Environmental hygiene in outdoor food markets in Africa: a scoping review

Outdoor food markets represent important locations where foodborne illnesses and other infectious diseases can spread. Countries in Africa face particular challenges given the importance of these markets in food supply and low rates of access to safely managed water and sanitation. We undertook a scoping review of evidence related to disease transmission in food markets in sub-Saharan Africa, North Africa and identified 46 papers for data extraction and synthesis. Vendor behaviour or awareness was reported in the majority of papers and about half reported on market infrastructure. Fewer studies have been reported on regulatory environments or food contamination. Studies on water supply, sanitation and handwashing facilities focused on the presence of services and did not evaluate quality, thus conclusions cannot be drawn on service adequacy. Studies of vendor behaviour were primarily based on self-reporting and subject to bias. Most studies reported high levels of vendor awareness of the need for hygiene, but where observations were also conducted, these showed lower levels of behaviours in practice. Our findings suggest that there are limited studies on environmental hygiene in outdoor food markets and this is an area warranting further research, including into the quality of services and addressing methodological weaknesses.

Food as a transmitter of viruses: A review

Viruses have been present throughout human history, causing diseases due to infections and food poisoning;they have caused frequent public health problems worldwide. These illnesses are usually mild, moderate, or severe in nature. The personal hygiene of food handlers and processing processes should be checked periodically. Virus detection protocols and safety measures should be continually reviewed as viruses change their mode of infection. The objective of this review was to discuss the possible routes of virus transmission to humans through food. Important topics have been reviewed such as: definition of food viruses, presence, and types of viruses in food, enteric viruses, zoonotic viruses, water as a means of transmission, risks of infection, other non-conventional foods as potential transmitters of viruses and food safety, in addition to current and future challenges, research work on viruses more resistant to heat treatments in food should be sought. Also, future work on survival time of active viruses on food surfaces. In addition, studies that determine the mechanisms of virus mutation in relation to the conditions of food handling and processing.

A Simplified Amplification-Free Strategy with Lyophilized CRISPR-CcrRNA System for Drug-Resistant Salmonella Detection.

Drug resistance in pathogenic bacteria has become a major threat to global health. The misuse of antibiotics has increased the number of resistant bacteria in the absence of rapid, accurate, and cost-effective diagnostic tools. Here, an amplification-free CRISPR-Cas12a time-resolved fluorescence immunochromatographic assay (AFC-TRFIA) is used to detect drug-resistant Salmonella. Multi-locus targeting in combination crRNA (CcrRNA) is 27-fold more sensitive than a standalone crRNA system. The lyophilized CRISPR system further simplifies the operation and enables one-pot detection. Induction of nucleic acid fixation via differentially charged interactions reduced the time and cost required for flowmetric chromatography with enhanced stability. The induction of nucleic acid fixation via differentially charged interactions reduces the time and cost required for flowmetric chromatography with enhanced stability. The platform developed for the detection of drug-resistant Salmonella has an ultra-sensitive detection limit of 84 CFU mL-1 within 30 min, with good linearity in the range of 102 -106 CFU mL-1 . In real-world applications, spiked recoveries range from 76.22% to 145.91%, with a coefficient of variation less than 10.59%. AFC-TRFIA offers a cost-effective, sensitive, and virtually equipment-independent platform for preventing foodborne illnesses, screening for drug-resistant Salmonella, and guiding clinical use.

Industry 4.0 technologies in agri-food sector and their integration in the global value chain: A review

