Common Cell Shape Evolution of Two Nasopharyngeal Pathogens

Respiratory infectious diseases are the third cause of worldwide death. The nasopharynx is the portal of entry and the ecological niche of many microorganisms, of which some are pathogenic to humans, such as Neisseria meningitidis and Moraxella catarrhalis. These microbes possess several surface structures that interact with the actors of the innate immune system. In our attempt to understand the past evolution of these bacteria and their adaption to the nasopharynx, we first studied differences in cell wall structure, one of the strongest immune-modulators. We were able to show that a modification of peptidoglycan (PG) composition (increased proportion of pentapeptides) and a cell shape change from rod to cocci had been selected for along the past evolution of N. meningitidis. Using genomic comparison across species, we correlated the emergence of the new cell shape (cocci) with the deletion, from the genome of N. meningitidis ancestor, of only one gene: yacF. Moreover, the reconstruction of this genetic deletion in a bacterium harboring the ancestral version of the locus together with the analysis of the PG structure, suggest that this gene is coordinating the transition from cell elongation to cell division. Accompanying the loss of yacF, the elongation machinery was also lost by several of the descendants leading to the change in the PG structure observed in N. meningitidis. Finally, the same evolution was observed for the ancestor of M. catarrhalis. This suggests a strong selection of these genetic events during the colonization of the nasopharynx. This selection may have been forced by the requirement of evolving permissive interaction with the immune system, the need to reduce the cellular surface exposed to immune attacks without reducing the intracellular storage capacity, or the necessity to better compete for adhesion to target cells

Host Heterogeneity and the Dynamics of Pathogen Diversity

A central goal of ecology is to explain the diversity of coexisting species. Analogously, fundamental questions in epidemiology center around coexistence in pathogen communities. Classical models of strain competition predict variable coexistence dynamics depending upon the strength of cross-immunity. However, heterogeneity among human hosts, through variation in population structure and immune responses, can also profoundly affect coexistence. This dissertation investigates the intersection of immune-mediated competition and host heterogeneity to explain the dynamics of pathogen diversity in two viral communities: human papillomavirus (HPV) and influenza A viruses. We test hypotheses about viral dynamics by fitting mechanistic models to longitudinal data. We show that the prevalence and coexistence of over 200 genetically distinct HPV types are maintained by recurring infection within individuals of type-specific highrisk subpopulations. We then show that the dynamics of immune protection after influenza infection differ between children and adults, signaling substantial variability in the population-level selective pressures that shape the diversity of influenza strains

Economic burden of neonatal sepsis in sub-Saharan Africa

Background and significance The third Sustainable Development Goal for child health, which aims to end preventable deaths of newborns and children less than 5 years of age by 2030, cannot be met without substantial reduction of infection-specific neonatal mortality in the developing world. Neonatal infections are estimated to account for 26% of annual neonatal deaths, with mortality rates highest in sub-Saharan Africa (SSA). Reliable and comprehensive estimates of the incidence and aetiology surrounding neonatal sepsis in SSA remain incompletely available. We estimate the economic burden of neonatal sepsis in SSA. Methods: Data available through global health agencies and in the medical literature were used to determine population demographics in SSA, as well as to determine the incidence, disease burden, mortality and resulting disabilities associated with neonatal sepsis. The disability-adjusted life years (DALY) associated with successful treatment or prevention of neonatal sepsis in SSA for 1 year were calculated. The value of a statistical life (VSL) methodology was estimated to evaluate the economic burden of untreated neonatal sepsis in SSA. Results: We conservatively estimate that 5.29–8.73 million DALYs are lost annually in SSA due to neonatal sepsis. Corresponding VSL estimates predict an annual economic burden ranging from $10 billion to$469 billion. Conclusions: Our results highlight and quantify the scope of the public health and economic burden posed by neonatal sepsis in SSA. We quantify the substantial potential impact of more successful treatment and prevention strategies, and we highlight the need for greater investment in strategies to characterise, diagnose, prevent and manage neonatal sepsis and its long-term sequelae in SSA

Common Cell Shape Evolution of Two Nasopharyngeal Pathogens.

International audienceRespiratory infectious diseases are the third cause of worldwide death. The nasopharynx is the portal of entry and the ecological niche of many microorganisms, of which some are pathogenic to humans, such as Neisseria meningitidis and Moraxella catarrhalis. These microbes possess several surface structures that interact with the actors of the innate immune system. In our attempt to understand the past evolution of these bacteria and their adaption to the nasopharynx, we first studied differences in cell wall structure, one of the strongest immune-modulators. We were able to show that a modification of peptidoglycan (PG) composition (increased proportion of pentapeptides) and a cell shape change from rod to cocci had been selected for along the past evolution of N. meningitidis. Using genomic comparison across species, we correlated the emergence of the new cell shape (cocci) with the deletion, from the genome of N. meningitidis ancestor, of only one gene: yacF. Moreover, the reconstruction of this genetic deletion in a bacterium harboring the ancestral version of the locus together with the analysis of the PG structure, suggest that this gene is coordinating the transition from cell elongation to cell division. Accompanying the loss of yacF, the elongation machinery was also lost by several of the descendants leading to the change in the PG structure observed in N. meningitidis. Finally, the same evolution was observed for the ancestor of M. catarrhalis. This suggests a strong selection of these genetic events during the colonization of the nasopharynx. This selection may have been forced by the requirement of evolving permissive interaction with the immune system, the need to reduce the cellular surface exposed to immune attacks without reducing the intracellular storage capacity, or the necessity to better compete for adhesion to target cells

Cell shape and PG structure evolution among the <i>Moraxellaceae</i> family.

