CID Annual Symposium 2024: Poster Abstracts

Monitoring the Prevalence of Hepatitis C through Surveillance Data and Use of Multiple Imputation.

Adewunmi Akingbola, De Angelis Group, MRC Biostatistics Unit

This research explores the prevalence of Hepatitis C, focusing on the comparison between complete-case analysis and multiple imputation techniques to handle missing values in surveillance data. Hepatitis C, a significant public health issue, affects millions globally, primarily spreading through needle sharing among drug users. This study leverages data from the Unlinked Anonymous Monitoring Survey in the UK, covering socio-demographic and behavioral factors from 1990 to 2019. The research aims to assess the impact of these factors on Hepatitis C prevalence, using two methods to handle missing data: traditional complete-case analysis and the more advanced multiple imputation technique. By comparing these methods, the project seeks to understand their effects on epidemiological research outcomes and inform public health policies. The methodology includes a detailed analysis of the survey data, focusing on variables such as age, gender, drug use behaviors, and health service utilization. The findings are expected to enhance the reliability of data interpretation and contribute to methodological advancements in public health research. The study acknowledges the limitations of both data handling methods and the survey's design, emphasizing the importance of considering these factors when interpreting the results.

Genotype-specific interaction of Drosophila melanogaster and its parasite sigma virus

Aleksei Belyi, Frank Jiggins group, Department of Genetics

Host-parasite interactions guide the evolution of both sides, determining levels of host resistance and parasite infectivity. These traits often show high levels of genetic variation maintained in the interacting populations, which may be explained by negative frequency-dependent selection (NFDS). We found that virus transmission rates varied considerably depending on both the host and virus genotypes. In particular, flies carrying resistant alleles of the genes ge1, CHKov1 and ref(2)p had lower transmission rates for the majority of the virus genotypes. Furthermore, there was a sex-specific interaction between the Drosophila and the virus genotypes on the transmission rate, such that flies that are adapted to one sigma virus genotype might be maladapted to other genotypes. This genotype-specific interaction has the potential to generate NFDS within both insect and parasite populations.

Estimating Geographic Spread of Streptococcus pneumoniae within Israel Using Genomic Data

Raymond Cheng,Wellcome Sanger Institute

Understanding how pathogens spread across geographic space is fundamental for control measures such as vaccination. Streptococcus pneumoniae (the pneumococcus) is a respiratory bacterium responsible for a large proportion of infectious disease morbidity and mortality globally. Even in the post-vaccination era, the rates of invasive pneumococcal disease (IPD) remain stable in most countries including Israel. To understand the geographic spread of the pneumococcus in Israel, we analysed 1,159 pneumococcal genomes from patients with IPD across multiple regions. We included the evolutionary distance between pairs of isolates inferred using whole genome data within a relative risk (RR) ratio framework to capture the geographical structure of S. pneumoniae. While we could not find geographic structure at the overall lineage level, the extra granularity provided by whole genome sequence data showed that it takes approximately 5 years for the pneumococcus to become fully mixed across the country.

The role of microbial genomics in supporting shigellosis vaccination programs

Charlotte Chong,Baker Group, Department of Genetics

Microbial genomics is transforming our understanding of bacterial populations and has incredible potential to shape management of diarrhoeal disease in resource poor settings. Our recent pathogenomic analysis of >1200 Shigella isolates from South Asia and sub-Saharan Africa isolated during the Global Enteric Multicentre Study (GEMS) examined vaccine target conservation and antimicrobial resistance to inform future treatment, prevention, and surveillance strategies. 

We found that Shigella sonnei (relative to other species) and protein antigen candidates (relative to serotype-specific targets) represented comparatively conserved vaccine targets and identified convergent evolution of resistance against ciprofloxacin, a current WHO recommended antimicrobial therapy. We also determined that serotype switching in S. flexneri, which may lead to immune escape from O-antigen based vaccines, is common (3% of isolates) and can occur in as little as 6 months, highlighting the need for ongoing monitoring of Shigella populations particularly around vaccine implementation. 

In this abstract we will present our extensions to this work demonstrating the shifts in Shigella population diversity that occur through natural immune pressures in endemic settings via longitudinal analysis of Shigella isolated in The Gambia during the follow-on Vaccine Impact on Diarrhoea in Africa (VIDA) trial. These analyses showed clonal replacement of the circulating subpopulations of S. flexneri in the Gambia and provide an important baseline of natural Shigella population shifts critical for monitoring for future vaccine escape. 

