Serotypes and Clonal Composition of Streptococcus pneumoniae Isolates Causing IPD in Children and Adults in Catalonia before 2013 to 2015 and after 2017 to 2019 Systematic Introduction of PCV13

Redin, Alba; Ciruela, Pilar; Sevilla, Mariona Fernández de; Gómez, Frederic; González‐Peris, Sebastià; Benítez, Miguel Ángel; Trujillo, Glòria; Díaz, Álvaro; Jou, Erin; Izquierdo, Conchita; Pérez-Moreno, Mar Olga; Llop, F.A. Moraga; Olsina, Montserrat; Viñado, Belén; Sanfeliu, Esther; García, A.; Lauro, S Gonzalez-di; García‐García, Juan José; Domı́nguez, Àngela; Sá-Leão, Raquel; Muñoz‐Almagro, Carmen

doi:10.1128/spectrum.01150-21

Cited by 11 publications

(5 citation statements)

References 63 publications

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“…IPD occurred in children with a median age of 2 years, and about 50% of the episodes occurred in the male population. Serotype 24F was the main capsular type detected (14.3%), followed by 14 (8.4%) and 15B/C (6.7%), which is in line with the epidemiology of pneumococcus reported in the region of Catalonia in children under 5 years of age ( 9 ).…”

Section: Discussionsupporting

confidence: 85%

“…However, continuous surveillance of pneumococcal serotypes causing IPD in multiple countries has demonstrated a phenomenon of serotype replacement due to the increase of IPD by non-vaccine serotypes. These pneumococcal strains can be virulent and multi-drug resistant ( 7 – 9 ). Of note, differences in serotype distribution have also been described according to geographical area ( 10 , 11 ).…”

Section: Introductionmentioning

confidence: 99%

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Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae

Henares,

Lo,

Perez-Argüello

et al. 2023

J Clin Microbiol

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Whole genome sequencing (WGS)-based approaches for pneumococcal capsular typing have become an alternative to serological methods. In silico serotyping from WGS has not yet been applied to long-read sequences produced by third-generation technologies. The objective of the study was to determine the capsular types of pneumococci causing invasive disease in Catalonia (Spain) using serological typing and WGS and to compare the performance of different bioinformatics pipelines using short- and long-read data from WGS. All invasive pneumococcal pediatric isolates collected in Hospital Sant Joan de Déu (Barcelona) from 2013 to 2019 were included. Isolates were assigned a capsular type by serological testing based on anticapsular antisera and by different WGS-based pipelines: Illumina sequencing followed by serotyping with PneumoCaT, SeroBA, and Pathogenwatch vs MinION-ONT sequencing coupled with serotyping by Pathogenwatch from pneumococcal assembled genomes. A total of 119 out of 121 pneumococcal isolates were available for sequencing. Twenty-nine different serotypes were identified by serological typing, with 24F ( n = 17; 14.3%), 14 ( n = 10; 8.4%), and 15B/C ( n = 8; 6.7%) being the most common serotypes. WGS-based pipelines showed initial concordance with serological typing (>91% of accuracy). The main discrepant results were found at the serotype level within a serogroup: 6A/B, 6C/D, 9A/V, 11A/D, and 18B/C. Only one discrepancy at the serogroup level was observed: serotype 29 by serological testing and serotype 35B/D by all WGS-based pipelines. Thus, bioinformatics WGS-based pipelines, including those using third-generation sequencing, are useful for pneumococcal capsular assignment. Possible discrepancies between serological typing and WGS-based approaches should be considered in pneumococcal capsular-type surveillance studies.

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Section: Discussionsupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae

Henares,

Lo,

Perez-Argüello

et al. 2023

J Clin Microbiol

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“…Similarly, a single serotype stood up among the others after the introduction of each conjugate vaccine: serotype 19A after PCV7 and serotype 8 after PCV13. In other places where PCV13 was introduced, similar decreases in PCV13 serotypes and increases in NVTs have also been documented (24,(29)(30)(31). In most of these studies, serotypes 8, 15A, 22F, and 24F were the most frequent post-PCV13 serotypes causing IPD, while the importance of serotype 3 varied.…”

