MERS-CoV recombination: implications about the reservoir and potential for adaptation

Gytis Dudas, Andrew Rambaut
doi: http://dx.doi.org/10.1101/020834

Recombination is a process that unlinks neighbouring loci allowing for independent evolutionary trajectories within genomes of many organisms. If not properly accounted for, recombination can compromise many evolutionary analyses. In addition, when dealing with organisms that are not obligately sexually reproducing, recombination gives insight into the rate at which distinct genetic lineages come into contact. Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has caused 1106 laboratory-confirmed infections, with 421 MERS-CoV associated deaths as of April 16, 2015. Although bats are considered as the likely ultimate source of zoonotic betacoronaviruses, dromedary camels have been consistently implicated as the source of current human infections in the Middle East. In this paper we use phylogenetic methods and simulations to show that MERS-CoV genome has likely undergone numerous recombinations recently. Recombination in MERS-CoV implies frequent co-infection with distinct lineages of MERS-CoV, probably in camels given the current understanding of MERS-CoV epidemiology.

Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005–2010: Potential for Molecular Surveillance of New Outbreaks

Mohammad A. Alkhamis, Brian R. Moore, Andrés M. Perez
doi: http://dx.doi.org/10.1101/020339

Previous Bayesian phylogeographic studies of H5N1 highly pathogenic avian influenza viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia, indicating that HPAIV circulated in Russia prior to its detection there in 2005. In this study, we extend this research to explore the evolution and spread of HPAIV within Europe during the 2005–2010 epidemic, using all available sequences of the HA and NA gene regions that were collected in Europe and Russia during the outbreak. We use discrete-trait phylodynamic models within a Bayesian statistical framework to explore the evolution of HPAIV. Our results indicate that the genetic diversity and effective population size of HPAIV peaked between mid-2005 and early 2006, followed by drastic decline in 2007, which coincides with the end of the epidemic in Europe. Our results also suggest that domestic birds were the most likely source of the spread of the virus from Russia into Europe. Additionally, estimates of viral dispersal routes indicate that Russia, Romania, and Germany were key epicenters of these outbreaks. Our study quantifies the dynamics of a major European HPAIV pandemic and substantiates the ability of phylodynamic models to improve molecular surveillance of novel AIVs.

Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species

Jeanneth Mosquera-Rendón, Ana M. Rada-Bravo, Sonia Cárdenas-Brito, Mauricio Corredor, Eliana Restrepo-Pineda, Alfonso Benítez-Páez
doi: http://dx.doi.org/10.1101/020305

Background. Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains. Results. The P. aeruginosa pangenome was estimated to contain almost 17,000 non-redundant genes, and approximately 15% of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates. Conclusions. We report the unprecedented pangenome characterization of P. aeruginosa on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein conjugates from pili, flagella, or secretion systems as antigens for vaccine design, which exhibit high genetic variation in terms of non-synonymous substitutions in P. aeruginosa strains.

Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing

Minh Duc Cao, Devika Ganesamoorthy, Alysha Elliott, Huihui Zhang, Matthew Cooper, Lachlan Coin
doi: http://dx.doi.org/10.1101/019356

Clinical pathogen sequencing has significant potential to drive informed treatment of patients with unknown bacterial infection. However, the lack of rapid sequencing technologies with concomitant analysis has impeded clinical adoption in infection diagnosis. Here we demonstrate that commercially-available Nanopore sequencing devices can identify bacterial species and strain information with less than one hour of sequencing time, initial drug-resistance profiles within 2 hours, and a complete resistance profile within 12 hours. We anticipate these devices and associated analysis methods may become useful clinical tools to guide appropriate therapy in time-critical clinical presentations such as bacteraemia and sepsis.

Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis.

Phelim Bradley , N Claire Gordon , Timothy M Walker , Laura Dunn , Simon Heys , Bill Huang , Sarah Earle , Louise J Pankhurst , Luke Anson , Mariateresa de Cesare , Paolo Piazza , Antonina A Votintseva , Tanya Golubchik , Daniel J Wilson , David H Wyllie , Roland Diel , Stefan Niemann , Silke Feuerriegel , Thomas A Kohl , Nazir Ismail , Shaheed V Omar , E Grace Smith , David Buck , Gil McVean , A Sarah Walker , Tim Peto , Derrick Crook , Zamin Iqbal
doi: http://dx.doi.org/10.1101/018564

Rapid and accurate detection of antibiotic resistance in pathogens is an urgent need, affecting both patient care and population-scale control. Microbial genome sequencing promises much, but many barriers exist to its routine deployment. Here, we address these challenges, using a de Bruijn graph comparison of clinical isolate and curated knowledge-base to identify species and predict resistance profile, including minor populations. This is implemented in a package, Mykrobe predictor, for S. aureus and M. tuberculosis, running in under three minutes on a laptop from raw data. For S. aureus, we train and validate in 495/471 samples respectively, finding error rates comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.3%/99.5% across 12 drugs. For M. tuberculosis, we identify species and predict resistance with specificity of 98.5% (training/validating on 1920/1609 samples). Sensitivity of 82.6% is limited by current understanding of genetic mechanisms. We also show that analysis of minor populations increases power to detect phenotypic resistance in second-line drugs without appreciable loss of specificity. Finally, we demonstrate feasibility of an emerging single-molecule sequencing technique.

Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections

Bethany L. Dearlove, Alison J. Cody, Ben Pascoe, Guillaume Méric, Daniel J. Wilson, Samuel K. Sheppard
(Submitted on 7 Apr 2015)

Campylobacter jejuni and Campylobacter coli are the biggest causes of bacterial gastroenteritis in the developed world, with human infections typically arising from zoonotic transmission associated with infected meat, especially poultry. Because this organism is not thought to survive well outside of the gut, host associated populations are genetically isolated to varying degrees. Therefore the likely origin of most Campylobacter strains can be determined by host-associated variation in the genome. This is instructive for characterizing the source of human infection at the population level. However, some common strains appear to have broad host ranges, hindering source attribution. Whole genome sequencing has the potential to reveal fine-scale genetic structure associated with host specificity within each of these strains.
We found that rates of zoonotic transmission among animal host species in ST-21, ST-45 and ST-828 clonal complexes were so high that the signal of host association is all but obliterated. We attributed 89% of clinical cases to a chicken source, 10% to cattle and 1% to pig. Our results reveal that common strains of C. jejuni and C. coli infectious to humans are adapted to a generalist lifestyle, permitting rapid transmission between different hosts. Furthermore, they show that the weak signal of host association within these complexes presents a challenge for pinpointing the source of clinical infections, underlining the view that whole genome sequencing, powerful though it is, cannot substitute for intensive sampling of suspected transmission reservoirs.

Variation in rural African gut microbiomes is strongly shaped by parasitism and diet

Elise R Morton , Joshua Lynch , Alain Froment , Sophie Lafosse , Evelyne Heyer , Molly Przeworski , Ran Blekhman , Laure Segurel
doi: http://dx.doi.org/10.1101/016949

The human gut microbiome is influenced by its host’s nutrition and health status, and represents an interesting adaptive phenotype under the influence of metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that geography is an important factor associated with the gut microbiome; however, studies have yet to disentangle the effects of factors such as climate, diet, host genetics, hygiene and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiomes of populations that inhabit similar environments but have different traditional subsistence modes and (ii) evaluate the effect of parasitism on microbiome composition and structure. We sampled rural Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon and found that the presence of Entamoeba is strongly correlated with microbial composition and diversity. Using a random forest classifier model, we show that an individual’s infection status can be predicted with 79% accuracy based on his/her gut microbiome composition. We identified multiple taxa that differ significantly in frequency between infected and uninfected individuals, and found that alpha diversity is significantly higher in infected individuals, while beta-diversity is reduced. Subsistence mode was another factor significantly associated with microbial composition, notably with some taxa previously shown to differ between Hadza East African hunter-gatherers and Italians also discriminating Pygmy hunter-gatherers from neighboring farming or fishing populations in Cameroon. In conclusion, these results provide evidence for a strong relationship between human gut parasites and the microbiome, and highlight how sensitive this microbial ecosystem is to subtle changes in host nutrition.

Current data show no signal of Ebola virus adapting to humans

Stephanie J. Spielman, Austin G. Meyer, Claus O. Wilke
doi: http://dx.doi.org/10.1101/011429

Gire et al. (Science 345:1369–1372, 2014) analyzed 81 complete genomes sampled from the 2014 Zaire ebolavirus (EBOV) outbreak and claimed that the virus is evolving far more rapidly in the current outbreak than it has been between previous outbreaks. This assertion has received widespread attention, and many have perceived Gire et al. (2014)’s results as implying rapid adaptation of EBOV to humans during the current outbreak. Here, we show that, on the contrary, sequence divergence in EBOV is rather limited, and that the currently available data contain no signal of rapid evolution or adaptation to humans. Gire et al.’s findings resulted from an incorrect application of a molecular-clock model to a population of sequences with minimal divergence and segregating polymorphisms. Our results highlight how indiscriminate use of off-the-shelf analysis techniques may result in highly-publicized, misleading statements about an ongoing public health crisis.

E. coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity

Shraddha Madhav Karve, Sachit Daniel, Yashraj Chavhan, Abhishek Anand, Somendra Singh Kharola, Sutirth Dey
doi: http://dx.doi.org/10.1101/011007

There is considerable understanding about how laboratory populations respond to predictable (constant or deteriorating-environment) selection for single environmental variables like temperature or pH. However, such insights may not apply when selection environments comprise multiple variables that fluctuate unpredictably, as is common in nature. To address this issue, we grew replicate laboratory populations of E. coli in nutrient broth whose pH and concentrations of salt (NaCl) and hydrogen peroxide (H2O2) were randomly changed daily. After ~170 generations, the fitness of the selected populations had not increased in any of the three selection environments. However, these selected populations had significantly greater fitness in four novel environments which have no known fitness-correlation with tolerance to pH, NaCl or H2O2. Interestingly, contrary to expectations, hypermutators did not evolve. Instead, the selected populations evolved an increased ability for energy dependent efflux activity that might enable them to throw out toxins, including antibiotics, from the cell at a faster rate. This provides an alternate mechanism for how evolvability can evolve in bacteria and potentially lead to broad-spectrum antibiotic resistance, even in the absence of prior antibiotic exposure. Given that environmental variability is increasing in nature, this might have serious consequences for public-health.

Counterinsurgency Doctrine Applied to Infectious Disease
Benjamin C Kirkup ​

Recent scientific discoveries lead inexorably to the conclusion that the ‘total human’ incorporates a necessary body of numerous microbes, including bacteria. These bacteria play a very important role in immunity by actively resisting infections by outside bacteria; however, under certain conditions they can degrade their community. They can arrogate to themselves resources that normally flow through other metabolic pathways and form persistent biological structures. In this situation, these bacteria constitute an insurgency, with strategic ramifications.