The presence of multiple variants of IncF plasmid alleles in a single genome sequence can hinder accurate replicon sequence typing using in silico pMLST tools
ABSTRACT IncF plasmids are mobile genetic elements found in bacteria from the Enterobacteriaceae family and often carry critical antibiotic and virulence gene cargo. The classification of IncF plasmids using the plasmid Multi-Locus Sequence Typing (pMLST) tool from the Center for Genomic Epidemiolog...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2025-05-01
|
| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.01010-24 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849326780050046976 |
|---|---|
| author | Michaela Ruzickova Jana Palkovicova Ivo Papousek Max L. Cummins Steven P. Djordjevic Monika Dolejska |
| author_facet | Michaela Ruzickova Jana Palkovicova Ivo Papousek Max L. Cummins Steven P. Djordjevic Monika Dolejska |
| author_sort | Michaela Ruzickova |
| collection | DOAJ |
| description | ABSTRACT IncF plasmids are mobile genetic elements found in bacteria from the Enterobacteriaceae family and often carry critical antibiotic and virulence gene cargo. The classification of IncF plasmids using the plasmid Multi-Locus Sequence Typing (pMLST) tool from the Center for Genomic Epidemiology (CGE; https://www.genomicepidemiology.org/) compares the sequences of IncF alleles against a database to create a plasmid sequence type (ST). Accurate identification of plasmid STs is useful as it enables an assessment of IncF plasmid lineages associated with pandemic enterobacterial STs. Our initial observations showed discrepancies in IncF allele variants reported by pMLST in a collection of 898 Escherichia coli ST131 genomes. To evaluate the limitations of the pMLST tool, we interrogated an in-house and public repository of 70,324 E. coli genomes of various STs and other Enterobacteriaceae genomes (n = 1247). All short-read assemblies and representatives selected for long-read sequencing were used to assess pMLST allele variants and to compare the output of pMLST tool versions. When multiple allele variants occurred in a single bacterial genome, the Python and web versions of the tool randomly selected one allele to report, leading to limited and inaccurate ST identification. Discrepancies were detected in 5,804 of 72,469 genomes (8.01%). Long-read sequencing of 27 genomes confirmed multiple IncF allele variants on one plasmid or two separate IncF plasmids in a single bacterial cell. The pMLST tool was unable to accurately distinguish allele variants and their location on replicons using short-read genome assemblies, or long-read genome assemblies if the same allele variant was present more than once.IMPORTANCEPlasmid sequence type is crucial for describing IncF plasmids due to their capacity to carry important antibiotic and virulence gene cargo and consequently due to their association with disease-causing enterobacterial lineages exhibiting resistance to clinically relevant antibiotics in humans and food-producing animals. As a result, precise reporting of IncF allele variants in IncF plasmids is necessary. Comparison of the FAB formulae generated by the pMLST tool with annotated long-read genome assemblies identified inconsistencies, including examples where multiple IncF allele variants were present on the same plasmid but missing in the FAB formula, or in cases where two IncF plasmids were detected in one bacterial cell, and the pMLST output provided information only about one plasmid. Such inconsistencies may cloud interpretation of IncF plasmid replicon type in specific bacterial lineages or inaccurate assumptions of host strain clonality. |
| format | Article |
| id | doaj-art-82fd1c3d58574820904b2573c2facd6d |
| institution | Kabale University |
| issn | 2379-5077 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj-art-82fd1c3d58574820904b2573c2facd6d2025-08-20T03:48:03ZengAmerican Society for MicrobiologymSystems2379-50772025-05-0110510.1128/msystems.01010-24The presence of multiple variants of IncF plasmid alleles in a single genome sequence can hinder accurate replicon sequence typing using in silico pMLST toolsMichaela Ruzickova0Jana Palkovicova1Ivo Papousek2Max L. Cummins3Steven P. Djordjevic4Monika Dolejska5Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, South Moravian Region, CzechiaCentral European Institute of Technology, University of Veterinary Sciences Brno, Brno, South Moravian Region, CzechiaDepartment of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, South Moravian Region, CzechiaAustralian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, AustraliaAustralian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, AustraliaCentral European Institute of Technology, University of Veterinary Sciences Brno, Brno, South Moravian Region, CzechiaABSTRACT IncF plasmids are mobile genetic elements found in bacteria from the Enterobacteriaceae family and often carry critical antibiotic and virulence gene cargo. The classification of IncF plasmids using the plasmid Multi-Locus Sequence Typing (pMLST) tool from the Center