Prediction of edapho-climatic parameters in the incidence of Campylobacter spp. in northwestern Mexico

Campylobacter spp. is one of the main causes of enteric zoonotic infections worldwide. In Mexico, although a commonly detected pathogen in both children and adults, there is limited surveillance and few studies. The northern part of Mexico stands out for an unnoticed outbreak of Campylobacter jejuni due to contaminated drinking water, which caused an abrupt increase in Guillain-Barré syndrome in the local population. Although it is suggested that its distribution in nature is related to edaphic and climatic factors, this relationship is scarcely known. To understand abiotic factors driving the occurrence and prevalence of Campylobacter spp. in three municipalities from three states in northwestern Mexico (Chihuahua, Sonora, and Baja California), we used the kriging interpolation method of unsampled areas and the correspondence analysis of 23 environmental variables. Of the three municipalities evaluated, Janos in Chihuahua (CHIH), has the highest number of geographic areas classified as high and medium incidence, followed by Santa Cruz, Sonora (SON) and Mexicali, Baja California (BC). Mexicali (BC) edaphic variables limit the potential incidence of the bacterium, mainly due to the lack of soil moisture and its difficulty of surviving on dry surfaces, related to electrical conductivity and salinity. Janos (CHIH) presents limitations in terms of soil water availability, although its presence is more heterogeneous (2 to 8 months). Santa Cruz (SON) has the highest soil water availability (4 to 5 months), and presents pH, texture and low percentage of salinity conditions for the potential incidence of Campylobacter spp. Mexicali (BC) reports a temperature in the warmest month of up to 43°C, which could influence the presence of thermophilic species. The annual precipitation is another limiting factor for the potential incidence of Campylobacter spp. since it does not exceed 509.5 mm, contributing to Janos (CHIH) as the municipality with the highest potential incidence of this bacterium.

Assessment of the prevalence, serotype, and antibiotic resistance pattern of Salmonella enterica in integrated farming systems in the Maryland-DC area

Implementation of organic/pasture farming practices has been increasing in the USA regardless of official certification. These practices have created an increasingly growing demand for marketing safe products which are produced through these systems. Products from these farming systems have been reported to be at greater risk of transmitting foodborne pathogens because of current trends in their practices. Salmonella enterica (SE) is a ubiquitous foodborne pathogen that remains a public health issue given its prevalence in various food products, but also in the environment and as part of the microbial flora of many domestic animals. Monitoring antibiotic resistance and identifying potential sources contamination are increasingly important given the growing trend of organic/pasture markets. This study aimed to quantify prevalence of SE at the pre- and post-harvest levels of various integrated farms and sites in Maryland-Washington D.C. area, as well as identify the most prevalent serovars and antibiotic resistance patterns. Samples from various elements within the farm environment were collected and screened for SE through culture and molecular techniques, which served to identify and serotype SE, using species and serovar-specific primers, while antibiotic resistance was evaluated using an antibiogram assay. Results showed a prevalence of 7.80% of SE pre-harvest and 1.91% post-harvest. These results also showed the main sources of contamination to be soil (2.17%), grass (1.28%), feces (1.42%) and unprocessed produce (1.48%). The most commonly identified serovar was Typhimurium (11.32%) at the pre-harvest level, while the only identified serovar from post-harvest samples was Montevideo (4.35%). With respect to antibiotic resistance, out of the 13 clinically relevant antibiotics tested, gentamycin and kanamycin were the most effective, demonstrating 78.93 and 76.40% of isolates, respectively, to be susceptible. However, ampicillin, amoxicillin and cephradine had the lowest number of susceptible isolates with them being 10.95, 12.36, and 9.83%, respectively. These results help inform farms striving to implement organic practices on how to produce safer products by recognizing areas that pose greater risks as potential sources of contamination, in addition to identifying serotypes of interest, while also showcasing the current state of antibiotic efficacy and how this can influence antibiotic resistance trends in the future.

