Open Access

New eight genes identified at the clinical multidrug-resistant Acinetobacter baumannii DMS06669 strain in a Vietnam hospital

Annals of Clinical Microbiology and Antimicrobials201716:74

https://doi.org/10.1186/s12941-017-0250-9

Received: 5 July 2017

Accepted: 8 November 2017

Published: 14 November 2017

Abstract

Background

Acinetobacter baumannii is an important nosocomial pathogen that can develop multidrug resistance. In this study, we characterized the genome of the A. baumannii strain DMS06669 (isolated from the sputum of a male patient with hospital-acquired pneumonia) and focused on identification of genes relevant to antibiotic resistance.

Methods

Whole genome analysis of A. baumannii DMS06669 from hospital-acquired pneumonia patients included de novo assembly; gene prediction; functional annotation to public databases; phylogenetics tree construction and antibiotics genes identification.

Results

After sequencing the A. baumannii DMS06669 genome and performing quality control, de novo genome assembly was carried out, producing 24 scaffolds. Public databases were used for gene prediction and functional annotation to construct a phylogenetic tree of the DMS06669 strain with 21 other A. baumannii strains. A total of 18 possible antibiotic resistance genes, conferring resistance to eight distinct classes of antibiotics, were identified. Eight of these genes have not previously been reported to occur in A. baumannii.

Conclusions

Our results provide important information regarding mechanisms that may contribute to antibiotic resistance in the DMS06669 strain, and have implications for treatment of patients infected with A. baumannii.

Keywords

Acinetobacter baumannii Multidrug resistanceDraft genome assemblyNext generation sequencing

Background

The nosocomial pathogen Acinetobacter baumannii has become a serious world-wide health concern, as it has in recent decades acquired resistance to an array of antibiotics [13]. The development of resistance to carbapenem is of particular concern [4, 5]. A. baumannii is responsible for 2–10% of all Gram-negative bacterial infections in intensive care units, and causes significant mortality in infected patients [6, 7]. Infection with multidrug resistant (MDR) Acinetobacter strains is associated both with elevated mortality rates and longer hospital treatment times [8].

Recent advances in next-generation sequencing have facilitated the rapid characterization of whole-genome sequences from microbial species [9]. In this study, we used the Illumina HiSeq® platform to carry out de novo assembly of the genome of the A. baumannii strain DMS06669 to identify genes related to antibiotic resistance. DNA samples were obtained from the sputum of a male patient with hospital-acquired pneumonia. Gene prediction and functional annotation were carried out using public databases, followed by construction of a phylogenetic tree and whole-genome comparison. Antibiotic resistance of DMS06669 to multiple antibiotics was characterized using an antibiotic susceptibility assay test, and potential antibiotic resistance genes in DMS06669 were predicted from functional annotation analysis. Identification of these genes is an important step in elucidating mechanisms underlying antibiotic resistance in A. baumannii.

Methods

Isolation and identification of A. baumannii strain DMS06669

The A. baumannii strain DMS06669 was isolated from a sputum specimen obtained from a 49-year-old male patient with hospital-acquired pneumonia at Thong Nhat Dong Nai General Hospital in Dong Nai, Vietnam. This isolate was cultured at 37 °C on blood agar and MacConkey agar. The presence of the blaOXA-51 gene was used to confirm that the isolate was a strain of A. baumannii [10].

Antibiotic susceptibility assay test

Microbiological isolation and identification of the A. baumannii strain DMS06669 was performed using classic methods and verified by the Phoenix system (BD Diagnostics, Sparks, MD, USA). Antimicrobial susceptibility testing was performed using the minimum inhibitory concentration (MIC) breakpoint method according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Antimicrobials tested included amikacin, aztreonam, ampicillin/sulbactam, ciprofloxacin, ceftazidime, ceftriaxone, colistin, cefepime, cefoxitin, ceftazolin, gentamicin, imipenem, meropenem, levofloxacin, trimethoprim/sulfamethoxazole, ticarcillin/clavulanic acid, tigecycline, and piperacillin/tazobactam.

DNA preparation and sequencing

Genomic DNA of A. baumannii DMS06669 was extracted using the Wizard DNA extraction kit (Promega, USA), and then sequenced (1st BASE, Singapore) on an Illumina HiSeq 2000, resulting in 150 base pair (bp) paired-end reads and an average coverage of 120-fold.