We will also present our extended analysis of Shigella isolated in GEMS that exploited the case-control study design to identify pathogen-specific factors responsible for the manifestation of clinical disease through bacterial genome wide association studies. Preliminary findings indicate that specific genotypes are significantly more associated with disease than others, while accessory genome elements that were associated with disease showed epidemiological interaction with genotype. These genetic factors could be developed as predictors of severe disease or as novel therapeutic targets. 

Our work highlights the importance and varied utility of microbial genomics for: evaluating and monitoring the efficacy of vaccination and other management approaches; developing diagnostics; and quantitating the potential control of antimicrobial resistance and disease burden through vaccination.

Secret Bugs: Charting the unknown diversity of the human microbiome

Ana Catarina da Silva,Microbiome Function and Diversity, Department of Veterinary Medicine

The human gut microbiome plays a pivotal role in maintaining overall health and influencing essential physiological processes. However, of the nearly 5,000 species known in the gut microbiome, >70% remain uncultured and inaccessible to experimental manipulation. To gain new insights into the role of uncultured gut bacteria in host health, we analysed a dataset of >17,000 human gut metagenomes from 13 diseases using the most comprehensive gut genomic catalog to date. Our results showed that >20% of microbiome species are associated with at least one disease, with most microbiome signatures found to be disease-specific. Notably, uncultured bacteria were overrepresented among health-associated species, with the genus named CAG-170 identified as the strongest biomarker of health. Functional prediction analyses revealed that disease-associated species are enriched in functions involved in osmotic and oxidative stress, whereas species linked to health encode a higher number of genes related with gut colonization and motility. This work expands our understanding of the role of the uncultured microbiome in health, identifying key species to be prioritized for targeted culturing efforts.

Temporal GWAS identifies a widely distributed putative adhesin contributing to pathogen success in Shigella spp   

P. Malaka De Silva, Baker group, Department of Genetics

Bacteria of the genus Shigella are a major contributor to the global diarrhoeal disease burden. Increasing antimicrobial resistance in Shigella and the lack of a licenced vaccine has led WHO to recognise Shigella as a priority organism for the development of new antimicrobials. Understanding drivers of long-term persistence and success of this pathogen is critical for ongoing shigellosis management and is relevant for other enteric bacteria.

To identify key genetic drivers of Shigella evolution over the past 100 years, we analysed S. flexneri from the historical Murray collection (n=45, isolated between 1917-1954) alongside a comparatively modern collection (n=262, isolated between 1950-2011) using a novel approach called temporal genome-wide association study (tGWAS). We identified SNPs (n=94), COGs (n=359) and significant kmers within 48 genes significantly positively associated with time in known genes and several unknown genes (28%, 49/172).

Among the unknown proteins we identified a novel plasmid borne putative adhesin, named Stv. Genomic epidemiological analyses reveal that Stv was associated with clonal expansions of multiple phylogroups of S. flexneri and its acquisition predates multidrug resistance acquisition and the global dissemination of Lineage III S. sonnei. Stv, and close relatives, are widely distributed in other Enterobactericeae and bacteria, indicating that its importance likely extends beyond shigellae. We also created a deletion mutant of stv in S. sonnei to explore the phenotypic effects of Stv.

This work highlights the effectiveness of using tGWAS on historical isolate collections for identifying novel contributors to pathogen success over time. This approach is readily translatable to other pathogens and our application in Shigella identified Stv, a putative adhesin and potential drug target that is widely distributed across the AMR priority group Enterobacteriaceae.

Insights into the dynamics, composition, and functionality of the respiratory microbiome

Luis Antonio Gonzalez Villaseca, Microbiome function and diversity lab - Almeida Group, Department of Veterinary Medicine

The respiratory tract microbiome (namely the lungs and the nasal and oral cavity) modulates local immune responses and acts as a physical barrier against external pathogens. Perturbations to this microbiome community, for instance through the use of antibiotics, may favor the growth of opportunistic pathogens and increase the risk of developing severe respiratory diseases (e.g., asthma, cystic fibrosis, chronic obstructive pulmonary disease, among others). Although previous studies have provided initial insights into the composition of the respiratory microbiome, they have mainly relied on marker-based methods (e.g., 16S rRNA genotyping), which have limited taxonomic resolution and do not provide meaningful functional insights. Here, we leveraged a dataset of >2,000 metagenomes from the respiratory tract to characterize the composition, diversity, and functionality of the microbiome in the lung, oral, and nasopharyngeal cavities. We showed that every niche possesses a unique microbiome and resistome composition, with the oral cavity in particular showing the highest microbial diversity. We are now generating a comprehensive collection of isolate and metagenome-assembled genomes from these same datasets to uncover novel species unique to the respiratory microbiome. This will enable us to provide the first high-resolution view of the biological role of the respiratory microbiome and its association with human health, age and lifestyle.

