2024_Characterisation and genomic analyses of non-baumannii acinetobacter clinical isolates from a tertiary hospital in Terengganu, Malaysia
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| country | Malaysia |
| date | 2024-12-22 02:55 |
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| id | 16810 |
| institution | UniSZA |
| originalfilename | CHARACTERISATION AND GENOMIC ANALYSES OF NON-BAUMANNII ACINETOBACTER CLINICAL ISOLATES FROM A TERTIARY HOSPITAL IN TERENGGANU, MALAYSIA (PHD_2024).pdf |
| person | Farahiyah Binti Mohd Rani |
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| resourceurl | https://intelek.unisza.edu.my/intelek/pages/view.php?ref=16810 |
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| spelling | 16810 https://intelek.unisza.edu.my/intelek/pages/view.php?ref=16810 https://intelek.unisza.edu.my/intelek/pages/search.php?search=!collection3 General Document Malaysia Library Staff (Top Management) Library Staff (Management) Library Staff (Support) Terengganu Faculty of Medicine English application/pdf 1.7 Server storage Scanned document Universiti Sultan Zainal Abidin UniSZA Private Access Universiti Sultan Zainal Abidin Copyright©PWB2025 318 Dissertations, Academic 2024_Characterisation and genomic analyses of non-baumannii acinetobacter clinical isolates from a tertiary hospital in Terengganu, Malaysia Farahiyah Binti Mohd Rani Bacteria of the genus Acinetobacter are causal agents of numerous nosocomial infections, in particular Acinetobacter baumannii, which was listed as a priority pathogen by the World Health Organisation. However, other non-baumannii Acinetobacters such as A. nosocomialis and A. pittii have emerged to cause outbreaks of infections in hospitals. The extent of their involvement in nosocomial infections is unknown in Malaysia due to the difficulties in identifying these bacteria at the species level by conventional microbiological identification methods. This study thus aims to determine the occurrence, antimicrobial resistance profiles, and genomic characteristics of non-baumannii Acinetobacters in Hospital Sultanah Nur Zahirah (HSNZ), the main tertiary hospital in Terengganu, Malaysia.Methodology: From 2015 to 2020, 384 Acinetobacter spp. isolates with background clinical data were collected from HSNZ. Their preliminary identification was performed by PCR amplification followed by sequencing of the rpoB gene. Antimicrobial susceptibility was determined by disc diffusion for a panel of 21 antibiotics encompassing eight antimicrobial classes. A selection of 50 non-baumannii isolates was subjected to whole genome sequencing (WGS) on the short-read Illumina platform. Various bioinformatic tools were used to analyse the assembled genome sequences. Results: Sequencing of the rpoB gene indicated that most of the isolates (84.1%, or 323/384) were A. baumannii. Higher resistance rates were observed in A. baumannii where 75.2% (or 243/323) of the isolates were multidrug-resistant (MDR), defined as resistance to at least three antimicrobial classes. In contrast, only 11.5% (or 7/61) of the non-baumannii isolates were MDR with all of them A. nosocomialis. From the 50 sequenced isolates, 33 were A. nosocomialis, 10 were A. pittii, with the rest being identified as A. soli (n=2), A. oleivorans (n=2), A. berezeniae (n=1), A. haemolyticus (n=1) and A. variabilis (n=1). The non-baumannii isolates were diverse with multiple sequence types (STs) detected. For A. nosocomialis, a total of 9 Oxford STs and 12 Pasteur STs were identified, with the majority being ST958 Oxford (n=6) and ST433 Pasteur (n=7). All ten A. pittii isolates belonged to ten separate ST Pasteur types. The core-genome phylogenetic trees of these isolates also indicated their diversity, suggesting that there was likely no clonal spread of these non-baumannii Acinetobacters in the hospital.One MDR A. nosocomialis strain AC1530 was found to harbour the bla<sub>NDM-1</sub> and bla<sub>OXA-58</sub> genes encoding the New Delhi metallo-β-lactamase-1 (NDM-1) and OXA-58 carbapenemase, respectively, on a large ~170 kb plasmid, pAC1530. This plasmid also harboured genes conferring resistance to aminoglycosides, sulphonamides, and macrolides. Interestingly, a similar plasmid was found on an MDR A. baumannii strain AC1633 that was isolated a year later, suggesting a possible spread of the plasmid.Conclusions: Although fewer MDR isolates of non-baumannii were found as compared to A. baumannii during the five-year period, the possible spread of a large MDR plasmid from A. nosocomialis to A. baumannii underlines the need for close monitoring of these pathogens. 2024-12-22 02:55 uuid:96664384-1EB6-45E4-8AC9-402F4546FF7F ConvertAPI CHARACTERISATION AND GENOMIC ANALYSES OF NON-BAUMANNII ACINETOBACTER CLINICAL ISOLATES FROM A TERTIARY HOSPITAL IN TERENGGANU, MALAYSIA (PHD_2024).pdf Acinetobacter Baumannii Hospital Sultanah Nur Zahirah (HSNZ) Acinetobacter Nosocomialis Nosocomial Infections Multidrug-Resistant Bacteria (MDR) Whole Genome Sequencing (WGS) Genomic Epidemiology Plasmid-Mediated Resistance Public Health Surveillance Acinetobacter infections — Malaysia Nosocomial infections — Malaysia Drug resistance in microorganisms — Malaysia Thesis |