Data preprocessing and de novo genome assembly

Raw paired-end reads were assessed and quality control was carried out using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Trimmomatic [11] (parameters: ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:10:30 MINLEN:100) to obtain a set of clean paired-end reads. After preprocessing, FastQC was again used to report features of the preprocessing libraries and to verify the effectiveness of read trimming. After filtering, short reads were assembled using the SPAdes Genome Assembler [12] and contigs longer than 300 bp were retained. Then, those contigs were launched in a multi-draft based analysis to reorder through MeDuSa software [13], using A. baumannii ATCC 17978 as a reference.

Genome annotation

Prodigal (version 2.6.2) [14] was used for gene prediction in the A. baumannii DMS06669 draft genome, while tRNAscan-SE [15] and RNAmmer [16] were used for tRNA and rRNA (5S, 16S, and 23S) identification. Tandem Repeat Finder (http://tandem.bu.edu/trf/trf.html) [17] and CRISPR Finder (http://crispr.u-psud.fr/Server/) [18] were used to find tandem repeat sequences and clustered regularly interspaced short palindromic repeats (CRISPRs). Insertion sequences (ISs) were identified using ISfinder (https://www-is.biotoul.fr//). For functional classification of the predicted genes, BLASTp [19] was used to align amino acids of predicted genes against the Clusters of Orthologous Groups (COG) database [20] with an expected value threshold of 10e−3 using the Conserved Domains Database (CDD) batch server [21] (https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi). Amino acid sequences were aligned using default parameters, and the description of the best hit (highest alignment length percentage and match identity) was assigned as the predicted gene. All annotated genes were then categorized based on their COG classification. ResFinder (version 2.1; https://cge.cbs.dtu.dk/services/ResFinder/) was used to identify potential antibiotic resistance genes, using recommended similarity thresholds [22].

Construction of phylogenetic tree

16S rRNA sequences were extracted from the draft genome of DMS06669, and 16S rRNA sequences of 21 A. baumannii strains (including 1656-2, AB0057, AB030, AB031, AB307-0294, AC29, ACICU, ATCC17978, AYE, AbH12O-A2, BJAB07104, BJAB0715, BJAB0868, D1279779, LAC-4, MDR-TJ, MDR-ZJ06, SDF, TCDC-AB0715, TYTH-1, and ZW85-1) were downloaded using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database [23]. Evolutionary analyses of 16S rRNA sequences were carried out using ClustalW (version 2.1) to multiple aligned sequences. The maximum-likelihood phylogenetic tree was then constructed using PHYLIP (version 3.695) [24] with the bootstrap algorithm set to 500, and the phylogenetic tree was visualized using FigTree (version 1.4.3) (http://tree.bio.ed.ac.uk/software/fgtree/).

Results and discussion

Antibiotic resistance of A. baumannii DMS06669

The antibiotic susceptibility profile for the DMS06669 strain is shown in Table 1. The A. baumannii DMS06669 strain was resistant to all antibiotics tested with high level of MIC values except colistin and tigecycline.
Table 1

Susceptibility profile of A. baumannii strain DMS06669

Antibiotic drug

MIC (µg/ml)

Ampicillin/sulbactam

32/16

Ceftazidime

32

Ciprofloxacin

4

Levofloxacin

4

Imipenem

16

Meropenem

16

Gentamicin

16

Colistin

1

Amikacin

64

Piperacillin/tazobactam

128/8

Ticarcillin/clavulanic acid

128/4

Cefepime

32

Cefoxitin

32

Cefazolin

16

Ceftriaxone

8

Tigecycline

1

Aztreonam

32

Trimethoprim/sulfamethoxazole

8/76

Assembly and annotation of the genomic sequence

Raw reads from the Illumina HiSeq mahcine were assessed with FastQC and filtered using Trimmomatic to produce a clean set of reads. These whole genome DNA samples yielded 4,750,865 raw paired-end reads with lengths of 150 bp. After removal of adapters and low-quality data (quality scores ≤ 30), 3,768,594 clean reads (79.3% of the initial total) remained (Table 2).
Table 2

Results of genome assembly and annotation of A. baumannii strain DMS06669

Feature

Statistics

Pair-end raw reads

4,750,865

Pair-end clean reads (remaining percentage)

3,768,594 (79.32%)

