Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina
- Autores
- Kovacec, Verónica Ivana; Di Gregorio, Sabrina Noelia; Pajon, Mario Ignacio; Crestani, Chiara; Poklepovich, Tomás; Campos, Josefina; Basit Khan, Uzma; Bentley, Stephen D.; Jamrozy, Dorota; Mollerach, Marta Eugenia; Bonofiglio, Laura
- Año de publicación
- 2024
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Group B Streptococcus (GBS) causes severe infections in neonates and adults with comorbidities. Prophages have been reported to contribute to GBS evolution and pathogenicity. However, no studies are available to date on the presence and diversity of prophages in GBS isolates from humans in South America. This study provides insights into the prophage content of 365 GBS isolates collected from clinical samples in the context of an Argentinean multicentric study. Using whole-genome sequence data, we implemented two previously proposed methods for prophage typing: a PCR approach (carried out in silico) coupled with a blastx-based method to classify prophages based on their prophage group and integrase type, respectively. We manually searched the genomes and identified 325 prophages. However, only 80% of prophages could be accurately categorized with the previous approaches. Integration of phylogenetic analysis, prophage group and integrase type allowed for all to be classified into 19 prophage types, which correlated with GBS clonal complex grouping. The revised prophage typing approach was additionally improved by using a blastn search after enriching the database with ten new genes for prophage group classification combined with the existing integrase typing method. This modified and integrated typing system was applied to the analysis of 615 GBS genomes (365 GBS from Argentina and 250 from public databases), which revealed 29 prophage types, including two novel integrase subtypes. Their characterization and comparative analysis revealed major differences in the lysogeny and replication modules. Genes related to bacterial fitness, virulence or adaptation to stressful environments were detected in all prophage types. Considering prophage prevalence, distribution and their association with bacterial virulence, it is important to study their role in GBS epidemiology. In this context, we propose the use of an improved and integrated prophage typing system suitable for rapid phage detection and classification with little computational processing.
Fil: Kovacec, Verónica Ivana. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina
Fil: Di Gregorio, Sabrina Noelia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Pajon, Mario Ignacio. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina
Fil: Crestani, Chiara. Institut Pasteur de Paris.; Francia
Fil: Poklepovich, Tomás. Dirección Nacional de Instituto de Investigación.Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"; Argentina
Fil: Campos, Josefina. Dirección Nacional de Instituto de Investigación.Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"; Argentina
Fil: Basit Khan, Uzma. Wellcome Genome Campus;
Fil: Bentley, Stephen D.. Wellcome Genome Campus;
Fil: Jamrozy, Dorota. Wellcome Genome Campus;
Fil: Mollerach, Marta Eugenia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Bonofiglio, Laura. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina - Materia
-
GBS
Streptococcus agalactiae
genomic analysis
group B Streptococcus
phage typing
prophage - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/248225
Ver los metadatos del registro completo
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Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from ArgentinaKovacec, Verónica IvanaDi Gregorio, Sabrina NoeliaPajon, Mario IgnacioCrestani, ChiaraPoklepovich, TomásCampos, JosefinaBasit Khan, UzmaBentley, Stephen D.Jamrozy, DorotaMollerach, Marta EugeniaBonofiglio, LauraGBSStreptococcus agalactiaegenomic analysisgroup B Streptococcusphage typingprophagehttps://purl.org/becyt/ford/3.3https://purl.org/becyt/ford/3Group B Streptococcus (GBS) causes severe infections in neonates and adults with comorbidities. Prophages have been reported to contribute to GBS evolution and pathogenicity. However, no studies are available to date on the presence and diversity of prophages in GBS isolates from humans in South America. This study provides insights into the prophage content of 365 GBS isolates collected from clinical samples in the context of an Argentinean multicentric study. Using whole-genome sequence data, we implemented two previously proposed methods for prophage typing: a PCR approach (carried out in silico) coupled with a blastx-based method to classify prophages based on their prophage group and integrase type, respectively. We manually searched the genomes and identified 325 prophages. However, only 80% of prophages could be accurately categorized with the previous approaches. Integration of phylogenetic analysis, prophage group and integrase type allowed for all to be classified into 19 prophage types, which correlated with GBS clonal complex grouping. The revised prophage typing approach was additionally improved by using a blastn search after enriching the database with ten new genes for prophage group classification combined with the existing integrase typing method. This modified and integrated typing system was applied to the analysis of 615 GBS genomes (365 GBS from Argentina and 250 from public databases), which revealed 29 prophage types, including two novel integrase subtypes. Their characterization and comparative analysis revealed major differences in the lysogeny and replication modules. Genes related to bacterial fitness, virulence or adaptation to stressful environments were detected in all prophage types. Considering prophage prevalence, distribution and their association with bacterial virulence, it is important to study their role in GBS epidemiology. In this context, we propose the use of an improved and integrated prophage typing system suitable for rapid phage detection and classification with little computational processing.Fil: Kovacec, Verónica Ivana. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; ArgentinaFil: Di Gregorio, Sabrina Noelia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Pajon, Mario Ignacio. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; ArgentinaFil: Crestani, Chiara. Institut Pasteur de Paris.; FranciaFil: Poklepovich, Tomás. Dirección Nacional de Instituto de Investigación.Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"; ArgentinaFil: Campos, Josefina. Dirección Nacional de Instituto de Investigación.Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"; ArgentinaFil: Basit Khan, Uzma. Wellcome Genome Campus;Fil: Bentley, Stephen D.. Wellcome Genome Campus;Fil: Jamrozy, Dorota. Wellcome Genome Campus;Fil: Mollerach, Marta Eugenia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bonofiglio, Laura. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaMicrobiology Society2024-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/248225Kovacec, Verónica Ivana; Di Gregorio, Sabrina Noelia; Pajon, Mario Ignacio; Crestani, Chiara; Poklepovich, Tomás; et al.; Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina; Microbiology Society; Microbial Genomics; 10; 10; 10-2024; 1-152057-5858CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001297info:eu-repo/semantics/altIdentifier/doi/10.1099/mgen.0.001297info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:16:16Zoai:ri.conicet.gov.ar:11336/248225instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:16:16.472CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina |
title |
Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina |
spellingShingle |
Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina Kovacec, Verónica Ivana GBS Streptococcus agalactiae genomic analysis group B Streptococcus phage typing prophage |
title_short |
Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina |
title_full |
Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina |
title_fullStr |
Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina |
title_full_unstemmed |
Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina |
title_sort |
Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina |
dc.creator.none.fl_str_mv |
Kovacec, Verónica Ivana Di Gregorio, Sabrina Noelia Pajon, Mario Ignacio Crestani, Chiara Poklepovich, Tomás Campos, Josefina Basit Khan, Uzma Bentley, Stephen D. Jamrozy, Dorota Mollerach, Marta Eugenia Bonofiglio, Laura |
author |
Kovacec, Verónica Ivana |
author_facet |
Kovacec, Verónica Ivana Di Gregorio, Sabrina Noelia Pajon, Mario Ignacio Crestani, Chiara Poklepovich, Tomás Campos, Josefina Basit Khan, Uzma Bentley, Stephen D. Jamrozy, Dorota Mollerach, Marta Eugenia Bonofiglio, Laura |
author_role |
author |
author2 |
Di Gregorio, Sabrina Noelia Pajon, Mario Ignacio Crestani, Chiara Poklepovich, Tomás Campos, Josefina Basit Khan, Uzma Bentley, Stephen D. Jamrozy, Dorota Mollerach, Marta Eugenia Bonofiglio, Laura |
author2_role |
author author author author author author author author author author |
dc.subject.none.fl_str_mv |
GBS Streptococcus agalactiae genomic analysis group B Streptococcus phage typing prophage |
topic |
GBS Streptococcus agalactiae genomic analysis group B Streptococcus phage typing prophage |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/3.3 https://purl.org/becyt/ford/3 |
dc.description.none.fl_txt_mv |
Group B Streptococcus (GBS) causes severe infections in neonates and adults with comorbidities. Prophages have been reported to contribute to GBS evolution and pathogenicity. However, no studies are available to date on the presence and diversity of prophages in GBS isolates from humans in South America. This study provides insights into the prophage content of 365 GBS isolates collected from clinical samples in the context of an Argentinean multicentric study. Using whole-genome sequence data, we implemented two previously proposed methods for prophage typing: a PCR approach (carried out in silico) coupled with a blastx-based method to classify prophages based on their prophage group and integrase type, respectively. We manually searched the genomes and identified 325 prophages. However, only 80% of prophages could be accurately categorized with the previous approaches. Integration of phylogenetic analysis, prophage group and integrase type allowed for all to be classified into 19 prophage types, which correlated with GBS clonal complex grouping. The revised prophage typing approach was additionally improved by using a blastn search after enriching the database with ten new genes for prophage group classification combined