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Displaying One Session

Session Type
Parallel Session
Date
Mon, 20.06.2022
Session Time
15:20 - 16:35
Room
Birchwood Ballroom
Session Description
Please note: Each presentation is followed by about 3 minutes of Q&A. The audience is encouraged to send questions to the speakers from the beginning of their presentations. Q&A time is included in each speaker’s presentation duration, accounting for at least 25% active learning for the maximum registrants anticipated.

Introduction (ID 42)

Session Type
Parallel Session
Date
Mon, 20.06.2022
Session Time
15:20 - 16:35
Room
Birchwood Ballroom
Lecture Time
15:20 - 15:25

O021 - RAPID, INTERACTIVE AND SECURE ANALYSIS OF PNEUMOCOCCAL SEQUENCING DATA FOR ON-SITE EPIDEMIOLOGY (ID 303)

Session Type
Parallel Session
Date
Mon, 20.06.2022
Session Time
15:20 - 16:35
Room
Birchwood Ballroom
Lecture Time
15:25 - 15:35

Abstract

Background

Genomic surveillance of pneumococci promises to revolutionize how we trace the global spread of strains, detect resistance, and make decisions on how to control disease. However, complex and cumbersome methods, barriers to data integration, and reproducibility issues with currently used genotyping schemes have prevented the translation of technological innovation into the clinic.

Methods

Our core method, PopPUNK, uses a machine learning approach to produce a stable, consistent genotyping scheme reflecting pneumococcal population biology. We have extended this software to use customised genome sketching techniques to enhance its flexibility, scalability, and portability. We also provide a machine-learning based approach for determining susceptibility to antimicrobials.

Results

We have defined the structure of the pneumococcal species by applying our method to over 50,000 globally sampled genomes. Users can rapidly integrate their own sequences into the context of this global population, directly from the browser, and visualise the results without the need for bioinformatics expertise. Phylogenetic analysis of sub-populations, for example to determine outbreak characteristics, has also been optimised and automated. Unlike some other platforms, users will not be required to give away any rights to their data, and sequence data never leaves the local machine.

Conclusions

Our software suite empowers local epidemiologists to perform analysis onsite, regardless of prior expertise, available computational resources, or location.

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O022 - CHARACTERISATION OF PNEUMOCOCCAL WITHIN-HOST DIVERSITY DURING TREATMENT, TRANSMISSION AND CARRIAGE VIA DEEP POPULATION SEQUENCING (ID 374)

Session Type
Parallel Session
Date
Mon, 20.06.2022
Session Time
15:20 - 16:35
Room
Birchwood Ballroom
Lecture Time
15:35 - 15:45

Abstract

Background

Typically studies investigating the genomics of Streptococcus pneumoniae have used whole genome sequencing (WGS) of single colony isolates obtained by sequencing DNA after selecting an individual colony from a culture plate. Such studies provide limited insight into within-host genomic diversity, and can obscure cases of multiple carriage.

Methods

More than 3500 nasopharyngeal swab samples from the longitudinal Maela pneumococcal colonization study were plated onto selective Columbia nalidixic acid agar plates. All colonies were harvested from plates and DNA extracted for deep within-host population sequencing.

Results

We demonstrate that population sequencing can accurately identify instances of multiple colonization and antimicrobial resistance elements. The increased resolution detected a greater prevalence of the invasive serotype 1 during carriage, and an elevated rate of transmission from mothers to their children in the first year of the child’s life. Accurate data on the administration of antimicrobials indicated that infants were at risk of both the acquisition and colonization of a multi drug resistant bacterium following antimicrobial treatment. Rates of co-colonisation imply that in the absence of treatment, susceptible lineages outcompete resistant lineages within the host.

Conclusions

The improved resolution and additional insights into co-colonisation, antimicrobial resistance, within-host selection and transmission indicate that deep within-host population sequencing can provide a general approach to enhance the genomic surveillance of S. pneumoniae and other pathogens.

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O023 - GENOME-WIDE ASSOCIATION STUDY OF PNEUMOCOCCAL CARRIAGE AMONG NEPALESE CHILDREN. (ID 435)

Session Type
Parallel Session
Date
Mon, 20.06.2022
Session Time
15:20 - 16:35
Room
Birchwood Ballroom
Lecture Time
15:45 - 15:55

Abstract

Background

Determining the host molecular genetic characteristics associated with pneumococcal colonisation may inform the development of new clinical interventions which could interrupt pneumococcal transmission and progression to disease. We performed a genome-wide association study to identify the genetic variants associated with pneumococcal carriage.

