Genotyping of Acinetobacter baumannii strains isolated at a Japanese hospital over five years using targeted next-generation sequencing

Alshahni, Mohamed Mahdi; Asahara, Miwa; Kawakami, Sayoko; Fujisaki, Ryuichi; Matsunaga, Naohisa; Furukawa, Taiji; Teramoto, Tamio; Makimura, Koichi

doi:10.1016/j.jiac.2015.03.009

Cited by 8 publications

(7 citation statements)

References 7 publications

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“…A recent study showed that unlike vancomycin-resistant Enterococcus faecium and methicillin-resistant Staphylococcus aureus, genomically identical A. baumannii isolates might be misclassified as different by PFGE, leading to incorrectly reconstructed transmission trees and an underestimation of the true extent of A. baumannii outbreaks (13). A large-scale sequencing study of A. baumannii strains was more discriminatory than MLST (48). These previous reports and the results from our study suggest that for A. baumannii in particular, NGS-based SNV typing can more informatively distinguish strains than can MLST or PFGE.…”

Section: Discussionmentioning

confidence: 99%

Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center

Kanamori

Parobek

Weber

et al. 2016

Antimicrob Agents Chemother

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f Next-generation sequencing (NGS) analysis has emerged as a promising molecular epidemiological method for investigating health care-associated outbreaks. Here, we used NGS to investigate a 3-year outbreak of multidrug-resistant Acinetobacter baumannii (MDRAB) at a large academic burn center. A reference genome from the index case was generated using de novo assembly of PacBio reads. Forty-six MDRAB isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and sequenced using an Illumina platform. After mapping to the index case reference genome, four samples were excluded due to low coverage, leaving 42 samples for further analysis. Multilocus sequence types (MLST) and the presence of acquired resistance genes were also determined from the sequencing data. A transmission network was inferred from genomic and epidemiological data using a Bayesian framework. Based on single-nucleotide variant (SNV) differences, this MDRAB outbreak represented three sequential outbreaks caused by distinct clones. The first and second outbreaks were caused by sequence type 2 (ST2), while the third outbreak was caused by ST79. For the second outbreak, the MLST and PFGE results were discordant. However, NGS-based SNV typing detected a recombination event and consequently enabled a more accurate phylogenetic analysis. The distribution of resistance genes varied among the three outbreaks. The first-and second-outbreak strains possessed a bla OXA-23-like group, while the thirdoutbreak strains harbored a bla OXA-40-like group. NGS-based analysis demonstrated the superior resolution of outbreak transmission networks for MDRAB and provided insight into the mechanisms of strain diversification between sequential outbreaks through recombination.H ealth care-associated infections (HAI) are a substantial cause of morbidity and mortality in acute-care hospitals (1). Acinetobacter baumannii is an important opportunistic pathogen causing HAI (2) and has become one of the most common colonizing pathogens in burn patients (3, 4). A. baumannii may cause serious outbreaks despite the implementation of rigorous infection prevention interventions and control measures, which occur most commonly in intensive care units (5-8). Furthermore, the emergence of multidrug-resistant A. baumannii (MDRAB), especially carbapenem-resistant A. baumannii (CRAB), has become a global concern (5, 9). Patients infected by multidrug-resistant Acinetobacter strains are likely to have higher mortality rates and longer lengths of hospitalization than those infected by susceptible strains (10).Pulsed-field gel electrophoresis (PFGE) has been the gold standard approach for bacterial strain typing in hospital outbreak investigations, but several disadvantages have been described, including that it is a time-consuming, labor-intensive, and technically demanding assay and that is has limited reproducibility among laboratories; also, the interpretation of the relative relatedness of strains using this method may be discordant and subjective (11-13). For these reasons, next...

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Section: Discussionmentioning

confidence: 99%

Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center

Kanamori

Parobek

Weber

et al. 2016

Antimicrob Agents Chemother

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“…In Japan, A. baumannii IC II is also reported to be strongly associated with multidrug or carbapenem resistance (8)(9)(10) and has caused nosocomial outbreaks (11)(12)(13). However, the prevalence of MDR Acinetobacter species isolates (criteria are described in Materials and Methods section) remains low in Japan.…”

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confidence: 99%

Distribution and Molecular Characterization of Acinetobacter baumannii International Clone II Lineage in Japan