for Genomic Epidemiology (CGE; https://www.genomicepidemiology.org/) compares the sequences of IncF alleles against a database to create a plasmid sequence type (ST). Accurate identification of plasmid STs is useful as it enables an assessment of IncF plasmid lineages associated with pandemic enterobacterial STs. Our initial observations showed discrepancies in IncF allele variants reported by pMLST in a collection of 898 Escherichia coli ST131 genomes. To evaluate the limitations of the pMLST tool, we interrogated an in-house and public repository of 70,324 E. coli genomes of various STs and other Enterobacteriaceae genomes (n = 1247). All short-read assemblies and representatives selected for long-read sequencing were used to assess pMLST allele variants and to compare the output of pMLST tool versions. When multiple allele variants occurred in a single bacterial genome, the Python and web versions of the tool randomly selected one allele to report, leading to limited and inaccurate ST identification. Discrepancies were detected in 5,804 of 72,469 genomes (8.01%). Long-read sequencing of 27 genomes confirmed multiple IncF allele variants on one plasmid or two separate IncF plasmids in a single bacterial cell. The pMLST tool was unable to accurately distinguish allele variants and their location on replicons using short-read genome assemblies, or long-read genome assemblies if the same allele variant was present more than once.IMPORTANCEPlasmid sequence type is crucial for describing IncF plasmids due to their capacity to carry important antibiotic and virulence gene cargo and consequently due to their association with disease-causing enterobacterial lineages exhibiting resistance to clinically relevant antibiotics in humans and food-producing animals. As a result, precise reporting of IncF allele variants in IncF plasmids is necessary. Comparison of the FAB formulae generated by the pMLST tool with annotated long-read genome assemblies identified inconsistencies, including examples where multiple IncF allele variants were present on the same plasmid but missing in the FAB formula, or in cases where two IncF plasmids were detected in one bacterial cell, and the pMLST output provided information only about one plasmid. Such inconsistencies may cloud interpretation of IncF plasmid replicon type in specific bacterial lineages or inaccurate assumptions of host strain clonality.https://journals.asm.org/doi/10.1128/msystems.01010-24plasmidsIncFpMLSTEnterobacteriaceaeantibiotic resistance |
| spellingShingle | Michaela Ruzickova Jana Palkovicova Ivo Papousek Max L. Cummins Steven P. Djordjevic Monika Dolejska The presence of multiple variants of IncF plasmid alleles in a single genome sequence can hinder accurate replicon sequence typing using in silico pMLST tools mSystems plasmids IncF pMLST Enterobacteriaceae antibiotic resistance |
| title | The presence of multiple variants of IncF plasmid alleles in a single genome sequence can hinder accurate replicon sequence typing using in silico pMLST tools |
| title_full | The presence of multiple variants of IncF plasmid alleles in a single genome sequence can hinder accurate replicon sequence typing using in silico pMLST tools |
| title_fullStr | The presence of multiple variants of IncF plasmid alleles in a single genome sequence can hinder accurate replicon sequence typing using in silico pMLST tools |
| title_full_unstemmed | The presence of multiple variants of IncF plasmid alleles in a single genome sequence can hinder accurate replicon sequence typing using in silico pMLST tools |
| title_short | The presence of multiple variants of IncF plasmid alleles in a single genome sequence can hinder accurate replicon sequence typing using in silico pMLST tools |
| title_sort | presence of multiple variants of incf plasmid alleles in a single genome sequence can hinder accurate replicon sequence typing using in silico pmlst tools |
| topic | plasmids IncF pMLST Enterobacteriaceae antibiotic resistance |
| url | https://journals.asm.org/doi/10.1128/msystems.01010-24 |
| work_keys_str_mv | AT michaelaruzickova thepresenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT janapalkovicova thepresenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT ivopapousek thepresenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT maxlcummins thepresenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT stevenpdjordjevic thepresenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT monikadolejska thepresenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT michaelaruzickova presenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT janapalkovicova presenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT ivopapousek presenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT maxlcummins presenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT stevenpdjordjevic presenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools AT monikadolejska presenceofmultiplevariantsofincfplasmidallelesinasinglegenomesequencecanhinderaccuraterepliconsequencetypingusinginsilicopmlsttools |