Ane Landajuela, Martha Braun, Christopher D.A. Rodrigues, Erdem Karatekin

Membrane fission is an essential process in all domains of life. The underlying mechanisms remain poorly understood in bacteria, partly because suitable assays are lacking. Here, we describe an assay to detect membrane fission during endospore formation in single Bacillus subtilis cells with a temporal resolution of ∼1 min. Other cellular processes can be quantified and temporally aligned to the membrane fission event in individual cells, revealing correlations and causal relationships.

STAR Protocols. March 2024

Branko Rihtman, Alberto Torcello-Requena, Alvetina Mikhaylina, Richard J Puxty, Martha RJ Clokie, Andrew D Millard, David J Scanlan

Phosphorus (P) is a major abiotic control on the marine cyanobacterium Synechococcus. Some viruses infecting Synechococcus have acquired, from their host, a gene encoding a P substrate binding protein (PstS), thought to improve virus replication under phosphate starvation. Yet, pstS is uncommon amongst cyanobacterial viruses. Thus, we asked how infections with viruses lacking PstS are affected by P scarcity. We show that production of infectious virus particles of such viruses is reduced in low P conditions. Our data shows how phage genomes, lacking obvious P-stress related genes, have evolved to exploit their host’s environmental sensing mechanisms to coordinate their own gene expression in response to resource limitation.

ISME Journal. March 2024

Anita Ramesh, Paula Oliveira, Mary Cameron, Priscila M S Castanha, Thomas Walker, Audrey Lenhart, Lucy Impoinvil, Neal Alexander, Zulma Medeiros, André Sá, Abraham Rocha, Wayner V Souza, Amélia Maciel, Cynthia Braga

Lymphatic filariasis (LF) is a leading cause of disability due to infectious disease worldwide. The Recife Metropolitan Region (RMR) is the only remaining focus of LF in Brazil, where the parasite Wuchereria bancrofti is transmitted solely by the mosquito Culex quinquefasciatus. This study reports the results of transmission assessment surveys and molecular xenomonitoring in the city of Olinda, RMR, after nearly 15 years (2015-2016) of interventions for LF elimination. Participants were screened for W. bancrofti antigen via immunochromatographic card tests (ICT), and all 1,170 children from MDA areas and the entire population sample of 990 residents in non-MDA areas were ICT negative. In MDA areas, a total of 3,152 female Cx. quinquefasciatus mosquitoes in 277 households were collected via aspiration. RT-qPCR of 233 pools of mosquitos were negative for W. bancrofti RNA; an independent reference laboratory confirmed these results. These results provide evidence that LF transmission has been halted in this setting.

American Journal of Tropical Medicine & Hygiene. March 2024

Brooks S, Weaver JA, Klomchit A, Alharthi SA, Onlamun T, Nurani R, Vong TK, Alberti F and Greco C

Endophytic fungi constitute a rich source of secondary metabolites that can be manipulated to produce desirable novel analogs for combating current agricultural challenges for crop production, especially controlling plant disease. The endophytic fungus Daldinia eschscholtzii MFLUCC 19-0629, was newly isolated from tropical ancient plants, Oncosperma sp., and displays a broad-spectrum of antifungal and antibacterial activities against several plant pathogens. The discovery that D. eschscholtzii MFLUCC 19-0629 has a broad spectrum of antimicrobial activity against seven major plant pathogenic microorganisms relevant to crop production and its complete genome sequence carries immense importance in the advancement of novel microbial biocontrol agents (MBCAs). This also unveils the prospect of uncovering new compounds that could be utilized for sustainable agriculture and pharmaceutical purposes.

Frontiers in Chemical Biology. March 2024

Kevin D. Whitley, James Grimshaw, David M. Roberts, Eleni Karinou, Phillip J. Stansfeld & Seamus Holden

Bacterial cell division requires septal peptidoglycan (sPG) synthesis by the divisome complex. Treadmilling of the essential tubulin homologue FtsZ has been implicated in septal constriction, though its precise role remains unclear. Here we used live-cell single-molecule imaging of the divisome transpeptidase PBP2B to investigate sPG synthesis dynamics in Bacillus subtilis. In contrast to previous models, we observed a single population of processively moving PBP2B molecules whose motion is driven by peptidoglycan synthesis and is not associated with FtsZ treadmilling. However, despite the asynchronous motions of PBP2B and FtsZ, a partial dependence of PBP2B processivity on FtsZ treadmilling was observed. Additionally, through single-molecule counting experiments we provide evidence that the divisome synthesis complex is multimeric. Our results support a model for B. subtilis division where a multimeric synthesis complex follows a single track dependent on sPG synthesis whose activity and dynamics are asynchronous with FtsZ treadmilling.

Nature Microbiology. March 2024

Camus Nimmo, Arturo Torres Ortiz, Cedric C. S. Tan, Juanita Pang, Mislav Acman, James Millard, Nesri Padayatchi, Alison D. Grant, Max O’Donnell, Alex Pym, Ola B. Brynildsrud, Vegard Eldholm, Louis Grandjean, Xavier Didelot, François Balloux & Lucy van Dorp

Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. We compiled a dataset of 3682 Mtb genomes, including 180 carrying variants in mmpR5, and its immediate background (i.e. mmpR5 promoter and adjacent mmpL5 gene), that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We characterised the occurrence of all nonsynonymous mutations in mmpR5 in this dataset and estimated, using time-resolved phylogenetic methods, the age of their emergence.

Genome Medicine. February 2024

Ryan Cook​, Nathan Brown​, Branko Rihtman​, Slawomir Michniewski​, Tamsin Redgwell, Martha Clokie​, Dov J. Stekel, Yin Chen​, David J. Scanlan​, Jon L. Hobman, Andrew Nelson​, Michael A. Jones​, Darren Smith​ and Andrew Millard

ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community. Thus, we constructed a mock bacteriophage community of previously sequenced phage genomes and sequenced them using Illumina, Nanopore and PacBio sequencing technologies and tested a number of different assembly approaches. Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short-read-only assemblies. When using a single technology, Illumina only was the best approach. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.

