Morning flash-talk session (12.10-12.40) – Chair: Prof Julian Parkhill
A multinational collaboration to estimate relative SARS-CoV-2 variant severity in six European countries based on a common protocol
Tommy Nyberg, MRC Biostatistics Unit
- Background: Several SARS-CoV-2 variants that evolved during the COVID-19 pandemic have appeared to differ in severity, based on analyses of single-country datasets. With decreased SARS-CoV-2 testing and sequencing, international collaborative studies will become increasingly important for timely assessment of the severity of newly emerged variants.
- Methods: The Joint WHO Regional Office for Europe and ECDC Infection Severity Working Group was formed to produce and pilot a standardised study protocol to estimate relative variant case-severity in settings with individual-level SARS-CoV-2 testing and COVID-19 outcome data during periods when two variants were co-circulating. To assess feasibility, the study protocol and its associated statistical analysis code was applied by local investigators in Denmark, England, Luxembourg, Norway, Portugal and Scotland to assess the case-severity of Omicron BA.1 relative to Delta cases.
- Results: After pooling estimates using meta-analysis methods, the risk of hospital admission (adjusted hazard ratio [aHR]=0.41, 95% CI 0.31-0.54), ICU admission (aHR=0.12, 95% CI 0.05-0.27), and death (aHR=0.31, 95% CI 0.28-0.35) was lower for Omicron BA.1 compared to Delta cases. The aHRs varied by age group and vaccination status.
- Conclusion: This study has demonstrated the feasibility of conducting variant severity analyses in a multinational collaborative framework. The results add further evidence for the reduced severity of the Omicron BA.1 variant.
Characterization of the essential lipopolysaccharide and multidrug ABC transporter MsbA from Gram-negative bacteria
Yakun Tang, Department of Pharmacology
The ATP-binding cassette (ABC) multidrug exporter MsbA mediates the translocation of lipopolysaccharides and phospholipids across the plasma membrane in Gram-negative bacteria. MsbA is essential for outer membrane formation, and is a potential target for the development of novel antibiotics against multidrug-resistant pathogens. Although MsbA is structurally well-characterised, biochemical studies on lipid transport are still limited. Using proteoliposomes containing purified MsbA and custom-made biotinylated-Lipid-A, we demonstrated for the first time the ability of MsbA to transport Lipid-A in an ATP-dependent fashion in a biochemical assay. We also report that, similar to the transport of small-molecule antibiotics and cytotoxic agents, the flopping of physiologically relevant long-acyl-chain 1,2-dioleoyl (C18)-phosphatidylethanolamine in proteoliposomes requires the simultaneous input of ATP binding and hydrolysis and the chemical proton gradient as sources of metabolic energy. Our mutational analyses indicate lipid and drug transport via the central binding chamber in MsbA. These results demonstrate that the energetics of lipid transport by MsbA is lipid dependent, and that the lipid availability in the membrane can affect the drug efflux activity by the transporter.
Uncovering commensal gut bacteria with antipathogen potential against the colonization of Enterobacteriaceae-associated species
Qi Yin, Department of Veterinary Medicine
The emergence of multidrug-resistant Enterobacteriaceae infections has become a major public health concern. Current antibiotic therapies face a dilemma in that they not only kill the targeted pathogens but also the normal resident intestinal microbial flora, leading to a disrupted gut microbiome. Therefore, there is an urgent need to explore novel antibacterial agents or therapies. To address this, we screened over 30,000 global human gut metagenomes to identify bacterial species and genes correlating with the presence of Enterobacteriaceae species in order to find those that may either aid or prevent their colonization. Our findings showed that bacterial species from the families Bacteroidaceae are overrepresented in gut microbiomes devoid of Enterobacteriaceae species, whereas the family Acutalibacteraceae usually co-occur with Enterobacteriaceae presence. In particular, the understudied species Ruthenibacterium lactatiformans was found to be most strongly associated with the presence of Enterobacteriaceae, suggesting a potential cooperative interaction. In contrast, the species Phocaeicola coprola (formerly Bacteroides coprola) was very strongly correlated with Enterobacteriaceaea absence, which may indicate a possible antagonistic relationship. We are currently investigating variations at a pangenomic and functional level to deduce novel mechanistic hypotheses that may help treat or prevent Enterobacteriaceae-associated infections.
