title: Molecular epidemiology of multidrug-resistant Acinetobacter baumannii isolates in a university hospital in Nepal reveals the emergence of a novel epidemic clonal lineage.
abstract: The emergence of multidrug-resistant (MDR) Acinetobacter baumannii has become a serious medical problem worldwide. To clarify the genetic and epidemiological properties of MDR A. baumannii strains isolated from a medical setting in Nepal, 246 Acinetobacter spp. isolates obtained from different patients were screened for MDR A. baumannii by antimicrobial disk susceptibility testing. Whole genomes of the MDR A. baumannii isolates were sequenced by MiSeq™ (Illumina), and the complete genome of one isolate (IOMTU433) was sequenced by PacBio RS II. Phylogenetic trees were constructed from single nucleotide polymorphism concatemers. Multilocus sequence types were deduced and drug resistance genes were identified. Of the 246 Acinetobacter spp. isolates, 122 (49.6%) were MDR A. baumannii, with the majority being resistant to aminoglycosides, carbapenems and fluoroquinolones but not to colistin and tigecycline. These isolates harboured the 16S rRNA methylase gene armA as well as bla(NDM-1), bla(OXA-23) or bla(OXA-58). MDR A. baumannii isolates belonging to clonal complex 1 (CC1) and CC2 as well as a novel clonal complex (CC149) have spread throughout a medical setting in Nepal. The MDR isolates harboured genes encoding carbapenemases (OXA and NDM-1) and a 16S rRNA methylase (ArmA).
authors.affiliation: Department of Microbiology, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal.
authors.forename: Shovita
authors.initials: S
authors.lastname: Shrestha
authors.affiliation: Department of Infectious Diseases, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Tada
authors.affiliation: Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan.
authors.forename: Tohru
authors.initials: T
authors.lastname: Miyoshi-Akiyama
authors.affiliation: Department of International Medical-Cooperation, National Center for Global Health and Medicine, Tokyo 162-8655, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ohara
authors.affiliation: Department of Infectious Diseases, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan.
authors.forename: Kayo
authors.initials: K
authors.lastname: Shimada
authors.affiliation: Okinawa Institute of Advanced Science, Okinawa 904-2234, Japan.
authors.forename: Kazuhito
authors.initials: K
authors.lastname: Satou
authors.affiliation: Okinawa Institute of Advanced Science, Okinawa 904-2234, Japan.
authors.forename: Kuniko
authors.initials: K
authors.lastname: Teruya
authors.affiliation: Okinawa Institute of Advanced Science, Okinawa 904-2234, Japan.
authors.forename: Kazuma
authors.initials: K
authors.lastname: Nakano
authors.affiliation: Okinawa Institute of Advanced Science, Okinawa 904-2234, Japan.
authors.forename: Akino
authors.initials: A
authors.lastname: Shiroma
authors.affiliation: Department of Microbiology, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal.
authors.forename: Jeevan Bdr
authors.initials: JB
authors.lastname: Sherchand
authors.affiliation: Department of Microbiology, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal.
authors.forename: Basista Psd
authors.initials: BP
authors.lastname: Rijal
authors.affiliation: Okinawa Institute of Advanced Science, Okinawa 904-2234, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Hirano
authors.affiliation: Department of Infectious Diseases, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan. Electronic address: tkirikae@ri.ncgm.go.jp.
authors.forename: Teruo
authors.initials: T
authors.lastname: Kirikae
authors.affiliation: Department of Microbiology, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal.
authors.forename: Bharat Mani
authors.initials: BM
authors.lastname: Pokhrel
mesh_terms: D000151:Acinetobacter Infections / Q000453:epidemiology* / Q000382:microbiology; D040981:Acinetobacter baumannii / Q000145:classification* / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D003428:Cross Infection / Q000453:epidemiology* / Q000382:microbiology; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D052978:Disk Diffusion Antimicrobial Tests; D024901:Drug Resistance, Multiple, Bacterial; D016680:Genome, Bacterial; D005838:Genotype; D006785:Hospitals, University; D006801:Humans; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D058889:Molecular Typing; D009390:Nepal / Q000453:epidemiology; D017422:Sequence Analysis, DNA
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial
keywords: 16S rRNA methylase; Carbapenemase; Clonal complex; Molecular epidemiology; Multidrug-resistant Acinetobacter baumannii