Matsui

Suzuki

et al. 2018

Antimicrob Agents Chemother

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Multidrug-resistant (MDR) spp. have been globally disseminated in association with the successful clonal lineage international clone II (IC II). Because the prevalence of MDR spp. in Japan remains very low, we characterized all spp. ( = 866) from 76 hospitals between October 2012 and March 2013 to describe the entire molecular epidemiology of spp. The most prevalent species was ( = 645; 74.5%), with IC II ( = 245) accounting for 28.3% of the total. Meropenem-resistant isolates accounted for 2.0% ( = 17) and carried IS ( = 10), ( = 4), or IS ( = 3). Multilocus sequence typing of 110 representative isolates revealed the considerable prevalence of domestic sequence types (STs). IC II isolates were divided into the domestic sequence type 469 (ST469) ( = 18) and the globally disseminated STs ST208 ( = 14) and ST219 ( = 4). ST469 isolates were susceptible to more antimicrobial agents, while ST208 and ST219 overproduced the intrinsic AmpC β-lactamase. IC II and some non-IC II STs (e.g., ST149 and ST246) were associated with fluoroquinolone resistance. This study revealed that carbapenem-susceptible IC II was moderately disseminated in Japan. The low prevalence of acquired carbapenemase genes and presence of domestic STs could contribute to the low prevalence of MDR A similar epidemiology might have appeared before the global dissemination of MDR epidemic lineages. In addition, fluoroquinolone resistance associated with IC II may provide insight into the significance of epidemic clones.

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“…A. baumannii clinical isolates were previously collected from Teikyo University Hospital, a 1,082-bed academic hospital in Tokyo, Japan, 4 and stored in glycerol at −80°C. During the MDRA outbreak from 2009 to 2010, 59 patients were infected and nine patients who had hematological diseases died as a result of the infection.…”

Section: Methodsmentioning

confidence: 99%

“…A fatal MDRA outbreak occurred in 2010 at Teikyo University Hospital (Tokyo, Japan). 3 , 4 In this study, we compared the pathogenicity of A. baumannii clinical isolates including MDRA strains. Despite many clinical studies, little is known regarding the virulence and microbial fitness of A. baumannii .…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of the pathogenicity between multidrug-resistant <em>Acinetobacter baumannii</em> clinical isolates: isolation of highly pathogenic multidrug-resistant <em>A. baumannii</em> and experimental therapeutics with fourth-generation cephalosporin cefozopran

Nishida

Ono

2018

IDR

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IntroductionThe pathogenicity of fatal-outbreak Acinetobacter baumannii isolates has not been fully investigated. This study aimed to compare the pathogenicity between A. baumannii clinical isolates, including multidrug-resistant A. baumannii (MDRA).Materials and methodsAntibiotic susceptibility was determined by the broth microdilution method, and drug-resistant genes were characterized by PCR and sequencing. The pathogenicity of A. baumannii and antibiotic responses were evaluated using the Galleria mellonella infection model. Clinical isolates from an A. baumannii outbreak at our hospital were categorized using the pulse-field gel electrophoresis. Of the 16 isolated A. baumannii clones, 12 clones were resistant to carbapenems (meropenem and imipenem), of which 10 clones were also resistant to amikacin and ciprofloxacin (MDRAs). MDRAs had OXA-51-like β-lactamase gene harboring an insertion sequence in the promoter region and armA gene encoding 16S rRNA methyltransferase.ResultsCarbapenem- and/or amikacin-resistant A. baumannii were more pathogenic than carbapenem- and/or amikacin-sensitive A. baumannii in G. mellonella. MDRA isolate TK1033 was more virulent than other A. baumannii isolates. However, TK1033 was sensitive to the fourth-generation cephalosporin cefozopran in addition to minocycline, tigecycline, and polymyxins (colistin and polymyxins B) in vitro and in vivo in the MDRA-G. mellonella infection model.ConclusionDifferences in pathogenicity among carbapenem-resistant A. baumannii clones are consistent with heterogeneous clinical outcomes. Strain TK1033, isolated frequently during the outbreak, was the most virulent, whereas preoutbreak isolate TK1032 was less virulent than other A. baumannii isolates. Infection by high-virulence isolates may be more prevalent during outbreaks. These strains may prove valuable for investigating MDRA virulence and novel therapeutics.

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Genotyping of Acinetobacter baumannii strains isolated at a Japanese hospital over five years using targeted next-generation sequencing

Cited by 8 publications

References 7 publications

Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center

Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center

Distribution and Molecular Characterization of Acinetobacter baumannii International Clone II Lineage in Japan

Comparative analysis of the pathogenicity between multidrug-resistant <em>Acinetobacter baumannii</em> clinical isolates: isolation of highly pathogenic multidrug-resistant <em>A. baumannii</em> and experimental therapeutics with fourth-generation cephalosporin cefozopran

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