Exploring scenarios for the food system-zoonotic risk interface

The unprecedented economic and health impacts of the COVID-19 pandemic have shown the global necessity of mitigating the underlying drivers of zoonotic spillover events, which occur at the human-wildlife and domesticated animal interface. Spillover events are associated to varying degrees with high habitat fragmentation, biodiversity loss through land use change, high livestock densities, agricultural inputs, and wildlife hunting-all facets of food systems. As such, the structure and characteristics of food systems can be considered key determinants of modern pandemic risks. This means that emerging infectious diseases should be more explicitly addressed in the discourse of food systems to mitigate the likelihood and impacts of spillover events. Here, we adopt a scenario framework to highlight the many connections among food systems, zoonotic diseases, and sustainability. We identify two overarching dimensions: the extent of land use for food production and the agricultural practices employed that shape four archetypal food systems, each with a distinct risk profile with respect to zoonotic spillovers and differing dimensions of sustainability. Prophylactic measures to curb the emergence of zoonotic diseases are therefore closely linked to diets and food policies. Future research directions should explore more closely how they impact the risk of spillover events.

Risk factors associated with the prevalence of Shiga-toxin-producing Escherichia coli in manured soils on certified organic farms in four regions of the USA

Introduction

Biological soil amendments of animal origin (BSAAO), including untreated amendments are often used to improve soil fertility and are particularly important in organic agriculture. However, application of untreated manure on cropland can potentially introduce foodborne pathogens into the soil and onto produce. Certified organic farms follow the USDA National Organic Program (NOP) standards that stipulate a 90- or 120-day interval between application of untreated manure and crop harvest, depending on whether the edible portion of the crop directly contacts the soil. This time-interval metric is based on environmental factors and does not consider a multitude of factors that might affect the survival of the main pathogens of concern. The objective of this study was to assess predictors for the prevalence of Shiga-toxin-producing Escherichia coli (non-O157 STEC) in soils amended with untreated manure on USDA-NOP certified farms.

Methods

A longitudinal, multi-regional study was conducted on 19 farms in four USA regions for two growing seasons (2017–2018). Untreated manure (cattle, horse, and poultry), soil, and irrigation water samples were collected and enrichment cultured for non-O157 STEC. Mixed effects logistic regression models were used to analyze the predictors of non-O157 STEC in the soil up to 180 days post-manure application.

Results and discussion

Results show that farm management practices (previous use with livestock, presence of animal feces on the field, season of manure application) and soil characteristics (presence of generic E. coli in the soil, soil moisture, sodium) increased the odds of STEC-positive soil samples. Manure application method and snowfall decreased the odds of detecting STEC in the soil. Time-variant predictors (year and sampling day) affected the presence of STEC. This study shows that a single metric, such as the time interval between application of untreated manure and crop harvest, may not be sufficient to reduce the food safety risks from untreated manure, and additional environmental and farm-management practices should also be considered. These findings are of particular importance because they provide multi-regional baseline data relating to current NOP wait-time standards. They can therefore contribute to the development of strategies to reduce pathogen persistence that may contribute to contamination of fresh produce typically eaten raw from NOP-certified farms using untreated manure.

Risk factors of Shiga toxin-producing Escherichia coli in livestock raised on diversified small-scale farms in California

The increasing number of diversified small-scale farms (DSSF) that raise outdoor-based livestock in the USA reflects growing consumer demand for sustainably produced food. Diversified farms are small scale and raise a combination of multiple livestock species and numerous produce varieties. This 2015–2016 cross-sectional study aimed to describe the unique characteristics of DSSF in California, estimate the prevalence of Shiga toxin-producing Escherichia coli (STEC) in livestock and evaluate the association between risk factors and the presence of STEC in livestock, using generalised linear mixed models. STEC prevalence was 13.62% (76/558). Significant variables in the mixed-effect logistic regression model included daily maximum temperature (OR 0.95; CI_95% 0.91–0.98), livestock sample source (cattle (OR 4.61; CI_95% 1.64–12.96) and sheep (OR 5.29; CI_95% 1.80–15.51)), multiple species sharing the same barn (OR 6.23; CI_95% 1.84–21.15) and livestock having contact with wild areas (OR 3.63; CI_95% 1.37–9.62). Identification of STEC serogroups of public health concern (e.g. O157:H7, O26, O103) in this study indicated the need for mitigation strategies to ensure food safety by evaluating risk factors and management practices that contribute to the spread and prevalence of foodborne pathogens in a pre-harvest environment on DSSF.