| spellingShingle | 2024_Characterisation and genomic analyses of non-baumannii acinetobacter clinical isolates from a tertiary hospital in Terengganu, Malaysia |
| state | Terengganu |
| subject | Dissertations, Academic Acinetobacter infections — Malaysia Nosocomial infections — Malaysia Drug resistance in microorganisms — Malaysia |
| summary | Bacteria of the genus Acinetobacter are causal agents of numerous nosocomial infections, in particular Acinetobacter baumannii, which was listed as a priority pathogen by the World Health Organisation. However, other non-baumannii Acinetobacters such as A. nosocomialis and A. pittii have emerged to cause outbreaks of infections in hospitals. The extent of their involvement in nosocomial infections is unknown in Malaysia due to the difficulties in identifying these bacteria at the species level by conventional microbiological identification methods. This study thus aims to determine the occurrence, antimicrobial resistance profiles, and genomic characteristics of non-baumannii Acinetobacters in Hospital Sultanah Nur Zahirah (HSNZ), the main tertiary hospital in Terengganu, Malaysia.Methodology: From 2015 to 2020, 384 Acinetobacter spp. isolates with background clinical data were collected from HSNZ. Their preliminary identification was performed by PCR amplification followed by sequencing of the rpoB gene. Antimicrobial susceptibility was determined by disc diffusion for a panel of 21 antibiotics encompassing eight antimicrobial classes. A selection of 50 non-baumannii isolates was subjected to whole genome sequencing (WGS) on the short-read Illumina platform. Various bioinformatic tools were used to analyse the assembled genome sequences. Results: Sequencing of the rpoB gene indicated that most of the isolates (84.1%, or 323/384) were A. baumannii. Higher resistance rates were observed in A. baumannii where 75.2% (or 243/323) of the isolates were multidrug-resistant (MDR), defined as resistance to at least three antimicrobial classes. In contrast, only 11.5% (or 7/61) of the non-baumannii isolates were MDR with all of them A. nosocomialis. From the 50 sequenced isolates, 33 were A. nosocomialis, 10 were A. pittii, with the rest being identified as A. soli (n=2), A. oleivorans (n=2), A. berezeniae (n=1), A. haemolyticus (n=1) and A. variabilis (n=1). The non-baumannii isolates were diverse with multiple sequence types (STs) detected. For A. nosocomialis, a total of 9 Oxford STs and 12 Pasteur STs were identified, with the majority being ST958 Oxford (n=6) and ST433 Pasteur (n=7). All ten A. pittii isolates belonged to ten separate ST Pasteur types. The core-genome phylogenetic trees of these isolates also indicated their diversity, suggesting that there was likely no clonal spread of these non-baumannii Acinetobacters in the hospital.One MDR A. nosocomialis strain AC1530 was found to harbour the bla<sub>NDM-1</sub> and bla<sub>OXA-58</sub> genes encoding the New Delhi metallo-β-lactamase-1 (NDM-1) and OXA-58 carbapenemase, respectively, on a large ~170 kb plasmid, pAC1530. This plasmid also harboured genes conferring resistance to aminoglycosides, sulphonamides, and macrolides. Interestingly, a similar plasmid was found on an MDR A. baumannii strain AC1633 that was isolated a year later, suggesting a possible spread of the plasmid.Conclusions: Although fewer MDR isolates of non-baumannii were found as compared to A. baumannii during the five-year period, the possible spread of a large MDR plasmid from A. nosocomialis to A. baumannii underlines the need for close monitoring of these pathogens. |
| title | 2024_Characterisation and genomic analyses of non-baumannii acinetobacter clinical isolates from a tertiary hospital in Terengganu, Malaysia |
| title_full | 2024_Characterisation and genomic analyses of non-baumannii acinetobacter clinical isolates from a tertiary hospital in Terengganu, Malaysia |
| title_fullStr | 2024_Characterisation and genomic analyses of non-baumannii acinetobacter clinical isolates from a tertiary hospital in Terengganu, Malaysia |
| title_full_unstemmed | 2024_Characterisation and genomic analyses of non-baumannii acinetobacter clinical isolates from a tertiary hospital in Terengganu, Malaysia |
| title_short | 2024_Characterisation and genomic analyses of non-baumannii acinetobacter clinical isolates from a tertiary hospital in Terengganu, Malaysia |
| title_sort | 2024_characterisation and genomic analyses of non-baumannii acinetobacter clinical isolates from a tertiary hospital in terengganu, malaysia |