Microbial Genomics. February 2024

Javier Sánchez Romano, Jaione Simón-Santamaria, Peter McCourt, Bård Smedsrød, Kim Erlend Mortensen, Antonia P. Sagona, Karen Kristine Sørensen, Anett Kristin Larsen

Blood-borne phages are believed to be captured by macrophages in the liver and spleen. Since liver sinusoids also consist of specialized scavenger liver sinusoidal endothelial cells (LSECs) and Kupffer cells (KCs), this study investigated the contribution of both cell types in the elimination of Escherichia coli phage K1Fg10b::gfp (K1Fgfp) in mice. The results presented herein contribute to increased knowledge about the pharmacokinetics of the T7-like phage K1F in the mammalian system. The cell types of the liver that are responsible for rapid phage blood clearance are identified. Our results highlight the need for more research about appropriate dose regimens when phage therapy is delivered intravenously and advise essential knowledge about cell systems that should be investigated further for detailed phage pharmacodynamics.

mSphere. February 2024

Elena Fiorin, Charlotte A. Roberts, Marica Baldoni, Erin Connelly, Christina Lee, Claudio Ottoni & Emanuela Cristiani

Leprosy was one of the most outwardly visible diseases in the European Middle Ages, a period during which leprosaria were founded to provide space for the sick. In the present study, microremains and DNA were analysed from the calculus of individuals buried in the late medieval cemetery of St Leonard, a leprosarium located in Peterborough, England. The results show the presence of ginger (Zingiber officinale), a culinary and medicinal ingredient, as well as evidence of consumption of cereals and legumes. This research suggests that affected individuals consumed ingredients mentioned in medieval medical textbooks that were used to treat regions of the body typically impacted by leprosy. To the authors' knowledge, this is the first study which has identified Zingiber officinale in human dental calculus in England or on the wider European continent.

Scientific Reports. January 2024

Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes

Y Wan, AC Myall, A Boonyasiri, F Bolt, A Ledda, S Mookerjee, AY Weiße, M Getino, JF Turton, H Abbas, R Prakapaite, A Sabnis, A Abdolrasouli, K Malpartida-Cardenas, L Miglietta, H Donaldson, M Gilchrist, KL Hopkins, MJ Ellington, JA Otter, G Larrouy-Maumus, M Edwards, J Rodriguez-Manzano, X Didelot, M Barahona, AH Holmes, E Jauneikaite, F Davies

Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of IMP-encoding CPE amongst diverse Enterobacterales species between 2016 and 2019 across a London regional network. Our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multi-modal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.

Journal of Infectious Diseases. January 2024

Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK

Emily T. Fotopoulou​, Claire Jenkins, Clare R. Barker​, Anais Painset​, Xavier Didelot​, Ameze Simbo​, Amy Douglas​, Gauri Godbole​, Frieda Jorgensen​, Saheer Gharbia​, Jim McLauchlin

Listeria monocytogenes is a food-borne pathogen, typically affecting the elderly, immunocompromised patients and pregnant women. The aim of this study was to determine the population structure of L. monocytogenes clonal complex 1 (CC1) in the UK and describe the genomic epidemiology of this clinically significant CC. We interrogated a working dataset of 4073 sequences of L. monocytogenes isolated between January 2015 and December 2020 from human clinical specimens, food and/or foodproduction environments. Analysis of demographic and clinical outcome data identified CC1 as a clinically significant cause of invasive listeriosis in the elderly population and in women of child-bearing age. Phylogenetic analysis revealed the population structure of CC1 in the UK comprised small, sparsely populated genomic clusters. Only clusters containing isolates from an implicated food vehicle, or food processing or farming environments, were resolved, emphasizing the need for clinical, food and animal-health agencies to share sequencing data in real time, and the importance of a One Health approach to public-health surveillance of listeriosis.

Microbial Genomics. January 2024

Arnold W. Lambisia, Nickson Murunga, Martin Mutunga, Robinson Cheruiyot, Grace Maina, Timothy O. Makori, D. James Nokes and Charles N. Agoti

The non-pharmaceutical interventions (NPIs) implemented to curb the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic, substantially disrupted the activity of other respiratory viruses. However, there is limited data from low-and-middle income countries (LMICs) to determine whether these NPIs also impacted the transmission of common enteric viruses. Here, we investigated the changes in the positivity rate of five enteric viruses among hospitalised children who presented with diarrhoea to a referral hospital in coastal Kenya, during COVID-19 pandemic period. Our study finds that in 2020 the transmission of common enteric viruses, especially RVA and astrovirus, in Kilifi Kenya may have been disrupted due to the COVID-19 NPIs. After 2020, local enteric virus transmission patterns appeared to return to pre-pandemic levels coinciding with the removal of most of the government COVID-19 NPIs.

Gut Pathogens. January 2024

Jake Carson, Matt Keeling, David Wyllie, Paolo Ribeca, Xavier Didelot

Here we present a new methodology that can use any number of genomes sampled from a set of individuals to reconstruct their transmission network. Furthermore, we remove the need for the assumption of a complete transmission bottleneck. We use simulated data to show that our method becomes more accurate as more genomes per host are provided, and that it can infer key infectious disease parameters such as the size of the transmission bottleneck, within-host growth rate, basic reproduction number and sampling fraction. We demonstrate the usefulness of our method in applications to real datasets from an outbreak of Pseudomonas aeruginosa amongst cystic fibrosis patients and a nosocomial outbreak of Klebsiella pneumoniae.

Molecular Biology & Evolution. January 2024

Guillermo Friis, Edward G. Smith, Catherine E. Lovelock, Alejandra Ortega, Alyssa Marshell, Carlos M. Duarte, John A. Burt

Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The grey mangroves (Avicennia marina) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyse fully sequenced genomes sampled from 19 locations across the Red Sea, the Arabian Sea and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Our results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.

