Comparison of 16S rRNA Sequencing and VITEK 2 Analysis for the Identification of Acinetobacter baumannii Clinical Isolates: A Study from Southwestern Province of Saudi Arabia
Correspondence Address :
Dr. Vinod Kumar Basode,
Assistant Professor, Unit of Medical Microbiology, Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.
E-mail: bvionodkumar2006@yahoo.com
Dear Editor,
Acinetobacter baumannii (A. baumannii) is one of the major causes of nosocomial infections in the hospital environment. Even the World Health Organisation (WHO) has designated A. baumannii as a priority pathogen that poses a significant health risk (1). A. baumannii rapidly develops resistance to antimicrobials, and multidrug-resistant strains have been reported in the literature. As a multidrug-resistant and invasive pathogen, it has been identified as an opportunistic pathogen that causes severe infections such as wound infections, pneumonia, meningitis, septicaemia, and urinary tract infections, resulting in high mortality and morbidity rates. Carbapenem-resistant A. baumannii is a major global public health threat and imposes a greater burden worldwide, including in Saudi Arabia (2).
Due to the close genetic relationship of some Acinetobacter species, it is difficult to distinguish them phenotypically using standard laboratory techniques. Several genotypic methods are used for the identification of bacterial species, with 16S ribosomal Ribonucleic Acid (rRNA) gene sequencing being one of the most commonly utilised methods for identifying bacterial isolates. Accurate bacterial and species identification is crucial for effective treatment of A. baumannii infections (2). However, to date, there have been no reports comparing 16S rRNA sequencing and VITEK 2 analysis for the identification of Acinetobacter baumannii clinical isolates from the Southwestern Province of Saudi Arabia.
Therefore, the present study aimed to compare the phenotypic identification system (VITEK 2) with 16S rRNA sequencing for the identification of A. baumannii hospital isolates. A total of 29 clinical isolates of A. baumannii were collected from a tertiary hospital in the Southwestern Province of Saudi Arabia and identified using the VITEK 2 system (bioMérieux, Marcy l’Etoile, France). Ethical approval (2016/50A) was obtained from King Fahd Central Hospital, and informed consent was obtained from the participants. All 29 strains were further subjected to identification based on 16S rRNA gene sequencing. The 16S rRNA gene sequencing was performed at Macrogen, Inc. (South Korea), using universal primer pairs (785F 5’(GGA TTA GAT ACC CTG GTA) 3’ and 907R 5’ (CCG TCA ATT CMT TTR AGT TT) 3’) and confirmation primers (27F 5’(AGA GTT TGA TCM TGG CTC AG) 3’ and 1492R 5’(TAC GGY TAC CTT GTT ACG ACT T) 3’) for A. baumannii.
In the present study, the VITEK 2 system correctly identified 93.10% of clinical isolates of A. baumannii when compared with the 16S rRNA gene sequencing method (Table/Fig 1). In contrast, Lee MJ et al., reported an accuracy rate of 76.6% for the VITEK 2 system in identifying A. baumannii clinical isolates (3). Additionally, other reports have shown that the VITEK 2 system correctly identified 87.5% of other bacterial clinical isolates compared with 16S rRNA gene sequencing analysis (4). The VITEK 2 system identifies bacterial isolates based on metabolic activities and/or morphological features. Misidentification of bacterial isolates in the VITEK 2 system can occur due to various reasons: (i) aged culture isolates may not display the expected biochemical characteristics; (ii) different strains of the same species may not express a specific characteristic; (iii) the same strain may produce different outcomes in subsequent testing; (iv) long-term antibiotic therapy may cause isolates from a host to change their typical metabolic features; (v) phenotypic variation can affect the accuracy of species-level identification by automated phenotypic systems; (vi) the databases only contain information on a few species; and (vii) phenotypic systems frequently propose two or more labels with similar probabilities (4). Therefore, 16S rRNA sequencing may be useful for the correct identification of A. baumannii clinical isolates when compared with the VITEK 2 system of identification.
Authors’ contributions: VKB conceived the study, contributed to the design, and drafted the manuscript. AA, NK, and MUA assisted with sample collection and provided overall support for the study. AAZH was responsible for collecting the samples. All authors have read and approved the final manuscript.
Antimicrobials, Gene sequencing, Ribosomal ribonucleic acid
DOI: 10.7860/JCDR/2024/65999.19152
Date of Submission: Jun 13, 2023
Date of Peer Review: Aug 08, 2023
Date of Acceptance: Dec 07, 2023
Date of Publishing: Mar 01, 2024
AUTHOR DECLARATION:
• Financial or Other Competing Interests: Funded under Grant No. RG-2-1, Research Group Funding Program, Division of Vector-borne Diseases, Jazan University.
• Was Ethics Committee Approval obtained for this study? Yes
• Was informed consent obtained from the subjects involved in the study? Yes
• For any images presented appropriate consent has been obtained from the subjects. NA
PLAGIARISM CHECKING METHODS:
• Plagiarism X-checker: Jun 15, 2023
• Manual Googling: Aug 16, 2023
• iThenticate Software: Nov 21, 2023 (20%)
ETYMOLOGY: Author Origin
EMENDATIONS: 6
- Emerging Sources Citation Index (Web of Science, thomsonreuters)
- Index Copernicus ICV 2017: 134.54
- Academic Search Complete Database
- Directory of Open Access Journals (DOAJ)
- Embase
- EBSCOhost
- Google Scholar
- HINARI Access to Research in Health Programme
- Indian Science Abstracts (ISA)
- Journal seek Database
- Popline (reproductive health literature)
- www.omnimedicalsearch.com