Comparative genomic analysis of clinical Acinetobacter nosocomialis isolates from Terengganu, Malaysia led to the discovery of a novel tetracycline-resistant plasmid
Comparative genomic analysis of clinical Acinetobacter nosocomialis isolates from Terengganu, Malaysia led to the discovery of a novel tetracycline-resistant plasmid
Objectives: To analyse the genome sequences of four archival Acinetobacter nosocomialis clinical isolates (designated AC13, AC15, AC21 and AC25) obtained from Terengganu, Malaysia in 2011 to determine their genetic relatedness and basis of antimicrobial resistance.
Methods: Antimicrobial susceptibility profiles of the A. nosocomialis isolates were determined by disk diffusion. Genome sequencing was performed using the Illumina NextSeq platform. Results: The four A. nosocomialis isolates were cefotaxime resistant whereas three isolates (namely, AC13, AC15 and AC25) were tetracycline resistant. The carriage of the bla ADC-255-encoded cephalosporinase gene is likely responsible for cefotaxime resistance in all four isolates. Phylogenetic analysis indicated that the three tetracycline-resistant isolates were closely related, with an average nucleotide identity of 99.9%, suggestive of nosocomial spread, whereas AC21 had an average nucleotide identity of 97.9% when compared to these three isolates. The tetracycline-resistant isolates harboured two plasmids: a 13476 bp Rep3-family plasmid of the GR17 group designated pAC13-1, which encodes the tetA(39) tetracycline-resistance gene, and pAC13-2, a 4872 bp cryptic PriCT-1-family plasmid of a new Acinetobacter plasmid group, GR60. The tetA(39) gene was in a 2 001 bp fragment flanked by XerC/XerD recombination sites characteristic of a mobile pdif module. Both plasmids also harboured mobilisation/transfer-related genes. Conclusions: Genome sequencing of A. nosocomialis isolates led to the discovery of two novel plasmids, one of which encodes the tetA(39) tetracycline-resistant gene in a mobile pdif module. The high degree of genetic relatedness among the three tetracycline-resistant A. nosocomialis isolates is indicative of nosocomial transmission.
Acinetobacter nosocomialis, Plasmids, Tetracycline resistance, Whole genome sequence, pdif modules
104-109
Mohd Rani, Farahiyah
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Lean, Soo Sum
b99842bf-0783-45cc-adf1-3a3979e7c567
A Rahman, Nor Iza
c8250dae-dd75-446b-8b17-c2763f98c121
Ismail, Salwani
beb95eb3-3e79-4c48-a040-9994c7b5abce
Alattraqchi, Ahmed Ghazi
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Amonov, Malik
8197b95e-e5c0-442f-a1c8-0a64d27e8498
Cleary, David W
f4079c6d-d54b-4108-b346-b0069035bec0
Clarke, Stuart C
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Yeo, Chew Chieng
fdccc646-7c5d-4231-a9fa-ff01c39f4e5a
1 December 2022
Mohd Rani, Farahiyah
1a1e50e5-e44e-445e-83ef-c7039a713620
Lean, Soo Sum
b99842bf-0783-45cc-adf1-3a3979e7c567
A Rahman, Nor Iza
c8250dae-dd75-446b-8b17-c2763f98c121
Ismail, Salwani
beb95eb3-3e79-4c48-a040-9994c7b5abce
Alattraqchi, Ahmed Ghazi
dade11e6-1d45-4351-96a5-ed751091e200
Amonov, Malik
8197b95e-e5c0-442f-a1c8-0a64d27e8498
Cleary, David W
f4079c6d-d54b-4108-b346-b0069035bec0
Clarke, Stuart C
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Yeo, Chew Chieng
fdccc646-7c5d-4231-a9fa-ff01c39f4e5a
Mohd Rani, Farahiyah, Lean, Soo Sum, A Rahman, Nor Iza, Ismail, Salwani, Alattraqchi, Ahmed Ghazi, Amonov, Malik, Cleary, David W, Clarke, Stuart C and Yeo, Chew Chieng
(2022)
Comparative genomic analysis of clinical Acinetobacter nosocomialis isolates from Terengganu, Malaysia led to the discovery of a novel tetracycline-resistant plasmid.
