CID Annual Symposium 2022 Programme: Flash Talks

Flash Talks Session (13.45 - 14.45) – Chair: James Wood

Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis

Noémie Lefrancq, Department of Genetics

Bordetella pertussis (Bp), which causes whooping cough, infects >24 million individuals annually despite widespread vaccination. Asymptomatic carriage and multiple circulating lineages hide the underlying dynamics of Bp from surveillance systems. Therefore, the extent of spread across spatial scales remains a mystery, as does the role of vaccines in driving changes in strain fitness. Models informed by pathogen sequences provide an exciting way to help. Here we use 3344 sequences from 23 countries to show on average there are 28.1 transmission chains circulating within a subnational region, with the number of chains strongly associated with host population size. It takes 5-10 years for Bordetella pertussis to be homogeneously distributed throughout Europe, with the same time frame required for the United States. Increased fitness of pertactin-deficient strains following implementation of acellular vaccines, but reduced fitness otherwise, can explain long-term genotype dynamics. These novel insights into Bp dynamics and its interactions with vaccine-induced immunity are highly relevant to vaccination policies.

Genomic insight holds promise to advance pneumococcal vaccine design

Dr Stephanie Lo, Parasites and Microbes – Wellcome Sanger Institute

Pneumococcal conjugate vaccine (PCV) is effective at reducing disease in young children. However, increasing replacement with non-vaccine serotypes and persistent circulation of vaccine serotypes compromise the benefit of the PCV programme. The Global Pneumococcal Sequencing project (GPS) conducts genomic surveillance across >60 countries creating an unprecedented resource to assess the evolution of vaccine evading lineages and to inform the design of future vaccine formulations. 

During the global deployment of PCV, we found that globally-spreading lineages expressing multiple serotypes are the major drivers of serotype replacement. Our in-depth analysis into one of these lineages GPSC10 revealed its ability to survive under vaccine-selective pressure by rapidly adapting serotype composition from vaccine serotype to non-vaccine serotype (24F) while quickly spreading between countries. The concern raised led to the inclusion of serotype 24F in the design of the upcoming 25-valent PCV. 

Reasons for the persistence of vaccine serotype are unclear. Our investigation into residual vaccine serotype 19F revealed that the persistence was mainly due to lineages that carry a distinct variant of the 19F capsule gene array, as compared with those which are decreasing post PCV. This finding highlights potential antigenic heterogeneity within a serotype that may result in vaccine escape. 

Genomic insight generated from the GPS project improved our understanding of how pneumococci respond to PCV and paves the way for continually-informed vaccine design.  

There’s more to the Kermack and McKendrick model than SIR!

Desmond Lai, Department of Applied Mathematics and Theoretical Physics

The Susceptible-Infectious-Recovered (SIR) model is often attributed to Kermack and McKendrick (KM) but in fact, their seminal paper in 1927 went much further, and this is often overlooked. And this work continues to have value in the face of modern challenges in disease modelling.

In this talk, I will share with you what the KM model comprises and why we should pay more attention to this generic framework, which introduces the concept of time since infection. I will show how this model can be extended to include waning immunity, and explain why it is important to consider waning immunity in mathematical models of disease transmission, not only for COVID-19, but also against the next disease X.

An in vitro 3D model of the vertebrate gut to study host-microbiome-parasite interactions

Dr Chrysanthi-Maria Moysidou, Department of Chemical Engineering and Biotechnology

In vitro models of the gut-microbiome axis are in high demand. Conventionally,  intestinal monolayers grown on Transwell culture setups are used to test the effects of commensals or pathogens on the integrity of the barrier under (patho-)physiological conditions. Such models remain valuable for deepening our understanding of host-microbe interactions, however, they often lack biological components that serve as key mediators of this intricate crosstalk. Here, we describe the establishment of stable host-microbe co-cultures, using a commensal bacterial strain, within a 3D in vitro model of the vertebrate intestinal epithelium, interfaced with immune cells. We show functional and morphological changes in the intestinal barrier induced by the presence of bacteria and we then demonstrate the applicability of this 3D cell system to proof-of-concept studies of host-microbe interactions. More specifically, we show that exposure of the vertebrate 3D in vitro gut-immune cell models co-cultured with live cultures of Escherichia coli to ‘excretory/secretory products’ (ESP) from the nematode Teladorsagia circumcincta induces in vivo-like immune cell responses, down-regulating secretion of pro- and anti-inflammatory cytokines. These findings support the robustness of our modular in vitro cell systems for investigating the dynamics of host-microbe crosstalk and pave the way toward new approaches for systems biology studies of pathogens that cannot be maintained in vitro, such as parasitic helminths. 

Challenges on the interaction of models and policy for pandemic control

Liza Hadley, Department of Veterinary Medicine

The COVID-19 pandemic has seen a hugely expanded involvement of epidemic modelling in political decision-making. In this talk, we introduce a framework for challenges on the interface of outbreak modelling and decision-making. This work arose from the ‘Infectious Dynamics of Pandemics’ program at the Isaac Newton Institute, and features in the upcoming Epidemics special issue on ‘Challenges for Future Pandemics’.

We start by considering the problems of long-term preparedness and international cooperation. Next, decisions on policy need to weigh up the different effects of a pandemic on society, especially on health and on the economy. We consider the integration of modellers into decision-making and explore the inclusion of economic and social science expertise. Communication (among scientists, with decision-makers, and with the public) is our third major topic. We then conclude discussions with a look at the main technical challenges for developing models that address key policy questions, and finish by presenting a collection of recommendations and suggestions for future outbreak response.

Viral ribonucleoprotein condensates and RNA chaperones as paradigms for segmented RNA genome assembly.

