Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina

Autores
Gagetti, Paula Silvana; Lo, Stephanie W; Hawkins, Paulina A.; Gladstone, Rebecca A.; Regueira, Mariana; Faccone, Diego Francisco; Klugman, Keith P.; Breiman, Robert F.; McGee, Lesley; Bentley, Stephen D; Corso, Alejandra
Año de publicación
2021
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998–1999 (pre-PCV), before the introduction of PCV13 2010–2011 (PCV7) and after the introduction of PCV13 2012–2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50% of the isolates. Resistance to penicillin was 34.9%, cefotaxime 10.6%, meropenem 4.9%, cotrimoxazole 45%, erythromycin 21.5%, tetracycline 15.4% and chloramphenicol 0.4%. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9%) were non-susceptible to at least one antibiotic and 235(13.7%) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococ-cal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0% in pre-PCV to 3.2% in the PCV13 period. Our analysis showed that 66.1% (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9% (49/413) were multidrug resistant. We found an agreement of 100% when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4% of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.
Fil: Gagetti, Paula Silvana. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; Argentina
Fil: Lo, Stephanie W. Wellcome Sanger Institute; Reino Unido
Fil: Hawkins, Paulina A.. University Of Emory. Rollins School Of Public Health; Estados Unidos. Centers for Disease Control and Prevention; Estados Unidos
Fil: Gladstone, Rebecca A.. Wellcome Sanger Institute; Reino Unido
Fil: Regueira, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Dirección Nacional de Instituto de Investigación.Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"; Argentina
Fil: Faccone, Diego Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; Argentina
Fil: Klugman, Keith P.. University Of Emory. Rollins School Of Public Health; Estados Unidos
Fil: Breiman, Robert F.. University Of Emory. Rollins School Of Public Health; Estados Unidos
Fil: McGee, Lesley. Centers for Disease Control and Prevention; Estados Unidos
Fil: Bentley, Stephen D. Wellcome Sanger Institute; Reino Unido
Fil: Corso, Alejandra. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; Argentina
Materia
ANTIMICROBIAL RESISTANCE
ARGENTINA
GLOBAL PNEUMOCOCCAL SEQUENCE CLUSTER
SEROTYPES
STREPTOCOCCUS PNEUMONIAE
WGS (WHOLE-GENOME SEQUENCING)
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/166317

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network_name_str CONICET Digital (CONICET)
spelling Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in ArgentinaGagetti, Paula SilvanaLo, Stephanie WHawkins, Paulina A.Gladstone, Rebecca A.Regueira, MarianaFaccone, Diego FranciscoKlugman, Keith P.Breiman, Robert F.McGee, LesleyBentley, Stephen DCorso, AlejandraANTIMICROBIAL RESISTANCEARGENTINAGLOBAL PNEUMOCOCCAL SEQUENCE CLUSTERSEROTYPESSTREPTOCOCCUS PNEUMONIAEWGS (WHOLE-GENOME SEQUENCING)https://purl.org/becyt/ford/3.3https://purl.org/becyt/ford/3Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998–1999 (pre-PCV), before the introduction of PCV13 2010–2011 (PCV7) and after the introduction of PCV13 2012–2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50% of the isolates. Resistance to penicillin was 34.9%, cefotaxime 10.6%, meropenem 4.9%, cotrimoxazole 45%, erythromycin 21.5%, tetracycline 15.4% and chloramphenicol 0.4%. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9%) were non-susceptible to at least one antibiotic and 235(13.7%) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococ-cal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0% in pre-PCV to 3.2% in the PCV13 period. Our analysis showed that 66.1% (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9% (49/413) were multidrug resistant. We found an agreement of 100% when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4% of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.Fil: Gagetti, Paula Silvana. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; ArgentinaFil: Lo, Stephanie W. Wellcome Sanger Institute; Reino UnidoFil: Hawkins, Paulina A.. University Of Emory. Rollins School Of Public Health; Estados Unidos. Centers for Disease Control and Prevention; Estados UnidosFil: Gladstone, Rebecca A.. Wellcome Sanger Institute; Reino UnidoFil: Regueira, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Dirección Nacional de Instituto de Investigación.Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"; ArgentinaFil: Faccone, Diego Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; ArgentinaFil: Klugman, Keith P.. University Of Emory. Rollins School Of Public Health; Estados UnidosFil: Breiman, Robert F.. University Of Emory. Rollins School Of Public Health; Estados UnidosFil: McGee, Lesley. Centers for Disease Control and Prevention; Estados UnidosFil: Bentley, Stephen D. Wellcome Sanger Institute; Reino UnidoFil: Corso, Alejandra. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; ArgentinaMicrobiology Society2021-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/166317Gagetti, Paula Silvana; Lo, Stephanie W; Hawkins, Paulina A.; Gladstone, Rebecca A.; Regueira, Mariana; et al.; Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina; Microbiology Society; Microbial Genomics; 7; 9; 9-2021; 1-152057-5858CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1099/mgen.0.000636info:eu-repo/semantics/altIdentifier/url/https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000636info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:40:56Zoai:ri.conicet.gov.ar:11336/166317instacron: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 09:40:56.841CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina
title Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina
spellingShingle Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina
Gagetti, Paula Silvana
ANTIMICROBIAL RESISTANCE
ARGENTINA
GLOBAL PNEUMOCOCCAL SEQUENCE CLUSTER
SEROTYPES
STREPTOCOCCUS PNEUMONIAE
WGS (WHOLE-GENOME SEQUENCING)
title_short Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina
title_full Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina
title_fullStr Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina
title_full_unstemmed Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina
title_sort Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina
dc.creator.none.fl_str_mv Gagetti, Paula Silvana
Lo, Stephanie W
Hawkins, Paulina A.
