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Key features of invasive pneumococcal isolates recovered in Lima, Peru determined through whole genome sequencing

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dc.contributor.author Hawkins, Paulina
dc.contributor.author Mercado, Erik
dc.contributor.author Chochua, Sopio
dc.contributor.author Castillo, Maria E.
dc.contributor.author Reyes, Isabel
dc.contributor.author Chaparro, Eduardo
dc.contributor.author Gladstone, Rebecca
dc.contributor.author Bentley, Stephen D.
dc.contributor.author Breiman, Robert F.
dc.contributor.author Metcalf, Benjamin J.
dc.contributor.author Beall, Bernard
dc.contributor.author Ochoa Woodell, Theresa Jean
dc.contributor.author McGee, Lesley
dc.date.accessioned 2019-01-25T15:28:04Z
dc.date.available 2019-01-25T15:28:04Z
dc.date.issued 2017
dc.identifier.uri https://hdl.handle.net/20.500.12866/4684
dc.description.abstract Before PCV7 introduction, invasive pneumococcal disease (IPD) was responsible for approximately 12,000-18,000 deaths annually among children <5years in Latin America. In Peru, PCV7 was introduced in 2009. We used whole genome sequencing to deduce key features of invasive strains collected in Lima, Peru from 2006 to 2011. We sequenced 212 IPD isolates from 16 hospitals in Lima pre (2006-2009; n=133) and post (2010-2011; n=79) PCV7 introduction; 130 (61.3%) isolates were from children≤5years old. CDC's Streptococcus lab bioinformatics pipeline revealed serotypes, sequence types (STs), pilus genes, PBP types and other resistance determinants. During the pre-PCV7 period, serotype 14 was the most common serotype (24.8%), followed by 6B (20.3%), 19F (10.5%), and 23F (6.8%). Post-PCV7, the proportion of PCV7 serotype 6B decreased significantly (to 6.3%), while 19F (16.3%), 14 (15.0%), 23F (7.5%), and 19A (7.5%) were the most common serotypes; only serotypes 3 and 10A increased significantly. Overall, 82% (n=173) of all isolates carried at least one resistance determinant, including 72 (34%) isolates that carried resistance determinants against 3 or more antimicrobial classes; of these 72 isolates, 56 (78%) belonged to a PCV7 serotype. Eighty-two STs were identified, with 53 of them organized in 14 clonal complexes. ST frequencies were distributed differently pre and post-PCV7 introduction, with only 18 of the 57 STs identified in years 2006-2009 isolates also observed in years 2010-2011 isolates. The apparent expansion of a 19F/ST1421 lineage with predicted β-lactam resistance (PBP type 13:16:20) and carrying resistance determinants against four additional antimicrobial classes was observed. en_US
dc.language.iso eng
dc.publisher Elsevier
dc.relation.ispartofseries International Journal of Medical Microbiology
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject Pneumococcal Vaccines/classification/genetics en_US
dc.subject Whole Genome Sequencing en_US
dc.subject Adult en_US
dc.subject Anti-Infective Agents/pharmacology en_US
dc.subject Antimicrobial resistance en_US
dc.subject Child, Preschool en_US
dc.subject Drug Resistance, Bacterial en_US
dc.subject Genotype en_US
dc.subject Humans en_US
dc.subject Infant en_US
dc.subject Peru en_US
dc.subject Pneumococcal Infections/microbiology/pathology/prevention & control en_US
dc.subject S. pneumoniae en_US
dc.subject Serogroup en_US
dc.subject Streptococcus pneumoniae/classification/drug effects/genetics/isolation & purification en_US
dc.subject Vaccines, Conjugate en_US
dc.subject Whole genome sequencing en_US
dc.title Key features of invasive pneumococcal isolates recovered in Lima, Peru determined through whole genome sequencing en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1016/j.ijmm.2017.07.008
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#1.06.01
dc.relation.issn 1618-0607


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