We use many kinds of digital technologies in our daily life and they lead to radical changes. These technologies are recently being adopted by agriculture and food industry and their use in various applications is tested. The results of the studies conducted with the use of these technologies, especially IoT (internet of things)-based systems, are quite promising for the solution of the chronic problems of agriculture and food industry such as food-borne diseases, mycotoxin contaminations, pesticide residues, increasing waste, etc. Under extraordinary conditions, just like the ones we have recently experienced due to COVID-19 pandemic, IoT-based systems are crucial to ensure the sustainability of agriculture and food supply chain. In this review, the fundamentals of IoT-based systems and recent developments in their use in agriculture and food supply chain are explained. Based on the literature, examples of successful applications of IoT-based systems for irrigation efficiency, pesticide treatments, supply chain management etc. are given. Nowadays, there is a great demand for the integration of IoT-based systems into the present agricultural practices and supply chains and it seems to increase exponentially. Experts in electronics and computer sciences have achieved noteworthy success in the simulations. On the other hand, only a few studies have been conducted in real agricultural and food systems. However, IoT-based systems should be tested on-site and their success in practical applications should be proved. It is obvious that new era will be one in which IoT-based technologies and their tools will be more commonly used in agriculture and food supply. © 2023 Elsevier Ltd

Tolerance Increase in Escherichia coli O157:H7 and Methicillin-Resistant Staphylococcus Aureus USA300 Exposed to Low-Power Continuous Ultraviolet Radiation from Narrow-Wavelength Sources

Escherichia coli O157:H7 is a major cause of foodborne disease outbreaks throughout the world, while methicillin-resistant Staphylococcus aureus (MRSA) is responsible for many difficult-to-treat infections in humans. Ultraviolet (UV) irradiation is commonly used for disinfection in food processing, medical facilities, and water treatment to prevent the transmission of these pathogen. With increased use of UV disinfection technologies over the last few years because of COVID-19 and concerns about other communicable disease, it has become a concern that microbial species could develop tolerance to UV irradiation, especially when it is applied continuously. To elucidate the effect of continuous UV exposure at different wavelengths and power levels on the tolerance development of bacteria, Escherichia coli O157:H7 and MRSA)USA300 growths were investigated by continuously exposing inoculated agar plates to six different commercially available UV sources at wavelengths of 222 nm, 254 nm, 275 nm, and 405 nm. The agar plates in these experiments were partially covered by a thin acrylic sheet, which provided either complete protection from the UV to the cells directly under the sheet, no protection if significantly away from the sheet, or partial protection near the edges of the sheet due to shading or small amounts of UV reflection under the sheet at the edges. In these experiments, tolerant cells of E. coli and S. aureus were found from the 222 nm, the 405 nm, and one of the 254 nm sources. Upon examination of the power of each UV source, it was shown that the 275 nm and 254 nm sources that resulted in no tolerant cells had surface power densities [at 25 cm (10 in.)] that were more than 10-200 times greater than those that had tolerant cells. These results suggests that bacterial cells have a higher chance to develop UV tolerance under lower power UV sources (under the experimental conditions in our laboratory). Genome investigation of the tolerant colonies revealed that there are no significant differences between the cells that developed tolerance and the original organism, hinting at the need to explore the role of epigenetics mechanisms in the development of UV tolerance in these bacteria. © 2023 American Society of Civil Engineers.

Use of Online Consumer Complaint Forms to Enhance Complaint-Based Surveillance for Foodborne Illness Outbreaks in Minnesota.

Foodborne illness complaint systems that collect consumer reports of illness following exposure at a food establishment or event are a primary tool for detecting outbreaks of foodborne illness. Approximately, 75% of outbreaks reported to the national Foodborne Disease Outbreak Surveillance System are detected through foodborne illness complaints. The Minnesota Department of Health added an online complaint form to their existing statewide foodborne illness complaint system in 2017. During 2018-2021, online complainants tended to be younger than those who used traditional telephone hotlines (mean age 39 vs 46 years; p value < 0.0001), reported illnesses sooner following onset of symptoms (mean interval 2.9 vs 4.2 days; p value = 0.003), and were more likely to still be ill at the time of the complaint (69% vs 44%; p value < 0.0001). However, online complainants were less likely to have called the suspected establishment to report their illness than those who used traditional telephone hotlines (18% vs 48%; p value < 0.0001). Of the 99 outbreaks identified by the complaint system, 67 (68%) were identified through telephone complaints alone, 20 (20%) through online complaints alone, 11 (11%) using a combination of both, and 1 (1%) through email alone. Norovirus was the most common outbreak etiology identified by both complaint system methods, accounting for 66% of outbreaks identified only via telephone complaints and 80% of outbreaks identified only via online complaints. Due to the COVID-19 pandemic in 2020, there was a 59% reduction in telephone complaint volume compared to 2019. In contrast, online complaints experienced a 25% reduction in volume. In 2021, the online method became the most popular complaint method. Although most outbreaks detected by complaints were reported by telephone complaints alone, adding an online form for complaint reporting increased the number of outbreaks detected.