Length of total draft genome length (bp)

4,369,281

Scaffolds

24

Length of scaffold (N50)

4,207,939

GC content (%)

38.9

Coding sequences

4101

tRNAs

63

rRNAs

3

CRISPR sequences

2a

Tandem repeat sequences

6

Insertion sequences

62

aIncludes one questionable (non-confirmed) sequence

The clean paired-end read dataset was used for de novo genome assembly using the SPAdes Genome Assembler and reordering by MeDuSa, and resulted in 24 scaffolds, with a total draft genome length of 4,369,281 bp (N50 of 4,207,939 bp and GC content of 38.9%). From genome annotation analysis, we detected 4101 coding sequences, 63 tRNA sequences, 3 rRNA sequences, 2 CRISPR sequences, 6 tandem repeat sequences, and 62 predicted ISs (Table 2).

Functional annotation of the genomic sequence of A. baumannii strain DMS06669

The COG database phylogenetically classifies proteins encoded by completely sequenced genomes. Of the 4101 coding sequences identified in the DMS06669 genome, 3066 sequences (74.8%) were annotated and classified into 25 functional categories (Fig. 1). The identity ratio in this study was similar to those obtained in studies of A. baumannii strains MDR-TJ, MDR-SHH02, and XH386 (ST208) [22, 25, 26]. Among the aligned COG classifications, the “transcription” category comprised the largest group (268 coding sequences, 8.7% of the total number), followed by “amino acid transport and metabolism” (263 coding sequences, 8.6%), “general function prediction only” (211 coding sequences, 6.9%), and “translation” (210 coding sequences, 6.8%). In addition, 193 coding sequences were classified as having “unknown function”. No coding sequences were assigned to functional categories of “chromatin structure and dynamics”, “nuclear structure”, or “cytoskeleton” (Fig. 1).
Fig. 1

COG functional classification of coding sequences. A total of 3066 coding sequences were annotated and assigned to 25 functional categories

Based on genomes from published A. baumannii strains on the KEGG database, we performed phylogenetic analysis of 16S rRNA to identify genetic relatedness of strains. Figure 2 shows that DMS06669 is most closely related to the ZW-85 and AbH120-A2 strains.
Fig. 2

16S rRNA phylogenetic analysis showing the evolutionary relationship between A. baumannii strains. The tree was generated with PHYLIP (version 3.695) with the bootstrap algorithm set to 500 and standard settings. The scale bar represents the branch lengths

Identification of antibiotic resistance genes

To identify A. baumannii DMS06669 genes related to antibiotic resistance, coding sequences were submitted to ResFinder [22]. Table 3 lists genes that may contribute to A. baumannii DMS06669 resistance to aminoglycosides, beta-lactams, macrolides, lincosamide streptogramin B, phenicols, rifampicin, sulphonamides, tetracyclines, and trimethoprim.
Table 3

Resistance-associated genes identified in A. baumannii strain DMS06669

Predicted gene

Resistance gene

Antibiotic class

% identity

HSP length/query length

DMS06669_scf_4_1

aadA16

Aminoglycoside resistance

99.7

846/846

DMS06669_scf_2_1

aadB

Aminoglycoside resistance

100.00

534/534

DMS06669_scf_23_3

aadA1

Aminoglycoside resistance

99.9

792/792

DMS06669_scf_22_2

rmtB

Aminoglycoside resistance

100.00

756/756

DMS06669_scf_2_2

blaVEB-7

Beta-lactam resistance

99.9

900/900

DMS06669_scf_23_2

blaOXA-10

Beta-lactam resistance

100.00

801/801

DMS06669_scf_18_1

blaOXA-58

Beta-lactam resistance

100.00

843/843

DMS06669_scf_1_2828

blaADC-25

Beta-lactam resistance

96.3

1152/1152

DMS06669_scf_11_9

blaNDM-1

Beta-lactam resistance

100.00

813/813

DMS06669_scf_1_1731

blaOXA-64

Beta-lactam resistance

100.00

825/825

DMS06669_scf_23_1

cmlA1

Phenicol resistance

99.1

1260/1260

DMS06669_scf_21_2

floR

Phenicol resistance

98.3

1214/1215

DMS06669_scf_5_1

sul1

Sulphonamide resistance

100.00

840/840

DMS06669_scf_8_3

tet(39)

