Epidemiology of campylobacteriosis and acute gastroenteritis from a human and health system's perspective in Switzerland

In humans, the zoonotic disease campylobacteriosis is caused by an infection with Campylobacter spp. The infection often leads to acute gastroenteritis (AG), a syndrome which is characterised by diarrhoea, nausea and other gastrointestinal symptoms. Infectious intestinal diseases (IID) other than campylobacteriosis such as salmonellosis or norovirus infections can also result in AG. The disease and health system burden of campylobacteriosis and AG in general is considerable and around 230,000 cases of campylobacteriosis alone are recorded annually in Europe. In Switzerland, the surveillance of IID is based on a mandatory notification system for laboratory-confirmed cases of certain IIDs while there is no distinct surveillance of AG. About 7000 cases of campylobacteriosis and 1200 cases of salmonellosis are recorded annually in the Swiss notification system. Cases suffering from a mild episode of IID often do not seek health care and consequently are never diagnosed and recorded. As a result the entire disease and health system burden of AG caused by IID is unknown. The present PhD thesis assesses causes for an infection with Campylobacter spp. in wintertime and the disease and health system burden of IID and AG at the primary care level in Switzerland. Determinants for the registration of IID cases along the burden-of-illness pyramid and the case management of AG patients in primary care are also explored

Time trends of positivity rates from foodborne pathogen testing in Switzerland, 2003 to 2012

Campylobacteriosis and salmonellosis are important foodborne diseases in Europe, including in Switzerland. In 2014, notification rates for Switzerland were 92.9 per 100 000 population for campylobacteriosis and 15.2 per 100 000 population for salmonellosis. These notification rates originate from laboratory-based surveillance whereby positive test results are reported to the National Notification System for Infectious Diseases. Consequently, notification rates do not directly correspond to the disease burden among the population as the number of positive tests depends on patients' healthcare-seeking behaviour, stool sampling rates and other factors.; We assessed laboratory positivity rates (proportion of positive tests among all tests performed) of diagnostic tests for Campylobacter and Salmonella from five private laboratories in Switzerland between 2003 and 2012. We analysed demographic characteristics, temporal and spatial distribution of test numbers and positivity rates. Predictors for a positive test and disease seasonality were assessed with logistic regression analyses.; A total of 135 122 (13 095 positive) Campylobacter tests and 136 997 (2832 positive) Salmonella tests were obtained with positive tests corresponding to 20.4% and 17.2% of notified campylobacteriosis and salmonellosis cases, respectively. The number of tests conducted annually increased for both pathogens by 51% from 2003 to 2012. Annual positivity rates of Campylobacter increased from 7.6 to 11.1% and rates of Salmonella decreased from 2.7 to 1.5%. The largest increases in annual Campylobacter positivity rates were observed for patients older than 85 years (+193.7%), followed by children aged 5-9 years (+131.9%). Positivity rates and test numbers for both diseases by month or calendar week showed a distinct seasonality, with peak rates for Salmonella occurring in autumn and for Campylobacter in summer and at the turn of the year. These findings were independent of patients' age and sex.; Both positivity rates and notification rates showed increasing trends for Campylobacter and decreasing trends for Salmonella, suggesting that these trends reflect changes in disease epidemiology at population level. The continuous assessment of positivity rates remains important to appropriately interpret changes observed in the notification system especially considering the increasing use of multiplex polymerase chain reaction test panels where multiple pathogens are tested simultaneously

A tradition and an epidemic: determinants of the campylobacteriosis winter peak in Switzerland