Evolution of epidemic Pseudomonas aeruginosa adapted to specific human hosts
Aaron Weimann, Department of Medicine
Pseudomonas aeruginosa is a leading cause of various hospital-acquired infections and the principal cause of severe chronic lung infections in cystic fibrosis (CF). Despite the success of this bacteria, the factors underlying the evolution of Pseudomonas are unknown. We therefore asked how epidemic clones of Pseudomonas emerge and subsequently adapt to the human host.
To this end, we analysed 10,000 P. aeruginosa clinical genomes and clinical meta-data from more than 2800 patients globally. We found that more than 50% of the infections were caused by just 21 epidemic clones that have sequentially expanded and then disseminated across the world over the last 120 years. Using graphical pan-genome analysis, we then identified key horizontal gene transfer events associated with increases fitness of these epidemic lineages. The epidemic clones differed in their intrinsic ability to cause infection in CF or non-CF individuals. This CF affinity is associated with specific transcriptional signatures and experimentally leads to enhanced survival within CF macrophages, highlighting this as a critical step in establishing chronic lung infections.
We then tracked pathoadaptive evolution through multiple rounds of person-to-person transmission and identified, through mutational burden analysis, convergent evolution of 224 genes linked to host adaptation. We find clear support for distinct and specific evolutionary trajectories between clones infecting CF and non-CF populations, that may explain the low levels of cross-transmission between these groups. Our results point to a model for the emergence of Pseudomonas epidemic clones through saltational evolution via gene acquisition of ancestral environmental isolates followed by host-specific lung adaptation that determines clinical outcomes and transmission potential, and reveals key therapeutic targets to modulate virulence.
Antibiotic-mediated remodelling of species trajectories in a polymicrobial airway infection model
Eva Bernadett Benyei, Department of Biochemistry
Pseudomonas aeruginosa (PA) is designated as a critical priority pathogen by the WHO. In airway infection scenarios, PA shares the niche with a “zoo” of other microbes, including Gram-negative, Gram-positive and fungal species – yet little is currently known about how these co-habiting species affect the response of PA to antibiotic challenge.
PA is a very aggressive pathogen, and has proven difficult to stably co-culture with other species in vitro. However, this problem has been recently overcome with the introduction of a robust experimental platform that allows us to stably co-culture PA in artificial sputum medium with other airway-associated microbes, Staphylococcus aureus (SA) and Candida albicans (CA), for long periods of time. All three species frequently co-colonise airways of people with cystic fibrosis.
We found that the presence of other species greatly enhances the survival of PA when challenged with antibiotics (compared with survival of the species in monoculture). Some elements of this enhanced resistance were heritable, whereas others are associated with phenotypic adaptation. The relative efficacy of anti-pseudomonal antibiotics could be improved when they were applied in combination. However, this combination therapy, which is a common tactic deployed in the clinic, inadvertently led to a “blooming” of the fungal pathogen.
Afternoon flash-talk session (14.40-15.10) – Chair: Prof Martin Welch
The importance of vaccinated individuals to population-level evolution of pathogens
Maria A. Gutierrez, Department of Applied Mathematics and Theoretical Physics
Host immunity may drive pathogen evolution towards antigenic escape at the individual level. Using compartmental SIR-style models with imperfect vaccination, we allow the probability of immune escape to differ in vaccinated and unvaccinated hosts. As the relative contribution to evolution at the population level varies, the overall effect of vaccination on the resultant antigenic escape pressure changes between two different regimes.
We find that this relative contribution is critical to understanding how vaccination affects the escape pressure. If vaccinated hosts do not contribute much more than unvaccinated hosts to the escape pressure, increasing vaccination reduces the overall escape pressure. In contrast, if vaccinated hosts contribute significantly more than unvaccinated hosts to the population level escape pressure, then the escape pressure is maximal at intermediate vaccination levels.
If reinfections are possible, different behaviour is possible. If vaccines give at least as much protection as infection, vaccination always reduces the escape pressure, regardless of the escape contribution from infections in partially immune hosts. Our research also shows the importance of heterogeneous contributions to escape from the unvaccinated, such as immunocompromised hosts.
This work highlights the potential value of understanding better how the contribution to antigenic escape depends on individual host immunity.
