Streptococcus pneumoniae Serotype 3 in Mexico (1994 to 2017): Decrease of the Unusual Clonal Complex 4909 Lineage following PCV13 Introduction

J Clin Microbiol. 2019 Jan 2;57(1):e01354-18. doi: 10.1128/JCM.01354-18. Print 2019 Jan.


Streptococcus pneumoniae expressing serotype 3 has a high virulence and a high case fatality ratio. Most studies of serotype 3 pneumococci have focused on a single lineage, the widespread sequence type 180 (ST180). To evaluate the serotype 3 lineages causing infections in Mexico, we characterized 196 isolates recovered from 1994 to 2017. The isolates were mostly susceptible to all antimicrobials tested. A single meningitis isolate was resistant to penicillin, and the resistance to erythromycin was 5.2%. The isolates represented the widely disseminated clonal complex 180 (CC180; n = 140), the unusual CC4909 (n = 42), CC260 (n = 11), and a few singletons (n = 3). CC260 was less frequent among pneumococcal invasive disease isolates than CC180 and CC4909 (P = 0.015). There was a decrease of CC4909 (P < 0.001) following PCV13 introduction (2012 to 2017). The CC4909 isolates were represented mostly by ST1119 (n = 40), seemingly having a restricted geographic origin, with isolates in the PubMLST database having been recovered only in Mexico, the United States, and Germany. A genomic analysis of publicly available genomes showed that ST1119 isolates have less than 32% similarity with ST180 isolates, indicating that these lineages are more separated than revealed by traditional multilocus sequence typing. Considering the suggestions of a lower efficacy of the 13-valent pneumococcal conjugate vaccine against serotype 3, the different dynamics of the two major serotype 3 lineages in Mexico following the introduction of PCV13 should be closely monitored.

Keywords: Streptococcus pneumoniae; antibiotic resistance; genomics; infectious clones; molecular subtyping; vaccines.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Anti-Bacterial Agents / pharmacology
  • Child
  • Child, Preschool
  • Drug Resistance, Bacterial
  • Epidemiological Monitoring
  • Female
  • Genome, Bacterial / genetics
  • Humans
  • Infant
  • Infant, Newborn
  • Male
  • Mexico / epidemiology
  • Microbial Sensitivity Tests
  • Middle Aged
  • Multilocus Sequence Typing
  • Pneumococcal Infections / epidemiology*
  • Pneumococcal Infections / microbiology*
  • Pneumococcal Infections / prevention & control
  • Pneumococcal Vaccines / administration & dosage*
  • Serogroup
  • Serotyping
  • Streptococcus pneumoniae / classification
  • Streptococcus pneumoniae / drug effects
  • Streptococcus pneumoniae / genetics*
  • Young Adult


  • 13-valent pneumococcal vaccine
  • Anti-Bacterial Agents
  • Pneumococcal Vaccines