Molecular Ecology. January 2024

Rysava, Kristyna and Tildesley, Michael J

Here, we present a quantitative framework using a series of progressively more biologically realistic models of canine rabies in domestic dogs and from dogs to humans, a suitable example system to characterize dynamical changes under varying levels of dog quarantine. We explicitly incorporate health-seeking behaviour data to inform the modelling of contact-tracing and exclusion of rabies suspect and probable dogs that can be identified through bite-histories of patients presenting at anti-rabies clinics. We find that a temporary quarantine of rabies suspect and probable dogs provides a powerful tool to curtail rabies transmission, especially in settings where optimal vaccination coverage is yet to be achieved, providing a critical stopgap to reduce the number of human and animal deaths due to rabid bites.

PLoS Computational Biology. December 2023

Huba L Marton, Apoorva Bhatt, Antonia P Sagona, Peter Kilbride, Matthew I Gibson

Bacteriophages have many biotechnological and therapeutic applications, but as with other biologics, cryopreservation is essential for storage and distribution. Macromolecular cryoprotectants are emerging for a range of biologics, but the chemical space for polymer-mediated phage cryopreservation has not been explored. Here we screen the cryoprotective effect of a panel of polymers against five distinct phages, showing that nearly all the tested polymers provide a benefit. This work shows that phages are amenable to protection with hydrophilic polymers and opens up new opportunities for advanced formulations for future phage therapies and to take advantage of the additional functionality brought by the polymers.

Biomacromolecules. December 2023

Jan Böhning, Miles Graham, Suzanne C. Letham, Luke K. Davis, Ulrike Schulze, Phillip J. Stansfeld, Robin A. Corey, Philip Pearce, Abul K. Tarafder, Tanmay A. M. Bharat

Inoviruses are filamentous phages infecting numerous prokaryotic phyla. Inoviruses can self-assemble into mesoscale structures with liquid-crystalline order, termed tactoids, which protect bacterial cells in Pseudomonas aeruginosa biofilms from antibiotics. Here, we investigate the structural, biophysical, and protective properties of tactoids formed by the P. aeruginosa phage Pf4 and Escherichia coli phage fd. This study provides insights into how filamentous molecules protect bacteria from extraneous substances in biofilms and in host-associated infections.

Nature Communications. December 2023

Kaisa Thorell, Zilia Y Muñoz-Ramírez, Difei Wang, Santiago Sandoval-Motta, Rajiv Boscolo Agostini, Silvia Ghirotto, Roberto C Torres; HpGP Research Network (inc. Xavier Didelot); Daniel Falush, M Constanza Camargo, Charles S Rabkin

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics.

Nature Communications. December 2023

Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons

D. Collins Owuor, Zaydah R. de Laurent, Bryan O. Nyawanda, Gideon O. Emukule, Rebecca Kondor, John R. Barnes, D. James Nokes, Charles N. Agoti and Sandra S. Chaves

Influenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making. We sequenced and phylogenetically analyzed A(H1N1)pdm09 virus genome sequences obtained from specimens collected from hospitalized patients of all ages with or without pneumonia between 2009 and 2018 from seven sentinel surveillance sites across Kenya. We compared these sequences with recommended vaccine strains during the study period to infer genetic and potential antigenic changes in circulating viruses and associations of clinical outcome. Our study highlights the necessity of timely genomic surveillance to monitor the evolutionary changes of influenza viruses. Routine influenza surveillance with broad geographic representation and whole genome sequencing capacity to inform on prioritization of antigenic analysis and the severity of circulating strains are critical to improved selection of influenza strains for inclusion in vaccines.

Scientific Reports. December 2023

Changes in the global hospitalisation burden or respiratory syncytial virus in young children during the COVID-19 pandemic: a systematic analysis

Bingbing Cong et al inc. D J Nokes.

We aimed to assess the hospitalisation burden of respiratory syncytial virus (RSV)-associated acute lower respiratory infection (ALRI) in children younger than 5 years during the pandemic period and the possible changes in RSV epidemiology from a global perspective. Our finding suggest that the hospitalisation burden of RSV-associated ALRI in children younger than 5 years was significantly reduced during the first year of the COVID-19 pandemic. The rebound in hospitalisation rates to pre-pandemic rates observed in the high-income region but not in the middle-income region by March, 2022, suggests a persistent negative impact of the pandemic on health-care systems and health-care access in the middle-income region. RSV surveillance needs to be established (or re-established) to monitor changes in RSV epidemiology, particularly in low-income and lower-middle-income countries.

Lancet Infectious Diseases. December 2023

Orin Courtenay, José F Marinho-Júnior, Maria Edileuza F Brito, Juliana FCLS Monteiro, Jeffrey J Shaw, Sinval P. Brandão-Filho

Human and wild rodent infection rates with Leishmania (Viannia) braziliensis are needed to differentiate transmission pathways in anthropogenically altered habitats.  In this study, human participants in northeast Brazil were tested by the leishmanin skin test (LST) and inspected for lesions/scars characteristic of American clinical leishmaniasis (ACL). Molecular (PCR/qPCR) test records of free-ranging rodents were available from a concurrent capture–mark–recapture study. Force of Infection (λ) and recovery (ρ) rates were estimated from cross-sectional and longitudinal datasets. The results show human exposure to L. (V.) braziliensis continues to be high despite the substantial drop in reported ACL cases in recent years. Spill-over transmission risk to humans from rodents in peridomestic habitats is likely supported by a rodent infection/transmission corridor linking houses, plantations, and the Atlantic Forest.

Pathogens. December 2023

Esther Ivorra-Molla, Dipayan Akhuli, Martin B. L. McAndrew, William Scott, Lokesh Kumar, Saravanan Palani, Masanori Mishima, Allister Crow & Mohan K. Balasubramanian

StayGold is an exceptionally bright and stable fluorescent protein that is highly resistant to photobleaching. Despite favorable fluorescence properties, use of StayGold as a fluorescent tag is limited because it forms a natural dimer. Here we report the 1.6 Å structure of StayGold and generate a derivative, mStayGold, that retains the brightness and photostability of the original protein while being fully monomeric.

