Genetic structure of penicillin non-susceptible invasive Streptococcus pneumoniae in Colombia

Background. Infections caused by Streptococcus pneumoniae are a public health problem worldwide, and penicillin-non-susceptible isolates are a priority for the World Health Organization, which requires further research and development of new antibiotics and vaccines. Aim. To describe the global pneumococcal sequence clusters (GPSCs) among penicillin non-susceptible S. pneumoniae isolates obtained from patients with invasive pneumococcal disease in Colombia after the introduction of PCV10 (Synflorix, GlaxoSmithKline) to generate data on the genetic structure of pneumococcal populations with different antimicrobial susceptibilities. Methods. A subset of 313 pneumococcal isolates with values of Minimum Inhibitory Concentration to penicillin of ≥0.125 µg ml −1 , collected through the National Reference Laboratory at the National Health Institute of Colombia, were characterized by whole-genome sequencing to determine the GPSCs, serotypes, sequence types, antimicrobial resistance determinants and pilus islets. Results. Most of the isolates (80%, n =251) were clustered in seven GPSCs: multidrug-resistant GPSC1 (40.6%, n =127) conformed principally to serotype 19A isolates and ST320, GPSC5 (10.5%, n =33) associated with ST338 and isolates of serogroups 23 and 6, GPSC13 (7.3%, n =23) which clustered 68% of 6A isolates, GPSC10 (7.0%, n =22) with 19A and 24F isolates, GPSC6 (5.4%, n =17) related to ST156, GPSC9 (4.8%, n =15) conformed to isolates 15A, 19 F/A and 6A and GPSC47 (4.5%, n =14) with 6C isolates. Only three isolates with PCV10 serotypes were recovered from children younger than 5 years old. Conclusion. The results revealed changes in the population structure expected after PCV10 introduction, with GPSC1 being the most important clone due to its association with multidrug resistance. Genome sequencing of clinical multidrug-resistant isolates contributes to elucidating the antibiotic resistance mechanism and understanding the global pneumococcal population structure.