Food safety concerns in "COVID-19 era"

In March 2020, the World Health Organization (WHO) declared that the COVID-19 outbreak can be characterized as a pandemic. Human-to-human transmission of the SARS-CoV-2 virus may initially be blamed as the first cause of spread, but can an infection be contracted by ingestion of contaminated food or touching contaminated food surfaces? Recently cold-chain food contamination has been indicated as a possible source of many human cases in China. However, the risk of a food-related COVID-19 infection is still debated since the virus may reach people through a fresh product or packaging, which have been touched/sneezed on by infected people. This review summarizes the most recent evidence on the zoonotic origin of the pandemic, reports the main results regarding the transmission of SARS-CoV-2 through food or a food chain, as well as the persistence of the virus at different environmental conditions and surfaces. Emphasis is also posed on how to manage the risk of food-related COVID-19 spread and potential approaches that can reduce the risk of SARS-CoV-2 contamination.Copyright © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Analysis of epidemic characteristics and related factors of norovirus in diarrhea patients in Guangxi, 2015-2020

To analyze the epidemiological characteristics and related factors of norovirus in Guangxi from 2015 to 2020, and to provide scientific recommendations for norovirus prevention and control. Methods The foodborne diseases surveillance data were collected from 11 sentinel hospitals through the National Foodborne Disease Monitoring and Reporting System from 2015 to 2020. R software with version 4.0.3 was used for descriptive and statistical analysis, including epidemic curve, chi-square test, and trend chi-square and so on. Logistic regression was used to analyze norovirus-related factors, OR values and 95% confidence intervals were calculated respectively with the statistical test level of P < 0.05. Results There were 1 008 norovirus cases detected, with a detection rate of 12.75% (1 008/7 903). Children with age less than 5 years (OR=1.43, 95%CI: 1.13-1.82) and patients at age 20-45 (OR=1.45, 95%CI: 1.13-1.87) were high risk population. The detection rate was higher in autumn (OR=1.29, 95%CI: 1.08-1.53) but lower in summer (OR=0.67, 95%CI: 0.55-0.80). In addition, the tourist area (Guilin City) presented a higher detection rate than other areas (OR=1.41, 95%CI: 1.10-1.80). Aquatic products (OR=1.40, 95%CI: 1.03-1.91), meat and dairy products (OR=1.31, 95%CI: 1.06-1.61) were high-risk foods for norovirus infection. The prevention and control policies of COVID-19 can reduce the possibility of norovirus by 61% (OR=0.39, 95%CI: 0.31-0.49) showed a declining trend (Trend X2=85.33, P < 0.001). In addition, prolonged visit time can lead to 19%-23% decrease in the detection rate of norovirus (OR24-48 hours=0.81, 95%CI: 0.70-0.95;OR>48 hours=0.77, 95%CI: 0.63-0.93). Conclusions The epidemic of norovirus presented seasonal and regional distribution in Guangxi with a declining detection rate trend in diarrhea patients during recent 6 years. Young children were high-risk population in infection norovirus. The intake of seafood can increase the risk of norovirus infection. The prevention and control policies of COVID-19 can sharply decrease the possibility of infection norovirus. The monitoring of key foods such as seafood should be strengthened, and the early screening of suspected cases should be taken. The norovirus monitoring should be improved to ensure the health of the population.

Coronaviruses - Potential human threat from foodborne transmission?