Using mathematical models to explore future meningitis vaccination strategies in Ghana
Mark Asare Owusu, Department of Veterinary Medicine
Meningitis, an infection of the protective membranes that surround the brain and the spinal cord, affects more than 2.5 million individuals each year across the globe. The African meningitis belt, which includes Ghana, has experienced irregular but periodic epidemics of meningitis, primarily due to Neisseria meningitidis over 100 years. MenAfriVac, a vaccine against meningococcal serogroup A (the predominant cause of meningitis epidemics before 2010) has contributed to the drastic decline of these cases in the belt. Previous works have shown that, the vaccine does not induce permanent immunity and hence, there is a risk of resurgence if the population immunity is not maintained. For this reason, we explored the possible population immunity profile induced by MenAfriVac using duration specific exponential decay function in Ghana. Our results showed that, approximately 52% among the 1-29-year-olds risk age group are estimated to be directly protected in the Northern region if the duration of vaccine protection is 20 years by 2030. Under the 5 years duration of vaccine protection, only 16% of individuals in this risk age group are estimated to experience direct protection due to the vaccine. The implication of this study suggests that the duration of vaccine protection is an important parameter in making projections on the population immunity. Further studies including employing transmission dynamics model and seroprevalence study are warranted to capture both direct and indirect impacts of MenAfriVac, as well as reducing the uncertainty in the duration of the vaccine protection to collectively refine the estimates of this work.
Growth-rate dependent action of cell-wall targeting antibiotics
Leonardo Mancini, Department of Biochemistry/Physics
Cell wall-targeting antibiotics are widely used in clinical settings owing to their low toxicity to humans and excellent bacteriolytic properties. Most of these drugs belong to the class of beta-lactams and their mechanism of action relies on blocking enzymes involved in the synthesis of novel cell wall, which promotes cell wall hydrolysis. As a result, treated cells display altered morphologies and growth-dependent death dynamics. Mecillinam is a beta-lactam that selectively inhibits PBP2, an enzyme involved in cell elongation. Cells treated with Mecillinam swell losing their rod-shape and eventually lyse. By using a combination of mathematical modelling, bulk and single cell observations we show that death dynamics can be predicted quantitatively by a model based on two key concepts: growth-medium dependent exponential increase in biomass, combined with surface area growth that is inhibited by the antibiotic. Mechanically limiting morphological abnormalities using microfluidics completely abolishes cell death supporting a killing mechanism that is exquisitely dependent on cell geometry.
Enabling the in vitro study of long noncoding RNAs to understand their role in Plasmodium falciparum
Joa Hoshizaki, Wellcome Sanger Institute
Long noncoding RNAs (lncRNAs) have been identified in Plasmodium falciparum, the parasitic cause for life-threatening malaria, yet their role remains largely undiscovered. Through interactions with nucleic acids and proteins, lncRNAs can modulate gene expression. Determining the role of lncRNAs in the regulation of the P. falciparum transcriptome is imperative to further our understanding of gene regulation in the parasite. The characterisation of P. falciparum lncRNAs has been hindered by an incomplete annotation and the absence of disruption methods that together would permit high-throughput systematic knockdown of lncRNAs. During my PhD, I addressed these challenges to enable the study of P. falciparum lncRNAs in vitro. I generated a high-quality lncRNA annotation using manual curation of sequencing data generated at the Sanger Institute, along with supportive datasets from the literature. I evaluated CRISPR-based approaches for in vitro disruption of lncRNAs including gene knockout, knockdown, and interference. Furthermore, I implemented these tools to interrogate a set of lncRNAs that were selected based on predicted biological significance and targetability. LncR¬NA-depleted parasites were phenotypically characterised by assessing changes in fitness, drug resistance, gametocytogenesis and transcription. By developing bioinformatics and molecular tools, this work enables future studies elucidating the specific roles of lncRNAs in P. falciparum.
The role of antigenic and genetic diversity in driving disease risk of dengue infection
Lin Wang, Department of Genetics
The infection and disease processes of dengue virus (DENV) are driven by multiple competing factors, including the antigenic and genetic diversity of DENV and the effect of pre-existing immunity. How these complex factors drive the epidemiological observations in the hospital remains unclear. To address this question, we combine detailed genetic (N=2,198 viruses) and antigenic (N=396 viruses) characterisation of DENV from Bangkok Thailand across a 21-year period from 1994 to 2014, with detailed long-term serotype- and age-specific case data (N=6,903 cases over 18 years) from a large children hospital in the city. We develop a Bayesian framework that integrates over birth-cohorts lifetime exposures to the virus to critically explore whether the antigenic distance between viruses causing primary and secondary infections was linked to disease risk. We found that the specific virus that first infects an individual largely determines future disease risk when they are exposed to future different viruses. This study provides a unified framework to integrate heterogeneous data from hospital-based surveillance and pathogen genomics for assessing the infection and disease risk of DENV for each birth cohort in the community.