1887

Abstract

Invasive disease caused by (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 defining pneumococcal lineages using Global Pneumococcal 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.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2021-09-29
2024-03-28
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References

  1. Constenla D, Gomez E, Pio de la Hoz F, O’Loughlin R, Sinha A. The Burden of Pneumococcal Disease and Cost-Effectiveness of a Pneumococcal Vaccine in Latin America and the Caribbean. A Review of the Evidence and a Preliminary Economic Analysis Washington, DC: Sabin Vaccine Institute; 2007
    [Google Scholar]
  2. Geno KA, Gilbert GL, Song JY, Skovsted IC, Klugman KP et al. Pneumococcal capsules and their types: past, present and future. Clin Microbiol Rev 2015; 28:871–899 [PubMed]
    [Google Scholar]
  3. Wahl B, O’Brien KL, Greenbaum A, Majumder A, Liu L et al. Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000-15. Lancet Glob Health 2018; 6:e744–e757
    [Google Scholar]
  4. O’Brien KL, Wolfson LJ, Watt JP, Henkle E, Deloria-Knoll M et al. Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates. Lancet 2019; 374:893–902
    [Google Scholar]
  5. WHO WHO vaccine-preventable diseases: monitoring system. 2018 global summary Coverage time series for Argentina; 2018 http://apps.who.int/immunization_monitoring/globalsummary/coverages?c=ARG
  6. Clinical Laboratory Standards Institute (CLSI) M100S 29th Edition: Performance Standards for Antimicrobial Susceptibility Testing Wayne, PA, USA: Clinical Laboratory Standards Institute; 2019
    [Google Scholar]
  7. Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME et al. Multidrugresistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 2012; 18:268–281 [PubMed]
    [Google Scholar]
  8. Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ et al. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine 2019; 43:338–346 [PubMed]
    [Google Scholar]
  9. Epping L, van Tonder AJ, Gladstone RA. The Global Pneumococcal Sequencing Consortium Bentley SD et al. SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data. Microb Genom 2018; 4:
    [Google Scholar]
  10. Page AJ, Taylor B, Keane JA. Multilocus sequence typing by blast from de novo assemblies against PubMLST. J Open Source Softw 2016; 8:118
    [Google Scholar]
  11. Li Y, Metcalf BJ, Chochua S, Li Z, Gertz RE et al. Penicillin-binding protein transpeptidase signatures for tracking and predicting β-lactam resistance levels in Streptococcus pneumoniae. mBio 2016; 7:e00756
    [Google Scholar]
  12. Li Y, Metcalf BJ, Chochua S, Li Z, Gertz RE et al. Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences. BMC Genomics 2017; 18:621
    [Google Scholar]
  13. Metcalf BJ, Chochua S, Gertz RE, Li Z, Walker H et al. Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States. Clin Microbiol Infect 2016; 22:1002e1-1002.e8 [PubMed]
    [Google Scholar]
  14. Metcalf B, Gertz RE, Gladstone RA, Walker H, Sherwood LK et al. Strain features and distributions in pneumococci from children with invasive disease before and after 13-valent conjugate vaccine implementation in the USA. Clin Microbiol Infect 2016; 22:60e9–29 [PubMed]
    [Google Scholar]
  15. Hunt M, Mather AE, Sanchez-Busó L, Page AJ, Parkhill J et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom 2017; 3:
    [Google Scholar]
  16. Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 2004; 186:1518–1530
    [Google Scholar]
  17. Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW et al. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Res 2019; 29:304–316
    [Google Scholar]
  18. Hanage WP, Bishop CJ, Lee GM, Lipsitch M, Stevenson A et al. Clonal replacement among 19A Streptococcus pneumoniae in Massachusetts, prior to 13 valent conjugate vaccination. Vaccine 2011; 29:8877–8881
    [Google Scholar]
  19. Bricio-Moreno L, Ebruke C, Chaguza C, Cornick J, Kwambana-Adams B et al. Comparative genomic analysis and in vivo modeling of Streptococcus pneumoniae ST3081 and ST618 isolates reveal key genetic and phenotypic differences contributing to clonal replacement of serotype 1 in The Gambia. J Infect Dis 2017; 216:1318–1327 [PubMed]
    [Google Scholar]
  20. Corso A, Faccone D, Galia C, Gagetti P, Rodriguez M et al. Prevalence of mef and ermB genes in invasive pediatric erythromycin-resistant Streptococcus pneumoniae isolates from Argentina. Rev Argent Microbiol 2009; 41:29–33 [PubMed]
    [Google Scholar]
  21. Reijtman V, Gagetti P, Faccone D, Fossati S, Sommerfleck P et al. Macrolide resistance in Streptococcus pneumoniae isolated from Argentinian pediatric patients suffering from acute otitis media. Rev Argent Microbiol 2013; 45:262–266 [PubMed]
    [Google Scholar]
  22. Gagetti P, Faccone D, Reijtman V, Fossati S, Rodriguez M et al. Characterization of Streptococcus pneumoniae invasive serotype 19A isolates from Argentina (1993–2014. Vaccine 2017; 16:4548–4553
    [Google Scholar]
  23. Lo SW, Gladstone RA, van Tonder AJ, Lees JA, du Plessis M et al. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study. Lancet Infect Dis 2019; 19:759–769
    [Google Scholar]