The COVID-19 pandemic has worldwide impact in terms of number of illnesses, deaths and long-term sequelae. While the main route for the spread of the SARS-CoV-2 virus is person to person from respiratory droplets, survival of the virus in the air and its ability to infect subsequently have raised concerns. COVID-19 outbreaks in meat and other food processing plants raise concern for potential foodborne spread. We focus on the survival of the virus in the food subjected to various unit operations during processing, storage and distribution and the risk to consumers. While the risk of contamination of food products is possibly due to survival of the virus in the air in food processing operations if preventive measures are not followed, survival of the virus on fresh foods is dependent on the intrinsic and extrinsic properties of the specific foods and antimicrobial interventions used during production. Even if the virus remains infective on contaminated foods, maintenance of infectivity after ingestion of food and subsequent invasion of tissue has not been reported. An alternate route of infection from contaminated foods can be during handling of foods and subsequent spread of the virus to other surfaces such as face, nose, leading to infection. However, due to the extensive treatments foods receive during processing, often inhospitable environs of the food products and further food preparation prior to consumption significantly reduce the risk of transmission of the SARS-CoV-2 virus.

[Viruses present in the environment: virological considerations and examples of their impact on human health]. / Les virus dans l'environnement, considérations virologiques et exemples de leur impact en santé humaine.

Animal viruses are present in most human environments. Their viability in these media is very variable and the most important element that conditions this viability is the existence or not of a phospholipid envelope surrounding the nucleocapsid. After some general considerations on the structure of viruses, their multiplication cycle and their resistance to different physico-chemical agents, some examples of the impact of animal viruses present in the environment on human health will be presented. The situations that are related concern recent epidemiological events: circulation of type 2 polioviruses derived from the Sabin vaccine strain in the wastewater of New York, London and Jerusalem; risk of transmission of Sars-CoV-2 during the spreading of sludge from wastewater treatment plants on agricultural land in the era of the Covid-19 pandemic; « new ¼ forms of food-borne poisoning of viral origin (hepatitis E, tick-borne encephalitis, Nipah virus infection); contamination by epidemic viruses of mobile phones used by pediatricians; role of fomites in the spread of orthopoxvirus infections (smallpox, cowpox, monkeypox). The risk attached to animal viruses present in the environment must be assessed in a measured way without overestimating or underestimating their potential consequences for human health.

Foodborne infections and intoxications in Poland in the years 2018-2020.

AIM: The purpose of this study is to assess the epidemiological situation of foodborne infections and intoxications in Poland in the years 2018-2020. MATERIALS AND METHODS: The evaluation was based on the analysis of information sent to Department of Epidemiology NIPH NIH - NRI through ROE (pol. Rejestr Ognisk Epidemicznych) - an electronic system created for uploading, transfer and analysis of data acquired during the outbreak investigations. Additional sources for the analysis were NIPH NIH - NRI annual bulletins (Czarkowski MP et al. "Infectious diseases and poisonings in Poland", 2014-2020. Warsaw, NIPH NIH and GIS). RESULTS: In the years 2018-2020 a total number of 2,108 foodborne outbreaks were reported in which 52,175 persons were exposed and 17,023 got sick (in 2016 n=916, in 2019 n=918, in 2020 n=274). In 2020 over 3 fold decrease in the number of outbreaks comparing to 2019 and over 4 fold decrease in the number of cases in those outbreaks was observed. Among outbreaks which took place in 3 most frequent settings (private household, food facility and hospital) the steepest decrease was in 12th week of 2020 (ISO 2020-W12). The most frequent etiological agent of outbreaks in the years 2018-2020 was Salmonella sp. (38.3% of outbreaks in 2018, 32.7% in 2019 and 47.8% in 2020) and specifically serotype Enteritidis (38.3%, 27% and 39.4% accordingly). The most frequent setting of outbreaks was private household (59.7% outbreaks in 2018, 66% in 2019 and 62% in 2020), followed by hospital (17.4%, 18.3% i 19.7% accordingly). Up until 2019 an increasing trend in the number of small outbreaks (up to 4 cases) caused by Salmonella sp. was observed (in 2018 - 605 and in 2019 - 612 were reported). CONCLUSIONS: Decrease in the number of outbreaks in selected settings from 12th ISO week of 2020 might have been due to introduction of restrictions during COVID-19 pandemic and enhancement of personal hygiene practices. An increase in identified and registered small outbreaks caused by Salmonella sp. comparing to the median of the number of those outbreaks from 2014-2016 could partly be a result of routine surveillance enhancement after introducing System for Registry of Epidemiological Interviews (pol. SRWE).

