Epidemiological Methods: About Time

Epidemiological studies often produce false positive results due to use of statistical approaches that either ignore or distort time. The three time-related issues of focus in this discussion are: (1) cross-sectional vs. cohort studies, (2) statistical significance vs. public health significance, and (3), how risk factors “work together” to impact public health significance. The issue of time should be central to all thinking in epidemiology research, affecting sampling, measurement, design, analysis and, perhaps most important, the interpretation of results that might influence clinical and public-health decision-making and subsequent clinical research

Epidemiological methods in diarrhoea studies—an update

Background Diarrhoea remains a leading cause of morbidity and mortality but is difficult to measure in epidemiological studies. Challenges include the diagnosis based on self-reported symptoms, the logistical burden of intensive surveillance and the variability of diarrhoea in space, time and person

Etiology and prognosis of spondyloarthropathies using family-based epidemiological methods

The spondyloarthropathies (SpA) are a group of chronic inflammatory diseases that share several disease characteristics such as inflammation of entheses and extramusculoskeletal manifestations like uveitis, psoriasis, and inflammatory bowel disease. These diseases, or symptoms thereof, are also known to run in families. The purpose of this thesis was to expand knowledge concerning the etiology and prognosis of SpA, using family-based epidemiological methods on data from Swedish health and population registers. In study I, we estimated the familial aggregation of a specific SpA subtype, ankylosing spondylitis (AS), in a nested case-control study of AS cases, population controls, and first-degree relatives of both groups. We were able to provide a precise estimate of the familial aggregation, corresponding to a 20-fold increased risk of AS among first-degree relatives of AS cases. We also estimated the heritability of AS to 77%, i.e. the proportion of susceptibility to AS in the population that is due to genetics. Our estimate can be seen as an upper limit for the heritability, as shared environmental effects were not considered. While both estimates are relatively high, they are lower than previous reports for AS, which have been based on small and often selected samples. In study II, a cohort study, we investigated whether family history of SpA, or its specific subtypes, were predictive of response to treatment with tumor necrosis factor inhibitors (TNFi) in patients with SpA. Despite being such a strong risk factor for disease development, we did not find family history to be associated with prognosis in terms of TNFi drug survival or treatment response at three or twelve months. In study III, we studied temporal trends in pregnancy outcomes among women with axial SpA. We found that women with axial SpA, compared to women from the general population, were at increased risk of pre-eclampsia, preterm birth, and serious infection in the infant. The proportion of cesarean deliveries was also significantly higher among women with axial SpA. The risks had, however, diminished over the last decade, to reach similar levels as in the general population, while the use of effective treatment in the form of TNFi increased before and during pregnancy over the same period. In study IV, we searched for environmental risk factors for AS, with a focus on perinatal characteristics and infections in childhood. In this nested case-control study, we found that having older siblings and a history of tonsillectomy in childhood were associated with AS in adulthood, even after adjustment for childhood socio-economic status and other family-shared confounders through a sibling comparison. By using data from national registers, we were able to perform the hitherto largest studies on these topics regarding etiology and prognosis of SpA. While the genetic influence is substantial in AS, there is a larger contribution of environmental risk factors than previously known. These seem partly related to early life, with a possible influence of childhood infections. We have also added to a growing body of evidence supporting the use of effective treatment in women with axial SpA, before and at least in the beginning of pregnancy, to minimize the risks active that SpA disease pose on pregnancy outcomes

Development and evaluation of new molecular epidemiological methods for analysis of salmonella TYPHI

A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfillment of requirements of the degree of Master of Science. Johannesburg, 2017The typhoid fever causing Salmonella Typhi remains an important public health problem in Africa. More importantly, the emergence of the highly antimicrobial resistant H58 Salmonella Typhi haplotype is of greater concern. Rapid and highly discriminatory molecular methods are essential for prompt and effective epidemiological investigation of typhoid fever outbreaks. Traditional methods, such as pulsed-field gel electrophoresis (PFGE) are time-consuming and offer subjective discrimination of highly homologous isolates. On the contrary, molecular subtyping based on multiple-locus variable-number tandem-repeats (VNTR) analysis (MLVA) is a rapid, PCR-based method which has been successfully used for subtyping homogenous isolates of the Salmonella genus. This study describes the development and application of a MLVA assay for molecular characterization of Salmonella Typhi isolates from sub-Saharan Africa (SSA). This involved evaluation of thirteen VNTR loci using a validation panel consisting of 50 diverse Salmonella Typhi isolates. A MLVA assay consisting of five highly variable VNTR loci was adopted. The developed MLVA assay was used, along with PFGE, to characterize 316 Salmonella Typhi isolates from SSA. A total of 226 MLVA types were identified as compared to 143 PFGE fingerprint types. MLVA typing results indicated intracontinental spread of Salmonella Typhi. For the rapid identification of H58 Salmonella Typhi, a conventional PCR targeting a mutation that is exclusive to the H58 haplotype was employed on 105 isolates from South Africa as well as 121 isolates from other SSA countries. Approximately 54% (105/214) of the Salmonella Typhi isolates from South Africa and 62% (75/121) of the isolates from other SSA countries were identified as H58 Salmonella Typhi. The MLVA tool was able to discriminate among H58 Salmonella Typhi isolates. MLVA is viable alternative to PFGE for subtyping Salmonella Typhi and can be used as first-line assay for routine screening of Salmonella Typhi isolates in SSA, providing excellent discrimination of isolates.MT201