  24. Camilli R, D’Ambrosio F, Del Grosso M, Pimentel de Araujo F, Caporali MG et al. Impact of pneumococcal conjugate vaccine (PCV7 and PCV13) on pneumococcal invasive diseases in Italian children and insight into evolution of pneumococcal population structure. Vaccine 2017; 35:4587–4593
    [Google Scholar]
  25. Andrews NJ, Waight PA, Burbidge P, Pearce E, Roalfe L et al. Serotype-specific effectiveness and correlates of protection for the 13-valent pneumococcal conjugate vaccine: a postlicensure indirect cohort study. Lancet Infect Dis 2014; 14:839–846 [PubMed]
    [Google Scholar]
  26. Prymula R, Peeters P, Chrobok V, Kriz P, Novakova E et al. Pneumococcal capsular polysaccharides conjugated to protein D for prevention of acute otitis media caused by both Streptococcus pneumoniae and non-typable Haemophilus influenzae: a randomised double-blind efficacy study. Lancet 2006; 367:740–748 [PubMed]
    [Google Scholar]
  27. Azarian T, Mitchell PK, Georgieva M, Thompson CM, Ghouila A et al. Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci. PLoS Pathog 2018; 14:e1007438
    [Google Scholar]
  28. Beall B, Chochua S, Gertz RE, Li Y, Li Z et al. A population-based descriptive atlas of invasive pneumococcal strains recovered within the U.S. during 2015-2016. Front Microbiol 2018; 19:2670
    [Google Scholar]
  29. Mothibeli KM, Du Plessis M, Von Gottberg A, De Gouveia L, Adrian P et al. An unusual pneumococcal sequence type is the predominant cause of serotype 3 invasive disease in South Africa. J Clin Microbiol 2010; 48:184–191 [View Article]
    [Google Scholar]
  30. Gladstone RA, Lo SW, Goater R, Yeats C, Taylor B et al. Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates. Microb Genom 2020 [View Article]
    [Google Scholar]
  31. Gagetti P, Menocal A, Faccone D, Fossati S, Napoli D et al. Emergence of multidrug resistant serotype 24 among children under 2 years old with invasive pneumococcal disease after the introduction of PCV13 in Argentina. (p1429) Idweek 2018, San Francisco, CA, USA, 3-7 October 2018; 2018
  32. Kavalari ID, Fuursted K, Krogfelt KA, Slotved HC. Molecular characterization and epidemiology of Streptococcus pneumoniae serotype 24F in Denmark. Sci Rep 2019; 9:5481 [View Article]
    [Google Scholar]
  33. Ouldali N, Levy C, Varon E, Bonacorsi S, Bechet S et al. Incidence of paediatric pneumococcal meningitis and emergence of new serotypes: a time-series analysis of a 16-year French national survey. Lancet Infect Dis 2018; 18:983–991 [View Article] [PubMed]
    [Google Scholar]
  34. Ubukata K, Takata M, Morozumi M, Chiba N, Wajima T et al. Effects of pneumococcal conjugate vaccine on genotypic penicillin resistance and serotype changes, Japan, 2010-2017. Emerg Infect Dis 2018; 24:2010–2020 [View Article]
    [Google Scholar]
  35. Kawabata T, Tenokuchi Y, Yamakuchi H, Sameshima H, Katayama H et al. Concurrent bacteremia due to non-vaccine serotype 24F pneumococcus in twins. Pediatr Infect Dis J 2020; 39:85–87 [View Article]
    [Google Scholar]
  36. Latasa Zamalloa P, Sanz Moreno JC, Ordobás Gavín M, Barranco Ordoñez MD, Insúa Marisquerena E et al. Trends of invasive pneumococcal disease and its serotypes in the Autonomous Community of Madrid. Enferm Infecc Microbiol Clin 2018; 36:612–620 [View Article]
    [Google Scholar]
  37. Esteva C, Codina G, de Sevilla MF, Diaz A, Ciruela P et al. The impact of serotype-specific distribution of Streptococcus pneumoniae in the clonal complex 230 after the subsidised PCV13 vaccine in a national immunization programme in Catalonia, Spain. (P0355) 29th ECCMID, the European Congress of Clinical Microbiology and Infectious Diseases, Amsterdam, Netherlands, 13–16 April 2019; 2019
  38. Kandasamy R, Voysey M, Collins S, Berbers G, Robinson H et al. Persistent circulation of vaccine serotypes and serotype replacement after 5 years of infant immunization with 13-valent Pneumococcal Conjugate Vaccine in the United Kingdom. J Infect Dis 2020; 221:1361–1370 [PubMed]
    [Google Scholar]
  39. Weinberger R, von Kries R, van der Linden M, Rieck T, Siedler A et al. Invasive pneumococcal disease in children under 16 years of age: Incomplete rebound in incidence after the maximum effect of pcv13 in 2012/13 in Germany. Vaccine 2018; 36:572–577 [View Article]
    [Google Scholar]
  40. Silva-Costa C, Brito MJ, Aguiar SI, Lopes JP, Ramirez M et al. Dominance of vaccine serotypes in pediatric invasive pneumococcal infections in Portugal (2012-2015. Sci Rep 2019; 9:6 [View Article]
    [Google Scholar]
  41. Balsells E, Dagan R, Yildirim I, Gounder PP, Steens A et al. The relative invasive disease potential of Streptococcus pneumoniae among children after PCV introduction: A systematic review and meta-analysis. J Infect 2018; 77:368–378 [View Article]
    [Google Scholar]
  42. Gradoux E, Asner S, Perez M-H, Crisinel PA. An invasive pneumococcal infection due to Streptococcus pneumoniae serotype 24. Pediatr Infect Dis J 2015; 34:1142 [View Article]
    [Google Scholar]
  43. del Amo E, Esteva C, Hernandez-Bou S, Galles C, Navarro M et al. Serotypes and clonal diversity of Streptococcus pneumoniae causing invasive disease in the era of PCV13 in Catalonia, Spain. PLoS ONE 2016; 11:e0151125 [View Article]
    [Google Scholar]
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