Background

Understanding the role of viral co-infection in defining the outcome of paediatric pneumonia will provide novel treatment and prevention strategies, improving patient’s outcome. The objective of this study was to determine the prevalence of viral infection in children with pneumonia

Methods

128 Nasopharyngeal swabs of children with clinically proven pneumonia collected from a tertiary care hospital in a duration of 1 year were tested. Multiplex real-time PCR assay- FTIyo Respiratory pathogens 33 test kit (Fast-Track Diagnosis, Luxembourg) was used for analysis.

Results

105/128(82%) of children included in the study tested positive for at least one pathogen: bacterial or viral. Viral infection was detected in 55/128(42%) of samples. Pure viral infection was present in 12%(7/55) of cases. Single viral co-infection accounted for 67%(37/55) of cases. Co-infection with duel virus was detected in 10 patients(18%) and triple infection in 1.8% (1/55).

The most common viruses identified were Adenovirus(47%), Bocavirus(32%), Rhinovirus (21%), Human Parainfluenza Viruses HPIV3(12%), HPIV4(3.63%) and Respiratory syncytial viruses A and B(3.63%) respectively

Conclusions

The study highlights the importance of evaluating viral co-infection in the context of pneumonia in children. It is an ideal approach for better understanding of the carriage with multiple viral agents and its relationship with the bacterial pathogen.

Background

Pneumococcal Conjugate Vaccine (PCV) use has resulted in decrease of vaccine serotypes (VTs) and emergence of non-vaccine types (NVTs). We applied whole genome sequence (WGS) to predict serotype, sequence type (ST) and antibiotic resistance of NVT invasive pneumococcal isolates collected during the pre-vaccine era from Indian population.

Methods

96 NVT invasive isolates (2009-2017) collected across the country were sequenced on Illumina platform. Bioinformatic pipelines SeroBA and CDC pneumococcal pipeline for AMR calls were used for data analysis.

Results

Serotypes 15B (n=11), 24 (n=9) were dominant NVT types followed by 8 (n=8) and 34,10A,11A,16F (n=5). MLST resolved strains into 67 known STs. ST13727 (n=6) and ST2234 (n=5) were most common. Strains clustered in 45 clonal complexes and 16 singletons. The dominant clonal complex CC230 (n=12) was from serotypes 15B,15C,24,10A and 11A. 78(81%) of isolates were multidrug-resistant. Resistance genes for tetracycline (n=44), cotrimoxazole (n=41), erythromycin (n=34), penicillin (n=13) and chloramphenicol (n=2) were identified.

Conclusions

With the introduction of PCV in 2018 in national immunization program our data provides information for post-vaccination assessments. With higher valency vaccines coming to market by Indian manufacturers, knowledge of PCV13 NVT disease is important to identify serotypes to expand vaccine coverage in India.

Background

Pneumococcal Conjugate Vaccine (PCV) use has resulted in decrease of vaccine serotypes (VTs) and emergence of non-vaccine types (NVTs). We applied whole genome sequence (WGS) to predict serotype, sequence type (ST) and antibiotic resistance of NVT invasive pneumococcal isolates collected during the pre-vaccine era from Indian population.

Methods

96 NVT invasive isolates (2009-2017) collected across the country were sequenced on Illumina platform. Bioinformatic pipelines SeroBA and CDC pneumococcal pipeline for AMR calls were used for data analysis.

Results

Serotypes 15B (n=11), 24 (n=9) were dominant NVT types followed by 8 (n=8) and 34,10A,11A,16F (n=5). MLST resolved strains into 67 known STs. ST13727 (n=6) and ST2234 (n=5) were most common. Strains clustered in 45 clonal complexes and 16 singletons. The dominant clonal complex CC230 (n=12) was from serotypes 15B,15C,24,10A and 11A. 78(81%) of isolates were multidrug-resistant. Resistance genes for tetracycline (n=44), cotrimoxazole (n=41), erythromycin (n=34), penicillin (n=13) and chloramphenicol (n=2) were identified.

Conclusions

With the introduction of PCV in 2018 in national immunization program our data provides information for post-vaccination assessments. With higher valency vaccines coming to market by Indian manufacturers, knowledge of PCV13 NVT disease is important to identify serotypes to expand vaccine coverage in India.