Nature Biotechnology. December 2023

George Muscatt, Ryan Cook, Andrew Millard, Gary D Bending, Eleanor Jameson

To investigate viral communities throughout the soil depth profile, we leveraged a publicly available metagenomic data set sampled from grassland soil in Northern California. In total, 10,196 non-redundant viral operational taxonomic units were recovered from soil between 20 cm and 115 cm below the surface. Viral diversity was assessed at both the population level and strain level to reveal diverse ecological and evolutionary patterns of virus-host interactions in surface and subsurface soils. Investigating viral microdiversity uncovered potential patterns of antagonistic co-evolution across both surface and subsurface soils. We have provided evidence for the potential of soil viruses to augment the remineralization of soil carbon. While we continue to yield a more comprehensive understanding of soil viral ecology, our work appeals to future researchers to further investigate subsurface viral communities.

Microbial Ecology. November 2023

T. Bertie Ansell, Wanling Song, Claire E. Coupland, Loic Carrique, Robin A. Corey, Anna L. Duncan, C. Keith Cassidy, Maxwell M. G. Geurts, Tim Rasmussen, Andrew B. Ward, Christian Siebold, Phillip J. Stansfeld, Mark S. P. Sansom

Cryo-electron microscopy (cryo-EM) enables the determination of membrane protein structures in native-like environments. Characterising how membrane proteins interact with the surrounding membrane lipid environment is assisted by resolution of lipid-like densities visible in cryo-EM maps. Nevertheless, establishing the molecular identity of putative lipid and/or detergent densities remains challenging. Here we present LipIDens, a pipeline for molecular dynamics (MD) simulation-assisted interpretation of lipid and lipid-like densities in cryo-EM structures.

Nature Communications. November 2023

McKendrick, James, Tennant, Warren S. D. and Tildesley, Michael J.

Lassa fever (Lf) is a viral haemorrhagic disease endemic to West Africa and is caused by the Lassa mammarenavirus. The rodent Mastomys natalensis serves as the primary reservoir and its ecology and behaviour have been linked to the distinct spatial and temporal patterns in the incidence of Lf. While previous research has modelled the case seasonality within Nigeria, this did not capture the seasonal variation in the reproduction of the zoonotic reservoir and its effect on case numbers. To this end, we introduce an approximate Bayesian computation scheme to fit our model to the case data from 2018–2020 supplied by the NCDC. In this study we used a periodically forced seasonal nonautonomous system of ordinary differential equations as a vector model to demonstrate that the population dynamics of the rodent reservoir may be responsible for the spikes in the number of observed cases in humans.

PLoS Neglected Tropical Diseases.November 2023

Yenew, B., et al. (incl. Didelot, X)

The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.

Nature Communications. November 2023

Massimo Cavallaro, Louise Dyson, Michael J Tildesley, Dan Todkill, Matt J Keeling

The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. Here we study the spatial invasion and early spread of the Alpha, Delta and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.

Journal of the Royal Society Interface. November 2023

Patrick Becker, Fiona B. Naughton, Deborah H. Brotherton, Raul Pacheco-Gomez, Oliver Beckstein, Alexander D. Cameron

The bile acid sodium symporter (BASS) family transports a wide array of molecules across membranes, including bile acids in humans, and small metabolites in plants. These transporters, many of which are sodium-coupled, have been shown to use an elevator mechanism of transport, but exactly how substrate binding is coupled to sodium ion binding and transport is not clear. Here, we solve the crystal structure at 2.3 Å of a transporter from Neisseria meningitidis (ASBTNM) in complex with pantoate, a potential substrate of ASBTNM.. Comparison of structures in the presence and absence of pantoate demonstrates that pantoate elicits a conformational change in one of the cross-over helices. This modifies the interface between the two domains that move relative to one another to elicit the elevator mechanism. These results have implications, not only for ASBTNM but for the BASS family as a whole and indeed other transporters that work through the elevator mechanism.

eLife. November 2023

Holly Acford-Palmer, Monica Campos, Janvier Bandibabone, Sévérin N’Do, Chimanuka Bantuzeko, Bertin Zawadi, Thomas Walker, Jody E. Phelan, Louisa A. Messenger, Taane G. Clark & Susana Campino

Vector control strategies have been successful in reducing the number of malaria cases and deaths globally, but the spread of insecticide resistance represents a significant threat to disease control. To support the continuous efficacy of vector control strategies, it is essential to monitor insecticide resistance using molecular surveillance tools. In this study, we developed an amplicon sequencing (“Amp-seq”) approach targeting An. funestus, and using multiplex PCR, dual index barcoding, and next-generation sequencing for high throughput and low-cost applications. Overall, our panel represents an extendable and much-needed method for the molecular surveillance of insecticide resistance in An. funestus populations.

Scientific Reports. October 2023

Yiying Yang, Haoxiang Chen, Robin A. Corey, Violette Morales, Yves Quentin, Carine Froment, Anne Caumont-Sarcos, Cécile Albenne, Odile Burlet-Schiltz, David Ranava, Phillip J. Stansfeld, Julien Marcoux, Raffaele Ieva

Insertion of lipopolysaccharide (LPS) into the bacterial outer membrane (OM) is mediated by a druggable OM translocon consisting of a β-barrel membrane protein, LptD, and a lipoprotein, LptE. The β-barrel assembly machinery (BAM) assembles LptD together with LptE at the OM. In the enterobacterium Escherichia coli, formation of two native disulfide bonds in LptD controls translocon activation. Here we report the discovery of LptM (formerly YifL), a lipoprotein conserved in Enterobacteriaceae, that assembles together with LptD and LptE at the BAM complex.. Our results suggest that, by mimicking LPS binding, LptM facilitates oxidative maturation of LptD, thereby activating the LPS translocon.

Nature Communications. October 2023

Chan, Y. L. Elaine, Irvine, Michael A., Prystajecky, Natalie, Sbihi, Hind, Marsha, Taylor, Joffres , Yayuk, Schertzer, Andrea, Rose, Caren, Dyson, Louise, Hill, Edward M., Tildesley, Michael J., Tyson, John R., Hoang, Linda M. N. and Galanis, Eleni

In British Columbia, Canada, initial growth of the SARS-CoV-2 Delta variant was slower than that reported in other jurisdictions. We describe the growth of Delta variant cases in British Columbia during March1 – June 20 2021, and apply retrospective counterfactual modelling to examine factors for the initially low COVID-19 case rate after Delta introduction, such as vaccination coverage and nonpharmaceutical interventions. Grwth of COVID-19 cases in the first 3 months after Delta emergence was likely limited in British Columbia because additional nonpharmaceutical interventions were implemented.

