The potential of different molecular biology methods in tracking clones of Acinetobacter baumannii in an ICU setting

Nithin Sam Ravi, Shalini Anandan, Saranya Vijayakumar, Radha Gopi, Bruno S Lopes, Balaji Veeraraghavan

Research output: Contribution to journalArticle

Abstract

PURPOSE: This study aimed to characterize A. baumannii strains isolated from patients in an intensive care unit (ICU) setting. Molecular techniques were used to study clonal relatedness and determine a fast, efficient and cost-effective way of detecting persistent clones.

METHODOLOGY: A. baumannii (n=17) were obtained in June and November 2015 from a single ICU setting in South India. DNA typing methods such as multilocus sequence typing (MLST), single-locus sequence-based typing (SBT) and DNA fingerprinting PCRs (M13, DAF4 and ERIC2) were employed to understand the association of clones. PCRs were performed for the antimicrobial resistance genes ISAba1-blaOXA-51-like, ISAba1-blaOXA-23-like, blaNDM-1, blaPER-7 and blaTEM-1, and the virulence genes cpa 1, cpa2 and pkf.

RESULTS: The MLST showed some degree of corroboration with the other DNA typing methods. The M13 PCR was found to give better results than the other fingerprinting methods. ST848 (CC92) was the dominant strain isolated in both June and November. All isolates were blaOXA-51-like-positive, with 16 having ISAba1 upstream of the blaOXA-51-like and blaOXA-23-like genes. Genes such as blaNDM-1 (23 %, n=4), blaPER-7 (58.8 %, n=10), pkf (82 %, n=14), blaTEM-1 (5.8 %, n=1), cpa1 (5.8 %, n=1) and cpa2 (5.8 %, n=1) were also detected.

CONCLUSION: M13 PCR can be used in routine environmental surveillance for the detection of persistent antibiotic resistant clones in an ICU setting because of its reliability and simplicity. Further studies based on greater sample size, conducted at the multi-centre level, can give us a better understanding of the reliability of the molecular methods that can be used for the detection of persistent clones in the hospital setting.

Original languageEnglish
Pages (from-to)1340-1347
Number of pages8
JournalJournal of Medical Microbiology
Volume67
Issue number9
Early online date17 Jul 2018
DOIs
Publication statusPublished - 1 Sep 2018

Fingerprint

Acinetobacter baumannii
Intensive Care Units
DNA Fingerprinting
Molecular Biology
Clone Cells
Multilocus Sequence Typing
Polymerase Chain Reaction
Genes
Environmental Monitoring
Sample Size
Virulence
India
Anti-Bacterial Agents
Costs and Cost Analysis

Keywords

  • A. baumannii
  • MLST
  • DNA fingerprinting
  • single locus sequence type basing
  • ST848

Cite this

The potential of different molecular biology methods in tracking clones of Acinetobacter baumannii in an ICU setting. / Ravi, Nithin Sam; Anandan, Shalini; Vijayakumar, Saranya; Gopi, Radha; Lopes, Bruno S; Veeraraghavan, Balaji.

In: Journal of Medical Microbiology, Vol. 67, No. 9, 01.09.2018, p. 1340-1347.

Research output: Contribution to journalArticle

Ravi, Nithin Sam ; Anandan, Shalini ; Vijayakumar, Saranya ; Gopi, Radha ; Lopes, Bruno S ; Veeraraghavan, Balaji. / The potential of different molecular biology methods in tracking clones of Acinetobacter baumannii in an ICU setting. In: Journal of Medical Microbiology. 2018 ; Vol. 67, No. 9. pp. 1340-1347.
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N2 - PURPOSE: This study aimed to characterize A. baumannii strains isolated from patients in an intensive care unit (ICU) setting. Molecular techniques were used to study clonal relatedness and determine a fast, efficient and cost-effective way of detecting persistent clones.METHODOLOGY: A. baumannii (n=17) were obtained in June and November 2015 from a single ICU setting in South India. DNA typing methods such as multilocus sequence typing (MLST), single-locus sequence-based typing (SBT) and DNA fingerprinting PCRs (M13, DAF4 and ERIC2) were employed to understand the association of clones. PCRs were performed for the antimicrobial resistance genes ISAba1-blaOXA-51-like, ISAba1-blaOXA-23-like, blaNDM-1, blaPER-7 and blaTEM-1, and the virulence genes cpa 1, cpa2 and pkf.RESULTS: The MLST showed some degree of corroboration with the other DNA typing methods. The M13 PCR was found to give better results than the other fingerprinting methods. ST848 (CC92) was the dominant strain isolated in both June and November. All isolates were blaOXA-51-like-positive, with 16 having ISAba1 upstream of the blaOXA-51-like and blaOXA-23-like genes. Genes such as blaNDM-1 (23 %, n=4), blaPER-7 (58.8 %, n=10), pkf (82 %, n=14), blaTEM-1 (5.8 %, n=1), cpa1 (5.8 %, n=1) and cpa2 (5.8 %, n=1) were also detected.CONCLUSION: M13 PCR can be used in routine environmental surveillance for the detection of persistent antibiotic resistant clones in an ICU setting because of its reliability and simplicity. Further studies based on greater sample size, conducted at the multi-centre level, can give us a better understanding of the reliability of the molecular methods that can be used for the detection of persistent clones in the hospital setting.

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