Traditional and innovative diagnostic tools: when and why they should be applied

The development of new technological methods surely improves the quality of the Diagnostic Services in Parasitology offered to the National Sanitary Service, however, cost and simplicity have not to be neglected, even when the prime consideration is efficiency. Moreover, the mere fact that something can be done by one of these new approaches does not mean that it should be done that way or that it is most cost-effective to do it that way. A review of diagnostic tools in Parasitology is proposed, to evaluate when and why each of them should be applied. Traditional procedures for the diagnosis of parasitosis are only based on the "direct" recovery and recognition of the parasite, with the microscope as main tool and few other instruments as co-operator. The innovative procedures, recently adjusted on the basis of new scientific knowledge and made possible by the development of the laboratory instrument weapons, can evidence the parasites both directly and indirectly. If it is obvious that the direct identification of a pathogen is more reliable than that indirect, is not so evident what is the most useful direct method, and when it would be better to use indirect diagnostic tools. Advantages and disadvantages of each procedure, cost as well as the purpose of the test (diagnosis, post-treatment, research), and the general condition in which the test have to been applied must be taken into account when we are choosing. In general, we can say that the rationale for their use can be summarised as follows: 1) The macroscopic/microscopic analysis of samples is always recommended (with the exception of samples coming from tissues that need surgery). This "old" procedure allows the identification in 20 minutes of all the parasites present in mixed infections, and the evaluation of the parasite load. It is a cost-effective method which relies ultimately on the skill of the observer to detect and identify parasite stages; 2) Parasite antigen detection is an innovative and expensive immunological diagnostic, which can suffer of sensitivity and specificity. It could be useful to directly diagnose "occult" infections; 3) Parasite DNA/RNA direct detection is an innovative, sensitive and specific procedure, which can also identify sibling species. It is expensive, therefore its use is restricted to reference laboratories; 4) Host antibody detection is an innovative indirect tool to evaluate the presence of a parasite by means the evaluation of the host response to infection. It can suffer of sensitivity and specificity, and the interpretation of the test results may be difficult. It could be applied as first step to evaluate the presence of tissue parasites, whose direct diagnosis would require surgery. Some tests can be performed in well-equipped laboratories; other tests are available through research laboratories. The specimens, appropriately collected and preserved, have always to be processed in security for potential risk of infection hazard, and submitted to tests appropriate to the laboratory's goals, where, therefore, field and research diagnostic tools shouldn't be applied. The test selected for routine use has to be chosen taking into account value and limitations of each method. Reduction in excessive and often unnecessary testing is mandatory, and therefore it is critical for the clinical Parasitology to perform relevant testing while maintaining appropriate quality. To date, the microscopic analysis of samples is the only direct method that allows all identifications in short times, at a reduced cost, independently from geographical origin and peculiar status of the patient. It has to be regarded as the first step in diagnostic procedures for all laboratories. Some molecular techniques have greater sensitivity than traditional methods, but at least at the present time, their costs may well preclude their routine use. It is difficult to know, exactly, where diagnostic Parasitology will be moving in the next few years, although many soothsayers feel very strongly that the area of molecular diagnostics will replace more traditional means. It is also possible that immunological or perhaps cytometric procedures will replace our more standard diagnostic approach; nevertheless they will continue to remain oddities on the outside of the general practice and be confined to a few reference laboratories. As far as semi-automated or automated instruments and robotics-based techniques, they are useful when large numbers of the same test are performed. Supposing that they will enter in our laboratory, that will happen in central facility rather than in each local facility. So, the great interest in using new technological methods to solve old problems probably will have to be seen in the right perspective.     

A mechanistic model of infection: why duration and intensity of contacts should be included in models of disease spread

Background  

Mathematical models and simulations of disease spread often assume a constant per-contact transmission probability. This assumption ignores the heterogeneity in transmission probabilities, e.g. due to the varying intensity and duration of potentially contagious contacts. Ignoring such heterogeneities might lead to erroneous conclusions from simulation results. In this paper, we show how a mechanistic model of disease transmission differs from this commonly used assumption of a constant per-contact transmission probability.     

Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn

Permutation tests are amongst the most commonly used statistical tools in modern genomic research, a process by which p-values are attached to a test statistic by randomly permuting the sample or gene labels. Yet permutation p-values published in the genomic literature are often computed incorrectly, understated by about 1/m, where m is the number of permutations. The same is often true in the more general situation when Monte Carlo simulation is used to assign p-values. Although the p-value understatement is usually small in absolute terms, the implications can be serious in a multiple testing context. The understatement arises from the intuitive but mistaken idea of using permutation to estimate the tail probability of the test statistic. We argue instead that permutation should be viewed as generating an exact discrete null distribution. The relevant literature, some of which is likely to have been relatively inaccessible to the genomic community, is reviewed and summarized. A computation strategy is developed for exact p-values when permutations are randomly drawn. The strategy is valid for any number of permutations and samples. Some simple recommendations are made for the implementation of permutation tests in practice.     