<p>Schematic phylogeny of the <i>Moraxellaceae</i> family, based on 16s analysis, along with scanning electronic microscopy images of representative species. The mean ratio (GM4+GM4_GM4)/(GM5+GM5_GM4) is presented (with standard deviation) for the different lineages (*** p≤0.001; ** p≤0.01; * p≤0.05). Each dote, represents an independent isolate (tested for <i>pbpX</i> presence) from the CNRM collection that have been classified as <i>M</i>. <i>catharrhalis</i> (3), <i>M</i>. <i>sp LNP20863</i> (1), <i>M</i>. <i>bovis (gift from Dr</i>. <i>S</i>. <i>Higlander—1) M</i>. <i>osloensis</i> (1), <i>M</i>. <i>sp</i>. LNP 26500 (1), <i>A</i>. <i>lwoffi</i> (2). Finally, the right part displays the deletion detected at the node of evolution by presenting the genomic organization of species that diverged before node 1 (assessed from the genome sequence of <i>M</i>. <i>bovis</i> and <i>A</i>. <i>lwoffi</i>) and after node 1 (from the <i>M</i>. <i>catharrhalis</i> genome).</p

Deleterious effects of <i>yacF</i> deletion can be fixed by inhibiting cell elongation.

<p>A) Scanning electron microscopy images showing similar morphology (coccus) of <i>N</i>. <i>elongata</i> Δ<i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i> and the double mutant Δ<i>yacF</i> Δ<i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i>. B) Same reverse-phase HPLC profile of muropeptides after mutanolysin digestion of purified insoluble PG of <i>N</i>. <i>elongata</i> Δ<i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i> and the double mutant Δ<i>yacF</i> Δ<i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i>. C) Similar ratio of GM4 quantity over GM5, GM4-GM3 over GM5-GM3 and finally GM4-GM4 over GM5-GM4 in the PG of Δ<i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i> and the double mutant Δ<i>yacF</i> Δ<i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i>. The raw quantification can be found in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005338#pgen.1005338.s002" target="_blank">S2 Fig</a> for <i>N</i>. <i>elongata</i> and the corresponding mutants. The ratio of wild type bacteria, the single mutant Δ<i>yacF</i> and the complemented strain Δ<i>yacF+yacF</i> are also presented. The increased proportion of GM5 in the PG of Δ<i>yacF</i> (as shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005338#pgen.1005338.g003" target="_blank">Fig 3</a>) can be again observed but this increase is less important than when the <i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i> locus, encoding for the elongation machinery, is deleted. (*** p≤0.001; ** p≤0.01; * p≤0.05 compare to wild-type).</p

Deleterious effects of <i>yacF</i> deletion can be fixed by inhibiting cell division.

<p>A) Scanning electron microscopy images showing similar morphology (filaments) of <i>N</i>. <i>elongata</i> wild type and Δ<i>yacF</i> grown in presence of sub-inhibitory concentrations of penicillin G. B) Similar reverse-phase HPLC profile of muropeptides after mutanolysin digestion of purified insoluble PG of <i>N</i>. <i>elongata</i> wild type and Δ<i>yacF</i> grown in presence of penicillin G. C) Similar ratio of GM4 over GM5, GM4-GM3 over GM5-GM3 and finally GM4-GM4 over GM5-GM4. (*** p≤0.001; ** p≤0.01; * p≤0.05 compare to wild-type).</p

Different properties of coccus cells.

<p>A) NF-κB luciferase expression in response to PG from <i>N</i>. <i>elongata</i> rod (wild-type) or cocci (Δ<i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i> Δ<i>yacF</i>) of HEK-293 cells transfected with human Nod1 (grey), human Nod2 (black) and murin Nod1 (white). The two controls measured the luciferase in absence of stimulation or in presence of purified specific agonist (MurTriDap for hNod1, MDP for hNod2, and MurTetraDap for mNod1). This is representative result of two independent experiments. All the results are statistically significant (p<0.05 rod vs cocci) except those noted ns (for non statistically significant). B) Estimated ratio surface/volume extracted from SEM images of around 20 cells (*** p≤0.001) and C) TEM image showing pili (red arrow) from <i>N</i>. <i>elongata</i> wild type (bacillus) and <i>N</i>. <i>elongata</i> Δ<i>yacF</i> Δ<i>mreBCD</i>,<i>pbpX</i>,<i>rodA</i> (coccus).</p

Distribution of <i>yacF</i> and other key components of the elongation machinery in proteobacteria.

<p>Representation of the proteobacteria taxonomy associated with a table presenting the information of the presence in all (white), absence in all (black). The presence/absence was assessed using the STRING database as previously described [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005338#pgen.1005338.ref045" target="_blank">45</a>]. A grey box indicates that the distribution was not uniform (presence of outliers) in the specific lineage. Finally, the cell morphology is also presented only for <i>yacF</i>-positive lineages to emphasize that the majority of <i>yacF</i>-positive strains are bacillus. A grey cell-shape indicates the presence of outliers in the lineage (herein <i>Methylococcus capsulatus</i>). Red asterisks indicate situation where the distribution is described more in details in the text. (e.g. the case of <i>Pseudomonadeles</i> is described more in detail in the text and in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005338#pgen.1005338.g009" target="_blank">Fig 9</a>).</p