Whole genome sequencing of an Enterococcus faecalis isolate from a patient with cholecystitis in a tertiary hospital in Kota Kinabalu, Sabah, Malaysia
Introduction: Enterococcus faecalis is a gram-positive bacterium that causes various human nosocomial infections including urinary tract infection, endocarditis, wound infection, and bacteremia. Objectives: This study aims to investigate the molecular characterization of local Enterococcus bacteria...
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2021
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| Online Access: | https://eprints.ums.edu.my/id/eprint/31003/1/Whole%20genome%20sequencing%20of%20an%20Enterococcus%20faecalis%20isolate%20from%20a%20patient%20with%20cholecystitis%20in%20a%20tertiary%20hospital%20in%20Kota%20Kinabalu%2C%20Sabah%2C%20Malaysia.pdf https://eprints.ums.edu.my/id/eprint/31003/2/Whole%20genome%20sequencing%20of%20an%20Enterococcus%20faecalis%20isolate%20from%20a%20patient%20with%20cholecystitis%20in%20a%20tertiary%20hospital%20in%20Kota%20Kinabalu_ABSTRACT.pdf https://eprints.ums.edu.my/id/eprint/31003/ https://migc-pgm.com/images/saintifik/program_book_MiGC14.pdf |
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| author | Nur Nashyiroh Mastor Vijay Kumar Subbiah Wan Nazirah Wan Abu Bakar Suzanah Silee Khurshida Begum M. Jahangir Alam Mohammad Zahirul Hoque |
| author_facet | Nur Nashyiroh Mastor Vijay Kumar Subbiah Wan Nazirah Wan Abu Bakar Suzanah Silee Khurshida Begum M. Jahangir Alam Mohammad Zahirul Hoque |
| author_sort | Nur Nashyiroh Mastor |
| building | UMS Library |
| collection | Institutional Repository |
| content_provider | Universiti Malaysia Sabah |
| content_source | UMS Institutional Repository |
| continent | Asia |
| country | Malaysia |
| description | Introduction: Enterococcus faecalis is a gram-positive bacterium that causes various human nosocomial infections including urinary tract infection, endocarditis, wound infection, and bacteremia. Objectives: This study aims to investigate the molecular characterization of local Enterococcus bacteria (isolate no. SHH039) isolated from a patient in a tertiary hospital in Kota Kinabalu, Sabah, using whole- genome sequencing. Methodology: A Tissue sample collected from a patient with cholecystitis was cultured for bacteria onto blood agar and identified and characterize by molecular methods. Bacterial DNA was extracted by using the Qiagen DNeasy Tissue Kit (Qiagen, Valencia, CA). The quantification of DNA was done using Qubit fluorometer (Qubit 3.0, Thermo Fisher Scientific). The sample was then sequenced using the Illumina HiSeq 4000 system. In addition, the 16S rRNA sequence was aligned with reference sequences using CLUSTAL W and subsequently, a phylogenetic tree was obtained using the maximum-likelihood method in MEGA 8.0. This research was approved by the Medical Research Ethics Committee (MREC), Ministry of Health, Malaysia (No. NMRR-19-1770-48622) and University Malaysia Sabah ethical committee (JKEtika 1/19(26). Result: Our phylogenetic tree analysis showed the isolate belongs to Enterococcus faecalis. The estimated whole genome size of the strain was 2,990,081 bp with a G + C content of 37.30%. The de novo assembly of the genome generated 77 contigs with an N50 of 270,652 bp. The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number JAEFCX000000000. The raw data were deposited as sequence read archieve (SRA) number SRR13153714. Conclusion: The molecular characterization data from our study might be helpful to understand the insights of the E. faecalis infection mechanism and molecular characteristics of the pathogen. |
| format | Conference or Workshop Item |
| id | my.ums.eprints-31003 |
| institution | Universiti Malaysia Sabah |
| language | en en |
| publishDate | 2021 |
| record_format | eprints |
| spelling | my.ums.eprints-310032021-10-22T01:44:01Z https://eprints.ums.edu.my/id/eprint/31003/ Whole genome sequencing of an Enterococcus faecalis isolate from a patient with cholecystitis in a tertiary hospital in Kota Kinabalu, Sabah, Malaysia Nur Nashyiroh Mastor Vijay Kumar Subbiah Wan Nazirah Wan Abu Bakar Suzanah Silee Khurshida Begum M. Jahangir Alam Mohammad Zahirul Hoque QR171 Microorganisms in the animal body Introduction: Enterococcus faecalis is a gram-positive bacterium that causes various human nosocomial infections including urinary tract infection, endocarditis, wound infection, and bacteremia. Objectives: This study aims to investigate the molecular characterization of local Enterococcus bacteria (isolate no. SHH039) isolated from a