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
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/248225
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/248225
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling 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 Técnicas2025-10-22T11:46:23Zoai: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:34982025-10-22 11:46:24.01CONICET 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
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str 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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