Campylobacteriosis is the most frequently reported food borne infection in Switzerland. We investigated determinants of infections and illness experience in wintertime. A case-control study was conducted in Switzerland between December 2012 and February 2013. Cases were recruited among laboratory-confirmed campylobacteriosis patients. Population-based controls were matched according to age group, sex and canton of residence. We determined risk factors associated with campylobacteriosis, and help seeking behaviour and illness perception. The multivariable analysis identified two factors associated with an increased risk for campylobacteriosis: consumption of meat fondue (matched odds ratio [mOR] 4.0, 95% confidence interval [CI] 2.3-7.1) and travelling abroad (mOR 2.7, 95% CI 1.1-6.4). Univariable analysis among meat fondue consumers revealed chicken as the type of meat with the highest risk of disease (mOR 3.8, 95% CI 1.1-13.5). Most frequently reported signs and symptoms among patients were diarrhoea (98%), abdominal pain (81%), fever (66%), nausea (44%) and vomiting (34%). The median perceived disease severity was 8 on a 1-to-10 rating scale. Patients reported a median duration of illness of 7days and 14% were hospitalised. Meat fondues, mostly "Fondue chinoise”, traditionally consumed during the festive season in Switzerland, are the major driver of the epidemic campylobacteriosis peak in wintertime. At these meals, individual handling and consumption of chicken meat may play an important role in disease transmission. Laboratory-confirmed patients are severely ill and hospitalisation rate is considerable. Public health measures such as decontamination of chicken meat and improved food handling behaviour at the individual level are urgently needed

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Prevalence and risk factors of Strongyloides stercoralis in Takeo Province, Cambodia

The threadworm Strongyloides stercoralis, the most neglected helminth, affects an estimated 30-100 million people worldwide. Information on S. stercoralis infection is scarce in tropical and sub-tropical resource poor countries, including Cambodia. We determined S. stercoralis infection prevalence and risk factors for infection in the general population in Southern Cambodia.; A cross-sectional study was carried out between January and April 2011 among 2,861 participants living in 60 villages of Takeo province, using Koga-agar plate culture, the Baermann technique and the Kato-Katz technique on a single stool sample.; Eight intestinal helminth species were diagnosed. Hookworm (31.4%) and S. stercoralis (21.0%) occurred most frequently. Prevalence of S. stercoralis infection increased with age. In all age groups a higher prevalence was found among males than among females (OR: 1.7; 95% CI: 1.4 - 2.0; P > 0.001). Participants who had a latrine at home were significantly less frequently infected with S. stercoralis than those who did not (OR: 0.7; 95% CI: 0.4 - 0.8; P = 0.003). Muscle pain (OR: 1.3; 95% CI: 1.0 - 1.6; P = 0.028) and urticaria (OR: 1.4; 95% CI: 1.1 - 1.8; P = 0.001) were significantly associated with S. stercoralis infection.; S. stercoralis is highly prevalent among the general Cambodian population and should no longer be neglected. Access to adequate diagnosis and treatment is urgently needed

Acute Gastroenteritis and Campylobacteriosis in Swiss Primary Care: The Viewpoint of General Practitioners.

Acute gastroenteritis (AG) is frequently caused by infectious intestinal diseases (IID) including food- and waterborne pathogens of public health importance. Among these pathogens, Campylobacter spp. plays a major role. Many European countries monitor selected IIDs within disease surveillance systems. In Switzerland, the information on IIDs is restricted to limited surveillance data, while no data is available for AG. We conducted a qualitative study among Swiss general practitioners (GPs) to investigate the case management of AG and campylobacteriosis patients, the associated disease burden and the determinants leading to registration in the National Notification System for Infectious Diseases (NNSID). Interviews were conducted with a semi-structured questionnaire and underwent inductive content analysis based on Grounded Theory. The questionnaire was repeatedly adapted to capture emerging themes until the point of theoretical saturation. GPs perceived AG and campylobacteriosis of little relevance to their daily work and public health in general. According to GP self-estimates each consults about two cases of AG per week and diagnoses a median of five campylobacteriosis cases per year. A large proportion of AG cases receives telephone consultations only and gets medical advice from the practice nurse. Antibiotic therapy is considered useful and stool diagnostics are performed for about a fifth of consulting AG patients. Stool diagnostics ("test") and antibiotic therapy ("treat") are interrelated and follow four strategies: "Wait & See", "Treat & See", "Treat & Test", and "Test & See". AG case management is diverse and includes different triage steps. A small proportion of AG patients have stool diagnostics performed and only positive tested patients are reported to the NNSID. As a result severe cases and cases with a history of travel abroad are overrepresented in the NNSID. The use of multiplex PCR panels in routine diagnostics likely leads to improved case management and higher case numbers in surveillance systems