Draft genome sequence of a multidrug-resistant beta-lactamase OXA-357-producing Acinetobacter pittii ST865 clinical isolate from China

Jianfeng Wang Yan Chen Liyan Wu Yu Chen Liqun Xu About the authors

Abstract

Worldwide increasing emergence of carbapenem-resistant Acinetobacter spp. has rendered the limited availability of effective antimicrobial agents and has become a major public health concern. In this study, we report the draft genome sequence of A. pittii TCM156, a multidrug-resistant isolate that harbored the blaOXA-357 gene. The genome sequence was further analyzed by various bioinformatics methods. The genome size was estimated to be 3,807,313 bp with 3508 predicted coding regions and G + C content is 38.7%. These findings have raised awareness of the possible emergence of OXA-type enzyme-producing A. pittii isolate in China.

Keywords:
Acinetobacter pittii; blaOXA-357; Whole genome sequencing (WGS); Multidrug-resistance

Acinetobacter pittii, formerly named Acinetobacter genomic species (gen. sp.) 3, is frequently associated with hospital-acquired infections and outbreaks that poses a particular concern due to its ability to acquire multidrug resistance to a wide range of antibiotics.11 Wang J, Ruan Z, Feng Y, et al. Species distribution of clinical Acinetobacter isolates revealed by different identification techniques. PLoS ONE. 2014;9:e104882. Carbapenems resistant Acinetobacter spp. isolates have been widely implicated in nosocomial infections and have also become an ongoing public health threat of global dimensions.22 Ruan Z, Chen Y, Jiang Y, et al. Wide distribution of CC92 carbapenem-resistant and OXA-23-producing Acinetobacter baumannii in multiple provinces of China. Int J Antimicrob Agents. 2013;42:322-328. The resistance rates to carbapenems among Acinetobacter spp., mainly caused by carbapenem-hydrolyzing class D-lactamases (CHDLs), have increased dramatically in the last decade.33 Ji S, Chen Y, Ruan Z, et al. Prevalence of carbapenem-hydrolyzing class D beta-lactamase genes in Acinetobacter spp. isolates in China. Eur J Clin Microbiol Infect Dis. 2014;33:989-997.

In this study, the strain A. pittii TCM156 was recovered from a blood sample of a male hospitalised patient with pneumonia at Hangzhou, Zhejiang province, China, in 2013. It was identified according to both 16S rRNA and rpoB gene sequencing. Genomic DNA was extracted using a QIAamp DNA minikit (Qiagen, Valencia, CA). The TruSeq DNA sample preparation kit (Illumina, USA) was used to create the libraries for genome sequencing. The genome of TCM156 was sequenced via the Illumina Hiseq 2500 platform using a TruSeq Rapid SBS Kit and a TruSeq PE (Paired-End) Cluster Kit v3. The draft genome sequence was assembled using CLC Genomics Workbench 9.0 and automatically annotated by the NCBI Prokaryotic Genomes Annotation Pipeline (PGAP) server. Resistance-related genes were analyzed using ResFinder 2.1.44 Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67:2640-2644. The multilocus sequence typing (MLST) analysis from the assembled genome was performed by BacWGSTdb.55 Ruan Z, Feng Y. BacWGSTdb, a database for genotyping and source tracking bacterial pathogens. Nucleic Acids Res. 2016;44:D682-D687. Further bioinformatics analysis, such as identification of genomic islands, insertion elements (IS), prophage sequences, clustered regularly interspaced short palindromic repeat (CRISPR) sequences and secondary metabolite gene clusters, were predicted by application of IslandViewer, ISfinder, PHASTER, CRISPRFinder and antiSMASH tools, respectively.66 Dhillon BK, Laird MR, Shay JA, et al. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res. 2015;43:W104-W108.1010 Weber T, Blin K, Duddela S, et al. antiSMASH 3.0 – a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015;43:W237-W243.

The draft genome sequence of A. pittii TCM156 consisted of 16 contigs with an average sequencing coverage of 100-fold, which comprised 3,807,313 bases, and PGAP server predicted a total of 3508 protein-coding sequences. The overall G + C content of this strain amounted to 38.7%. In total, 63 tRNA genes and 4 rRNA operons were identified, respectively. We also identified the aminoglycoside resistance genes strA, strB and aph(3′)-VIa, beta-lactam resistance gene blaADC-25 and blaOXA-357, macrolide resistance genes msr(E) and mph(E), and tetracycline resistance gene tet(39). The genome also contains at least 18 genomic islands and several IS elements: the majority belonging to the IS3, IS5, and IS110 families. The presence of three putative secondary metabolite gene clusters, including the arylpolyne, bacteriocin and siderophore biosynthetic gene clusters can also be predicted. The MLST analysis showed that TCM156 belongs to sequence type (ST) 865, according to the MLST scheme of A. baumannii.

In summary, these findings have raised awareness of the emergence of a multidrug-resistant OXA-357-producing A. pittii isolate in China. The possible emergence of a novel OXA-type enzyme is worrying and must be monitored to avoid their major spread to more clinically relevant bacterial species. To our knowledge, this is the first draft genome sequence of a multidrug-resistant OXA-357-producing clinical A. pittii isolate in China.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LSAL00000000. The version described in this paper is the first version, LSAL01000000.

Declarations

Funding

This study was supported by research grant from the National Natural Science Foundation of China [31600108], and the Zhejiang Provincial Medical and Health Science and Technology plan [2015KYA167].

Ethical approval

Not required.

References

  • 1
    Wang J, Ruan Z, Feng Y, et al. Species distribution of clinical Acinetobacter isolates revealed by different identification techniques. PLoS ONE 2014;9:e104882.
  • 2
    Ruan Z, Chen Y, Jiang Y, et al. Wide distribution of CC92 carbapenem-resistant and OXA-23-producing Acinetobacter baumannii in multiple provinces of China. Int J Antimicrob Agents 2013;42:322-328.
  • 3
    Ji S, Chen Y, Ruan Z, et al. Prevalence of carbapenem-hydrolyzing class D beta-lactamase genes in Acinetobacter spp. isolates in China. Eur J Clin Microbiol Infect Dis 2014;33:989-997.
  • 4
    Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012;67:2640-2644.
  • 5
    Ruan Z, Feng Y. BacWGSTdb, a database for genotyping and source tracking bacterial pathogens. Nucleic Acids Res 2016;44:D682-D687.
  • 6
    Dhillon BK, Laird MR, Shay JA, et al. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res 2015;43:W104-W108.
  • 7
    Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006;34:D32-D36.
  • 8
    Arndt D, Grant JR, Marcu A, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016;44:W16-W21.
  • 9
    Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35:W52-W57.
  • 10
    Weber T, Blin K, Duddela S, et al. antiSMASH 3.0 – a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 2015;43:W237-W243.

Publication Dates

  • Publication in this collection
    Apr-Jun 2017

History

  • Received
    12 July 2016
  • Accepted
    5 Oct 2016
Sociedade Brasileira de Microbiologia USP - ICB III - Dep. de Microbiologia, Sociedade Brasileira de Microbiologia, Av. Prof. Lineu Prestes, 2415, Cidade Universitária, 05508-900 São Paulo, SP - Brasil, Ramal USP 7979, Tel. / Fax: (55 11) 3813-9647 ou 3037-7095 - São Paulo - SP - Brazil
E-mail: bjm@sbmicrobiologia.org.br