Nagaraj Geetha, India

Kempegowda Institute Of Medical Sciences Central Research Laboratory

Poster Author Of 5 e-Posters

Author Of 5 Presentations

GENOME ANALYSIS OF INVASIVE SEROTYPE 1 STREPTOCOCCUS PNEUMONIAE ISOLATES FROM INDIA (ID 768)

Abstract

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.

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SEROTYPE, GENOTYPE AND ANTIBIOTIC RESISTANCE OF NON-VACCINE TYPE INVASIVE PNEUMOCOCCAL ISOLATES FROM PRE-VACCINE ERA (BEFORE 2018) - AN INDIAN STUDY (ID 1125)

Abstract

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.

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ZMPB ALLELIC VARIATION IN STREPTOCOCCUS PNEUMONIAE ISOLATES CAUSING MENINGITIS IN INDIAN POPULATION (ID 1138)

Abstract

Background

Streptococcus pneumoniae is a leading cause of meningitis. Intense inflammatory response observed in meningitis is partially attributed to zinc metalloprotease encoded by zmpB in pneumococcal strains. We aimed to study allelic variations of zmpB among isolates obtained from Meningitis patients

Methods

36 cerebrospinal fluid (CSF) isolates collected across the country from 2009-2016 were sequenced on Illumina platform. The CRL in-house bioinformatics pipeline was used to extract gene sequences, alignment and phylogeny analysis. SeroBA was used to determine serotype. Allelic variations of zmpB gene was analyzed by comparing the identity with the virulent strain S. pneumoniae TIGR4.

Results

36 pneumococcal isolates belong to 24 serotypes with 19F(n=5) as dominant type. Non-PCV13 vaccine serotypes constituted 50% of the isolates(n=18). The isolates were assigned to 28 sequence clusters, among them GPSC10(n=4) & GPSC2(n=3) were predominant.32 of 36 isolates showed 21 to 88% of sequence variation, while remaining 4 isolates showed sequence similarity of 98% with the TIGR4. Allelic variations did not affect the protein coding region analysis and conserved domains of ZmpB protein was identified in all isolates.

Conclusions

The findings provide insight on the allelic variations of zmpB, indicating there is a high degree of polymorphism in the sequence of zmpB in pneumococci causing meningitis.

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GENETIC DIVERSITY OF CBPA AMONG INVASIVE STREPTOCOCCUS PNEUMONIAE ISOLATES FROM INDIA (ID 1152)

Abstract

Background

Streptococcus pneumoniae is a human opportunistic pathogen responsible for morbidity and mortality worldwide. Pneumococcal surface protein, Choline-binding protein A (CbpA) plays a key biological role in nasopharyngeal colonization and modulating the immune response to pneumococci. We have analyzed the genetic diversity of cbpA in invasive isolates.

Methods

264 invasive S.pneumoniae isolates collected from 2010-2018, were sequenced on Illumina Platform. The CRL in-house bioinformatics pipeline was used to extract gene sequences, alignment and phylogeny analysis. Allelic variations of CbpA gene was analyzed by comparing the identity with a well-defined virulent strain of S. pneumoniae TIGR4.

Results

Gene cbpA was identified in 261(99%) of the 264 genomes. The sequences were highly polymorphic at both nucleotide and amino acid levels. Similarity of cbpA gene ranged from 65 – 98%, while 80- 99% homology was observed at amino acid level. Amino acid residues with similar physicochemical properties aligned allowing the identification of broadly conserved CbpA domains.

Conclusions

Due to high polymorphism at the cbpA locus, analysis of this loci from different isolates highlights how sequence diversity correlates with structural variation. The conserved epitope regions of the CbpA protein fragments can be exploited to develop more efficacious serotype-independent vaccines.

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PREDOMINANCE OF CLONAL COMPLEX 320 AMONG INVASIVE STREPTOCOCCUS PNEUMONIAE SEROTYPE 19F ISOLATES FROM INDIA IN PRE-VACCINE ERA. (ID 1203)

Abstract

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.

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