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Complete genome sequencing of Acinetobacter baumannii AC1633 and Acinetobacter nosocomialis AC1530 unveils a large multidrug-resistant plasmid encoding the NDM-1 and OXA-58 carbapenemases

Complete genome sequencing of Acinetobacter baumannii AC1633 and Acinetobacter nosocomialis AC1530 unveils a large multidrug-resistant plasmid encoding the NDM-1 and OXA-58 carbapenemases
Complete genome sequencing of Acinetobacter baumannii AC1633 and Acinetobacter nosocomialis AC1530 unveils a large multidrug-resistant plasmid encoding the NDM-1 and OXA-58 carbapenemases

Carbapenem-resistant Acinetobacter spp. are considered priority drug-resistant human-pathogenic bacteria. The genomes of two carbapenem-resistant Acinetobacter spp. clinical isolates obtained from the same tertiary hospital in Terengganu, Malaysia, namely, A. baumannii AC1633 and A. nosocomialis AC1530, were sequenced. Both isolates were found to harbor the carbapenemase genes blaNDM-1 and blaOXA-58 in a large (ca. 170 kb) plasmid designated pAC1633-1 and pAC1530, respectively, that also encodes genes that confer resistance to aminoglycosides, sulfonamides, and macrolides. The two plasmids were almost identical except for the insertion of ISAba11 and an IS4 family element in pAC1633-1, and ISAba11 along with relBE toxin-antitoxin genes flanked by inversely orientated pdif (XerC/XerD) recombination sites in pAC1530. The blaNDM-1 gene was encoded in a Tn125 composite transposon structure flanked by ISAba125, whereas blaOXA-58 was flanked by ISAba11 and ISAba3 downstream and a partial ISAba3 element upstream within a pdif module. The presence of conjugative genes in plasmids pAC1633-1/pAC1530 and their discovery in two distinct species of Acinetobacter from the same hospital are suggestive of conjugative transfer, but mating experiments failed to demonstrate transmissibility under standard laboratory conditions. Comparative sequence analysis strongly inferred that pAC1633-1/pAC1530 was derived from two separate plasmids in an IS1006-mediated recombination or transposition event. A. baumannii AC1633 also harbored three other plasmids designated pAC1633-2, pAC1633-3, and pAC1633-4. Both pAC1633-3 and pAC1633-4 are cryptic plasmids, whereas pAC1633-2 is a 12,651-bp plasmid of the GR8/GR23 Rep3-superfamily group that encodes the tetA(39) tetracycline resistance determinant in a pdif module.IMPORTANCE Bacteria of the genus Acinetobacter are important hospital-acquired pathogens, with carbapenem-resistant A. baumannii listed by the World Health Organization as the one of the top priority pathogens. Whole-genome sequencing of carbapenem-resistant A. baumannii AC1633 and A. nosocomialis AC1530, which were isolated from the main tertiary hospital in Terengganu, Malaysia, led to the discovery of a large, ca. 170-kb plasmid that harbored genes encoding the New Delhi metallo-β-lactamase-1 (NDM-1) and OXA-58 carbapenemases alongside genes that conferred resistance to aminoglycosides, macrolides, and sulfonamides. The plasmid was a patchwork of multiple mobile genetic elements and comparative sequence analysis indicated that it may have been derived from two separate plasmids through an IS1006-mediated recombination or transposition event. The presence of such a potentially transmissible plasmid encoding resistance to multiple antimicrobials warrants vigilance, as its spread to susceptible strains would lead to increasing incidences of antimicrobial resistance.

Acinetobacter baumannii, Acinetobacter nosocomialis, NDM-1, OXA-58, Tn125, carbapenem resistance, pdif modules, plasmids
2379-5042
1-21
Alattraqchi, Ahmed Ghazi
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Mohd Rani, Farahiyah
1a1e50e5-e44e-445e-83ef-c7039a713620
A Rahman, Nor Iza
c8250dae-dd75-446b-8b17-c2763f98c121
Ismail, Salwani
beb95eb3-3e79-4c48-a040-9994c7b5abce
Cleary, David W
f4079c6d-d54b-4108-b346-b0069035bec0
Clarke, Stuart C
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Yeo, Chew Chieng
fdccc646-7c5d-4231-a9fa-ff01c39f4e5a
Alattraqchi, Ahmed Ghazi
18fbc2de-7327-470c-b502-645133a4424a
Mohd Rani, Farahiyah
1a1e50e5-e44e-445e-83ef-c7039a713620
A Rahman, Nor Iza
c8250dae-dd75-446b-8b17-c2763f98c121
Ismail, Salwani
beb95eb3-3e79-4c48-a040-9994c7b5abce
Cleary, David W
f4079c6d-d54b-4108-b346-b0069035bec0
Clarke, Stuart C
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Yeo, Chew Chieng
fdccc646-7c5d-4231-a9fa-ff01c39f4e5a

Alattraqchi, Ahmed Ghazi, Mohd Rani, Farahiyah, A Rahman, Nor Iza, Ismail, Salwani, Cleary, David W, Clarke, Stuart C and Yeo, Chew Chieng (2021) Complete genome sequencing of Acinetobacter baumannii AC1633 and Acinetobacter nosocomialis AC1530 unveils a large multidrug-resistant plasmid encoding the NDM-1 and OXA-58 carbapenemases. mSphere, 6 (1), 1-21, [e01076-20]. (doi:10.1128/mSphere.01076-20).