Targeted nanopore sequencing for Plasmodium falciparum molecular surveillance in endemic settings

Alexandria Harrott, GSU, Wellcome Sanger Institute

Despite global efforts to control malaria, the World Health Organization (WHO) has estimated that there were 249 million cases and 608,000 deaths caused by malaria in 2022. Major threats to malaria control include parasite antimalarial resistance and evasion of diagnostic tests, vector dynamics, and the changing climate. The WHO has highlighted the need for enhanced molecular surveillance in Africa to monitor the emergence and spread of antimalarial resistance, which could have devastating public health consequences. However, historically, genomics has been limited to large centres outside of highly endemic regions.

In a collaboration between the Wellcome Sanger Institute and University of Ghana, we are developing amplicon-based approaches to malaria molecular surveillance using nanopore sequencing, suitable for deployment in endemic settings. Nanopore offers several advantages including relatively low up-front costs, portability, and long sequence reads. Using a multiplex PCR, we target key antimalarial resistance markers from readily collected clinical samples, followed by a rapid analysis pipeline that can run on commercial gaming laptop computers. Following an initial implementation phase in Ghana in 2022, we have expanded the surveillance panel to include additional markers of drug resistance and diverse surface proteins that act as markers of mixed infections. We have engaged in regional capacity strengthening by linking with the ARTIC Consortium, delivering a training workshop on nanopore sequencing for malaria surveillance to representatives of six west African countries in November 2023. 

In summary, we will present the latest data on this ongoing project to harness nanopore amplicon sequencing for malaria surveillance in endemic regions. Ultimately, a regular flow of molecular data will empower national malaria control programmes to make optimal and informed decisions in the fight against this ancient and evolving foe.

Qualitative studies on farmers’ perception and implementation of biosecurity measures​ on UK poultry farms in relation to HPAIV

Paniz Hosseini,Department of Veterinary Medicine

Objectives:

• Explore biosecurity and disease management on commercial poultry farms in the UK.
• Research into farmers’ experiences and perceptions of diseases such as avian influenza (AI).
• Understand how the spread of avian influenza can be prevented in the future amongst poultry farms.

Methods:  A total of 13 qualitative interviews with farm managers across various poultry farms in the UK were conducted, consisting of ""case"" farms (farms that have had an AI outbreak since 2021) and ""non-case"" farms (farms that have not had an AI outbreak before). Interviews were semi-structured and allowed for in-depth discussions on farming practices and biosecurity, including any associated challenges.

Ethnographic observations were also conducted on each farm, completed during and after each interview to help identify which biosecurity measures were physically being used on the farm, allowing for analysis of both farmers’ reported experiences and physical evidence of any biosecurity management/mismanagement.

Interviews, observation notes/diary entries and other information gathered were analysed using NVivo 12 to generate codes, patterns and themes amongst the data. 

Results: Biosecurity measures such as the use of foot-dips, changing boots and regular disinfection routines were some of the most popular and adhered to measures across a majority of the farms. Some of the weaker biosecurity measures related to the old age and poor maintenance of sheds and buildings; poor structure and layout of the farms and poor biosecurity surrounding wild birds. Additionally, farm managers expressed high levels of stress and anxiety surrounding the threat of AI. 

Analysis of the findings suggest that the level of adherence to biosecurity was impacted by factors such as the farmers own perceptions of risk; general knowledge surrounding the spread of AI; financial limitations; communication with other actors and the age/length of experience of the staff members on the farm.

Conclusions: We recommend further guidance and support services that acknowledge the mental health impacts which farmers may face during times of disease outbreaks. Providing services where farmers can speak to other individuals in the industry that have had experiences of an AI outbreak would be beneficial, as would access to further training and educational materials to better understand biosecurity and the risks associated with AI. Finally, further research with other actors in the poultry industry would help to better understand the factors influencing biosecurity implementation, and how best to approach this in the future from an industry perspective. 