Tetracycline resistance

99.9

1122/1122

DMS06669_scf_13_10

mph(E)

Macrolide resistance

100.00

885/885

DMS06669_scf_13_11

msr(E)

Macrolide, lincosamide, and streptogramin B resistance

100.00

1476/1476

DMS06669_scf_16_1

ARR-3

Rifampicin resistance

100.00

453/453

DMS06669_scf_4_2

dfrA27

Trimethoprim resistance

100.00

474/474

Among 22 A. baumannii strains, the DMS06669 strain had resistance to the highest number of types of antibiotics (including eightHo Chi Minh City of nine antibiotic classes, with susceptibility only to fluoroquinolones; Fig. 3). DMS06669 was followed by AYE, BJAB0868, MDR-ZJ06, MDR-TJ, and BJAB07104 strains, all of which have been reported to be MDR strains. The absence of resistance to fluoroquinolones in the DMS06669 strain was consistent with MIC analysis (Table 1) when the antibiotic susceptibility profile shows that MIC values of ciprofloxacin and levofloxacin was at intermediate level (4 µg/ml for each antibiotic). Detailed results of all antibiotic resistance genes in each class of antibiotics are included in Additional file 1: Table S1.
Fig. 3

Antibiotic resistance in A. baumannii strain DMS06669 and 21 other A. baumannii strains

Genes related to gentamicin (aadB [27]) and amikacin (rmtB [28]) resistance were found in the DMS06669 strain. MIC values for DMS06669 susceptibility to gentamicin and amikacin were high, measured at 16 and 64 µg/ml, respectively (Table 1). The rmtB aminoglycoside resistance gene has not previously been reported to occur in A. baumannii. Additionally, we found the aadA1 gene [29], involved in streptomycin resistance, and the aadA16 gene (not reported in A. baumannii before) [30], involved in spectinomycin resistance, in the DMS06669 genome.

Two genes related to macrolide, lincosamide, and streptogramin B resistance were found in the DMS06669 strain: mphE [31], associated with resistance to erythromycin (a macrolide antibiotic), and msrE [32], associated with streptogramin resistance. The presence of these genes in other MDR strains, including BJAB0868, BJAB07104, TYTH-1, MDR-ZJ06, AC29, and MDR-TJ, has previously been reported (Additional file 1: Table S1).

We found genes associated with resistance to phenicol, rifapicin, and sulphonamide antibiotics, including two genes already known to occur in A. baumannii: cmlA1, associated with chloramphenicol resistance [33], and sul1, associated with sulfamethoxazole resistance [34]. We identified two additional genes in this category that occur only in the DMS06669 strain: floR, associated with chloramphenicol and florfenicol resistance [35]; and arr-3, associated with rifampin (also known as rifampicin), rifaximin, rifabutin, and rifapentine antibiotic resistant groups [36].

Two predicted DMS06669 genes were similar to the tet(39) and dfrA27 genes, which are associated with resistance to tetracycline and trimethoprim, respectively. The presence of homologs to these genes in A. baumannii has not previously been reported. The tet(39) gene has been reported to confer resistance to tetracycline [37], which has a structure similar to that of tigecycline [38]. However, according to our analysis (Table 1), DMS06669 was weakly resistant to tigecycline (MIC value of 1 µg/ml), suggesting that tet(39) is not associated with tigecycline resistance. It has been reported that the dfrA27 gene confers trimethoprim resistance, and the complex of dfrA27 and aadA16 genes have been reported in the MDR E. coli strain 1387 [30]. We found that this complex was also present in the DMS06669 strain.

Interestingly, DMS06669 contained six genes associated with resistance to beta-lactamase. The blaVEB-7 and blaADC-25 genes have been associated with resistance to cephalosporins (a group that includes cefepime, cefoxitin, cefazolin, and ceftriaxone) and aztreonam [39, 40], in agreement with MIC analysis (Table 1). DMS06669 also contained the genes blaOXA-10 [41], blaOXA-58 [42], blaOXA-64 [43], and blaNDM-1 [44], which are thought to confer resistance to carbapenems (a group that includes meropenem and imipenem). Among these genes, blaOXA-64 and blaVEB-7 genes have not previously been reported to occur in A. baumannii strains. Moreover, both blaNDM-1 and blaOXA-58 genes that are found in the DMS06669 strain have not previously been reported to occur in the same strain.

