PubMed · 8255859
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P Simmons. 1993. Non-specific urethritis.. https://pubmed.ncbi.nlm.nih.gov/8255859/
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Phylodynamics bridges the gap between classical epidemiology and pathogen genome sequence data by estimating epidemiological parameters from time-scaled pathogen phylogenetic trees. The models used in phylodynamics typically assume that the sampling procedure is independent between infected individuals. However, this assumption does not hold for many epidemics, in particular for such sexually transmitted infections as HIV-1, for which contact tracing schemes are included in health policies of many countries. We extended phylodynamic multi-type birth-death (MTBD) models with contact tracing (CT), and developed a simulator to generate trees under MTBD and MTBD-CT models. We proposed a non-parametric test for detecting contact tracing in pathogen phylogenetic trees. Its application to simulated data showed that it is both highly specific and sensitive. For the simplest representative of the MTBD-CT family, the BD-CT(1) model, where only the last contact can be notified, we solved the differential equations and proposed a closed form solution for the likelihood function. We implemented a maximum-likelihood program, which estimates the BD-CT(1) model parameters and their confidence intervals from phylogenetic trees. It performed accurate parameter inference on BD and BD-CT(1) simulated data, and detected contact tracing in HIV-1 B epidemics in Zurich and the UK. Importantly, we showed that not accounting for contact tracing when it is present, leads to bias in parameter estimation with the BD model (overestimation of the becoming-non-infectious rate). This bias is also present, but greatly reduced, when the BD-CT(1) model is used on data where multiple contacts can be notified. Our CT test, MTBD-CT tree simulator and BD-CT(1) parameter estimator are freely available at GitHub (evolbioinfo/treesimulator and evolbioinfo/bdct).
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CONTEXT: This large outbreak of foodborne disease highlights the challenge of investigating outbreaks caused by intentional contamination and demonstrates the vulnerability of self-service foods to intentional contamination. OBJECTIVE: To investigate a large community outbreak of Salmonella Typhimurium infections. DESIGN: Epidemiologic investigation of patients with Salmonella gastroenteritis and possible exposures in The Dalles, Oregon. Cohort and case-control investigations were conducted among groups of restaurant patrons and employees to identify exposures associated with illness. SETTING: A community in Oregon. Outbreak period was September and October 1984. PATIENTS: A total of 751 persons with Salmonella gastroenteritis associated with eating or working at area restaurants. Most patients were identified through passive surveillance; active surveillance was conducted for selected groups. A case was defined either by clinical criteria or by a stool culture yielding S Typhimurium. RESULTS: The outbreak occurred in 2 waves, September 9 through 18 and September 19 through October 10. Most cases were associated with 10 restaurants, and epidemiologic studies of customers at 4 restaurants and of employees at all 10 restaurants implicated eating from salad bars as the major risk factor for infection. Eight (80%) of 10 affected restaurants compared with only 3 (11%) of the 28 other restaurants in The Dalles operated salad bars (relative risk, 7.5; 95% confidence interval, 2.4-22.7; P<.001). The implicated food items on the salad bars differed from one restaurant to another. The investigation did not identify any water supply, food item, supplier, or distributor common to all affected restaurants, nor were employees exposed to any single common source. In some instances, infected employees may have contributed to the spread of illness by inadvertently contaminating foods. However, no evidence was found linking ill employees to initiation of the outbreak. Errors in food rotation and inadequate refrigeration on ice-chilled salad bars may have facilitated growth of the S Typhimurium but could not have caused the outbreak. A subsequent criminal investigation revealed that members of a religious commune had deliberately contaminated the salad bars. An S Typhimurium strain found in a laboratory at the commune was indistinguishable from the outbreak strain. CONCLUSIONS: This outbreak of salmonellosis was caused by intentional contamination of restaurant salad bars by members of a religious commune.