Impact of the COVID-19 Pandemic on the Reported Incidence of Select Bacterial Enteric Diseases in Canada, 2020.

The aim of this study was to describe the impact of the COVID-19 pandemic on reported cases and clusters of select enteric diseases in Canada, for the period of March 2020 to December 2020. Weekly counts of laboratory confirmed cases of Salmonella, Shigella, Shiga toxin-producing Escherichia coli (STEC), and Listeria monocytogenes were obtained from laboratory surveillance data. These data were supplemented with epidemiological information on the suspected source of illness, collected for cases identified within whole genome sequencing clusters. Incidence rate ratios were calculated for each pathogen. All data were compared with a prepandemic reference period. Decreases in the number of reported cases in 2020 compared with the previous 5-year period were noted for Salmonella, Shigella, Escherichia coli O157, and non-O157 STEC. Reported number of cases for L. monocytogenes in 2020 remained similar to those of the previous 5-year period. There was a considerable decline (59.9%) in the number of cases associated with international travel compared with a 10% decline in the number of domestic cases. Comparison of reported incidence rates of clustered versus sporadic cases for each pathogen showed little variation. This study represents the first formal assessment of the impact of COVID-19 on reported enteric diseases in Canada. Reported case counts across several pathogens saw notable declines in 2020 compared with prepandemic levels, with restrictions on international travel playing a key role. Additional research is needed to understand how limitations on social gatherings, lock downs, and other public health measures have impacted enteric diseases.

Yersiniosis in Poland in 2018-2020.

AIM: The aim of the study was to assess the epidemiological situation of yersiniosis in Poland in 2018-2020 and compare it to previous years. MATERIAL AND METHODS: To assess the epidemiological situation of yersiniosis in Poland, data from individual case reports prepared by Sanitary Epidemiological Stations as part of routine epidemiological surveillance were used. Incidence, number of cases and data on hospitalizations by voivodship included in the bulletins "Infectious Diseases and Poisons in Poland" for 2015-2020 were also used. RESULTS: In 2018-2020, a total number of 542 cases of yersiniosis were registered, including 456 intestinal and 86 extraintestinal forms. The incidence in 2018 was 0.53/100,000 in 2019 0.59/100,000 and in 2020 0.29/100,000. The number of cases in 2020 compared to 2019 decreased by 52%, and compared to 2018 by 45.8%. The percentage of hospitalizations in each year was at a similar level of 65.5% in 2018, 62.4% in 2019, and 60% in 2020. The highest incidence was noted in the 0-4 age group at 44.7% of cases in 2018, 42.9% in 2019 and 55.6% in 2020, respectively (all cases of the intestinal form). The predominant species was Y. enterocolitica in both intestinal and extraintestinal forms. The most common serotype was serotype O:3, which was identified in 34 isolates in 2018, 43 isolates in 2019 and 9 isolates in 2020. SUMMARY AND CONCLUSIONS: Since 2009, Poland has had a decreasing trend in the incidence of yersiniosis. In 2020, both Poland and Europe saw a sharp decline in the number of cases compared to previous years. This is a result of the occurrence of the COVID-19 pandemic in March 2020, during which many measures were introduced to limit the spread of the SARS-CoV-2 virus, which may also have affected the number of other infections. Although the numbers of cases and incidence of yersiniosis among children under the age of 5 are the highest compared to other age groups, the highest number of hospitalizations was reported in the 10-19 age group, which most likely reflects the decreasing number of laboratory tests ordered on an outpatient basis with age and the significant underreporting of cases in this and older age groups.

Socioeconomic impacts of COVID-19 pandemic on foodborne illnesses in the United States.