Emerging Infectious Diseases.October 2023

Aina Mercant Osuna, Alexandra Gidley, Marie Paul Audrey Mayi, Roland Bamou, Vishaal Dhokiya, Christophe Antonio-Nkondjio, Claire Louise Jeffries, Thomas Walker

The endosymbiotic bacterium Wolbachia infects numerous species of insects and Wolbachia transinfection of Aedes mosquito species is now being used for biocontrol programs as Wolbachia strains can both inhibit arboviruses and invade wild mosquito populations. The discovery of novel, resident Wolbachia strains in mosquito species warrants further investigation as potential candidate strains for biocontrol strategies. We obtained mosquito specimens from diverse Culicine mosquitoes from Cameroon including ecologically diverse locations in the Central and West Regions. Wolbachia prevalence rates were assessed in addition to the environmentally acquired bacterial species Asaia in major Culicine genera Our study provides further evidence that Wolbachia is widespread within wild mosquito populations of diverse Culicine species and provides further candidate strains that could be investigated as future options for Wolbachia-based biocontrol to inhibit arbovirus transmission.

Wellcome Open Research. September 2023

Arturo Torres Ortiz, Michelle Kendall, Nathaniel Storey, James Hatcher, Helen Dunn, Sunando Roy, Rachel Williams, Charlotte Williams, Richard A Goldstein, Xavier Didelot, Kathryn Harris, Judith Breuer, Louis Grandjean

Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is partially maintained among repeated serial samples from the same host, it can transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.

eLife. September 2023

Katherine E. Gallagher & Joyce Nyiro, Charles N. Agoti, Eric Maitha, James Nyagwange, Angela Karani, Christian Bottomley, Nickson Murunga, George Githinji, Martin Mutunga, Lynette Isabella Ochola-Oyier, Ivy Kombe, Amek Nyaguara, E. Wangeci Kagucia, George Warimwe, Ambrose Agweyu, Benjamin Tsofa, Philip Bejon, J. Anthony G. Scott, David James Nokes 

We estimated the secondary attack rate of SARS-CoV-2 among household contacts of PCR-confirmed cases of COVID-19 in rural Kenya and analysed risk factors for transmission. We enrolled incident PCR-confirmed cases and their household members. At baseline, a questionnaire, a blood sample, and naso-oropharyngeal swabs were collected. Household members were followed 4, 7, 10, 14, 21 and 28 days after the date of the first PCR-positive in the household; naso-oropharyngeal swabs were collected at each visit and used to define secondary cases. Blood samples were collected every 1–2 weeks. Symptoms were collected in a daily symptom diary. We used binomial regression to estimate secondary attack rates and survival analysis to analyse risk factors for transmission. Households in our setting experienced a lower 7-day attack rate than a recent meta-analysis indicated as the global average (23%–43% depending on variant), and infection is mostly asymptomatic in our setting.

Influenza & other Respiratory Diseases. September 2023

Hill, Edward M, Prosser, Naomi S, Brown, Paul E, Ferguson, Eamonn, Green, Martin J, Kaler, Jasmeet, Keeling, Matt J and Tildesley, Michael J

Human behaviour is critical to effective responses to livestock disease outbreaks, especially with respect to vaccination uptake. Traditionally, mathematical models used to inform this behaviour have not taken heterogeneity in farmer behaviour into account. We address this by exploring how heterogeneity in farmers vaccination behaviour can be incorporated to inform mathematical models. We developed and used a graphical user interface to elicit farmers (n = 60) vaccination decisions to an unfolding fast-spreading epidemic and linked this to their psychosocial and behavioural profiles. We identified, via cluster analysis, robust patterns of heterogeneity in vaccination behaviour. By incorporating these vaccination behavioural groupings into a mathematical model for a fast-spreading livestock infection, using computational simulation we explored how the inclusion of heterogeneity in farmer disease control behaviour may impact epidemiological and economic focused outcomes.

Preventive Veterinary Medicine. September 2023

Joanna N de Klerk, Erin E Gorsich, John D Grewar, Benjamin D Atkins, Warren S D Tennant, Karien Labuschagne, Michael J Tildesley

African horse sickness is an equine orbivirus transmitted by Culicoides Latreille biting midges. The disease is endemic in South Africa; however, a unique control area has been set up in the Western Cape where increased surveillance and control measures have been put in place. A deterministic metapopulation model was developed to explore if an outbreak might occur, and how it might develop, if a latently infected horse was to be imported into the control area, by varying the geographical location and months of import. A sensitivity analysis indicated that control measures such as vaccination and vector control are potentially effective to manage the spread of an outbreak, and shortening the vaccination window to July to September may reduce the risk of vaccine-associated outbreaks.

PLoS Computational Biology. September 2023

Margo Chase-Topping, Timothy J. Dallman, Lesley Allison , Nadejda Lupolova, Louise Matthews, Sonia Mitchell, Christopher J. Banks, Jamie Prentice, Helen Brown, Sue Tongue, Madeleine Henry, Judith Evans, George Gunn, Deborah Hoyle, Tom N. McNeilly, Stephen Fitzgerald, Alison Smith-Palmer, Sharif Shaaban, Anne Holmes, Mary Hanson, Mark Woolhouse, Xavier Didelot, Claire Jenkins and David L. Gall

For the last two decades, the human infection frequency of Escherichia coli O157 (O157) in Scotland has been 2.5-fold higher than in England and Wales. Results from national cattle surveys conducted in Scotland and England and Wales in 2014/2015 were combined with data on reported human clinical cases from the same time frame to determine if strain differences in national populations of O157 in cattle could be associated with higher human infection rates in Scotland. There was evidence of limited cattle strain migration between nations and clinical isolates from one nation were more similar to cattle isolates from the same nation, with sub-lineage Ic (mainly PT21/28) exhibiting clear national association and evidence of local transmission in Scotland. While we propose the higher rate of O157 clinical cases in Scotland is a consequence of the nationally higher level of Stx2a+O157 strains in Scottish cattle, we discuss the multiple additional factors that may also contribute to the different infection rates between these nations.

