Salmonella is one of the main causes of human foodborne illness. It is endemic worldwide, with different animals and animal-based food products as reservoirs and vehicles of infection. Identifying animal reservoirs and potential transmission pathways of Salmonella is essential for prevention and control. There are many approaches for source attribution, each using different statistical models and data streams. Some aim to identify the animal reservoir, while others aim to determine the point at which exposure occurred. With the advance of whole-genome sequencing (WGS) technologies, new source attribution models will greatly benefit from the discriminating power gained with WGS. This review discusses some key source attribution methods and their mathematical and statistical tools. We also highlight recent studies utilizing WGS for source attribution and discuss open questions and challenges in developing new WGS methods. We aim to provide a better understanding of the current state of these methodologies with application to Salmonella and other foodborne pathogens that are common sources of illness in the poultry and human sectors.

Hyderabad, Pakistan, was the first city to witness an outbreak of extensively drug resistant (XDR) typhoid fever. The outbreak strain is resistant to ampicillin, chloramphenicol, trimethoprim-sulfamethoxazole, fluoroquinolones, and third-generation cephalosporin, thus greatly limiting treatment options. However, despite over 5000 documented cases, information on mortality and morbidity has been limited.
To address the existing knowledge gap, this study aimed to assess the morbidity and mortality associated with XDR and non-XDR Salmonella serovar Typhi infections in Pakistan.
We reviewed the medical records of culture-confirmed typhoid cases in 5 hospitals in Hyderabad from October 1, 2016, to September 30, 2018. We recorded data on age, gender, onset of fever, physical examination, serological and microbiological test results, treatment before and during hospitalization, duration of hospitalization, complications, and deaths.
A total of 1452 culture-confirmed typhoid cases, including 947 (66%) XDR typhoid cases and 505 (34%) non-XDR typhoid cases, were identified. Overall, ≥1 complications were reported in 360 (38%) patients with XDR typhoid and 89 (18%) patients with non-XDR typhoid (P<.001). Ileal perforation was the most commonly reported complication in both patients with XDR typhoid (n=210, 23%) and patients with non-XDR typhoid (n=71, 14%) (P<.001). Overall, mortality was documented among 17 (1.8%) patients with XDR S Typhi infections and 3 (0.6%) patients with non-XDR S Typhi infections (P=.06).
As this first XDR typhoid outbreak continues to spread, the increased duration of illness before hospitalization and increased rate of complications have important implications for clinical care and medical costs and heighten the importance of prevention and control measures.

Low-moisture foods have been responsible for a number of salmonellosis outbreaks worldwide over the last few decades, with cross contamination from contaminated equipment being the most predominant source. To date, actions have been focused on stringent hygienic practices prior to production, namely periodical sanitization of the processing equipment and lines. Not only does optimum sanitization require in-depth knowledge on the type and source of contaminants, but also the heat resistance of microorganisms is unique and often dependent on the heat transfer characteristics of the low-moisture foods. Rheological properties, including viscosity, degree of turbulence, and flow characteristics (for example, Newtonian or non-Newtonian) of both liquid and semisolid foods are critical factors impacting the flow behavior that consequently interferes heat transfer and related control elements. The demand for progressively more accurate prediction of complex fluid phenomena has called for the employment of computational fluid dynamics (CFD) to model mass and heat transfer during processing of various food products, ranging from drying to baking. With the aim of improving the quality and safety of low-moisture foods, this article critically reviewed the published literature concerning microbial survival in semisolid low-moisture foods, including chocolate, honey, and peanut butter. Critical rheological properties and state-of-the-art CFD application relevant to quality production of those products were also addressed. It is anticipated that adequate prediction of specific transport properties during optimum sanitization through CFD could be used to solve current and future food safety challenges.