Foodborne diseases continue to impact human health and the economy. The COVID-19 pandemic has dramatically affected the food system from production to consumption. This project aims to determine the impact of the COVID-19 pandemic on the spread of foodborne diseases and the factors that may have contributed, including environmental, behavioral, political, and socioeconomic. Data for this study were collected from The Foodborne Diseases Active Surveillance Network (FoodNet) for 2015-2020. FoodNet personnel located at state health departments regularly contact the clinical laboratories in Connecticut (CT), Georgia (GA), Maryland (MD), Minnesota (MN), New Mexico (NM), Oregon (OR), Tennessee (TN), and selected counties in California (CA), Colorado (CO), and New York (NY). Data were analyzed using SAS to determine the changes in rates of foodborne pathogens reported in FoodNet before and during the COVID-19 pandemic in the ten reporting states. Results of the study showed a significant decline in the incidences of foodborne diseases ranging between 25% and 60%. A geographical variation was also observed between California and states with the highest decline rate of foodborne illnesses. Policies and restrictions, in addition to environmental and behavioral changes during the COVID-19 pandemic, may have reduced rates of foodborne diseases.

Impact of COVID-19 on foodborne illness in Africa - A perspective piece.

Food safety investments in Africa, through international donors or national programs, were primarily focused on the formal market sector. However, increasing consumer food safety concerns about foods sold in the growing informal food markets, the rising foodborne disease burden in Africa, and the emergence of COVID-19 have all made food safety a major concern and ultimately brought it to an inflection point in Africa. In addition, Data on foodborne disease outbreaks revealed a scarcity of reported cases before and during the pandemic. The lack of information on foodborne disease reporting in Africa translates into one of the reasons why food safety in Africa is becoming a rising subject matter. This perspective discusses the situation of food safety in Africa before and after the COVID-19 pandemic. Finally, challenges confronting ongoing efforts to improve food safety in the post-COVID era in Africa are summarized and highlighted.

Norovirus and Coronavirus Risks in Food Service Settings: A Systematic Review for Future Research

This study discusses norovirus- and coronavirus-related health risks, foodborne illnesses, and outbreak risks associated with food and personal hygiene in the food service industry. Norovirus and coronavirus are global concerns. Employing a systematic review, the study focuses on the epidemiology of the viruses, including risk factors, possible transmission stages, and food safety regulations and practices. It is clear that the health risks related to norovirus have not received much attention from food service and hospitality management scholars. However, coronavirus risks and transmission route are well acknowledged by public and food service industry due to the current global pandemic. This study is one of the first studies that presents scholarly research results and discussions on the norovirus and coronavirus risks in food service settings providing implications and suggestions for future research. © 2021 Taylor & Francis.

Food safety knowledge and changes in practices and concerns of Indian families during the COVID-19 pandemic

Purpose>Unsafe food can lead to various foodborne diseases and even death, especially among children. This paper aims to assess food safety knowledge and changes in practices and concerns among adults ≥ 18 years during the coronavirus disease 2019 (COVID-19) pandemic.Design/methodology/approach>A cross-sectional, web-based survey was conducted among 325 adults living in Northern India. Demographic data and information regarding their knowledge, practices and concerns about various food safety issues were collected to see if there were any changes due to the COVID-19 pandemic.Findings>The results showed that the participants had slightly higher than average knowledge and good food safety practices with mean scores of 9.75 ± 2.23 and 24.87 ± 2.28, respectively. Contracting COVID-19 from food and food packaging materials was of high concern for more than 70% of the participants. Majority (> 80%) of them reported an increase in the frequency of handwashing. About 16% of the participants used chemical disinfectants for washing fruits and vegetables. An increase (57.5%) in the frequency of food label reading was also noted during the pandemic. Freshness and the general quality of food items (49.5%), safety of food (30.8%) and cost (18.2%) were the top drivers that influenced the purchase decision.Originality/value>This study highlighted the need to send out clear messages on safe food handling practices and keeping the tempo up for sustaining good hygienic practices. This will help in reducing the risk of foodborne diseases.

The European Union One Health 2021 Zoonoses Report.

