Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data
Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing...
| Main Authors: | , , , , , |
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| Format: | Journal Article |
| Language: | English |
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NATURE PUBLISHING GROUP
2017
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| Subjects: | |
| Online Access: | http://hdl.handle.net/20.500.11937/80735 |
| _version_ | 1848764261457723392 |
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| author | Mobegi, Fredrick Cremers, A.J.H. De Jonge, M.I. Bentley, S.D. Van Hijum, S.A.F.T. Zomer, A. |
| author_facet | Mobegi, Fredrick Cremers, A.J.H. De Jonge, M.I. Bentley, S.D. Van Hijum, S.A.F.T. Zomer, A. |
| author_sort | Mobegi, Fredrick |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics. With the premise that accumulation of putative resistance-conferring SNPs, potentially in combination with specific resistance genes, precedes full resistance, we retrogressively surveyed the hotspot loci and quantified the number of SNPs and/or genes, which if accumulated would confer full resistance to an otherwise susceptible strain. We name this approach the € distance to resistance'. It can be used to identify the creep towards complete antibiotics resistance in bacteria using genome sequencing. This approach serves as a basis for the development of future sequencing-based methods for predicting resistance profiles of bacterial strains in hospital microbiology and public health settings. |
| first_indexed | 2025-11-14T11:16:33Z |
| format | Journal Article |
| id | curtin-20.500.11937-80735 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T11:16:33Z |
| publishDate | 2017 |
| publisher | NATURE PUBLISHING GROUP |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-807352021-01-07T07:46:47Z Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data Mobegi, Fredrick Cremers, A.J.H. De Jonge, M.I. Bentley, S.D. Van Hijum, S.A.F.T. Zomer, A. Science & Technology Multidisciplinary Sciences Science & Technology - Other Topics PENICILLIN-BINDING PROTEINS INVASIVE STREPTOCOCCUS-PNEUMONIAE BETA-LACTAM ANTIBIOTICS SICKLE-CELL-DISEASE FLUOROQUINOLONE RESISTANCE UNITED-STATES MOLECULAR EPIDEMIOLOGY PRESCRIPTION RATES IN-VITRO MUTATIONS Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics. With the premise that accumulation of putative resistance-conferring SNPs, potentially in combination with specific resistance genes, precedes full resistance, we retrogressively surveyed the hotspot loci and quantified the number of SNPs and/or genes, which if accumulated would confer full resistance to an otherwise susceptible strain. We name this approach the € distance to resistance'. It can be used to identify the creep towards complete antibiotics resistance in bacteria using genome sequencing. This approach serves as a basis for the development of future sequencing-based methods for predicting resistance profiles of bacterial strains in hospital microbiology and public health settings. 2017 Journal Article http://hdl.handle.net/20.500.11937/80735 10.1038/srep42808 English http://creativecommons.org/licenses/by/4.0/ NATURE PUBLISHING GROUP fulltext |
| spellingShingle | Science & Technology Multidisciplinary Sciences Science & Technology - Other Topics PENICILLIN-BINDING PROTEINS INVASIVE STREPTOCOCCUS-PNEUMONIAE BETA-LACTAM ANTIBIOTICS SICKLE-CELL-DISEASE FLUOROQUINOLONE RESISTANCE UNITED-STATES MOLECULAR EPIDEMIOLOGY PRESCRIPTION RATES IN-VITRO MUTATIONS Mobegi, Fredrick Cremers, A.J.H. De Jonge, M.I. Bentley, S.D. Van Hijum, S.A.F.T. Zomer, A. Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data |
| title | Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data |
| title_full | Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data |
| title_fullStr | Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data |
| title_full_unstemmed | Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data |
| title_short | Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data |
| title_sort | deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data |
| topic | Science & Technology Multidisciplinary Sciences Science & Technology - Other Topics PENICILLIN-BINDING PROTEINS INVASIVE STREPTOCOCCUS-PNEUMONIAE BETA-LACTAM ANTIBIOTICS SICKLE-CELL-DISEASE FLUOROQUINOLONE RESISTANCE UNITED-STATES MOLECULAR EPIDEMIOLOGY PRESCRIPTION RATES IN-VITRO MUTATIONS |
| url | http://hdl.handle.net/20.500.11937/80735 |