Background

Worldwide Streptococcus pneumoniae serotype 19F, often multi-drug resistant, has emerged as an important pathogen associated with invasive pneumococcal disease (IPD). The aim of the study was to characterize invasive serotype 19F isolates collected from India in pre-vaccine era.

Methods

Among 480 pneumococcal isolates collected across India from 2010-2018, 38 belonged to serotype 19F (8%). These were sequenced on Illumina Platform. The sequence data was analysed for serotype, clonal complex, pilus islets and MLST using the CDC pipeline

Results

Overall, 11 STs encompassing in 4 GPSCs and 3 clonal complexes (CCs) were identified. The most prevalent strain of serotype 19F was GPSC1 (n=31, CC320), followed by GPSC10 (n=3, CC10879). CC320 was the major clonal complex (n=33) with ST236 (n=7), ST271 (n=7), ST320 (n=7), ST2697 (n=7), ST2854 (n=2) and ST651, ST1396, ST8359 (n=1 each). A majority of GPSC1 isolates (30/31) had pilus 1 & 2 while GPSC10 isolates were negative for both. All GPSC1 isolates and GPSC10 isolates were resistance to at least three antibiotic classes

Conclusions

This analysis identified CC320 as the major lineage among serotype 19F isolates pre-PCV vaccination in India. Overall, serotype 19F isolates were found to be multi-drug resistant with a high percentage of pili genes present.

Background

Serotype 1 Streptococcus pneumoniae is a common cause of IPD in India. The present study describes the phylogeny, clonality and antimicrobial susceptibility pattern of the isolates collected in the pre-PCV era in India.

Methods

21 invasive serotype 1 pneumococcal isolates collected across India during 2009-2016, were sequenced on Illumina platform. Phylogenetic tree was built with REALPHY 1.12. Abricate software with VFDB was used to analyse virulence genes and CDC Pneumococcal specific pipeline was used for antimicrobial resistance gene identification.

Results

Population structure analysis of the strains showed that 20 of them belong to sequence cluster GPSC2 and one to GPSC31. MLST resolved the isolates to 8 known STs and four clonal complexes CC217, CC5191, CC5316 and CC303. CC217 (n=16) was the most prevalent clonal complex, followed by CC5191 (n= 3). 90% (n=19) of the isolates harboured the virulence factors, lytA, nanA, hasC, pspA, srtG1, srtG2. Phenotypic and genomic analysis demonstrated sensitivity to penicillin, erythromycin and vancomycin of all 21 isolates; six isolates were resistant to cotrimoxazole and one to tetracycline.

Conclusions

With the introduction of pneumococcal vaccine in the national immunization programme in 2017, this study provides baseline data for future analyses.

Background

Understanding the role of viral co-infection in defining the outcome of paediatric pneumonia will provide novel treatment and prevention strategies, improving patient’s outcome. The objective of this study was to determine the prevalence of viral infection in children with pneumonia

Methods

128 Nasopharyngeal swabs of children with clinically proven pneumonia collected from a tertiary care hospital in a duration of 1 year were tested. Multiplex real-time PCR assay- FTIyo Respiratory pathogens 33 test kit (Fast-Track Diagnosis, Luxembourg) was used for analysis.

Results

105/128(82%) of children included in the study tested positive for at least one pathogen: bacterial or viral. Viral infection was detected in 55/128(42%) of samples. Pure viral infection was present in 12%(7/55) of cases. Single viral co-infection accounted for 67%(37/55) of cases. Co-infection with duel virus was detected in 10 patients(18%) and triple infection in 1.8% (1/55).

The most common viruses identified were Adenovirus(47%), Bocavirus(32%), Rhinovirus (21%), Human Parainfluenza Viruses HPIV3(12%), HPIV4(3.63%) and Respiratory syncytial viruses A and B(3.63%) respectively

Conclusions

The study highlights the importance of evaluating viral co-infection in the context of pneumonia in children. It is an ideal approach for better understanding of the carriage with multiple viral agents and its relationship with the bacterial pathogen.