with the existing integrase typing method. This modified and integrated typing system was applied to the analysis of 615 GBS genomes (365 GBS from Argentina and 250 from public databases), which revealed 29 prophage types, including two novel integrase subtypes. Their characterization and comparative analysis revealed major differences in the lysogeny and replication modules. Genes related to bacterial fitness, virulence or adaptation to stressful environments were detected in all prophage types. Considering prophage prevalence, distribution and their association with bacterial virulence, it is important to study their role in GBS epidemiology. In this context, we propose the use of an improved and integrated prophage typing system suitable for rapid phage detection and classification with little computational processing. Fil: Kovacec, Verónica Ivana. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina Fil: Di Gregorio, Sabrina Noelia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Pajon, Mario Ignacio. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina Fil: Crestani, Chiara. Institut Pasteur de Paris.; Francia Fil: Poklepovich, Tomás. Dirección Nacional de Instituto de Investigación.Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"; Argentina Fil: Campos, Josefina. Dirección Nacional de Instituto de Investigación.Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"; Argentina Fil: Basit Khan, Uzma. Wellcome Genome Campus; Fil: Bentley, Stephen D.. Wellcome Genome Campus; Fil: Jamrozy, Dorota. Wellcome Genome Campus; Fil: Mollerach, Marta Eugenia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Bonofiglio, Laura. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina |
description |
Group B Streptococcus (GBS) causes severe infections in neonates and adults with comorbidities. Prophages have been reported to contribute to GBS evolution and pathogenicity. However, no studies are available to date on the presence and diversity of prophages in GBS isolates from humans in South America. This study provides insights into the prophage content of 365 GBS isolates collected from clinical samples in the context of an Argentinean multicentric study. Using whole-genome sequence data, we implemented two previously proposed methods for prophage typing: a PCR approach (carried out in silico) coupled with a blastx-based method to classify prophages based on their prophage group and integrase type, respectively. We manually searched the genomes and identified 325 prophages. However, only 80% of prophages could be accurately categorized with the previous approaches. Integration of phylogenetic analysis, prophage group and integrase type allowed for all to be classified into 19 prophage types, which correlated with GBS clonal complex grouping. The revised prophage typing approach was additionally improved by using a blastn search after enriching the database with ten new genes for prophage group classification combined with the existing integrase typing method. This modified and integrated typing system was applied to the analysis of 615 GBS genomes (365 GBS from Argentina and 250 from public databases), which revealed 29 prophage types, including two novel integrase subtypes. Their characterization and comparative analysis revealed major differences in the lysogeny and replication modules. Genes related to bacterial fitness, virulence or adaptation to stressful environments were detected in all prophage types. Considering prophage prevalence, distribution and their association with bacterial virulence, it is important to study their role in GBS epidemiology. In this context, we propose the use of an improved and integrated prophage typing system suitable for rapid phage detection and classification with little computational processing. |
publishDate |
2024 |
dc.date.none.fl_str_mv |
2024-10 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/248225 Kovacec, Verónica Ivana; Di Gregorio, Sabrina Noelia; Pajon, Mario Ignacio; Crestani, Chiara; Poklepovich, Tomás; et al.; Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina; Microbiology Society; Microbial Genomics; 10; 10; 10-2024; 1-15 2057-5858 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/248225 |
identifier_str_mv |
Kovacec, Verónica Ivana; Di Gregorio, Sabrina Noelia; Pajon, Mario Ignacio; Crestani, Chiara; Poklepovich, Tomás; et al.; Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina; Microbiology Society; Microbial Genomics; 10; 10; 10-2024; 1-15 2057-5858 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/url/https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001297 info:eu-repo/semantics/altIdentifier/doi/10.1099/mgen.0.001297 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Microbiology Society |
publisher.none.fl_str_mv |
Microbiology Society |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
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CONICET Digital (CONICET) |
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CONICET Digital (CONICET) |
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Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.name.fl_str_mv |
CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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1844614105747423232 |
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13.070432 |