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PNEUMOCOCCAL LINEAGES ASSOCIATED WITH ANTIBIOTIC RESISTANCE IN CHILDHOOD INVASIVE DISEASE IN COLOMBIA USING WHOLE-GENOME SEQUENCING (WGS).
Abstract
Background
Pneumococcal conjugate vaccines (PCVs) have reduced the proportion of vaccine-types isolates and resistance to antibiotics. In 2011, Colombia introduced PCV10 in routine childhood immunization program.
Aims
To determine pneumococcal lineages and antimicrobial resistance (AMR) genes in post-vaccine childhood using WGS.
Methods
Hundred and ten Streptococcus pneumoniae isolates recovered from children under 5 years old by passive laboratory surveillance during 2015-2018 were analyzed. Isolates were serotyped by Quellung and antimicrobial susceptibility was determined by broth micro-dilution. All isolates had resistance to one or more antibiotics. WGS was performed by Illumina in Sanger Institute. Global Pneumococcal Sequencing Cluster (GPSC) and penicillin-binding protein (PBPs) variants were assigned using Pathogenwatch. AMR genes were determined using GHRU-AMR pipelines protocols. Data was visualized on Microreact.
Results
Isolates were collected from patients with pneumonia (36.4%), sepsis (18.2%) and meningitis (10.9%). Eighteen lineages were identified. GPSC1 was the most abundant (n=66; 60%), composed by multidrug-resistant serotype 19A-ST320 (n=57), 19A-ST1451 (n=5) and 19A-ST13455 (n=3), which predominantly contained PBP1a, PBP2b, and PBP2x profile 13-11-16 with penicillin MIC >4ug/ml and AMR genes ermB-mefA-msr, tetM, and folP were found. GPSC10 included 19A-ST276 (n=10) and 24-ST230 (n=2), 75% with PBP profile 17-39-18 and penicillin MIC of 2-4ug/ml and carried ermB and tetM genes. GPSC5 and GPSC48 contained non-PVC10 isolates exhibited different PBP profiles and two had mefA-msrD and tetM genes.
Conclusions
WGS is a tool useful for surveillance and understanding the genetic composition of GPSCs associated with resistance that could be used to predict the impact of the vaccine and to design strategies for pneumococcal disease control.