Conclusions

In this study, the genome of the A. baumannii strain DMS06669 was sequenced and de novo genome assembly was carried out, yielding 24 scaffolds. Phylogeny analysis was conducted from 16S rRNA extracted from the assembled genome. A total of 4101 coding sequences were predicted and annotated, leading to identification of 18 predicted genes associated with resistance to eight classes of antibiotics. Eight of these genes have not previously been reported to occur in A. baumannii. Furthermore, there were two antibiotic resistance genes (blaNDM-1 and blaOXA-58 genes) found in the DMS06669 strain that have not been reported together in any A. baumannii strain. Our analysis significantly expands understanding of the A. baumannii genome, and represents an important step in elucidating the molecular mechanisms of antibiotic resistance in this species.

Abbreviations

MDR: 

multidrug resistant

MIC: 

minimum inhibitory concentration

CLSI: 

Clinical and Laboratory Standards Institute

bp: 

base pair

CRISPRs: 

clustered regularly interspaced short palindromic repeats

IS: 

insertion sequences

COG: 

Clusters of Orthologous Groups

CDD: 

conserved domains database

KEGG: 

Kyoto Encyclopedia of Genes and Genomes

Declarations

Authors’ contributions

NST and NTH were responsible for designing experiment, carrying out the experiment and writing manuscript. HMN, PTTH and PHV were responsible for carrying out the experiments. CN and NST responsible for all bioinformatics analysis. All authors read and approved the final manuscript.

Acknowledgements

We would like to thank the members of Microbiology department—Thongnhat Dongnai General Hospital and Department of Biotechnology—Faculty of Chemical Engineering—Ho Chi Minh City University of Technology for their assistance in sample collection.

Competing interests

The authors declare that they have no competing interests.

Availability of data and materials

Raw dataset was deposited in the NCBI Sequence Read Archive (SRA) (the BioProject accession number, BioSample accession number and SRA accession numbers will be provided upon acceptance).

Funding

This work was financially supported by Dongnai General Hospital.

Ethics approval and consent to participate

This study was approved by the Ethics Committee in Biomedical research of the Thongnhat Dongnai General Hospital, Dongnai province, Vietnam (the committee’s reference number: 09/BVDKTNDN-HD).

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Authors’ Affiliations

(1)
Department of Biotechnology, Faculty of Chemical Engineering, Ho Chi Minh City University of Technology, HCM National University
(2)
Molecular Medicine Laboratory, Faculty of Medical Microbiology, Thong Nhat Dong Nai General Hospital
(3)
Department of Microbiology, Faculty of Biology, Ho Chi Minh City University of Natural Science, HCM National University
(4)
Department of Bioinformatics and Medical Statistics, Vinmec Research Institute of Stem Cell and Gene Technology
(5)
The HCM Society of Clinical Microbiologists
(6)
Faculty of Medical Biochemistry, Thong Nhat Dong Nai General Hospital