Molecular-genetic analysis of Mycobacterium tuberculosis strains spread in different patient groups in St.Petersburg (Russia)

Molecular epidemiological features of M.tuberculosis strains spread among different patient groups in Russia is not studied well. The aim of our study was to compare genotypes of M.tuberculosis strains circulating among TB patients from different groups: homeless, HIV-infected, prisoners and general population of St.Petersburg citizens. 
One hundred fifty M.tuberculosis complex isolates from different TB patient groups were studied using spoligotyping method. 
The majority of studied M.tuberculosis isolates in all groups belonged to Beijing family (56% among homeless; 77% among HIV-infected; 60% among general population; 83% among prisoners). There were no significant difference in Beijing family prevalence among homeless patients, HIV/TB co-infected and general population of TB patients. The lowest genetic diversity of the pathogen was detected among imprisoned patients. 
Results of our study demonstrate that M.tuberculosis strains circulating among homeless and HIV-infected people are also spread among general population of St.Petersburg citizens. Thus, we have investigated participation of high-risk groups in the TB infection spread in the city

Exploring the integration of traditional and molecular epidemiological methods for infectious disease outbreaks

BACKGROUND: Understanding the transmission dynamics of infectious pathogens is critical to developing effective public health strategies. Traditionally, time consuming epidemiological methods were used, often limited by incomplete or inaccurate datasets. Novel phylogenetic techniques can determine transmission events, but have rarely been used in real-time outbreak settings to inform interventions and limit the impact of outbreaks. METHODS: I undertook a series of novel studies to explore the utility of combining phylogenetics with traditional epidemiological analysis to enhance the understanding of transmission dynamics. I investigated HIV in an endemic South African setting and Ebola in an acute outbreak in Sierra Leone. The strengths and limitations of this combined approach are explored, ethical issues investigated and recommendations made regarding the implications of this work for public health. RESULTS: Phylogenetics provides an exciting and synergistic tool to epidemiological analysis in outbreak investigation and control. These combined methods enable a more detailed understanding than is possible through either discipline alone. My key findings include: • Identification of infection source: Phylogenetics gives new insight into the role of external introductions (e.g. migrators) in driving and sustaining the high incidence of HIV. • Earlier identification of new emerging clusters: I identified a new cluster of HIV from around a mining community. This is one of the first examples of molecular methods detecting a previously unknown outbreak. • Identification of novel mechanisms of transmission: This work suggests that children may have been infected by playing in puddles contaminated with Ebola, a previously unrecognised route of transmission. CONCLUSION: The integration of these two methods facilitate sophisticated real-time techniques to maximise understanding of transmission dynamics, allowing faster and more effectively targeted interventions. Moving forwards, sequence data should be incorporated into standard outbreak investigation. This is critical at a time when infectious disease outbreaks have led to the some of the most significant global health threats of the recent past

Measuring the effect of enhanced cleaning in a UK hospital : a prospective cross-over study

Increasing hospital-acquired infections have generated much attention over the last decade. There is evidence that hygienic cleaning has a role in the control of hospital-acquired infections. This study aimed to evaluate the potential impact of one additional cleaner by using microbiological standards based on aerobic colony counts and the presence of Staphylococcus aureus including meticillin-resistant S. aureus. We introduced an additional cleaner into two matched wards from Monday to Friday, with each ward receiving enhanced cleaning for six months in a cross-over design. Ten hand-touch sites on both wards were screened weekly using standardised methods and patients were monitored for meticillin-resistant S. aureus infection throughout the year-long study. Patient and environmental meticillin-resistant S. aureus isolates were characterised using molecular methods in order to investigate temporal and clonal relationships. Enhanced cleaning was associated with a 32.5% reduction in levels of microbial contamination at handtouch sites when wards received enhanced cleaning (P < 0.0001: 95% CI 20.2%, 42.9%). Near-patient sites (lockers, overbed tables and beds) were more frequently contaminated with meticillin-resistant S. aureus/S. aureus than sites further from the patient (P = 0.065). Genotyping identified indistinguishable strains from both handtouch sites and patients. There was a 26.6% reduction in new meticillin-resistant S. aureus infections on the wards receiving extra cleaning, despite higher meticillin-resistant S. aureus patient-days and bed occupancy rates during enhanced cleaning periods (P = 0.032: 95% CI 7.7%, 92.3%). Adjusting for meticillin-resistant S. aureus patient-days and based upon nine new meticillin-resistant S. aureus infections seen during routine cleaning, we expected 13 new infections during enhanced cleaning periods rather than the four that actually occurred. Clusters of new meticillin-resistant S. aureus infections were identified 2 to 4 weeks after the cleaner left both wards. Enhanced cleaning saved the hospital £30,000 to £70,000.Introducing one extra cleaner produced a measurable effect on the clinical environment, with apparent benefit to patients regarding meticillin-resistant S. aureus infection. Molecular epidemiological methods supported the possibility that patients acquired meticillin-resistant S. aureus from environmental sources. These findings suggest that additional research is warranted to further clarify the environmental, clinical and economic impact of enhanced hygienic cleaning as a component in the control of hospital-acquired infection