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Updated: Jun 13, 2025
Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Genomic diversity of clinically relevant bacterial pathogens from an acute care hospital in Suva, Fiji
Jane Hawkey1, Michael J Loftus1, Amitesh Prasad2
1Department of Infectious Diseases, the Alfred Hospital and School of Translational Medicine, Monash University, Melbourne 3004, Australia.
Objectives:
Antimicrobial resistance (AMR) is a global health threat, with third-generation cephalosporin-resistant (3GCR) and carbapenem-resistant infections of particular concern. There is currently a lack of genomic data on AMR organisms in the Pacific region.
Methods:
We aimed to address this gap by examining the genetic diversity of a collection of 788 Gram-negative and Gram-positive clinical isolates collected between July 2020 and October 2022 from a single hospital in Suva, Fiji. We sampled sensitive and resistant isolates, focusing on 3GCR and carbapenem-resistant Gram-negatives, and methicillin-resistant Staphylococcus and vancomycin-resistant Enterococcus.
Results:
We detected 29 distinct species across 12 different genera. Amongst Gram-negative genomes, Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii and Pseudomonas aeruginosa were the most common. Carbapenem resistance was mostly detected in A. baumannii ST2 and P. aeruginosa ST773, with both STs carrying NDM-1 and showing evidence of transmission within Fiji. Carbapenem resistance was relatively rare amongst the Enterobacterales; however, we observed evidence of transmission of OXA-232-carrying K. pneumoniae ST395 and NDM-7 E. coli ST410. For Gram-positive bacteria, Staphylococcus aureus ST1 was the dominant clone, and phylogenetic analysis revealed a single clade harbouring the majority of Fijian genomes, with close relationships to genomes from neighbouring Samoa. Enterococcus was relatively rare, with only 22 genomes detected.
Conclusions:
This study provides crucial genomic data on AMR organisms in Fiji, highlighting the diversity of resistant species in the region. Local transmission of four carbapenem-resistant clones within Fiji was observed, underscoring the importance of local spread of these resistant strains.
Insights
Genomic data reveals antimicrobial resistance (AMR) in Fiji, with carbapenem-resistant clones spreading locally. This study highlights the diversity of resistant bacteria in the Pacific region, crucial for public health.
Area of Science:
- Genomics
- Microbiology
- Public Health
Background:
- Antimicrobial resistance (AMR) is a significant global health challenge.
- Third-generation cephalosporin-resistant (3GCR) and carbapenem-resistant infections are of particular concern.
- Genomic data on AMR organisms in the Pacific region is limited.
Purpose of the Study:
- To investigate the genetic diversity of antimicrobial-resistant organisms in Fiji.
- To address the gap in genomic data for AMR in the Pacific.
- To identify specific resistant clones and their transmission patterns.
Main Methods:
- Analysis of 788 Gram-negative and Gram-positive clinical isolates from Fiji (July 2020 - October 2022).
- Focus on third-generation cephalosporin-resistant and carbapenem-resistant Gram-negatives, methicillin-resistant *Staphylococcus*, and vancomycin-resistant *Enterococcus*.
- Genomic sequencing and phylogenetic analysis.
Main Results:
- 29 species across 12 genera were identified.
- Common Gram-negative bacteria included *Klebsiella pneumoniae*, *Escherichia coli*, *Acinetobacter baumannii*, and *Pseudomonas aeruginosa*.
- Carbapenem resistance was primarily found in *A. baumannii* ST2 and *P. aeruginosa* ST773 (NDM-1 positive), and *K. pneumoniae* ST395 (OXA-232) and *E. coli* ST410 (NDM-7) showed local transmission. *Staphylococcus aureus* ST1 was the dominant Gram-positive clone.
Conclusions:
- This study provides essential genomic insights into AMR in Fiji.
- Local transmission of four carbapenem-resistant clones was identified within Fiji.
- The findings underscore the importance of understanding and controlling local spread of resistant strains in the region.
