Molecular Epidemiology of Clinical Carbapenem-Resistant Acinetobacter baumannii-calcoaceticus complex Isolates in Tertiary Care Hospitals in Java and Sulawesi Islands, Indonesia
Abstract
:1. Introduction
2. Materials and Methods
2.1. Setting and Study Design
2.2. Bacterial Isolates
2.3. DNA Extraction and Carbapenemase Genes’ Identification
2.4. Multi-Locus Variable-Number Tandem Repeat Analysis (MLVA)
2.5. Multilocus Sequence Typing (MLST)
2.6. Clonal Complex (CC) Analysis
2.7. Phylogenetic Analysis
3. Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Targeted Gene | Primer Designation | Amplicon Size | Tm °C | Primer Sequence |
---|---|---|---|---|
blaKPC | blaKPC-F blaKPC-R | 798 bp | 58 | CGTCTAGTTCTGCTGTCTTG CTTGTCATCCTTGTTAGGCG |
blaNDM | blaNDM-F blaNDM-R | 621 bp | 65 | GGTTTGGCGATCTGGTTTTC CGGAATGGCTCATCACGATC |
blaOXA23 | blaOXA23-F blaOXA23-R | 501 bp | 52 | GATCGGATTGGAGAACCAGA ATTCTGACCGCATTTCCAT |
VNTR Marker | Primer Designation | Primer Sequence (5′→3′) | Annealing Temperature (°C) | Repeat Size (bp) | Size of Flanking Regions |
---|---|---|---|---|---|
Abaum-1988 | Abaum-1988-F | GGCAAGGCATGCTCAAGGGCC | 55 | 26 | 77 |
Abaum-1988-R | CAGTAGACTGCTGGTTAATGAG | 55 | |||
Abaum-3530 | Abaum-3530-F | TGCAACCGGTATTCTAGGAAC | 55 | 60 | 121 |
Abaum-3530-R | CCTTGAACAACATCGATTACTGGA | 55 | |||
Abaum-3002 | Abaum-3002-F | GACTGAAGCAAGACTAAAACGT | 55 | 57 | 121 |
Abaum-3002-R | TCTGGGCAGCTTCTTCTTGAGC | 55 | |||
Abaum-2240 | Abaum-2240-F | CCCGCAGTACATCATGGTTC | 55 | 99 | 494 |
Abaum-2240-R | AGAACATGTATACGCAACTG | 55 | |||
Abaum-0826 | Abaum-0826-F | TGACTACTGAAACAGTTTTTG | 50 | 9 | 208 |
Abaum-0826-R | ATGATTGTACCGAGTAAAAGA | 50 | |||
Abaum-2396 | Abaum-2396-F | CAAGTCCAATCAACTCATGATG | 55 | 6 | 105 |
Abaum-2396-R | CTCCTGTAAGTGCTGTTCAGCC | 55 | |||
Abaum-3468 | Abaum-3468-F | CAGAAGTCACTGCATCTGCAAC | 55 | 6 | 147 |
Abaum-3468-R | CGGTTGAAATTTTTTATAATGAAG | 55 | |||
Abaum-0845 | Abaum-0845-F | AATTTTAATTCCAAATTGCTCC | 50 | 7 | 105 |
Abaum-0845-R | ACTTAAAATCGCATTTTTATCA | 50 |
Gene | Primer Suquence | Amplicon Size |
---|---|---|
cpn60-F | ACTGTACTTGCTCAAGC | 405 bp |
cpn60-R | TTCAGCGATGATAAGAAGTGG | |
fusA-F | ATCGGTATTTCTGCKCACATYGAT | 633 bp |
fusA-R | CCAACATACKYTGWACACCTTTGTT | |
gltA-F | AATTTACAGTGGCACATTAGGTCCC | 483 bp |
gltA-R | GCAGAGATACCAGCAGAGATACACG | |
pyrG-F | GGTGTTGTTTCATCACTAGGWAAAGG | 297 bp |
pyrG-R | ATAAATGGTAAAGAYTCGATRTCACCMA | |
recA-F | CCTGAATCTTCYGGTAAAAC | 372 bp |
recA-R | GTTTCTGGGCTGCCAAACATTAC | |
rplB-F | GTAGAGCGTATTGAATACGATCCTAACC | 330 bp |
rplB-R | CACCACCACCRTGYGGGTGATC | |
rpoB-F | GGTCCTGGTGGTTTAACACG | 456 bp |
rpoB-R | CGAATAACGATACGAGAAGCA |
No. | MT | MLVA Loci | Number of Isolates (%) | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Abaum-1988 | Abaum-3530 | Abaum-3002 | Abaum-2240 | Abaum-0826 | Abaum-2396 | Abaum-3468 | Abaum-0845 | Dr. Saiful Anwar Hospital, Malang | Prof. Dr. R. D. Kandou Hospital, Manado | ||