patient in a tertiary hospital in Kota Kinabalu, Sabah, using whole- genome sequencing. Methodology: A Tissue sample collected from a patient with cholecystitis was cultured for bacteria onto blood agar and identified and characterize by molecular methods. Bacterial DNA was extracted by using the Qiagen DNeasy Tissue Kit (Qiagen, Valencia, CA). The quantification of DNA was done using Qubit fluorometer (Qubit 3.0, Thermo Fisher Scientific). The sample was then sequenced using the Illumina HiSeq 4000 system. In addition, the 16S rRNA sequence was aligned with reference sequences using CLUSTAL W and subsequently, a phylogenetic tree was obtained using the maximum-likelihood method in MEGA 8.0. This research was approved by the Medical Research Ethics Committee (MREC), Ministry of Health, Malaysia (No. NMRR-19-1770-48622) and University Malaysia Sabah ethical committee (JKEtika 1/19(26). Result: Our phylogenetic tree analysis showed the isolate belongs to Enterococcus faecalis. The estimated whole genome size of the strain was 2,990,081 bp with a G + C content of 37.30%. The de novo assembly of the genome generated 77 contigs with an N50 of 270,652 bp. The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number JAEFCX000000000. The raw data were deposited as sequence read archieve (SRA) number SRR13153714. Conclusion: The molecular characterization data from our study might be helpful to understand the insights of the E. faecalis infection mechanism and molecular characteristics of the pathogen. 2021 Conference or Workshop Item PeerReviewed text en https://eprints.ums.edu.my/id/eprint/31003/1/Whole%20genome%20sequencing%20of%20an%20Enterococcus%20faecalis%20isolate%20from%20a%20patient%20with%20cholecystitis%20in%20a%20tertiary%20hospital%20in%20Kota%20Kinabalu%2C%20Sabah%2C%20Malaysia.pdf text en https://eprints.ums.edu.my/id/eprint/31003/2/Whole%20genome%20sequencing%20of%20an%20Enterococcus%20faecalis%20isolate%20from%20a%20patient%20with%20cholecystitis%20in%20a%20tertiary%20hospital%20in%20Kota%20Kinabalu_ABSTRACT.pdf Nur Nashyiroh Mastor and Vijay Kumar Subbiah and Wan Nazirah Wan Abu Bakar and Suzanah Silee and Khurshida Begum and M. Jahangir Alam and Mohammad Zahirul Hoque (2021) Whole genome sequencing of an Enterococcus faecalis isolate from a patient with cholecystitis in a tertiary hospital in Kota Kinabalu, Sabah, Malaysia. In: 14th Malaysia International Genetics Congress (MIGC14), 15 -17 March 2021, Malaysia (Virtual Conference). https://migc-pgm.com/images/saintifik/program_book_MiGC14.pdf |
| spellingShingle | QR171 Microorganisms in the animal body Nur Nashyiroh Mastor Vijay Kumar Subbiah Wan Nazirah Wan Abu Bakar Suzanah Silee Khurshida Begum M. Jahangir Alam Mohammad Zahirul Hoque Whole genome sequencing of an Enterococcus faecalis isolate from a patient with cholecystitis in a tertiary hospital in Kota Kinabalu, Sabah, Malaysia |
| title | Whole genome sequencing of an Enterococcus faecalis isolate from a patient with cholecystitis in a tertiary hospital in Kota Kinabalu, Sabah, Malaysia |
| title_full | Whole genome sequencing of an Enterococcus faecalis isolate from a patient with cholecystitis in a tertiary hospital in Kota Kinabalu, Sabah, Malaysia |
| title_fullStr | Whole genome sequencing of an Enterococcus faecalis isolate from a patient with cholecystitis in a tertiary hospital in Kota Kinabalu, Sabah, Malaysia |
| title_full_unstemmed | Whole genome sequencing of an Enterococcus faecalis isolate from a patient with cholecystitis in a tertiary hospital in Kota Kinabalu, Sabah, Malaysia |
| title_short | Whole genome sequencing of an Enterococcus faecalis isolate from a patient with cholecystitis in a tertiary hospital in Kota Kinabalu, Sabah, Malaysia |
| title_sort | whole genome sequencing of an enterococcus faecalis isolate from a patient with cholecystitis in a tertiary hospital in kota kinabalu, sabah, malaysia |
| topic | QR171 Microorganisms in the animal body |
| url | https://eprints.ums.edu.my/id/eprint/31003/1/Whole%20genome%20sequencing%20of%20an%20Enterococcus%20faecalis%20isolate%20from%20a%20patient%20with%20cholecystitis%20in%20a%20tertiary%20hospital%20in%20Kota%20Kinabalu%2C%20Sabah%2C%20Malaysia.pdf https://eprints.ums.edu.my/id/eprint/31003/2/Whole%20genome%20sequencing%20of%20an%20Enterococcus%20faecalis%20isolate%20from%20a%20patient%20with%20cholecystitis%20in%20a%20tertiary%20hospital%20in%20Kota%20Kinabalu_ABSTRACT.pdf https://eprints.ums.edu.my/id/eprint/31003/ https://migc-pgm.com/images/saintifik/program_book_MiGC14.pdf |
| url_provider | http://eprints.ums.edu.my/ |