Microbial Genomics. September 2023

Julie Rushmore, Brianna R. Beechler, Hannah Tavalire, Erin E. Gorsich, Bryan Charleston, Anne Devan-Song, Caroline K. Glidden, Anna E. Jolles

Here, we analyzed African buffalo social networks to quantify variation in close contacts, examined drivers of contact heterogeneity, and investigated how the observed contact patterns affect pathogen invasion likelihoods for a wild social ungulate. Although the observed herd was well connected, with most individuals contacting each other during each bimonthly interval, our analyses revealed striking heterogeneity in close-contact associations among herd members. Network analysis showed that individual connectivity was stable over time and that individual age, sex, reproductive status, and pairwise genetic relatedness were important predictors of buffalo connectivityThese findings highlight the role susceptible calves may play in the transmission of pathogens within the herd. We also demonstrate that, at time scales relevant to infectious pathogens found in nature, the observed level of connectivity affects pathogen invasion likelihoods for a wide range of infectious periods and transmissibilities. Ultimately, our study identifies key predictors of social connectivity in a social ungulate and illustrates how contact heterogeneity, even within a highly connected herd, can shape pathogen invasion likelihoods.

Ecology and Evolution. August 2023

Rie Nygaard, Chris L. B. Graham, Meagan Belcher Dufrisne, Jonathan D. Colburn, Joseph Pepe, Molly A. Hydorn, Silvia Corradi, Chelsea M. Brown, Khuram U. Ashraf, Owen N. Vickery, Nicholas S. Briggs, John J. Deering, Brian Kloss, Bruno Botta, Oliver B. Clarke, Linda Columbus, Jonathan Dworkin, Phillip J. Stansfeld, David I. Roper & Filippo Mancia

Peptidoglycan (PG) assembly requires a glycosyltransferase (GT) to generate a glycan polymer using a Lipid II substrate, which is then crosslinked to the existing PG via a transpeptidase (TP) reaction. A Shape, Elongation, Division and Sporulation (SEDS) GT enzyme and a Class B Penicillin Binding Protein (PBP) form the core of the multi-protein complex required for PG assembly. Here we used single particle cryo-electron microscopy to determine the structure of a cell elongation-specific E. coli RodA-PBP2 complex. We combine this information with biochemical, genetic, spectroscopic, and computational analyses to identify the Lipid II binding sites and propose a mechanism for Lipid II polymerization. Our data suggest a hypothesis for the movement of the glycan strand from the Lipid II polymerization site of RodA towards the TP site of PBP2, functionally linking these two central enzymatic activities required for cell wall peptidoglycan biosynthesis.

Nature Communications. August 2023

Suhad AA Al-Salihi and Fabrizio Alberti

Fungi represents a rich repository of taxonomically restricted, yet chemically diverse, secondary metabolites that are synthesised via specific metabolic pathways. An enzyme’s specificity and biosynthetic gene clustering are the bottleneck of secondary metabolite evolution. Trichoderma harzianum M10 v1.0 produces many pharmaceutically important molecules; however, their specific biosynthetic pathways remain uncharacterised. Our genomic-based analysis of this species reveals the biosynthetic diversity of its specialised secondary metabolites, where over 50 BGCs were predicted, most of which were listed as polyketide-like compounds associated clusters. Revealing the biogenetic background of these natural molecules is a step forward towards the expansion of their chemical diversification via engineering their biosynthetic genes heterologously, and the identification of their role in the interaction between this fungus and its biotic/abiotic conditions as well as its role as bio-fungicide. 

Journal of Fungi. August 2023

Louisa A Messenger, Nancy S Matowo, Chad L Cross, Mohamed Jumanne, Natalie M Portwood, Jackline Martin, Eliud Lukole, Elizabeth Mallya, Jacklin F Mosha, Robert Kaaya, Oliva Moshi, Bethanie Pelloquin, Katherine Fullerton, Alphaxard Manjurano, Franklin W Mosha, Thomas Walker, Mark Rowland, Manisha A Kulkarni, Natacha Protopopof

Insecticide resistance among malaria-vector species is a pervasive problem that might jeopardise global disease-control efforts. Novel vector-control tools with different modes of action, including long-lasting insecticidal nets (LLINs) incorporating new active ingredients, are urgently needed to delay the evolution and spread of insecticide resistance. We aimed to measure phenotypic and genotypic insecticide-resistance profiles among wild Anopheles collected over 3 years to assess the longitudinal effects of dual-active-ingredient LLINs on insecticide resistance.

Lancet Planetary Health. August 2023

Chatzichristofi, Agathangelos, Sagris, Vasileios, Pallaris, Aristos, Eftychiou, Marios, Kalvari, Ioanna, Price, Nicholas, Theodosiou, Theodosios, Iliopoulos, Ioannis, Nezis, Ioannis P. and Promponas, Vasilis J

Several selective macroautophagy receptor and adaptor proteins bind members of the Atg8 (autophagy related 8) family using short linear motifs (SLiMs), most often referred to as Atg8-family interacting motifs (AIMs) or LC3-interacting regions (LIRs). AIM/LIR motifs have been extensively studied during the last fifteen years, since they can uncover the underlying biological mechanisms and possible substrates for this key catabolic process of eukaryotic cells. Prompted by the fact that experimental information regarding LIR motifs can be found scattered across heterogeneous literature resources, we have developed LIRcentral (https://lircentral.euLink opens in a new window), a freely available online repository for user-friendly access to comprehensive, high-quality information regarding LIR motifs from manually curated publications. Herein, we describe the development of LIRcentral and showcase currently available data and features, along with our plans for the expansion of this resource.