1. | MT1 | 5 | 6 | 7 | 3 | 15 | 17 | 12 | 20 | 4 (9.3%) | |
2. | MT2 | 9 | 7 | 7 | 4 | 17 | 12 | 12 | 20 | 18 (41.9%) | 17 (56.6%) |
3. | MT3 | 5 | 6 | 8 | 3 | 17 | 22 | 12 | 22 | 21 (48.8%) | 4 (13.3%) |
3. | MT4 | 5 | 1 | 7 | 3 | 17 | 12 | 12 | 22 | 5 (16.7%) | |
5. | MT5 | 8 | 6 | 8 | 3 | - | 17 | 13 | 20 | 2 (6.7%) | |
6. | MT6 | 9 | 1 | - | - | - | 17 | 9 | 20 | 2 (6.7%) |
No. | MT | Sample Code | Locus Sequence and Allele Number | ST | CC | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
cpn60 | fusA | gltA | pyrG | recA | rpIB | rpoB | |||||
1. | MT1 | MLG-42 | 1 | 1 | 1 | 1 | 9 | 1 | 1 | 642 | 1 |
2. | MT2 MT2 MT2 MT2 | MLG-30 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
3. | MLG-41 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | |
4. | MDO-18 | 2 | 125 | 2 | 2 | 2 | 2 | 2 | 823 | 2 | |
5. | MDO-26 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | |
6. | MT3 MT3 MT3 | MLG-8 | 1 | 1 | 1 | 1 | 9 | 1 | 1 | 642 | 1 |
7. | MLG-31 | 1 | 1 | 1 | 1 | 9 | 1 | 1 | 642 | 1 | |
8. | MLG-32 | 1 | 1 | 1 | 1 | 9 | 1 | 1 | 642 | 1 | |
9. | MT4 | MDO-6 | 382 | 267 | 14 | 188 | 9 | 17 | 1 | 642 | 1 |
10. | MT5 | MDO-2 | 192 | 26 | 91 | 14 | 192 | 16 | 47 | 1276 | singleton |
11. | MT6 | MDO-9 | 2 | 1 | 1 | 2 | 68 | 2 | 201 | 641 | 2 |
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Homenta, H.; Julyadharma, J.; Susianti, H.; Noorhamdani, N.; Santosaningsih, D. Molecular Epidemiology of Clinical Carbapenem-Resistant Acinetobacter baumannii-calcoaceticus complex Isolates in Tertiary Care Hospitals in Java and Sulawesi Islands, Indonesia. Trop. Med. Infect. Dis. 2022, 7, 277. https://doi.org/10.3390/tropicalmed7100277
Homenta H, Julyadharma J, Susianti H, Noorhamdani N, Santosaningsih D. Molecular Epidemiology of Clinical Carbapenem-Resistant Acinetobacter baumannii-calcoaceticus complex Isolates in Tertiary Care Hospitals in Java and Sulawesi Islands, Indonesia. Tropical Medicine and Infectious Disease. 2022; 7(10):277. https://doi.org/10.3390/tropicalmed7100277
Chicago/Turabian StyleHomenta, Heriyannis, Julyadharma Julyadharma, Hani Susianti, Noorhamdani Noorhamdani, and Dewi Santosaningsih. 2022. "Molecular Epidemiology of Clinical Carbapenem-Resistant Acinetobacter baumannii-calcoaceticus complex Isolates in Tertiary Care Hospitals in Java and Sulawesi Islands, Indonesia" Tropical Medicine and Infectious Disease 7, no. 10: 277. https://doi.org/10.3390/tropicalmed7100277
APA StyleHomenta, H., Julyadharma, J., Susianti, H., Noorhamdani, N., & Santosaningsih, D. (2022). Molecular Epidemiology of Clinical Carbapenem-Resistant Acinetobacter baumannii-calcoaceticus complex Isolates in Tertiary Care Hospitals in Java and Sulawesi Islands, Indonesia. Tropical Medicine and Infectious Disease, 7(10), 277. https://doi.org/10.3390/tropicalmed7100277