Gladstone, Rebecca A.
Regueira, Mariana
Faccone, Diego Francisco
Klugman, Keith P.
Breiman, Robert F.
McGee, Lesley
Bentley, Stephen D
Corso, Alejandra
author Gagetti, Paula Silvana
author_facet Gagetti, Paula Silvana
Lo, Stephanie W
Hawkins, Paulina A.
Gladstone, Rebecca A.
Regueira, Mariana
Faccone, Diego Francisco
Klugman, Keith P.
Breiman, Robert F.
McGee, Lesley
Bentley, Stephen D
Corso, Alejandra
author_role author
author2 Lo, Stephanie W
Hawkins, Paulina A.
Gladstone, Rebecca A.
Regueira, Mariana
Faccone, Diego Francisco
Klugman, Keith P.
Breiman, Robert F.
McGee, Lesley
Bentley, Stephen D
Corso, Alejandra
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv ANTIMICROBIAL RESISTANCE
ARGENTINA
GLOBAL PNEUMOCOCCAL SEQUENCE CLUSTER
SEROTYPES
STREPTOCOCCUS PNEUMONIAE
WGS (WHOLE-GENOME SEQUENCING)
topic ANTIMICROBIAL RESISTANCE
ARGENTINA
GLOBAL PNEUMOCOCCAL SEQUENCE CLUSTER
SEROTYPES
STREPTOCOCCUS PNEUMONIAE
WGS (WHOLE-GENOME SEQUENCING)
purl_subject.fl_str_mv https://purl.org/becyt/ford/3.3
https://purl.org/becyt/ford/3
dc.description.none.fl_txt_mv Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998–1999 (pre-PCV), before the introduction of PCV13 2010–2011 (PCV7) and after the introduction of PCV13 2012–2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50% of the isolates. Resistance to penicillin was 34.9%, cefotaxime 10.6%, meropenem 4.9%, cotrimoxazole 45%, erythromycin 21.5%, tetracycline 15.4% and chloramphenicol 0.4%. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9%) were non-susceptible to at least one antibiotic and 235(13.7%) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococ-cal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0% in pre-PCV to 3.2% in the PCV13 period. Our analysis showed that 66.1% (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9% (49/413) were multidrug resistant. We found an agreement of 100% when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4% of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.
Fil: Gagetti, Paula Silvana. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; Argentina
Fil: Lo, Stephanie W. Wellcome Sanger Institute; Reino Unido
Fil: Hawkins, Paulina A.. University Of Emory. Rollins School Of Public Health; Estados Unidos. Centers for Disease Control and Prevention; Estados Unidos
Fil: Gladstone, Rebecca A.. Wellcome Sanger Institute; Reino Unido
Fil: Regueira, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Dirección Nacional de Instituto de Investigación.Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"; Argentina
Fil: Faccone, Diego Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; Argentina
Fil: Klugman, Keith P.. University Of Emory. Rollins School Of Public Health; Estados Unidos
Fil: Breiman, Robert F.. University Of Emory. Rollins School Of Public Health; Estados Unidos
Fil: McGee, Lesley. Centers for Disease Control and Prevention; Estados Unidos
Fil: Bentley, Stephen D. Wellcome Sanger Institute; Reino Unido
Fil: Corso, Alejandra. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; Argentina
description Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998–1999 (pre-PCV), before the introduction of PCV13 2010–2011 (PCV7) and after the introduction of PCV13 2012–2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50% of the isolates. Resistance to penicillin was 34.9%, cefotaxime 10.6%, meropenem 4.9%, cotrimoxazole 45%, erythromycin 21.5%, tetracycline 15.4% and chloramphenicol 0.4%. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9%) were non-susceptible to at least one antibiotic and 235(13.7%) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococ-cal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0% in pre-PCV to 3.2% in the PCV13 period. Our analysis showed that 66.1% (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9% (49/413) were multidrug resistant. We found an agreement of 100% when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4% of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.
publishDate 2021
dc.date.none.fl_str_mv 2021-09
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
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info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/166317
Gagetti, Paula Silvana; Lo, Stephanie W; Hawkins, Paulina A.; Gladstone, Rebecca A.; Regueira, Mariana; et al.; Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina; Microbiology Society; Microbial Genomics; 7; 9; 9-2021; 1-15
2057-5858
CONICET Digital
CONICET
url http://hdl.handle.net/11336/166317
identifier_str_mv Gagetti, Paula Silvana; Lo, Stephanie W; Hawkins, Paulina A.; Gladstone, Rebecca A.; Regueira, Mariana; et al.; Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina; Microbiology Society; Microbial Genomics; 7; 9; 9-2021; 1-15
2057-5858
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
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reponame_str CONICET Digital (CONICET)
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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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