Estimating individuals’ genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data

Individuals differ widely in their contribution to the spread of infection within and across populations. Three key epidemiological host traits affect infectious disease spread: susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection to others) and recoverability (propensity to recover quickly). Interventions aiming to reduce disease spread may target improvement in any one of these traits, but the necessary statistical methods for obtaining risk estimates are lacking. In this paper we introduce a novel software tool called SIRE (standing for “Susceptibility, Infectivity and Recoverability Estimation”), which allows for the first time simultaneous estimation of the genetic effect of a single nucleotide polymorphism (SNP), as well as non-genetic influences on these three unobservable host traits. SIRE implements a flexible Bayesian algorithm which accommodates a wide range of disease surveillance data comprising any combination of recorded individual infection and/or recovery times, or disease diagnostic test results. Different genetic and non-genetic regulations and data scenarios (representing realistic recording schemes) were simulated to validate SIRE and to assess their impact on the precision, accuracy and bias of parameter estimates. This analysis revealed that with few exceptions, SIRE provides unbiased, accurate parameter estimates associated with all three host traits. For most scenarios, SNP effects associated with recoverability can be estimated with highest precision, followed by susceptibility. For infectivity, many epidemics with few individuals give substantially more statistical power to identify SNP effects than the reverse. Importantly, precise estimates of SNP and other effects could be obtained even in the case of incomplete, censored and relatively infrequent measurements of individuals’ infection or survival status, albeit requiring more individuals to yield equivalent precision. SIRE represents a new tool for analysing a wide range of experimental and field disease data with the aim of discovering and validating SNPs and other factors controlling infectious disease transmission.     

Mesotheliomas and asbestos type in asbestos textile workers: a study of lung contents.

The asbestos contents of the lungs of former employees of an asbestos textile factory were determined at necropsy using a transmission electron microscope. Those who had died of mesothelioma were compared with a matched sample of those who had died of other causes. The predominant fibre processed in the factory was chrysotile, but crocidolite had also been used. The lung content was consistent with the known exposure to chrysotile, but the crocidolite content was also high, being about 300 times that of the general population of the United Kingdom. The lungs of those with mesothelioma did not contain more of either chrysotile or crocidolite than the lungs of the controls, so no particular type of asbestos could be implicated in causing the mesotheliomas. The evidence of substantial exposure to crocidolite means that the mesotheliomas that occurred in this factory could not be attributed with any certainty to the exposure to chrysotile.     

Turnover and spreading of old wall during surface growth of Bacillus subtilis.

The steady-state concentration of cell wall turnover products in the medium of Bacillus subtilis 168 growing exponentially on a casein hydrolysate-supplemented medium is equivalent to an overall rate of turnover of less than 10% per generation. After transfer of a steady-labeled culture to nonradioactive medium, the rate of release of labeled turnover products increased exponentially for up to two generations. The rate of turnover finally attained by this culture reached an apparently first-order rate of about 50% per generation. The addition of soluble autolytic activity to growing cultures of a mutant possessing a reduced rate of wall turnover resulted in a marked stimulation in the rate of solubilization of the cell wall fraction. The increased rate of solubilization produced was proportional to the concentration of added enzyme and remained constant until less than 20% of the wall originally present was left. Autolytic activity added under these conditions was bound entirely to wall at least one generation old. The results are interpreted in terms of a model for cell wall growth in which wall two or more generations old covers a total surface area at least four times larger than that occupied at the time of synthesis, forming a shallow outer layer (overlying newer wall) from which all turnover takes place. The model is discussed in relation to previous attempts to determine the pattern of surface expansion in bacilli.     

A periplasm in Bacillus subtilis.

