Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii
ABSTRACT Mutation rates in bacteria are an important determinant of adaptation to new environments and success in different niches. In some bacterial pathogens, “hypermutator” variants—most often associated with mutations in components of the DNA mismatch repair system—are associated with increased...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2025-08-01
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| Series: | mBio |
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| Online Access: | https://journals.asm.org/doi/10.1128/mbio.00966-25 |
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| author | Francesca L. Short Ram Maharjan Liping Li Nusrat Afrin Natasha Delgado Christine J. Boinett Julian Parkhill Amy K. Cain Ian T. Paulsen |
| author_facet | Francesca L. Short Ram Maharjan Liping Li Nusrat Afrin Natasha Delgado Christine J. Boinett Julian Parkhill Amy K. Cain Ian T. Paulsen |
| author_sort | Francesca L. Short |
| collection | DOAJ |
| description | ABSTRACT Mutation rates in bacteria are an important determinant of adaptation to new environments and success in different niches. In some bacterial pathogens, “hypermutator” variants—most often associated with mutations in components of the DNA mismatch repair system—are associated with increased antibiotic resistance and poorer patient outcomes. We report the serendipitous finding of novel hypermutator genes in Acinetobacter baumannii through genome-scale mutant fitness screening. Exposure of a transposon insertion mutant library of A. baumannii to extended weak antibiotic selection resulted in selection for mutations that directly increased fitness as expected, but also revealed genes where transposon insertion indirectly increased fitness due to elevated general mutation rates. Three novel hypermutator genes were confirmed in A. baumannii: nusB, encoding a transcription antiterminator; ABUW_0208, encoding a hypothetical protein; and ABUW_2121, which encodes a sulfite transporter. We find selection for hypermutator variants in transposon insertion sequencing (TIS) data sets from diverse bacteria under various antibiotic treatments. Our results expand the range of biological functions linked to hypermutator phenotypes in bacteria and provide a workflow for the identification of putative hypermutators by TIS.IMPORTANCEAll organisms have the capacity for evolution through mutation. Bacteria with high mutation rates have a survival advantage in some stressful environments because they generate beneficial mutations more frequently. “Hypermutators” are bacterial strains that carry gene inactivations that increase general mutation rates. These variants are important in chronic infections, as their increased genetic diversity allows higher drug resistance and prolonged survival in the host. Only a few different hypermutator genes are known, and there is no high-throughput method for their identification. We have made the serendipitous finding that hypermutator genes can be identified by genome-wide mutant fitness screening under specific selection conditions. We have identified novel hypermutator alleles in the notorious hospital pathogen Acinetobacter baumannii and show that hypermutator variants can be detected in screens of a wide range of pathogens. |
| format | Article |
| id | doaj-art-53f7a253759949d2b2cf19c5ccdae530 |
| institution | Kabale University |
| issn | 2150-7511 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj-art-53f7a253759949d2b2cf19c5ccdae5302025-08-20T04:00:49ZengAmerican Society for MicrobiologymBio2150-75112025-08-0116810.1128/mbio.00966-25Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumanniiFrancesca L. Short0Ram Maharjan1Liping Li2Nusrat Afrin3Natasha Delgado4Christine J. Boinett5Julian Parkhill6Amy K. Cain7Ian T. Paulsen8Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, AustraliaARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, New South Wales, AustraliaARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, New South Wales, AustraliaARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, New South Wales, AustraliaARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, New South Wales, AustraliaWellcome Sanger Institute, Hinxton, United KingdomWellcome Sanger Institute, Hinxton, United KingdomARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, New South Wales, AustraliaARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, New South Wales, AustraliaABSTRACT Mutation rates in bacteria are an important determinant of adaptation to new environments and success in different niches. In some bacterial pathogens, “hypermutator” variants—most often associated with mutations in components of the DNA mismatch repair system—are associated with increased antibiotic resistance and poorer patient outcomes. We report the serendipitous finding of novel hypermutator genes in Acinetobacter baumannii through genome-scale mutant fitness screening. Exposure of a transposon insertion mutant library of A. baumannii to extended weak antibiotic selection resulted in selection for mutations that directly increased fitness as expected, but also revealed genes where transposon insertion indirectly increased fitness due to elevated general mutation rates. Three novel hypermutator genes were confirmed in A. baumannii: nusB, encoding a transcription antiterminator; ABUW_0208, encoding a hypothetical protein; and ABUW_2121, which encodes a sulfite transporter. We find selection for hypermutator variants in transposon insertion sequencing (TIS) data sets from diverse bacteria under various antibiotic treatments. Our results expand the range of biological functions linked to hypermutator phenotypes in bacteria and provide a workflow for the identification of putative hypermutators by TIS.IMPORTANCEAll organisms have the capacity for evolution through mutation. Bacteria with high mutation rates have a survival advantage in some stressful environments because they generate beneficial mutations more frequently. “Hypermutators” are bacterial strains that carry gene inactivations that increase general mutation rates. These variants are important in chronic infections, as their increased genetic diversity allows higher drug resistance and prolonged survival in the host. Only a few different hypermutator genes are known, and there is no high-throughput method for their identification. We have made the serendipitous finding that hypermutator genes can be identified by genome-wide mutant fitness screening under specific selection conditions. We have identified novel hypermutator alleles in the notorious hospital pathogen Acinetobacter baumannii and show that hypermutator variants can be detected in screens of a wide range of pathogens.https://journals.asm.org/doi/10.1128/mbio.00966-25hypermutatortn-seqtradismutation rateAcinetobacter |
| spellingShingle | Francesca L. Short Ram Maharjan Liping Li Nusrat Afrin Natasha Delgado Christine J. Boinett Julian Parkhill Amy K. Cain Ian T. Paulsen Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii mBio hypermutator tn-seq tradis mutation rate Acinetobacter |
| title | Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii |
| title_full | Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii |
| title_fullStr | Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii |
| title_full_unstemmed | Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii |
| title_short | Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii |
| title_sort | transposon insertion sequencing reveals novel hypermutator genes in acinetobacter baumannii |
| topic | hypermutator tn-seq tradis mutation rate Acinetobacter |
| url | https://journals.asm.org/doi/10.1128/mbio.00966-25 |
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