Genomic characterization of Streptococcus pneumoniae isolates obtained from carriage and disease among paediatric patients in Addis Ababa, Ethiopia

<b>Background and aims.</b> Despite the introduction of pneumococcal conjugate vaccines (PCVs), <i>Streptococcus pneumoniae</i> still remains an important cause of morbidity and mortality, especially among children under 5 years in sub-Saharan Africa. We sought to determine the distribution of serotypes, lineages and antimicrobial resistance of <i>S. pneumoniae</i> from carriage and disease among children presenting to health facilities, 5-6 years after the introduction of PCV10 in Ethiopia.<b>Methods.</b> Whole-genome sequencing (WGS) was performed on 103 <i>S. pneumoniae</i> (86 from nasopharyngeal swabs, 4 from blood and 13 from middle ear discharge) isolated from children aged <15 years at 3 healthcare facilities in Addis Ababa, Ethiopia, from September 2016 to August 2017. Using the WGS data, serotypes were predicted, isolates were assigned to clonal complexes, global pneumococcal sequence clusters (GPSCs) were inferred and screening for alleles and mutations that confer resistance to antibiotics was performed using multiple bioinformatic pipelines.<b>Results.</b> The 103 <i>S</i>. <i>pneumoniae</i> isolates were assigned to 38 serotypes (including nontypeable) and 46 different GPSCs. The most common serotype was serotype 19A. Common GPSCs were GPSC1 [14.6% (15/103), sequence type (ST) 320, serotype 19A], GPSC268 [8.7% (9/103), ST 6882 and novel STs; serotypes 16F, 11A and 35A] and GPSC10 [8.7% (9/103), STs 2013, 230 and 8804; serotype 19A]. The four invasive isolates were serotype 19A (<i>n</i>=2) and serotype 33C (<i>n</i>=2). Resistance to penicillin (>0.06 µg ml^-1, CLSI meningitis cutoff) was predicted in 57% (59/103) of the isolates, and 43% (25/58) penicillin-binding protein allele combinations were predicted to be associated with penicillin resistance. Resistance mutations in <i>folA</i> (<i>I100L</i>) and/or <i>folP</i> (indel between fifty-sixth and sixty-seventh aa) were identified among 66% (68/103) of the isolates, whilst tetracycline (<i>tetM</i>) and macrolide (<i>ermB</i> and <i>mefA</i>) resistance genes were found in 46.6% (48/103), 20.4% (21/103) and 20.4% (21/103) of the isolates, respectively. Multidrug resistance (MDR) (≥3 antibiotic classes) was observed in 31.1% (32/103) of the isolates. GPSC1 and GPSC10 accounted for 46.8% (15/32) and 18.7% (6/32) of the overall MDR.<b>Conclusion.</b> Five to 6 years after the introduction of PCV10 in Ethiopia, the <i>S. pneumoniae</i> obtained from carriage and disease among paediatric patients showed diverse serotype and pneumococcal lineages. The most common serotype identified was 19A, expressed by the MDR lineages GPSC1 and GPSC10, which is not covered by PCV10 but is included in PCV13. Continued assessment of the impact of PCV on the population structure of <i>S. pneumoniae</i> in Ethiopia is warranted during and after PCV13 introduction.