Record type: Article

Abstract

Carbapenem-resistant Acinetobacter spp. are considered priority drug-resistant human-pathogenic bacteria. The genomes of two carbapenem-resistant Acinetobacter spp. clinical isolates obtained from the same tertiary hospital in Terengganu, Malaysia, namely, A. baumannii AC1633 and A. nosocomialis AC1530, were sequenced. Both isolates were found to harbor the carbapenemase genes blaNDM-1 and blaOXA-58 in a large (ca. 170 kb) plasmid designated pAC1633-1 and pAC1530, respectively, that also encodes genes that confer resistance to aminoglycosides, sulfonamides, and macrolides. The two plasmids were almost identical except for the insertion of ISAba11 and an IS4 family element in pAC1633-1, and ISAba11 along with relBE toxin-antitoxin genes flanked by inversely orientated pdif (XerC/XerD) recombination sites in pAC1530. The blaNDM-1 gene was encoded in a Tn125 composite transposon structure flanked by ISAba125, whereas blaOXA-58 was flanked by ISAba11 and ISAba3 downstream and a partial ISAba3 element upstream within a pdif module. The presence of conjugative genes in plasmids pAC1633-1/pAC1530 and their discovery in two distinct species of Acinetobacter from the same hospital are suggestive of conjugative transfer, but mating experiments failed to demonstrate transmissibility under standard laboratory conditions. Comparative sequence analysis strongly inferred that pAC1633-1/pAC1530 was derived from two separate plasmids in an IS1006-mediated recombination or transposition event. A. baumannii AC1633 also harbored three other plasmids designated pAC1633-2, pAC1633-3, and pAC1633-4. Both pAC1633-3 and pAC1633-4 are cryptic plasmids, whereas pAC1633-2 is a 12,651-bp plasmid of the GR8/GR23 Rep3-superfamily group that encodes the tetA(39) tetracycline resistance determinant in a pdif module.IMPORTANCE Bacteria of the genus Acinetobacter are important hospital-acquired pathogens, with carbapenem-resistant A. baumannii listed by the World Health Organization as the one of the top priority pathogens. Whole-genome sequencing of carbapenem-resistant A. baumannii AC1633 and A. nosocomialis AC1530, which were isolated from the main tertiary hospital in Terengganu, Malaysia, led to the discovery of a large, ca. 170-kb plasmid that harbored genes encoding the New Delhi metallo-β-lactamase-1 (NDM-1) and OXA-58 carbapenemases alongside genes that conferred resistance to aminoglycosides, macrolides, and sulfonamides. The plasmid was a patchwork of multiple mobile genetic elements and comparative sequence analysis indicated that it may have been derived from two separate plasmids through an IS1006-mediated recombination or transposition event. The presence of such a potentially transmissible plasmid encoding resistance to multiple antimicrobials warrants vigilance, as its spread to susceptible strains would lead to increasing incidences of antimicrobial resistance.

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More information

Accepted/In Press date: 8 January 2021
e-pub ahead of print date: 27 January 2021
Published date: 27 January 2021
Additional Information: Copyright © 2021 Alattraqchi et al.
Keywords: Acinetobacter baumannii, Acinetobacter nosocomialis, NDM-1, OXA-58, Tn125, carbapenem resistance, pdif modules, plasmids

Identifiers

Local EPrints ID: 446855
URI: http://eprints.soton.ac.uk/id/eprint/446855
ISSN: 2379-5042
PURE UUID: d87a5cd0-f5e4-4a75-8f08-bb7cf8af228c
ORCID for David W Cleary: ORCID iD orcid.org/0000-0003-4533-0700
ORCID for Stuart C Clarke: ORCID iD orcid.org/0000-0002-7009-1548

Catalogue record

Date deposited: 24 Feb 2021 17:32
Last modified: 23 Jul 2021 01:44

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Contributors

Author: Ahmed Ghazi Alattraqchi
Author: Farahiyah Mohd Rani
Author: Nor Iza A Rahman
Author: Salwani Ismail
Author: David W Cleary ORCID iD
Author: Stuart C Clarke ORCID iD
Author: Chew Chieng Yeo

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