Section: Discussionmentioning

confidence: 61%

Impact of the progressive uptake of pneumococcal conjugate vaccines on the epidemiology and antimicrobial resistance of invasive pneumococcal disease in Gipuzkoa, northern Spain, 1998–2022

Manzanal,

Vicente,

Alonso

et al. 2023

Front. Public Health

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ObjectivesTo analyze the impact of pneumococcal conjugate vaccines (PCVs) on the incidence of invasive pneumococcal diseases (IPDs) and pneumococcal antibiotic resistance in Gipuzkoa, northern Spain for a 25 years period.MethodsAll cases of IPD confirmed by culture between 1998 and 2022 in a population of around 427,416 people were included. Pneumococci were serotyped and antimicrobial susceptibility was assessed by the EUCAST guidelines.ResultsOverall, 1,516 S. pneumoniae isolates were collected. Annual IPD incidence rates (per 100,000 people) declined from 19.9 in 1998–2001 to 11.5 in 2017–19 (42.2% reduction), especially in vaccinated children (from 46.7 to 24.9) and non-vaccinated older adult individuals (from 48.0 to 23.6). After PCV13 introduction, the decrease in the incidence of infections caused by PCV13 serotypes was balanced by the increase in the incidence of non-PCV13 serotypes. In the pandemic year of 2020, IPD incidence was the lowest: 2.81. The annual incidence rates of penicillin-resistant isolates also decreased, from 4.91 in 1998–2001 to 1.49 in 2017–19 and 0.70 in 2020. Since 2017, serotypes 14, 19A, and 11A have been the most common penicillin-resistant types. The incidence of erythromycin-resistant strains declined, from 3.65 to 1.73 and 0.70 in the same years.ConclusionPCV use was associated with declines in the incidence of IPD and the spread of non-vaccine serotypes, that balanced the beneficial effect off PCV13, some of them showing high rates of antibiotic resistance.

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“…Analysis of the impact of PCVs on the incidence of IPD in Spain has been difficult because variations in vaccination policies, evaluation periods and surveillance systems could account for differences in reported data between geographical areas [ 7 , 8 ]. Andalusia is the most populous region of Spain.…”

Section: Introductionmentioning

confidence: 99%

Molecular Epidemiology of Paediatric Invasive Pneumococcal Disease in Andalusia, Spain

et al. 2022

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This study aimed to assess the impact of the introduction of PCV13 on the molecular epidemiology of invasive pneumococcal disease (IPD) in children from Andalusia. A population-based prospective surveillance study was conducted on IPD in children aged <14 years from Andalusia (2018-2020). Pneumococcal invasive isolates collected between 2006-2009 in the two largest tertiary hospitals in Andalusia were used as pre-PCV13 controls for comparison of serotype/genotype distribution. Overall IPD incidence rate (IR) was 3.55 cases per 100.000 in 2018; increased non significantly to 4.20 cases per 100.000 in 2019, and declined in 2020 to 1.69 cases per 100.000 ( incidence rate ratio 2020 vs. 2019: 0.40, 95% CI 0.20-0.89, p=0.01). Proportion of IPD cases due to PCV13 serotypes in 2018-2020 was 28% (P=0.0001 for comparison with 2006-2009) . Serotypes 24F (15%) and 11A (8.3%) were the most frequently identified non-PCV13 serotypes (NVT) in 2018-2020. Penicillin-and/or ampicillin-resistant clones mostly belonged to CC156 (serotype 14-ST156 and ST2944 and serotype 11A-ST6521). The proportion of IPD cases caused by PCV13 serotypes declined significantly after the initiation of the PCV13 vaccination program in 2016. Certain NVT, such as serotypes 24F and 11A, warrant future monitoring in IPD owing to invasive potential and/or antibiotic resistance rates.

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Serotypes and Clonal Composition of Streptococcus pneumoniae Isolates Causing IPD in Children and Adults in Catalonia before 2013 to 2015 and after 2017 to 2019 Systematic Introduction of PCV13

Cited by 11 publications

References 63 publications

Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae

Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae

Impact of the progressive uptake of pneumococcal conjugate vaccines on the epidemiology and antimicrobial resistance of invasive pneumococcal disease in Gipuzkoa, northern Spain, 1998–2022

Molecular Epidemiology of Paediatric Invasive Pneumococcal Disease in Andalusia, Spain

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