The evolutionary dynamics of the β-lactamase locus and its relationship with methicillin resistance in Staphylococcus aureus

Alasdair Fletcher, Murray Group, University College London 

The β-lactamase (bla) locus confers penicillin resistance in Staphylococcus aureus. It consists of a structural gene (blaZ) and its regulators; a repressor (blaI) and signal transducer (blaR). Previous studies show that blaI and blaR additionally regulate mecA, a gene that confers resistance to numerous β-lactam antibiotics, including methicillin. Little is known about the dynamics of mobile genetic elements (MGEs) that carry the bla locus, and how this influences the gain and loss of mecA. Here, we present the first comprehensive characterisation of the MGEs carrying blaZ in a S. aureus clonal complex (CC). Using 1181 genomes, we describe the diversity and dynamics of MGEs carrying blaZ in CC398, the dominant livestock-associated MRSA in Europe. We find that while blaZ is rarely absent, this superficial stability is underpinned by the carriage of multiple MGEs. Using ancestral state reconstruction, we determine acquisition dates for MGEs and contextualise them to lineage events. We identify a correlation between losses of mecA and blaZ, indicating a selective benefit of blaZ retention after mecA acquisition. We also find that a similar correlation is observed across other staphylococci. These results suggest that the bla locus plays an important role in the evolution and persistence of broad-spectrum β-lactam resistance in staphylococci. 

Examining the 'structure-function' relationships of global and European clinical societies in the light of some disease-related research

Anett Győri, University of Szeged 

My interdisciplinary research focuses on NGOs and their activities for the development and innovation of medicine in an international context. My research also covers the practice of 'medical' NGOs in the UK and Austria. 
For example, the primary actors in the Austrian COVID fight are the "St. Marx" institutes - IMBA is a good example. In response to a WWTF appeal, the non-profit organisations (B&C Private Foundation, Berndorf Private Foundation) have raised millions of euros to fund 24 priority research projects. Further COVID projects are jointly funded by the state and NGOs (BMBWF and WWTF) and as an inter-institutional collaboration, VBC and MUW have redeployed their existing resources - creating the VCDI laboratory, which has been included in the list of recommended laboratories of the Austrian Ministry of Health with an excellent rating based on the quality assessment of ÖQUASTA SARS-CoV-2 PCR.
The NGO sector is the only viable way to achieve the SDGs, and not merely an alternative. NGOs, through their fundamental research, bring about mind-blowing changes in our daily lives. Generally speaking, the information society has been elevated to another dimension of development by the global partnership revolution.

Trivalent MVA-based vaccine candidate against Ebola, Lassa and Marburg virus protects against lethal challenge with all three viruses

Nina Krause,Heeney Group, Department of Veterinary Medicine

Lassa fever, Ebola, and Marburg virus cause severe diseases often with fatal outcomes. Besides millions of people in Africa living at risk of acquiring an infection with one of these viruses, preventative measures are limited. 

We designed a trivalent MVA-based vaccine candidate and evaluated its immunogenicity and efficacy in Balb/c mice and Hartley guinea pigs. After three immunisations, animals developed significant levels of binding antibodies against all three antigens and neutralising antibodies against several circulating Filovirus strains. Balb/c mice further developed significant numbers of Lassa nucleoprotein-specific T cells. Following the confirmation of immunogenicity of all three antigens, Hartley guinea pigs were challenged with a lethal dose of guinea pig-adapted strains of the Lassa fever, Ebola Sudan and Marburg virus. All immunised animals survived the challenge and showed no signs of severe infections.

We showed that a multivalent vaccine candidate induces a robust immune response against several viruses and can effectively protect against severe haemorrhagic fever caused by these viruses. 

Unravelling the ecological shift to zoonosis and pathogenicity in Streptococcus suis in tonsils using FISH and confocal microscopy

Chenxi Liu, Weinert Lab, Department of Veterinary Medicine

Streptococcus suis is a ubiquitous and dominant member of the pig respiratory microbiota, but can also be an economically devastating bacterial pig pathogen, causing pneumonia and invasive disease. Our group has shown that this pathogenic phenotype largely comes from several recently emerged lineages from within this microbiota diversity. One of these pathogenic lineages also causes zoonotic infection among farm workers and people who eat undercooked pig products. 

The emergence of pathogenic lineages is associated with the acquisition of three genomic islands that altogether suggest a change of pathogenic S. suis within its microniche in the pig host. Since, the tonsils are the main ecological niche and transmission site of S. suis, we sought to test whether there are differences in the distribution of pathogenic and commensal S. suis strains within the tonsil tissues. 