Methods

DNA samples collected from healthy Nepalese children were genotyped using Illumina Global Screening Arrays. Array data underwent QC and filtering before undergoing imputation using the HRC R1.1 2016 reference panel. Nasopharyngeal swabs collected from participants were processed for the presence of pneumococci by conventional microbiological techniques. Association analysis was performed using PLINK 2.

Results

Following filtering, 1355 carriers (cases) and 766 non-carriers (controls) were analysed. 10 variants within a single region on chromosome 12, were associated with pneumococcal carriage (p<10-8). The variant that had the strongest association with pneumococcal carriage (MAF carriers = 0.07 vs MAF non-carriers = 0.13, OR 0.52, 95% CI 0.42-0.64, p=2.3x10-8), was located in PPFIA2 (PTPRF Interacting Protein Alpha 2).

Conclusions

We identified host genetic variants in PPFIA2 (which encodes a protein involved in cell adhesion, integrin expression, and cell-matrix interactions) are associated with pneumococcal carriage. Further studies confirming this association and the biological role in pneumococcal carriage are needed.

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O024 - PHYLOGENETIC INFERENCE OF THE TRANSMISSION DIRECTION OF PNEUMOCOCCAL INFECTIONS, A VALIDATION STUDY (ID 782)

Session Type
Parallel Session
Date
Mon, 20.06.2022
Session Time
15:20 - 16:35
Room
Birchwood Ballroom
Lecture Time
15:55 - 16:05

Abstract

Background

Sustaining herd protection via reduced-dose schedules of pneumococcal vaccine may ameliorate some of the associated costs but necessitates a better understanding of Streptococcus pneumoniae (Sp) transmission. We ran a pilot study to explore a phylogenetic approach for detecting pneumococcal occurrence and direction of transmission.

Methods

Five putative transmission pairs and their same days’ nasopharyngeal swabs were selected from a longitudinal household study of asymptomatic carriage. Deep-sequencing of the infecting Sp populations was performed from culture sweeps and the direction of transmission was inferred using Phyloscanner. Transmission bottlenecks were assessed by comparing the frequency of single nucleotide polymorphism (SNPs) within transmission pairs.

Results

Phylogenetic clustering of all five transmission pairs was concordant with epidemiological information. The concordance of the direction of transmission inferred from phylogenies and from epidemiological criteria depended on the genome fragment size and the minimum number of SNPs included; with seemingly increasing concordance if phylogenetic inference is based on longer fragment sizes. In 4 of 5 instances, the putative source of transmission had higher number of unique SNPs than the recipient.

Conclusions

This study is one of the first to attempt inference of transmission directionality from bacteria using whole-genome NGS data. While our sample size was small, we show promise for detecting linked pneumococcal infection and their direction of transmission, particularly if read length is high.

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O025 - MECHANISMS OF VIRULENCE REGULATION AND GLOBAL DISTRIBUTION OF VACCINE CANDIDATE ANTIGENS IN THE HIGH VIRULENT STREPTOCOCCUS PNEUMONIAE STRAINS (ID 285)

Session Type
Parallel Session
Date
Mon, 20.06.2022
Session Time
15:20 - 16:35
Room
Birchwood Ballroom
Lecture Time
16:05 - 16:15

Abstract

Background

Metabolic flexibility is a prerequisite for successful transition of Streptococcus pneumoniae (Spn) from colonizing to invasive state. The aim of this study was to investigate the common metabolic features of pneumococcus invasive strains and propose vaccine candidate antigens.

Methods

The dataset (1058 PubMLST Spn strains) was stratified by genotype and included all known epidemically significant invasive and non-invasive clones. Genomes (495) were analyzed with GenomeComparator. Core gene variant matrix was used to run machine learning algorithms (RandomForest, XGBoost) to find gene variants associations with genotypes and invasiveness. Topology and composition of phylogenetic trees clusters comparison was performed using Visual TreeCmp.