This report of the European Food Safety Authority and the European Centre for Disease Prevention and Control presents the results of zoonoses monitoring and surveillance activities carried out in 2021 in 27 MSs, the United Kingdom (Northern Ireland) and nine non-MSs. Key statistics on zoonoses and zoonotic agents in humans, food, animals and feed are provided and interpreted historically. In 2021, the first and second most reported zoonoses in humans were campylobacteriosis and salmonellosis, respectively. Cases of campylobacteriosis and salmonellosis increased in comparison with 2020, but decreased compared with previous years. In 2021, data collection and analysis at the EU level were still impacted by the COVID-19 pandemic and the control measures adopted in the MSs, including partial or total lockdowns. Sixteen MSs and the United Kingdom (Northern Ireland) achieved all the established targets in poultry populations for reduction in Salmonella prevalence for the relevant serovars. Salmonella samples from carcases of various animal species and samples for Campylobacter quantification from broiler carcases were more frequently positive when performed by the competent authorities than when own-checks were conducted. Yersiniosis was the third most reported zoonosis in humans, followed by Shiga toxin-producing Escherichia coli (STEC) and Listeria monocytogenes infections. L. monocytogenes and West Nile virus infections were the most severe zoonotic diseases, with the most hospitalisations and highest case fatality rates. Overall, MSs reported more foodborne outbreaks and cases in 2021 than in 2020. S. Enteritidis remained the most frequently reported causative agent for foodborne outbreaks. Salmonella in 'eggs and egg products' and in 'mixed foods' were the agent/food pairs of most concern. Outbreaks linked to 'vegetables and juices and products thereof' rose considerably compared with previous years. This report also provides updates on brucellosis, Coxiella burnetii (Q fever), echinococcosis, rabies, toxoplasmosis, trichinellosis, tuberculosis due to Mycobacterium bovis or M. caprae, and tularaemia.

Standing up FungiNet: Genomic epidemiology and surveillance of fungal diseases

Objectives: With the advent of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing, the public health landscape for genomic epidemiology and surveillance has transformed for a variety of pathogens. For fungal diseases, the U. S. Centers for Disease Control and Prevention (CDC) is working with global partners to stand up FungiNet, a network that aims to equip scientists with laboratory, bioinformatics, and informatics resources to harness genomic data. FungiNet partners will use genomic and epidemiologic data to detect outbreaks, identify introductions, and characterize transmission of fungal infections. In 2022, FungiNet aims to onboard nine state and local health departments in the United States and two global partners, the Instituto Nacional de Salud in Colombia and the National Institute for Communicable Diseases in South Africa, with a focus on Candida auris. Method(s): To streamline the onboarding process, CDC generated standardized operating procedures (SOPs) specific to C. auris. For DNA extraction, SOPs were created for workflows using the Zymo Research Quick-DNA TM (ZR) Fungal/Bacterial Miniprep, Qiagen Dneasy Blood and Tissue, and Epicentre (Illumina) MasterPure Yeast DNA Purification kits. For library preparation and Illumina sequencing, PulseNet methods used for foodborne pathogens were validated for C. auris. For NCBI data submissions, required data elements were defined. For SNP and phylogenetic analyses, the bioinformatics workflow My-coSNP was adapted to use Nextflow software and the Terra platform. For visualization with epidemiologic data, guidance documents and tutorials for Microreact were created. Finally, for data reporting, processes are being designed in REDCap and in laboratory information management systems to rapidly share genomic-related data. Result(s): To date, 11 partners have committed to building capacity for C. auris genomic sequencing and analysis as a FungiNet partner. Of these, seven have validated methods for DNA extraction, and nine have generated high-quality sequencing data. Only one partner has installed and locally run MycoSNP, and none have submitted raw sequence data to NCBI. Conclusion(s): Currently, 11 FungiNet partners are working to onboard C. auris genomic sequencing and bioinformatics analysis in 2022. This process is complex, requiring several laboratories, bioinformatics, and informatics workflows. For many partners, bioinformatics analysisand NCBIsubmission are themost challenging activities with the installationof MycoSNPand the ability to batch upload data to NCBI as the main barriers. Next steps will focus on the validation of informatics methods to link genomic and epidemiologic data.