In this study, we combine fluorescence in situ hybridization (FISH) and confocal microscopy to develop a method for S. suis strain mapping in tonsils. These results aim to demonstrate how genomic and ecological changes lead to the emergence of pathogenicity in bacteria. This pattern is reminiscent of more ancient shifts of the human microbiota giving rise to pathogens such as Streptococcus pneumoniae and Streptococcus pyogenes.

Streptococcus equi whole genome sequencing data shed new light on endemic persistence of strangles in the United Kingdom

Abigail McGlennon,Equine Infectious Disease Surveillance, Department of Veterinary Medicine

Background: Strangles, caused by Streptococcus equi, remains endemic in the UK horse population. Subclinically infected long-term carrier horses intermittently shedding Streptococcus equi are considered the principal driver of strangles endemicity. Monitoring genomic changes in circulating strains may provide valuable information on pathogen adaptation driving its endemic persistence. 

Objectives: Utilise whole genome sequencing (WGS) data to determine the population structure and diversity of UK field-derived Streptococcus equi bacterial isolates. 

Methods: Streptococcus equi isolates (n=510) from field-based clinical samples taken between 2016 and 2022 underwent DNA extraction prior to WGS. Assembled WGS sequences were compared with the Streptococcus equi 4047 reference genome to identify genomic differences and determine the collection’s population structure via Bayesian Analysis of Population Structure (fastBAPS).

Results: Nine fastBAPS groups were identified, although 82% of strains belonged to only two groups (fastBAPS3, n=230, 45%; fastBAPS5, n=189, 37%). There was a statistically significant association (p<0.001) between year of recovery and the relative proportion of groups, with linear trends over the study period for increasing proportions of fastBAPS3 isolates (7% in 2017 to 93% in 2022) and decreasing proportions of fastBAPS5 isolates (69% in 2017 to <1% in 2022). 

Conclusions: The rapid change in genomic population structure observed among Streptococcus equi isolates here cannot be explained by transmission via subclinical long-term carriers. Instead, it suggests transmission from acutely infected or recently recovered horses may be a far more significant contributor to strangles endemicity than previously thought.

A new approach to laboratory diagnosis of diphtheria

Vyacheslav Melnikov, Department of Veterinary Medicine

Diphtheria treatment is administered based on clinical manifestations. But the onset of the disease, when it is easily amenable to therapy with diphtheria antitoxin, is virtually indistinguishable from widespread streptococcal acute tonsillitis. Therefore, diagnostic laboratories need accelerated procedure for detection of diphtheria toxin (DT)-producing corynebacteria in clinical samples. Since taxonomic determination of the respective species of toxigenic corynebacteria is not urgently required for laboratory confirmation of clinical diphtheria diagnosis, we tested the following concise algorithm for indication of toxigenic corynebacteria: 1) inoculation of a clinical sample on tellurite agar, selective for corynebacteria; 2) examination of the primary culture agar after 24–48 hours of incubation for the presence of grey/black colonies resembling those of C. diphtheriae/C. ulcerans and determination of their DT-producing capacity using newly developed Lateral Flow Immunoassay (LFIA) on monoclonal antibodies to DT. Our results showed that the concomitant pharyngeal microbiota, which sparsely grow on tellurite plates and could have entered the colony mixture sample for testing, did not interfere with neither the growth of the diphtheria corynebacteria nor their DT expression. In conclusion, a simple algorithm for early diagnosing diphtheria is developed, which promotes the testing be performed in laboratories closer to the patient.

Exploring the role of PfAAT1 in the emergence of Plasmodium falciparum chloroquine resistance in Colombia

Kyle Michie,Rayner Group, Clinical Biochemistry

Malaria control relies heavily on antimalarial drugs, but the Plasmodium falciparum parasites that cause the majority of malaria mortality have evolved resistance to all widely released antimalarials. Resistance often evolves first in areas of low transmission before spreading globally, and can be multifactorial. Chloroquine resistance depends primarily on the multi-domain transmembrane protein PfCRT, but recent studies suggest that polymorphisms in a second such protein, PfAAT1, may modulate chloroquine resistance. Previous studies of PfAAT1 have all focused on Africa and Asia, but chloroquine resistance also emerged independently in Colombia, and the specific role of SNPs in PfAAT1 on Colombian parasites has not been explored. Using both historical and contemporary P. falciparum patient isolates that had been collected along the Pacific Coast of Colombia and adapted to in vitro  culture, we identify a putative Latin America-specific SNP in PfAAT1 and characterise the drug sensitivity of isolates both with and without this SNP. We are currently using CRISPR/Cas9 technology to make transgenic lines in lab strains of P. falciparum to directly test the role of this unique SNP and thereby further elucidate the multifactorial nature of antimalarial drug resistance and unique epidemiology of P. falciparum transmission in Colombia. 