Autophagy. August 2023

Tayseer Jibreel, Altayeb Khogali, Maribel Jiménez, Raiyed, Adeel, Osman Dakein, Bashir Alsharif, Noteila M. Khalid, Omran F. Osman, Bakri Y M Nour, Gamal Hassan Mohamed, Ricardo Molina, Ana Vidal, Ramón Díaz-Regañón, Margriet den Boer, Jorge Alvar, Orin Courtenay, D. A. Elnaiem

Visceral leishmaniasis (VL, kala azar), caused by Leishmania donovani, transmitted by Phlebotomus orientalis, is a serious systemic disease that causes high morbidity and mortality rates in Sudan and other parts of East Africa and the world. Despite progress in understanding the epidemiology of the disease in East Africa, little is known about the host preference of P. orientalis in kala azar endemic villages of Sudan, which have some of the highest VL incidence rates in the world. The present study used host choice experiments and blood-meal identification approaches to determine the host preference of P. orientalis in kala azar endemic villages in Gedarif state, eastern Sudan. Although the order of host preference varied by location, it was clear that cows are the most preferred host of P. orientalis in the area. Results are discussed in relation to the role of domestic/livestock animals in VL zoopotentiation and zooprophylaxis. Inference is made on the potential impact of insecticide treatment of cows in control of the vector and the transmission of VL in Sudan and other parts of East Africa.

Medical and Veterinary Entomology. August 2023

D Xu, W Jiang, . Wu, RG Gaudet, E-S Park, M Su, SK Cheppali, NR Cheemarla, P Kumar, PD Uchil, JR Grover, EF Foxman, CM Brown, PJ Stansfeld, J Bewersdorf, W Mothes, E Karatekin, CB Wilen, and JD MacMicking

Understanding protective immunity to COVID-19 facilitates preparedness for future pandemics and combats new SARS-CoV-2 variants emerging in the human population. Neutralizing antibodies have been widely studied; however, on the basis of large-scale exome sequencing of protected versus severely ill patients with COVID-19, local cell-autonomous defence is also crucial. Here we identify phospholipid scramblase 1 (PLSCR1) as a potent cell-autonomous restriction factor against live SARS-CoV-2 infection in parallel genome-wide CRISPR–Cas9 screens of human lung epithelia and hepatocytes before and after stimulation with interferon-γ (IFNγ). IFNγ-induced PLSCR1 not only restricted SARS-CoV-2 USA-WA1/2020, but was also effective against the Delta B.1.617.2 and Omicron BA.1 lineages. . Our mechanistic studies, together with reports that COVID-associated PLSCR1 mutations are found in some susceptible people, identify an anti-coronavirus protein that interferes at a late entry step before viral RNA is released into the host-cell cytosol.

Nature. July 2023

Samuel P. C. Brand, Massimo Cavallaro, Fergus Cumming , Charlie Turner , Isaac Florence, Paula Blomquist, Joe Hilton, Laura M. Guzman-Rincon, Thomas House, D. James Nokes and Matt J. Keeling 

Beginning in May 2022, Mpox virus spread rapidly in high-income countries through close human-to-human contact primarily amongst communities of gay, bisexual and men who have sex with men (GBMSM). Behavioural change arising from increased knowledge and health warnings may have reduced the rate of transmission and modified Vaccinia-based vaccination is likely to be an effective longer-term intervention. We investigated the UK epidemic presenting 26-week projections using a stochastic discrete-population transmission model. The Mpox cases peaked in mid-July; our analysis is that the decline was due to decreased transmission rate per infected individual and infection-induced immunity among GBMSM, especially those with the highest rate of new partners. Vaccination did not cause Mpox incidence to turn over, however, we predict that a rebound in cases due to behaviour reversion was prevented by high-risk group-targeted vaccination.

Nature Communications. July 2023

Fuss MF, Wieferig JP, Corey RA, Hellmich Y, Tascón I, Sousa JS, Stansfeld PJ, Vonck J, Hänelt I

Cyclic di-AMP is the only known essential second messenger in bacteria and archaea, regulating different proteins indispensable for numerous physiological processes. In particular, it controls various potassium and osmolyte transporters involved in osmoregulation. In this study, we reveal the molecular basis of how c-di-AMP binding inhibits KimA. We report cryo-EM structures of KimA with bound c-di-AMP in detergent solution and reconstituted in amphipols. By combining structural data with functional assays and molecular dynamics simulations we reveal how c-di-AMP modulates transport. We show that an intracellular loop in the transmembrane domain interacts with c-di-AMP bound to the adjacent cytosolic domain. This reduces the mobility of transmembrane helices at the cytosolic side of the K+ binding site and therefore traps KimA in an inward-occluded conformation.

Nature Communications. June 2023

Joshua Williams, Jaimee Kerven, Yin Chen, Antonia P. Sagona 

Many bacterial pathogens, such as Escherichia coli, can cause diseases intracellularly via cell entry and avoidance of the host immune system. Antibiotic resistance has caused such infections to be problematic, which has necessitated the development of new antimicrobials. Bacteriophages are a potent alternative due to their specificity and ease of genetic modification. We have engineered phage K1F, which is specific to E. coli K1 to express an epidermal growth factor (EGF) and green fluorescent protein (GFP) fusion on the minor capsid protein. Here, we demonstrate that EGF-labeled phage K1F can be internalized more readily in human cell lines to eradicate E. coli K1 infection intracellularly. Further, we establish that K1F-GFP-EGF enters human cells primarily through endocytosis following EGF receptor (EGFR) induction, subverting the phagocytic mode of entry and permitting its accretion in the cytosol to seek out its bacterial host.

ACS Synthetic Biology. June 2023

Helekal D, Keeling M, Grad YH, Didelot X

Resistance to an antibiotic provides a fitness benefit when the bacteria are exposed to this antibiotic, but resistance also often comes at a cost to the resistant pathogen relative to susceptible counterparts. We lack a good understanding of these benefits and costs of resistance for many bacterial pathogens and antibiotics, but estimating them could lead to better use of antibiotics in a way that reduces or prevents the spread of resistance. Here, we propose a new model for the joint epidemiology of susceptible and resistant variants, which includes explicit parameters for the cost and benefit of resistance. We show how Bayesian inference can be performed under this model using phylogenetic data from susceptible and resistant lineages and that by combining data from both we are able to disentangle and estimate the resistance cost and benefit parameters separately.

