefoxitin | >256 |
| Cefepime | 16 |
| Aztreonam | 8 |
| Imipenem | 8 |
| Meropenem | 32 |
| Ertapenem | 128 |
| Levofloxacin | 8 |
| Amikacin | 128 |
| Gentamicin | 1 |
| Tigecycline | 4 |
| Colistin | 16 |
Furthermore, the isolate also exhibited high MICs for levofloxacin, amikacin, tigecycline, and colistin (Table 1). Colistin has reemerged in several countries as a first-line treatment for multidrug-resistant Acinetobacter spp.; however, A. colistiniresistens is known to be naturally resistant to colistin (3, 14). β-Lactams, including carbapenems, play an essential role in the treatment of this species. If this species was to acquire a carbapenemase gene(s), such as IMP-34, outbreaks of health care-associated infections caused by this species could become a serious issue because limited treatment options would be available.
In conclusion, to the best of our knowledge, this is the first report of an IMP-34- and OXA-58-producing Acinetobacter sp. Moreover, this is the first description of carbapenemase-producing A. colistiniresistens, which is naturally resistant to colistin. Because antimicrobial susceptibility profiles differ among Acinetobacter spp., correct identification at the species level is necessary, in particular for those Acinetobacter spp. causing severe and nosocomial infections. The dissemination trend of this species should be monitored, and further studies examining the clinical and microbial significance of non-baumannii Acinetobacter, including A. colistiniresistens, are required.
Accession number(s).
The draft nucleotide sequence has been deposited in GenBank under the accession no. BGNT00000000.1.
ACKNOWLEDGMENTS
This work was supported by JSPS KAKENHI grant no. 16K09940, 17K10027, and 18K09935.
We thank Yasutoshi Kuroki, Kentaro Miyamoto, Kentaro Oka, and Motomichi Takahashi from Miyarisan Pharmaceutical Co., Ltd., Tokyo, Japan, for participating in next-generation sequencing analysis. We are also grateful to the staff at the microbiology laboratory of Tohoku University Hospital for their technical support.
We declare that we have no conflicts of interest.
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