A novel integrated physical-electrochemical approach for fighting biofilms

Sivan Nir,Zhang group, Yusuf Hamied Department of Chemistry

Biofilms are communities of bacterial cells connected within a matrix of extracellular polymeric substances (EPS), and are implicated in over 80% of infections. Antimicrobials are commonly deployed to treat biofilm-related infections; however, multi-drug resistance is increasingly common, with biofilm cell communities being up to 1000-fold more resistant to antibiotics than individual cells. Novel strategies to combat pathogenic biofilms are urgently needed. 

Promisingly, many new strategies have emerged across medicinal chemistry for the treatment of tumor cell communities that can also be used on biofilms. Furthermore, we are beginning to understand that the redox chemistry of the biofilm EPS can be controlled to modulate biofilm growth.

We aim to develop a novel integrated approach for fighting microbial infections that synergistically combines the physical disruption of biofilm EPS structure and function, with the chemical disruption of the EPS redox chemistry to inhibit biofilm metabolism. This approach uniquely combines/enhances both effects for inhibiting biofilms and minimises their ability to develop resistance. It will also benefit the wider field of bio/antifouling, as biofilms are also widely problematic in food, energy, and transport industries.

The emergence of multidrug-resistant Enterobacteriaceae infections has become a major public health concern.

Qi Yin,Department of Veterinary Medicine

Microbiome-based therapeutics utilizing beneficial species and/or functions found in the human gut represent promising alternative strategies. Here we investigated nearly 30,000 global human gut metagenomes across more than 50 countries to explore gut microbiome patterns associated with Enterobacteriaceae colonization. Differential abundance and network analyses revealed that over 700 gut microbiome species are associated with Enterobacteriaceae colonization status. In particular, bacterial species from the families Bacteroidaceae were overrepresented in gut microbiomes devoid of Enterobacteriaceae species, whereas the family Acutalibacteraceae usually co-occurs with Enterobacteriaceae presence. In particular, the understudied species Ruthenibacterium lactatiformans was found to be the strongest biomarker of Enterobacteriaceae presence, while Alistipes and Prevotella were the most promising competitive targets associated with the absence of Enterobacteriaceae. Functional prediction of the microbiome candidates associated with Enterobacteriaceae colonization showed that the number of biosynthetic gene clusters per genome was higher among microbiome species negatively associated with Enterobacteriaceae, particularly those belonging to the cyclic lactone autoinducer and RRE containing types. Our work provides novel ecological insights into how the microbiome functional and taxonomic diversity may influence the colonization success of Enterobacteriaceae in the human gut.

Genomic characterisation of Streptococcus pneumoniae vaccine and non-serotypes pre- and post-PCV introduction in Nijmegen, The Netherlands.

Ana Daniela Ferreira,Wellcome Sanger Institute

Background: In 2006, the Netherlands introduced PCV7 vaccine for pediatric immunization, followed by PCV10 in 2011. This study focuses on characterizing Streptococcus pneumoniae isolates from patients in Nijmegen, the Netherlands.

Methods: Genome sequences from 1004 S. pneumoniae isolates were analyzed, categorized into four periods: Pre-PCV (n=191; 2000-2005), PCV7 (n=226; 2006-2010), early-PCV10 (n=311; 2011-2015), and late-PCV10 (n=251; 2016-2020). The genomes were clustered using PopPUNK into Global Pneumococcal Sequence Clusters (GPSC). Serotypes were determined with SeroBA, and changes in serotype groups were identified using Fisher’s Exact Test and odds ratio.

Results: Analysis of 1004 pneumococcal isolates revealed 46 serotypes across 64 GPSCs. The prevalent serotypes included serotype 8 (n=178; 18%), 7F (n=102; 10%), 3 (n=77; 8%), 19A (n=69; 7%), and 1 (n=66; 7%), collectively accounting for 49% (492/1,004) of the collection. PCV20 (Pfizer) demonstrated increased serotype coverage from 31-40% to 81-89% across all three age groups. PCV20 also outperformed PCV10 (GSK) in serotype coverage across different vaccine periods. The introduction of PCV10 led to a significant increase in non-vaccine serotypes (NVTs), alongside a decrease in vaccine serotypes (VTs).

Conclusions: The rise in pneumococcal NVTs suggests that the introduction of PCV impacted the invasive S. pneumoniae population in the Netherlands.