The possibility of there being a periplasm in Bacillus subtilis, in the distinct cell compartment bounded by the cytoplasmic membrane and the thick cell wall, has been investigated quantitatively and qualitatively. Cytoplasmic, membrane, and protoplast supernatant fractions were obtained from protoplasts which were prepared isotonically from cells grown under phosphate limitation. The contents of the protoplast supernatant fraction represent an operational definition of the periplasm. In addition, this cell fraction includes cell wall-bound proteins, exoproteins in transit, and contaminating cytoplasmic proteins arising through leakage from, or lysis of a fraction of, protoplasts. The latter, measured by assay of enzyme markers and by radiolabeled RNA and protein, was found to represent 7.6% of total cell protein, yielding a mean of 9.8% +/- 4.8% for B. subtilis 168 protein considered periplasmic. Qualitatively, after subjection of all cell fractions to polyacrylamide gel electrophoresis, RNase and DNase, zymographs revealed that (i) each cell fraction had a unique profile of nucleases and (ii) multiple species and a major fraction of both nucleases were concentrated in the periplasm. We conclude that the operationally defined periplasmic fraction corresponds closely, both quantitatively and qualitatively, to the contents of the periplasm of Escherichia coli. We discuss evidence that the maintenance of the components of this surface compartment in B. subtilis is compatible with the thick negatively charged cell wall acting as an external permeability barrier.     

Nest opening response of the Nile crocodile Crocodylus niloticus

Observations on captive Nile crocodiles, Crocodylus niloticus confirm earlier reports on parental care of nests and of young. Male and female appear to form a pair bond after courtship, the male defending nesting territory with the female rarely leaving the nest until the sounds of the young hatching stimulate her to open the nest to release them. The female transports unhatched eggs and live young in her buccal pouch to water and establishes a nursery where the young are defended for several weeks. Experiments involving playback of distress calls by tape recorder, offering of live young and eggs to the adults, the parent opening an artificial nest and vocalisations and resultant interactions between adults and young are described.     

An analysis of effects of heterozygosity in dairy cattle for bovine tuberculosis resistance

Genetic selection of cattle more resistant to bovine tuberculosis (bTB) may offer a complementary control strategy. Hypothesising underlying non‐additive genetic variation, we present an approach using genome‐wide high density markers to identify genomic loci with dominance effects on bTB resistance and to test previously published regions with heterozygote advantage in bTB. Our data comprised 1151 Holstein–Friesian cows from Northern Ireland, confirmed bTB cases and controls, genotyped with the 700K Illumina BeadChip. Genome‐wide markers were tested for associations between heterozygosity and bTB status using marker‐based relationships. Results were tested for robustness against genetic structure, and the genotypic frequencies of a significant locus were tested for departures from Hardy‐Weinberg equilibrium. Genomic regions identified in our study and in previous publications were tested for dominance effects. Genotypic effects were estimated through ASReml mixed models. A SNP (rs43032684) on chromosome 6 was significant at the chromosome‐wide level, explaining 1.7% of the phenotypic variance. In the controls, there were fewer heterozygotes for rs43032684 (P < 0.01) with the genotypic values suggesting that heterozygosity confers a heterozygote disadvantage. The region surrounding rs43032684 had a significant dominance effect (P < 0.01). SNP rs43032684 resides within a pseudogene with a parental gene involved in macrophage response to infection and within a copy‐number‐variation region previously associated with nematode resistance. No dominance effect was found for the region on chromosome 11, as indicated by a previous candidate region bTB study. These findings require further validation with large‐scale data.     

Identification of cell wall subunits in bacillus subtilis and analysis of their segregation during growth.

Continuous as well as pulse-labeling and chase experiments with Bacillus subtilis demonstrated that the cell wall (both peptidoglycan and teichoic acid) is composed of a limited number of blocks which, once completed, segregate during subsequent growth without undergoing any mixing with newly synthesized blocks. This observation suggests that new wall material is inserted in a limited number of zones. Previously reported observations which suggested diffuse intercalation of new wall material are reinterpreted on the basis of our results. Experiments performed on different media showed that the number of segregation units per unit of cell length and thus the density of insertion zones increases with medium richness. This finding suggests analogies between the regulation of cell wall and DNA synthesis.