Results

Phylogenetic analysis (based on MLST concatenates) revealed clustering of global pneumococcal population into the three groups (A, B1, B2), which may be associated with virulence. 181 genes were significant for the formation of A/B1/B2 groups: the components of various metabolic pathways (fatty acid biosynthesis, phenylalanine, biotin, arginine, galactose, fructose, mannose, purine bases, pyruvate, cysteine and methionine, alanine, aspartate and glutamate) and different virulence factors. Invasiveness is regulated by network of interacting genes variants: strH (exo-β-D-N-acetylglucosaminidase), carbohydrate metabolism components (gnd, dexB), aromatic amino acid synthesis pathways (aroE), relA regulatory gene (GTP pyrophosphokinase), peptidoglycan synthesis and cell division genes (murD, pbp1A), regulatory genes of polysaccharide capsule expression (wzg-wzh-wze).

Conclusions

Carbohydrates and aromatic amino acids metabolism pathways are involved in the regulation of cellular processes and phenotypic features of pneumococcus, including virulence. We achieved the list of vaccine candidates, which must be confirmed by reverse vaccinology.

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O026 - WEIGHT SYSTEM ADJUSTS INVASIVE PNEUMOCOCCAL DISEASE SURVEILLANCE DATA TO REPRESENT THE GENOMIC COMPONENTS OF CARRIAGE POPULATION (ID 785)

Session Type
Parallel Session
Date
Mon, 20.06.2022
Session Time
15:20 - 16:35
Room
Birchwood Ballroom
Lecture Time
16:15 - 16:25

Abstract

Background

Invasive pneumococcal disease datasets can reflect the carriage population, but with invasive serotypes overrepresented. To enrich the genomic data-usage of population-based invasive disease data for studying evolutionary dynamics, we aimed to develop a weight system to adjust the invasive disease data to represent carriage population.

Methods

We calculated the weight for each serotype as the ratio of percentage of the serotype in the carriage data to its percentage in all invasive cases, during the pre-vaccine era 1998-2000, in the US. We applied the weights to the accessory gene absence/presence matrix for each sequence in the invasive dataset (n = 11,784), after we conducted a bioinformatic pipeline to generate the set of accessory genes existing in 5% to 95% of the bacteria population.

Results

The weight system significantly improved the correlation of accessory gene frequency between invasive data and carriage population, for pre-vaccine, post-PCV7, and post-PCV13. The correlations of gene frequency between different vaccine periods in invasive data became more similar to those in carriage population. As the negative frequency dependent selection is one of the evolutionary mechanisms for Streptococcus Pneumonia, the accessory gene frequency “rebounce” after vaccine perturbance found in previous studies was observed in the invasive data during post-PCV13, after the weights were applied.

Conclusions

The proper weight system can adjust invasive disease datasets to represent the genomic components of the carriage population of Streptococcus Pneumoniae. Our methods enrich the value of genomic sequences from invasive disease surveillance, as it is common, easy to collect, and of direct interest of public health.

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O027 - DIFFERENTIAL EXPRESSION OF COMPETENCE GENES ASSOCIATED WITH VARIATION IN TRANSFORMATION FREQUENCIES AMONG SEROTYPE 3 STREPTOCOCCUS PNEUMONIAE (ID 176)

Session Type
Parallel Session
Date
Mon, 20.06.2022
Session Time
15:20 - 16:35
Room
Birchwood Ballroom
Lecture Time
16:25 - 16:35

Abstract

Background

Recombination has shaped the evolutionary history of Streptococcus pneumoniae, allowing rapid adaptation to interventions. Pneumococci can undergo recombination through natural competence – a state in which bacteria can uptake DNA from the environment. Recombination frequencies vary considerably across pneumococcal populations; yet the underlying mechanisms for these variations are not well understood.

Methods

We sought to elucidate differences in transformation frequency and the underlying genetic mechanisms among strains from two distinct phylogenetic clades of Serotype 3 belonging clonal complex (CC) 180 and a well-characterized non-CC180 comparison strain D39. To this end, we performed in-vitro competence assays and measured differential expression of early and late competence genes using RNA-sequencing.

Results

We found consistent differences in transformation frequencies among CC180 clades and D39 (Figure 1), which correlated with variation in differentially expressed genes during competence. While all strains exhibited a similar response to competence stimulating peptide for early competence genes, expression of late competence genes encoding the DNA uptake apparatus, DNA repair and recombination proteins needed for recombination were attenuated among strains demonstrating lower transformation frequencies. We also observed differences in expression of genes linked to bacteriocin production, which may partially explain observed population genomic-level differences. Further genomic analysis suggests variation in promoter sequences governing late competence genes may be slowing transition from early to late components of the competence pathway.

isppd_fig1.png

Conclusions

We show that there is considerable variation in competence even among closely related strains and that this variation may be the result of subtle genomic differences.

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