Dr Alex Borodavka, Department of Biochemistry

A key process in the replication cycle of RNA viruses is the formation of dynamic organelles called viral factories. Multiple lines of evidence suggest that viral factories supporting replication of e.g., SARS-CoV-2, influenza, measles and respiratory syncytial viruses form via liquid-liquid phase separation (LLPS). We have recently shown that replication factories of rotaviruses, also known as viroplasms, represent protein-RNA granules formed by condensation of viroplasm-forming proteins NSP5 and the RNA chaperone NSP2. At physiologically relevant concentrations, these proteins spontaneously form condensates and absorb both single-stranded and double-stranded RNAs, as well as the viral RNA-dependent RNA polymerase. Using single-molecule fluorescence tools, we dissected individual steps of the RNA chaperone activity of NSP2, as well as of its functional analogue Reovirus sNS. We show that some aspects of the viral RNA chaperone regulation mirror the conserved autoregulation mechanisms employed by unrelated RNA chaperones. We propose that viral replication factories of several members of the Reoviridae family represent specialised ribonucleoprotein condensates enriched in viral RNA chaperones that support segment assortment and replication of their segmented genomes.

Investigating the mechanisms underpinning preferential invasion of reticulocytes by Plasmodium falciparum parasites

Dr Viola Introini, Cambridge Institute for Medical Research

Several malaria parasite species prefer to invade young immature red blood cells called reticulocytes, with Plasmodium vivax having an absolute requirement for these cells. However, Plasmodium falciparum, which causes most of the malaria morbidity and mortality for humans, has long been considered indifferent to host cell age. In this study, we show that while P. falciparum can invade red blood cells of any age, it also preferentially invades reticulocytes by investigating ligand-receptor interactions and reticulocyte biophysical properties. Reticulocytes represent a few percent of all circulating blood cells, and mature into erythrocytes within 24 hours, undergoing significant changes in their morphology and surface composition. We developed a protocol to routinely isolate reticulocytes from whole blood, and we studied invasion efficiency and dynamics of P. falciparum lines in which key parasite invasion ligands had been genetically deleted. Multiple wild-type lines had a clear preference for reticulocytes, but this was lost in EBA181 and Rh4 knock-out parasites. Finally, membrane fluctuation analysis was used to link the mechanics of reticulocytes to invasion. These findings shed a light on a long-standing mystery in the malaria field, why malaria parasites prefer young red blood cells and provide novel insights into the essential process of parasite invasion.

Testing the sit-and-wait hypothesis for the evolution of virulence in Streptococcus suis

Eliza Rayner, Department of Veterinary Medicine

Streptococcus suis is a commensal of the pig respiratory tract which can also cause respiratory and systemic infections in pigs and zoonotic disease in humans. In theory, pathogenicity should represent an evolutionary dead-end for S. suis, but phylogenetic trees exhibit significant clusters of pathogenic isolates and diversification within pathogenic lineages. This suggests there are fitness benefits of pathogenicity promoting its maintenance within S. suis which are not currently understood. 

One hypothesis of virulence evolution is the ‘sit-and-wait hypothesis’, which predicts a positive correlation between virulence and environmental persistence. It predicts that better outside-host survival would allow increased environmental transmission via fomites, reducing dependence on host activity for transmission and thus enabling the evolution of increased virulence. 

We used a comparative desiccation tolerance assay to test the survival of S. suis on environmental surfaces, sampling 74 strains at regular intervals up to approximately four weeks after desiccation to quantify the remaining viable bacteria. We found that pathogenic strains died out significantly later than commensals at the p=0.05 significance level, suggesting that pathogenic isolates exhibit greater average desiccation tolerance. Our results provide empirical support for the sit-and-wait hypothesis in S. suis, which could inform the control and prevention of disease outbreaks.

Functional characterization of the HIV-regulating protein, CHD1L, showing Africa-specific human genetic variation 

Dr Harriet Groom, Department of Medicine

Human Immunodeficiency Virus-1 (HIV-1) remains a global health crisis, highlighting the need to identify new therapies. Given the marked human genome diversity in Africa, we assessed the genetic determinants of control of HIV-1 setpoint viral load (spVL) in 3,879 individuals of African ancestry. We identify a novel association signal on chromosome 1 where the peak variant associates with a ~0.3 log10 copies/ml lower spVL and is specific to populations of African descent. The top associated variant is intergenic and lies between a long intergenic noncoding RNA (LINC00624) and the coding gene CHD1L, a helicase that binds to PARP1, a known HIV-1 host dependency factor. Infection assays in iPSC-derived macrophages demonstrated increased HIV-1 replication in CHD1L knockdown and knockout cells in a dose-dependent manner. We provide evidence from population genetic and experimental studies suggesting that CHD1L is a novel host HIV-1 restriction factor in human populations. Studies are ongoing to determine the mechanism underlying this important observation.

Investigating the Role of Tryptophanase in E. coli biofilms

Cameron Croft, Department of Genetics

Tryptophanase (TnaA), an enzyme present in many species of bacteria, is best known for the conversion of L-tryptophan to indole, pyruvate, and ammonia. However, TnaA can also metabolise other amino acids. We recently observed that a clumping phenotype seen during the exponential growth phase of a uropathogenic E. coli strain (ATCC® 25922™) was absent in a tnaA knock-out. We also found that this phenotype, which is characteristic of early-stage biofilm development, was reduced by novel TnaA inhibitors. Using clinical isolates from urinary tract infections (UTIs), which produce biofilms with indwelling catheters, we developed an assay to demonstrate that these compounds also reduce their biofilm development. The compounds are of interest because they could lead to the use of a TnaA inhibitor as a combination therapy with existing antibiotics to mitigate recurrent UTIs and biofilms.