References

  1. Poirel L, Nordmann P. Carbapenem resistance in Acinetobacter baumannii: mechanisms and epidemiology. Clin Microbiol Infect. 2006;12:826–36.View ArticlePubMedGoogle Scholar
  2. Dijkshoorn L, Nemec A, Seifert H. An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii. Nat Rev Microbiol. 2007;5:939–51.View ArticlePubMedGoogle Scholar
  3. Peleg AY, Seifert H, Paterson DL. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev. 2008;21:538–82.View ArticlePubMedPubMed CentralGoogle Scholar
  4. Poirel L, Menuteau O, Agoli N, Cattoen C, Nordmann P. Outbreak of extended-spectrum β-Lactamase VEB-1-Producing Isolates of Acinetobacter baumannii in a French Hospital. J Clin Microbiol. 2003;41:3542–7.View ArticlePubMedPubMed CentralGoogle Scholar
  5. Lockhart SR, Abramson MA, Beekmann SE, Gallagher G, Riedel S, Diekema DJ, et al. Antimicrobial Resistance among Gram-Negative bacilli causing infections in intensive care unit patients in the United States between 1993 and 2004. J Clin Microbiol. 2007;45:3352–9.View ArticlePubMedPubMed CentralGoogle Scholar
  6. Falagas ME, Karveli EA. The changing global epidemiology of Acinetobacter baumannii infections: a development with major public health implications. Clin Microbiol Infect. 2007;13:117–9.View ArticlePubMedGoogle Scholar
  7. Zarrilli R, Pournaras S, Giannouli M, Tsakris A. Global evolution of multidrug-resistant Acinetobacter baumannii clonal lineages. Int J Antimicrob Agents. 2013;41:11–9.View ArticlePubMedGoogle Scholar
  8. Sunenshine RH, Wright M-O, Maragakis LL, Harris AD, Song X, Hebden J, et al. Multidrug-resistant Acinetobacter infection mortality rate and length of hospitalization. Emerg Infect Dis. 2007;13:97–103.View ArticlePubMedPubMed CentralGoogle Scholar
  9. Metzker ML. Sequencing technologies—the next generation. Nat Rev Genet. 2010;11:31–46.View ArticlePubMedGoogle Scholar
  10. Kinzler KW, Bigner SH, Bigner DD, Trent JM, Law ML, O&amp SJ, et al. Identification of an amplified, highly expressed gene in a human glioma. Science. 1987;236:70–4.View ArticlePubMedGoogle Scholar
  11. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014. https://doi.org/10.1093/bioinformatics/btu170.PubMedPubMed CentralGoogle Scholar
  12. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.View ArticlePubMedPubMed CentralGoogle Scholar
  13. Bosi E, Donati B, Galardini M, Brunetti S, Sagot M-F, Lió P, et al. MeDuSa: a multi-draft based scaffolder. Bioinformatics. 2015;31:2443–51.View ArticlePubMedGoogle Scholar
  14. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.View ArticlePubMedPubMed CentralGoogle Scholar
  15. Tm L, Sr E. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–64.View ArticleGoogle Scholar
  16. Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100–8.View ArticlePubMedPubMed CentralGoogle Scholar
  17. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–80.View ArticlePubMedPubMed CentralGoogle Scholar
  18. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35:W52–7.View ArticlePubMedPubMed CentralGoogle Scholar
  19. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.View ArticlePubMedPubMed CentralGoogle Scholar
  20. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2001;29:22–8.View ArticlePubMedPubMed CentralGoogle Scholar
  21. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, et al. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 2011;39:D225–9.View ArticlePubMedGoogle Scholar
  22. Wang H, Wang J, Yu P, Ge P, Jiang Y, Xu R, et al. Identification of antibiotic resistance genes in the multidrug-resistant Acinetobacter baumannii strain, MDR-SHH02, using whole-genome sequencing. Int J Mol Med. 2017;39:364–72.View ArticlePubMedGoogle Scholar
  23. Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28:27–30.View ArticlePubMedPubMed CentralGoogle Scholar
  24. Fedelstein J. PHYLIP (Phylogeny Inference Package). 1993.Google Scholar
  25. Gao F, Wang Y, Liu Y-J, Wu X-M, Lv X, Gan Y-R, et al. Genome sequence of Acinetobacter baumannii MDR-TJ. J Bacteriol. 2011;193:2365–6.View ArticlePubMedPubMed CentralGoogle Scholar
  26. Fang Y, Quan J, Hua X, Feng Y, Li X, Wang J, et al. Complete genome sequence of Acinetobacter baumannii XH386 (ST208), a multi-drug resistant bacteria isolated from pediatric hospital in China. Genom Data. 2016;7:269–74.View ArticlePubMedGoogle Scholar