Journal of Global Antimicrobial Resistance, 31 (12), .
(doi:10.1016/j.jgar.2022.08.019).
Abstract
Objectives: To analyse the genome sequences of four archival Acinetobacter nosocomialis clinical isolates (designated AC13, AC15, AC21 and AC25) obtained from Terengganu, Malaysia in 2011 to determine their genetic relatedness and basis of antimicrobial resistance.
Methods: Antimicrobial susceptibility profiles of the A. nosocomialis isolates were determined by disk diffusion. Genome sequencing was performed using the Illumina NextSeq platform. Results: The four A. nosocomialis isolates were cefotaxime resistant whereas three isolates (namely, AC13, AC15 and AC25) were tetracycline resistant. The carriage of the bla ADC-255-encoded cephalosporinase gene is likely responsible for cefotaxime resistance in all four isolates. Phylogenetic analysis indicated that the three tetracycline-resistant isolates were closely related, with an average nucleotide identity of 99.9%, suggestive of nosocomial spread, whereas AC21 had an average nucleotide identity of 97.9% when compared to these three isolates. The tetracycline-resistant isolates harboured two plasmids: a 13476 bp Rep3-family plasmid of the GR17 group designated pAC13-1, which encodes the tetA(39) tetracycline-resistance gene, and pAC13-2, a 4872 bp cryptic PriCT-1-family plasmid of a new Acinetobacter plasmid group, GR60. The tetA(39) gene was in a 2 001 bp fragment flanked by XerC/XerD recombination sites characteristic of a mobile pdif module. Both plasmids also harboured mobilisation/transfer-related genes. Conclusions: Genome sequencing of A. nosocomialis isolates led to the discovery of two novel plasmids, one of which encodes the tetA(39) tetracycline-resistant gene in a mobile pdif module. The high degree of genetic relatedness among the three tetracycline-resistant A. nosocomialis isolates is indicative of nosocomial transmission.
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More information
Accepted/In Press date: 23 August 2022
e-pub ahead of print date: 29 August 2022
Published date: 1 December 2022
Additional Information:
Funding Information:
This study was supported by the Fundamental Research Grant Scheme FRGS/1/2018/SKK11/UNISZA/01/1 from the Ministry of Higher Education Malaysia. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Ethical approval for the collection of Acinetobacter spp. isolates was obtained from the Malaysian Ministry of Health's Medical Research Ethics Council (approval no. NMRR-14-1650-23625-IIR). We thank Dr. Fatimah Haslina Abdullah and Dr. Norlela Othman of Hospital Sultanah Nur Zahirah, Kuala Terengganu, for the Acinetobacter nosocomialis strains used in this study.
Funding Information:
This study was supported by the Fundamental Research Grant Scheme FRGS/1/2018/SKK11/UNISZA/01/1 from the Ministry of Higher Education Malaysia.
Publisher Copyright:
© 2022 The Author(s)
Keywords:
Acinetobacter nosocomialis, Plasmids, Tetracycline resistance, Whole genome sequence, pdif modules
Identifiers
Local EPrints ID: 470050
URI: http://eprints.soton.ac.uk/id/eprint/470050
ISSN: 2213-7165
PURE UUID: bf8f8d15-abd0-4685-a508-27d1a1356bf9
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Date deposited: 30 Sep 2022 17:01
Last modified: 17 Mar 2024 03:35
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Contributors
Author:
Farahiyah Mohd Rani
Author:
Soo Sum Lean
Author:
Nor Iza A Rahman
Author:
Salwani Ismail
Author:
Ahmed Ghazi Alattraqchi
Author:
Malik Amonov
Author:
Chew Chieng Yeo
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