Journal of the Royal Society Interface. June 2023

Jonathan Cook, Tyler C Bavistock, Martin BL McAndrew, David I Roper, Phillip J Stansfeld and Allister Crow

Here, we present a high-resolution structure of the isolated AmiA protein, confirming that it is autoinhibited in the same manner as AmiB and AmiC, and a complex of the AmiB enzymatic domain bound to the activating EnvC LytM domain. In isolation, the active site of AmiA is blocked by an autoinhibitory helix that binds directly to the catalytic zinc and fills the volume expected to accommodate peptidoglycan binding. In the complex, binding of the EnvC LytM domain induces a conformational change that displaces the amidase autoinhibitory helix and reorganizes the active site for activity. Our structures, together with complementary mutagenesis work, defines the conformational changes required to activate AmiA and/or AmiB through their interaction with other cognate activator EnvC.

PNAS.; June 2023

Ramón Garcia Maset, Alexia Hapeshi, John Lapage, Niamh Harrington, Jenny Littler, Sébastien Perrier & Freya Harrison

Biofilm infections are associated with a high mortality risk for patients. Antibiotics perform poorly against biofilm communities, so high doses and prolonged treatments are often used in clinical settings. We investigated the pairwise interactions of two synthetic nano-engineered antimicrobial polymers (SNAPs). The g-D50 copolymer was synergistic with penicillin and silver sulfadiazine against planktonic Staphylococcus aureus USA300 in synthetic wound fluid. Furthermore, the combination of g-D50 and silver sulfadiazine showed a potent synergistic antibiofilm activity against S. aureus USA300 using in vitro and ex vivo wound biofilm models. The a-T50 copolymer was synergistic with colistin against planktonic Pseudomonas aeruginosa in synthetic cystic fibrosis medium, and this pair showed a potent synergistic antibiofilm activity against P. aeruginosa in an ex vivo cystic fibrosis lung model. SNAPs thus have the potential for increased antibiofilm performance in combination with certain antibiotics to shorten prolonged treatments and reduce dosages against biofilm infection.

npj biofilms and microbiomes. June 2023

Model design for nonparametric phylodynamic inference and applications to pathogen surveillance

Xavier Didelot, Vinicius Franceschi, Simon D W Frost, Ann Dennis, Erik M Volz

The methodology for nonparametric inference of effective population size is well-developed in the Bayesian setting, but here we develop a frequentist approach based on nonparametric latent process models of population size dynamics. We appeal to statistical principles based on out-of-sample prediction accuracy in order to optimize parameters that control shape and smoothness of the population size over time. Our methodology is implemented in a new R package entitled mlesky. We demonstrate the flexibility and speed of this approach in a series of simulation experiments and apply the methodology to a dataset of HIV-1 in the USA. We also estimate the impact of non-pharmaceutical interventions for COVID-19 in England using thousands of SARS-CoV-2 sequences. By incorporating a measure of the strength of these interventions over time within the phylodynamic model, we estimate the impact of the first national lockdown in the UK on the epidemic reproduction number.

Virus Evolution. May 2023

Phylogenetic analysis of the origin and spread of plague in Madagascar

Luis Roger Esquivel Gomez, Cyril Savin, Voahangy Andrianaivoarimanana, Soloandry Rahajandraibe, Lovasoa Nomena Randriantseheno, Zhemin Zhou, Arthur Kocher, Xavier Didelot, Minoarisoa Rajerison, Denise Kühnert

After a plague-free period of over 60 years in the northwestern coast city of Mahajanga, the disease reappeared in 1991 and caused several outbreaks until 1999. Previous research indicates that the disease was reintroduced to the city of Mahajanga from the Central Highlands instead of reemerging from a local reservoir. In this study we applied a Bayesian phylogeographic model to detect and date migrations of Y. pestis between the two locations that could be linked to the re-emergence of plague in Mahajanga. Our results indicate that two independent migrations from the Central Highlands caused the plague outbreaks in Mahajanga during the 1990s, with both introductions occurring during the early 1980s. They happened over a decade before the detection of human cases, thus the pathogen likely survived in wild reservoirs until the spillover to humans was possible diseases.

PLoS Neglected Tropical Diseases. May 2023

Sutthirat Sitthisak, Suphattra Manrueang, Supat Khongfak, Udomluk Leungtongkam, Rapee Thummeepak, Aunchalee Thanwisai, Nathan Burton, Gurneet K Dhanoa, Panagiotis Tsapras, Antonia P Sagona

Phage lytic enzymes are promising antimicrobial agents. In this study, an endolysin derived from vB_AbaM_PhT2 (vPhT2), was identified. This endolysin represented the conserved lysozyme domain. Recombinant endolysin (lysAB- vT2) and hydrophobic fusion endolysin (lysAB-vT2-fusion) were expressed and purified. Both endolysins showed lytic activity against bacterial crude cell wall of Gram-negative bacteria. The MIC of lysAB-vT2-fusion was 2 mg/ml corresponding to 100 µM, while the MIC of lysAB-vT2 was more than 10 mg/ml (400 µM). Combination of lysAB-vT2-fusion with colistin, polymyxin B or copper was synergistic against A. baumannii (FICI value as 0.25). Antibacterial activity of lysAB-vT2-fusion plus colistin at the fractional inhibitory concentrations (FICs) revealed that it can inhibit Escherichia coli, Klebsiella pneumoniae and various strains of extremely drug-resistant A. baumannii (XDRAB) and phage resistant A. baumannii. The lysAB- vT2-fusion still retained its antibacterial activity after incubating the enzyme at 4, 20, 40 and 60 °C for 30 min. The lysAB-vT2-fusion could inhibit the mature biofilm, and incubation of lysAB-vT2-fusion with T24 human cells infected with A. baumannii led to a partial reduction of LDH release from T24 cells. In summary, our study highlights the antimicrobial ability of engineered lysAB-vT2-fusion endolysin, which can be applied for the control of A. baumannii infection.

Scientific Reports. May 2023