Clonal diversity of Acinetobacter baumannii clinical isolates in Myanmar: identification of novel ST1407 harbouring blaNDM-1.

Recent Acinetobacter baumannii clinical isolates in a teaching hospital in Myanmar comprised three major sequence types (ST2, ST16 and ST23) and two sporadic STs, showing a high resistance rate to carbapenem associated with blaOXA-23 . The NDM-1 encoding gene was identified in only one isolate exhibiting novel ST1407 (a triple-locus variant of ST16).

Acinetobacter baumannii is opportunistic pathogen with a remarkable capacity to acquire antimicrobial resistance. Global spread of carbapenem-resistant A. baumannii has been noted as a public health concern since 2000 as a result of intra- and interhospital dissemination and international transfer of resistant strains [1]. According to the Institute Pasteur scheme of multilocus sequence typing (MLST) [2], sequence type (ST) 2 is considered to be the predominant clone with carbapenem resistance globally [1,2], while other STs such as ST10, clonal complex (CC) 32 and ST589 (CC1) were also described as major lineages, depending on the country [[3], [4], [5]]. In Myanmar, only limited information is available regarding the clonal lineage of A. baumannii responsible for carbapenem resistance in medical settings.

From January to November 2018, a total of 1270 bacterial isolates were recovered from clinical specimens as putative causes of infectious diseases in North Okkalapa General and Teaching Hospital, Yangon, Myanmar. Gram-negative bacteria accounted for 80.6% (1023 isolates), with Klebsiella pneumoniae being dominant, followed by Escherichia coli. Forty isolates (3.1%) were identified as Acinetobacter species by biochemical test kit (API 20NE strip; bioMérieux), among which 25 isolates were genetically confirmed to be A. baumannii by PCR detection of blaOXA-51-like gene [6] and sequencing of cpn60 (one MLST locus) [2]. The most common specimen associated with Acinetobacter spp. was sputum, followed by wound swab and urine (Supplementary Table S1). Most Acinetobacter spp. isolates were derived from male patients of older age (>40 years) (Supplementary Table S2).

Antimicrobial susceptibility of A. baumannii was measured by broth microdilution test, and ST was determined as per the Institute Pasteur scheme [2]. Carbapenemase genes were detected and typed as described previously [[7], [8], [9]]. Nucleotide sequences of the bla family were determined by PCR direct sequencing using primers designed in this study (Supplementary Table S3).

Among 25 A. baumannii isolates, five STs were identified (Table 1), including three common STs (ST2, ST16 and ST23) and two novel STs (ST1406 and ST1407). We identified five different genotypes of the bla family, which were correlated with each of the five STs. bla was detected in all the isolates except ST23 (detection rate, 72%), and bla was identified in a single isolate of ST1407. Resistance rate to carbapenem was 76%, although a lower rate was found for ST23 isolates than other STs.

Table 1

ST, carbapenemase genes and drug resistance of Acinetobacter baumannii clinical isolates from North Okkalapa General Hospital, Myanmar, January to November 2018

ST (no. of isolates)	Allelic profile of ST	Carbapenemase gene (no. of isolates)			Resistance rate (%) to:				Specimen (no. of isolates)
		blaOXA-51 family	Other blaOXA	blaNDM	CAZ, CTX, GEN	IPM, MEM	AMK	DOX
ST2 (8)	2-2-2-2-2-2-2	blaOXA-66 (8)	blaOXA-23 (8)	—	100	87.5	75	100	Sputum (5), urine (1), blood (1), suction tip (1)
ST16 (8)	7-7-2-2-8-4-4	blaOXA-70 (8)	blaOXA-23 (8)	—	100	100	37.5	87.5	Sputum (4), wound (2), pus (1), blood (1)
ST23 (7)	1-3-10-1-4-4-4	blaOXA-68 (7)	—	—	100	28.6	28.6	100	Sputum (4), wound (2), urine (1)
ST1406 (1)	1-3-2-1-137-4-92	blaOXA-144 (1)	blaOXA-23 (1)	—	R	R	R	R	Sputum (1)
ST1407 (1)	7-190-2-2-8-82-123	blaOXA-402 (1)	blaOXA-23 (1)	blaNDM-1 (1)	R	R	R	R	Sputum (1)
Total (25)			blaOXA-23 (18)	blaNDM-1 (1)	100	76	52	96

For each single isolate of ST1406 and ST1407, only R (resistant) is shown. All isolates were susceptible to colistin and tigecycline.

Abbreviations: AMK, amikacin; CAZ, ceftazidime; CTX, cefotaxime; DOX, doxycycline; GEN, gentamicin; IPM, imipenem; MEM, meropenem; ST, sequence type.

A recent study of A. baumannii clinical isolates in Myanmar described the dominance of ST2 (50%), high prevalence of bla (87%) and detection of bla in four STs (ST1, ST16, ST23 and ST109) [10]. However, in spite of the low number of isolates obtained in our study, ST2 was not dominant but rather showed isolation frequency similar to ST16 and ST23. A novel ST1407, which was assigned to one isolate harbouring bla, was sporadic type but a triple-locus variant of ST16 as well as ST1480. While being a minor lineage of A. baumannii, ST16 was found in the Netherlands, the United States, Malaysia and Thailand [2,11]. ST1480 was registered as an isolate in Thailand (strain ID 4657; PubMLST, at https://pubmlst.org/). Accordingly, ST16-related clones were suggested to be potentially prevalent in South-East Asian countries and responsible for carbapenem resistance carrying bla. Further epidemiologic surveillance of A. baumannii and its carbapenem resistance may be necessary, particularly on ST16-related lineage in Myanmar and neighbouring countries.

Conflict of interest

None declared.