  27. Cameron FH, Obbink JDO, Ackerman VP, Hall RM. Nucleotide sequence of the AAD(2′) aminoglycoside adenylyltransferase determinant aadB. Evolutionary relationship of this region with those surrounding aadA in R538-1 and dhfrll in R388. Nucleic Acids Res. 1986;14:8625–35.View ArticlePubMedPubMed CentralGoogle Scholar
  28. Zhou Y, Yu H, Guo Q, Xu X, Ye X, Wu S, et al. Distribution of 16S rRNA methylases among different species of Gram-negative bacilli with high-level resistance to aminoglycosides. Eur J Clin Microbiol Infect Dis. 2010;29:1349–53.View ArticlePubMedGoogle Scholar
  29. Hollingshead S, Vapnek D. Nucleotide sequence analysis of a gene encoding a streptomycin/spectinomycin adenyltransferase. Plasmid. 1985;13:17–30.View ArticlePubMedGoogle Scholar
  30. Wei Q, Jiang X, Yang Z, Chen N, Chen X, Li G, et al. dfrA27, a new integron-associated trimethoprim resistance gene from Escherichia coli. J Antimicrob Chemother. 2009;63:405–6.View ArticlePubMedGoogle Scholar
  31. Bhullar K, Waglechner N, Pawlowski A, Koteva K, Banks ED, Johnston MD, et al. Antibiotic resistance is prevalent in an isolated cave microbiome. PLoS ONE. 2012;7:e34953.View ArticlePubMedPubMed CentralGoogle Scholar
  32. Bonnin RA, Nordmann P, Carattoli A, Poirel L. Comparative Genomics of IncL/M-Type Plasmids: evolution by acquisition of resistance genes and insertion sequences. Antimicrob Agents Chemother. 2013;57:674–6.View ArticlePubMedPubMed CentralGoogle Scholar
  33. Bissonnette L, Champetier S, Buisson JP, Roy PH. Characterization of the nonenzymatic chloramphenicol resistance (cmlA) gene of the In4 integron of Tn1696: similarity of the product to transmembrane transport proteins. J Bacteriol. 1991;173:4493–502.View ArticlePubMedPubMed CentralGoogle Scholar
  34. Sköld O. Resistance to trimethoprim and sulfonamides. Vet Res. 2001;32:261–73.View ArticlePubMedGoogle Scholar
  35. Arcangioli M-A, Leroy-Sétrin S, Martel J-L, Chaslus-Dancla E. A new chloramphenicol and florfenicol resistance gene flanked by two integron structures in Salmonella typhimurium DT104. FEMS Microbiol Lett. 1999;174:327–32.View ArticlePubMedGoogle Scholar
  36. Chowdhury G, Pazhani GP, Nair GB, Ghosh A, Ramamurthy T. Transferable plasmid-mediated quinolone resistance in association with extended-spectrum β-lactamases and fluoroquinolone-acetylating aminoglycoside-6′-N-acetyltransferase in clinical isolates of Vibrio fluvialis. Int J Antimicrob Agents. 2011;38:169–73.PubMedGoogle Scholar
  37. Agersø Y, Guardabassi L. Identification of Tet 39, a novel class of tetracycline resistance determinant in Acinetobacter spp. of environmental and clinical origin. J Antimicrob Chemother. 2005;55:566–9.View ArticlePubMedGoogle Scholar
  38. Greer ND. Tigecycline (Tygacil): the first in the glycylcycline class of antibiotics. Proc Bayl Univ Med Cent. 2006;19:155–61.PubMedPubMed CentralGoogle Scholar
  39. Poirel L, Naas T, Guibert M, Chaibi EB, Labia R, Nordmann P. Molecular and biochemical characterization of VEB-1, a novel class a extended-spectrum β-Lactamase encoded by an Escherichia Coli integron gene. Antimicrob Agents Chemother. 1999;43:573–81.PubMedPubMed CentralGoogle Scholar
  40. Zong Z, Lü X, Valenzuela JK, Partridge SR, Iredell J. An outbreak of carbapenem-resistant Acinetobacter baumannii producing OXA-23 carbapenemase in western China. Int J Antimicrob Agents. 2008;31:50–4.View ArticlePubMedGoogle Scholar
  41. Paetzel M, Danel F, de Castro L, Mosimann SC, Page MGP, Strynadka NCJ. Crystal structure of the class D β-lactamase OXA-10. Nat Struct Mol Biol. 2000;7:918–25.View ArticleGoogle Scholar
  42. Poirel L, Marqué S, Héritier C, Segonds C, Chabanon G, Nordmann P. OXA-58, a novel class D β-lactamase involved in resistance to carbapenems in Acinetobacter baumannii. Antimicrob Agents Chemother. 2005;49:202–8.View ArticlePubMedPubMed CentralGoogle Scholar
  43. Brown S, Amyes SGB. The sequences of seven class D β-lactamases isolated from carbapenem-resistant Acinetobacter baumannii from four continents. Clin Microbiol Infect. 2005;11:326–9.View ArticlePubMedGoogle Scholar
  44. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, et al. Characterization of a new metallo-β-lactamase gene, blaNDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother. 2009;53:5046–54.View ArticlePubMedPubMed CentralGoogle Scholar

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