Krzysztof Trzciński, Netherlands
Wilhelmina's Children Hospital, University Medical Centre Department of Pediatric Immunology and Infectious DiseasesAuthor Of 3 Presentations
ANTIBIOTIC RESISTANCE PREDICTION WITH WHOLE GENOME SEQUENCING OF STREPTOCOCCUS PNEUMONIAE CARRIAGE ISOLATES COLLECTED BETWEEN 2009-2018 IN THE NETHERLANDS (ID 566)
Abstract
Background
We investigated the use of whole genome sequencing (WGS) to predict antibiotic resistance of circulating S. pneumoniae (pneumococcus) carriage isolates collected among PCV7 and PCV10-vaccinated toddlers in the Netherlands.
Methods
All Pneumococcal strains (n=737) isolated between 2009-2018 from 24-months old carriers were subjected to WGS. Genome assembly of short reads into contigs was performed using SPAdes, which were subsequently assigned a taxonomic origin with Kraken2. All DNA sequences identified as pneumococcus were used for resistance gene identification with RGI. Predicted resistance genes with ≥50 bitscore and ≥80% sequence identity were further analyzed and compared against phenotypical antibiotic resistance data. Susceptibility testing was performed according to EUCAST guidelines.
Results
Based on WGS data 9.8% (72/737) of pneumococcal isolates were predicted to harbor resistance genes. Genetic markers of antibiotic resistance predicted by WGS were in concordance with resistotypes determined using the EUCAST-recommended method. Lack of susceptibility to penicillins was primarily observed for serotypes 19A (13% of 128) and 23B (19% of 63), respectively.
Conclusions
We have observed good congruence between antibiotic resistance prediction with WGS and standard phenotypical antibiotic sensitivity testing. Antibiotic resistance among pneumococcal carriage isolates in the Netherlands is relatively rare and is characterized by circulation of resistant serotype 19A and 23B strains.
DYNAMICS OF PNEUMOCOCCAL CARRIAGE ASSOCIATED WITH INFLUENZA-LIKE ILLNESS IN COMMUNITY-DWELLING OLDER ADULTS (ID 975)
Abstract
Background
In older adults, pneumococcal disease is strongly associated with viral respiratory infections, though the impact of viruses on pneumococcal carriage remains poorly understood. Here, we have investigated effects of influenza-like illness (ILI) on pneumococcal carriage in older adults.
Methods
Pneumococcal presence was determined in saliva samples that were collected in the 2014/2015 influenza season from individuals aged ≥60 years, including 232 individuals with ILI sampled trice and 194 controls sampled twice. Pneumococcal carriage was detected with quantitative-PCRs targeting piaB and lytA genes in minimally-processed saliva and culture-enriched saliva. Bacterial and pneumococcal abundances were determined in minimally-processed saliva. Respiratory viruses were detected in nasopharyngeal and oropharyngeal samples using qPCR.
Results
In general, pneumococcal carriage was significantly associated with exposure to young children and rhinovirus infection. The prevalence of pneumococcal carriage was highest at ILI-onset (18%) and lowest among controls (11-13%). Compared with controls, both absolute and relative pneumococcal abundances were significantly elevated at ILI-onset and remained elevated 7-9 weeks later. Pneumococcal abundances were highest in individuals with carriage acquisition between ILI-onset and 2-3 weeks later.
Conclusions
Our findings support the notion that in older adults acute respiratory infections favor pneumococcal colonization of the upper respiratory tract and this impact persists beyond recovery from ILI.
IMPACT OF CULTURE-ENRICHMENT ON RANKED PNEUMOCOCCAL SEROTYPE CO-PRESENCE DETERMINED USING MOLECULAR DIAGNOSTIC METHOD OF QUANTITATIVE PCR (ID 875)
Abstract
Background
We investigated impact of culture-enrichment on the rank of serotypes when detected quantitatively in nasopharyngeal samples from toddlers co-carrying multiple pneumococcal strains.
Methods
Pneumococcal serotypes were detected in nasopharyngeal swabs (collected in a cross-sectional study from children aged <5 years) using conventional culture method followed by testing in serotype-specific qPCRs the DNA extracted from all bacterial growth harvested from culture-plates. Next, we quantified with qPCR serotypes in uncultured samples and compared serotype ranks before and after culture-enrichment.
Results
Co-presence of multiple serotypes has been detected in 37 (5.6%) of 658 nasopharyngeal samples. The number of serotype carriage events detected by any method in these 37 samples was 83 (2-5 per sample) while the number of strains cultured was 42 (1-2 per sample). For the majority of samples (n=27 or 73%) the serotype ranks in uncultured and culture-enriched samples matched. A shift in serotype rank was observed in 11% of the samples (4 of 37) whereas in another 16% (6 of 37) the discordance was due to fewer serotypes detected in uncultured samples.
Conclusions
While increasing sensitivity of carriage detection, culture-enrichment has limited impact on the rank of serotypes present in nasopharyngeal swabs and can therefore be used to provide insight into co-carriage dynamics.