Whole-genome sequencing of extended spectrum beta lactamases (ESBLs)-producing Klebsiella pneumoniae (kp) isolates from selected hospitals in Malaysia
Abstract The resistance of ESBLs-producing Kp to various groups of antibiotics commonly used against infections they caused had become a global threat and required urgent attention. This study assessed the extended spectrum beta-lactamases (ESBLs)-producing Klebsiella pneumoniae isolates in terms of...
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2025-03-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11215-7 |
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| author | Salawudeen Adamu Mika’ila Bawa Ali Mohd Nasir Mohd Desa Hui-min Neoh Siti Norbaya Masri Narcisse Joseph Tengku Zetty Maztura Tengku Jamaluddin |
| author_facet | Salawudeen Adamu Mika’ila Bawa Ali Mohd Nasir Mohd Desa Hui-min Neoh Siti Norbaya Masri Narcisse Joseph Tengku Zetty Maztura Tengku Jamaluddin |
| author_sort | Salawudeen Adamu |
| collection | DOAJ |
| description | Abstract The resistance of ESBLs-producing Kp to various groups of antibiotics commonly used against infections they caused had become a global threat and required urgent attention. This study assessed the extended spectrum beta-lactamases (ESBLs)-producing Klebsiella pneumoniae isolates in terms of their genomic resistance. An analytical profile index (API) 20E kit was used to confirm a total of 100 clinical isolates of ESBL Klebsiella pneumoniae. The disc diffusion method was used to perform the antimicrobial susceptibility testing (AST), which was followed by the phenotypic detection of ESBLs. Six profiled representative ESBL positive strains were subjected to whole genome sequencing (WGS), multilocus sequence typing (MLST), and phylogenetic tree construction using the sequence data. The study showed that 46(46%) of the 100 isolates were positive for ESBL production and antibiotic susceptibility testing revealed significant resistance to β-lactam antibiotics including monobactam especially ampicillin/sulbactam (40%), cephalosporin groups (cefuroxime, cefotaxime, and ceftriaxone) stood at 51%, 49% and 48% respectively and aztreonam with 49%. The WGS analysis of the representative strains revealed genes encoding resistance to aminoglycoside (StrA4, StrB1, aac(3’)-IIa, aac(6’)-1b, aac(6’)1b-cr-1, aadA16, aph(3’)-VIa and aadA15), trimethoprim (dfrA14 and dfrA27), sulphonamide (sul1_11, sul2_2 and sul2_3), quinolone (QnrB40-1, QnrB10, QnrS2, OqxA and OqxB), tetracycline (tet(A)_4), fosfomycin (fosA3, floR2 and fosA7), macrolid (mph(A)_1), rifampicin (ARR-3), β-lactam (blaCTX-M-15_23, blaCTX-M-55, blaSHV-1_22, blaSHV11_18, blaSHV-11, blaSHV-1_1.1, blaSHV-11_3, blaSHV-11_19, blaTEM-1_1, blaTEM-1_5, blaOXA-51_10, blaOXA-30_1, blaNDM-1, blaLEN6, blaLEN8 and blaLEN21 were detected. The MLST analysis revealed two novel sequence types of representative strains (2 with ST NF* and 12 with ST NF) and four other heterogeneous STs which include ST394, ST985, ST17 and ST11 while the phylogenetic tree of the strains showed closed clonal relationship and lineages with other reference isolates. In conclusion, the study’s results showed a high prevalence of ESBL-producing Kp in the study area, and the representative strains’ genomic contents demonstrated that ESBL-producing Kp in a clinical setting could serve as a reservoir for resistance genes and be the source of genetic transfer to other bacterial species. As a result, ongoing surveillance is required to monitor this endemic situation to prevent an epidemiological outbreak of K. pneumoniae- carrying ESBL. |
| format | Article |
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| institution | DOAJ |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-cf91d2fb036945f7a343bbd8a3bb257a2025-08-20T03:08:05ZengBMCBMC Genomics1471-21642025-03-0126111310.1186/s12864-025-11215-7Whole-genome sequencing of extended spectrum beta lactamases (ESBLs)-producing Klebsiella pneumoniae (kp) isolates from selected hospitals in MalaysiaSalawudeen Adamu0Mika’ila Bawa Ali1Mohd Nasir Mohd Desa2Hui-min Neoh3Siti Norbaya Masri4Narcisse Joseph5Tengku Zetty Maztura Tengku Jamaluddin6Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra MalaysiaMolecular Genetics and Infectious Diseases Research Laboratory, Abubakar Tafawa Balewa UniversityDepartment of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra MalaysiaUKM Medical Molecular Biology Institute (UMBI), UKM Medical CentreDepartment of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra MalaysiaDepartment of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra MalaysiaDepartment of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra MalaysiaAbstract The resistance of ESBLs-producing Kp to various groups of antibiotics commonly used against infections they caused had become a global threat and required urgent attention. This study assessed the extended spectrum beta-lactamases (ESBLs)-producing Klebsiella pneumoniae isolates in terms of their genomic resistance. An analytical profile index (API) 20E kit was used to confirm a total of 100 clinical isolates of ESBL Klebsiella pneumoniae. The disc diffusion method was used to perform the antimicrobial susceptibility testing (AST), which was followed by the phenotypic detection of ESBLs. Six profiled representative ESBL positive strains were subjected to whole genome sequencing (WGS), multilocus sequence typing (MLST), and phylogenetic tree construction using the sequence data. The study showed that 46(46%) of the 100 isolates were positive for ESBL production and antibiotic susceptibility testing revealed significant resistance to β-lactam antibiotics including monobactam especially ampicillin/sulbactam (40%), cephalosporin groups (cefuroxime, cefotaxime, and ceftriaxone) stood at 51%, 49% and 48% respectively and aztreonam with 49%. The WGS analysis of the representative strains revealed genes encoding resistance to aminoglycoside (StrA4, StrB1, aac(3’)-IIa, aac(6’)-1b, aac(6’)1b-cr-1, aadA16, aph(3’)-VIa and aadA15), trimethoprim (dfrA14 and dfrA27), sulphonamide (sul1_11, sul2_2 and sul2_3), quinolone (QnrB40-1, QnrB10, QnrS2, OqxA and OqxB), tetracycline (tet(A)_4), fosfomycin (fosA3, floR2 and fosA7), macrolid (mph(A)_1), rifampicin (ARR-3), β-lactam (blaCTX-M-15_23, blaCTX-M-55, blaSHV-1_22, blaSHV11_18, blaSHV-11, blaSHV-1_1.1, blaSHV-11_3, blaSHV-11_19, blaTEM-1_1, blaTEM-1_5, blaOXA-51_10, blaOXA-30_1, blaNDM-1, blaLEN6, blaLEN8 and blaLEN21 were detected. The MLST analysis revealed two novel sequence types of representative strains (2 with ST NF* and 12 with ST NF) and four other heterogeneous STs which include ST394, ST985, ST17 and ST11 while the phylogenetic tree of the strains showed closed clonal relationship and lineages with other reference isolates. In conclusion, the study’s results showed a high prevalence of ESBL-producing Kp in the study area, and the representative strains’ genomic contents demonstrated that ESBL-producing Kp in a clinical setting could serve as a reservoir for resistance genes and be the source of genetic transfer to other bacterial species. As a result, ongoing surveillance is required to monitor this endemic situation to prevent an epidemiological outbreak of K. pneumoniae- carrying ESBL.https://doi.org/10.1186/s12864-025-11215-7Whole-genomeSequencingExtended spectrum β-lactamasesKlebsiella pneumoniaeAntibiogram and resistance genes |
| spellingShingle | Salawudeen Adamu Mika’ila Bawa Ali Mohd Nasir Mohd Desa Hui-min Neoh Siti Norbaya Masri Narcisse Joseph Tengku Zetty Maztura Tengku Jamaluddin Whole-genome sequencing of extended spectrum beta lactamases (ESBLs)-producing Klebsiella pneumoniae (kp) isolates from selected hospitals in Malaysia BMC Genomics Whole-genome Sequencing Extended spectrum β-lactamases Klebsiella pneumoniae Antibiogram and resistance genes |
| title | Whole-genome sequencing of extended spectrum beta lactamases (ESBLs)-producing Klebsiella pneumoniae (kp) isolates from selected hospitals in Malaysia |
| title_full | Whole-genome sequencing of extended spectrum beta lactamases (ESBLs)-producing Klebsiella pneumoniae (kp) isolates from selected hospitals in Malaysia |
| title_fullStr | Whole-genome sequencing of extended spectrum beta lactamases (ESBLs)-producing Klebsiella pneumoniae (kp) isolates from selected hospitals in Malaysia |
| title_full_unstemmed | Whole-genome sequencing of extended spectrum beta lactamases (ESBLs)-producing Klebsiella pneumoniae (kp) isolates from selected hospitals in Malaysia |
| title_short | Whole-genome sequencing of extended spectrum beta lactamases (ESBLs)-producing Klebsiella pneumoniae (kp) isolates from selected hospitals in Malaysia |
| title_sort | whole genome sequencing of extended spectrum beta lactamases esbls producing klebsiella pneumoniae kp isolates from selected hospitals in malaysia |
| topic | Whole-genome Sequencing Extended spectrum β-lactamases Klebsiella pneumoniae Antibiogram and resistance genes |
| url | https://doi.org/10.1186/s12864-025-11215-7 |
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