Molecular epidemiology reports
A molecular epidemiology study is an observational study that collects and measures biological material, so its report also explains why the biomarkers were chosen, how the specimens were collected, processed and stored, and how the assays were run and analysed. The report of a study of an infectious disease also covers the pathogen population, its strains and the markers that type them, and, where transmission chains are investigated, how consistent the molecular and the epidemiological evidence are.
The reporting guidelines
STROBE-ME (2011) extends the STROBE statement for molecular epidemiology, and STROME-ID (2014) extends it for the molecular epidemiology of infectious diseases. Each sets its own items beside the STROBE items.
Biomarker studies
STROBE-ME asks a report to state the use of specific biomarkers in the title or the abstract, or both, if they contribute substantially to the findings. Explain in the background how and why the specific biomarkers were chosen, potentially among many others. Where one or more biomarkers are used as proxy measures, state the a priori hypothesis on their expected values. Describe the special study designs for molecular epidemiology, among them the nested case-control design.
Report the setting of the biological sample collection, the amount of sample, the nature of the collecting procedures, the participants' conditions, and the time between sample collection and the relevant clinical or physiological endpoints. Describe how the samples were processed and how they were stored until biomarker analysis. Report the biomarker's half-life and its chemical and physical characteristics. Report any habit, clinical condition, physiological factor, or working or living condition that might affect the characteristics or concentrations of the biomarker.
Report the type of assay used, the detection limit, the quantity of biological sample used, outliers, the timing in the assay procedures where it applies, and the calibration procedures or any standard used. Describe how biomarkers were introduced into statistical models. Report the validity and reliability of the biomarker measurement as the literature gives them, and any internal or external validation used in the study. Give the reason for the loss of biological samples at each stage. Give the distribution of the biomarker measurement, including its mean, median, range and variance.
Describe the main limitations in laboratory procedures, and interpret the results in terms of a priori biological plausibility. Describe informed consent and approval from ethics committees, and specify whether samples were anonymous, anonymized or identifiable.
Infectious-disease studies
STROME-ID recommends that the term 'molecular epidemiology' be applied to the study in the title or abstract and in the key words when molecular and epidemiological methods contribute substantially to it. Give background on the pathogen population and the distribution of its strains in the host population at risk, and state the epidemiological objectives of using molecular typing. Define, or cite definitions for, the key molecular terms, such as strain, isolate and clone, clearly define the molecular markers used, and clearly state the infectious-disease case definitions. State the sources of participants and clinical specimens, and clearly describe the sampling frame and strategy. Describe the sample collection and the laboratory methods, including any methods used to minimise and measure cross-contamination, and give the criteria used to interpret strain classification. Clearly state the study's timeframe, and consider and appropriately reference the molecular clock of the markers, if it is known, and the natural history of the infection.
Describe any methods used to detect multiple-strain infections and measure their effect on the findings, and any efforts to address discovery or ascertainment bias. State how the study took account of the non-independence of sample data, where appropriate, and how it dealt with missing data. Report the numbers of participants and samples at each stage, including the numbers of samples obtained, typed and yielding data. Where the study investigates molecular clusters, groups of genetically indistinguishable pathogens, state the sampling fraction, the distribution of cluster sizes and, if known, the turnover of the study population. Give information by strain type where appropriate, in standardised nomenclature.
Consider showing the molecular relatedness of strain types with a dendrogram or a phylogenetic tree. Where transmission chains are being investigated, consider alternative explanations for the findings and report how consistent the molecular and the epidemiological evidence are. Report any ethical considerations with specific implications for infectious-disease molecular epidemiology.