SIR epidemics and vaccination on random graphs with clustering

Journal of Mathematical Biology - In this paper we consider Susceptible $$\rightarrow $$ Infectious $$\rightarrow $$ Recovered (SIR) epidemics on random graphs with clustering. To incorporate group...     

Networks, epidemics and vaccination through contact tracing

We consider a (social) network whose structure can be represented by a simple random graph having a pre-specified degree distribution. A Markovian susceptible-infectious-removed (SIR) epidemic model is defined on such a social graph. We then consider two real-time vaccination models for contact tracing during the early stages of an epidemic outbreak. The first model considers vaccination of each friend of an infectious individual (once identified) independently with probability ρ. The second model is related to the first model but also sets a bound on the maximum number an infectious individual can infect before being identified. Expressions are derived for the influence on the reproduction number of these vaccination models. We give some numerical examples and simulation results based on the Poisson and heavy-tail degree distributions where it is shown that the second vaccination model has a bigger advantage compared to the first model for the heavy-tail degree distribution.     

Evaluation of the medical curriculum: why, when, by whom and for whom should questionnaires be used

The undergraduate medical curriculum has been modified or even totally reorganized in many countries in recent years, and there are plans to make departmental budgets and the salaries of university professors partially dependent on the outcome of teaching. Questionnaires are often used in such situations as a means of curriculum evaluation. Based on our own experience such evaluations should be done not only during and immediately after a course in the curriculum, but also at later time points, e.g., at the end of the undergraduate and also the postgraduate phase. The clinical relevance of lectures and courses can only be graded adequately after some years of clinical experience. Gross anatomy was graded top at all time points evaluated and reached higher levels of 'clinical relevance' than other typical preclinical and even clinical subjects. Efforts should be made to obtain a high response rate for representative results. After modifying parts of a course detailed questionnaires should also include space for students' suggestions. The results of such evaluations are not only relevant to the head of department as feedback on the individual lecturers but also important for the curriculum committee and the dean. Anatomists should utilize these evaluations to improve teaching.     

Models of epidemics and endemicity in genetically variable host populations

A discrete time genetics model is developed for populations that are undergoing selection due to infectious disease. It is assumed that the generation time of the host and infectious agent are non-synchronous and that only the host population is evolving. Two classes of epidemic processes are considered. The first class is for infectious agents that confer immunity following infection, while the second class is for those that do not confer immunity. The necessary and sufficient conditions are found in order for the disease to persist in a stable polymorphic host population. These conditions are shown to depend on the density of susceptibles, the selection coefficients, and the severity and class of the disease process.     

Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated

It has long been known, from the distribution of multiple amino acid replacements, that not all amino acids of a sequence are replaceable. More recently, the phenomenon was observed at the nucleotide level in mitochondrial DNA even after allowing for different rates of transition and transversion substitutions. We have extended the search to globin gene sequences from various organisms, with the following results: (1) Nearly every data set showed evidence of invariable nucleotide positions. (2) In all data sets, substitution rates of transversions and transitions were never in the ratio of 2/1, and rarely was the ratio even constant. (3) Only rarely (e.g., the third codon position of beta hemoglobins) was it possible to fit the data set solely by making allowance for the number of invariable positions and for the relative rates of transversion and transition substitutions. (4) For one data set (the second codon position of beta hemoglobins) we were able to simulate the observed data by making the allowance in (3) and having the set of covariotides (concomitantly variable nucleotides) be small in number and be turned over in a stochastic manner with a probability that was appreciable. (5) The fit in the latter case suggests, if the assumptions are correct and at all common, that current procedures for estimating the total number of nucleotide substitutions in two genes since their divergence from their common ancestor could be low by as much as an order of magnitude. (6) The fact that only a small fraction of the nucleotide positions differ is no guarantee that one is not seriously underestimating the total amount of divergence (substitutions). (7) Most data sets are so heterogeneous in their number of transition and transversion differences that none of the current models of nucleotide substitution seem to fit them even after (a) segregation of coding from noncoding sequences and (b) splitting of the codon into three subsets by codon position. (8) These frequently occurring problems cannot be seen unless several reasonably divergent orthologous genes are examined together.