Association of Common Zoonotic Pathogens With Concentrated Animal Feeding Operations

Animal farming has intensified significantly in recent decades, with the emergence of concentrated animal feeding operations (CAFOs) in industrialized nations. The congregation of susceptible animals in CAFOs can lead to heavy environmental contamination with pathogens, promoting the emergence of hyper-transmissible, and virulent pathogens. As a result, CAFOs have been associated with emergence of highly pathogenic avian influenza viruses, hepatitis E virus, Escherichia coli O157:H7, Streptococcus suis, livestock-associated methicillin-resistant Staphylococcus aureus, and Cryptosporidium parvum in farm animals. This has led to increased transmission of zoonotic pathogens in humans and changes in disease patterns in general communities. They are exemplified by the common occurrence of outbreaks of illnesses through direct and indirect contact with farm animals, and wide occurrence of similar serotypes or subtypes in both humans and farm animals in industrialized nations. Therefore, control measures should be developed to slow down the dispersal of zoonotic pathogens associated with CAFOs and prevent the emergence of new pathogens of epidemic and pandemic potential.

Cooked broiler meat quality affected by different Mediterranean medicinal plants in the diet

Objective

This study was conducted to investigate the effects of adding oregano (Origanum syriacum L.) and germander (Teucrium polium L.) to poultry diets individually and/or in combination: i) on cooked chicken meat quality and storage stability, ii) to compare this effect with those of the synthetic antioxidant butylated hydroxyanisole (BHA) and with the normal basic diet (Control: without supplements).

Methods

Broilers (140 birds) were raised for 21 days and then equally divided into five different treatment groups of 28 birds each. The dietary treatments were as follows: i) control; ii) germander (GER, 1.5%); iii) oregano (ORE, 2.5%); iv) combination of GER and ORE (CM, 1.5%, and 2.5%); v) BHA (0.02%). Meat patties from the five treatments were prepared, cooked, and stored at 4°C prior to analysis. During storage, samples were measured for thiobarbituric acid-reactive substances (TBARS) and total carbonyl levels at 0, 4, and 7 days. In addition, cooked thigh meat was prepared separately to evaluate cooking loss and sensory attributes.

Results

The CM dietary treatment showed the highest antioxidant effect, with decreasing TBARS values (breast and thigh meat) throughout the storage time (4 to 7 days). Furthermore, ORE showed a higher antioxidant effect, decreasing the rancidity development (TBARS values), compared to the GER during the storage period (days 0 to 7). The anti-carbonyl effect of the CM supplement was the highest among all treatments from day 0 to 7. Generally, the antioxidant effect of GER was lower compared to that of ORE and BHA alone. The CM treatment most significantly decreased off-odor and rancidity development, with the lowest oxidation odor scores.

Conclusion

The results indicate that the combination of oregano and germander in the diet of boilers improves meat quality and prolongs shelf life.

Detection of Toxoplasma gondii oocysts on organic and conventionally grown produce

Toxoplasma gondii infection can result in toxoplasmosis and potential psychological effects. Research commonly focuses on infection through contact with cat fecal matter or consumption of contaminated meat. However, T. gondii oocysts can persist in the environment for years and may be present in soils and on soil-grown produce. Rates of oocyst DNA recovery from produce were high, with 18% of vegetable samples testing positive for T. gondii via PCR test and melt curve analysis. Radishes had significantly higher oocyst counts than arugula, collard greens, kale, lettuce, and spinach. There were no significant differences in oocyst detection rates between samples taken from organic farmer's markets and conventional grocery stores. This study demonstrates that these oocysts can transfer to produce grown both conventionally and using organic techniques.

Gastrointestinal microbiomes of broilers and layer hens in alternative production systems

Alternative poultry production systems consisting of free-range or pasture flock raised poultry continues to increase in popularity. Based on the perceived benefits of poultry products generated from these alternative poultry production systems, they have commercial appeal to consumers. Several factors impact the health and well being of birds raised and maintained in these types of production systems. Exposure to foodborne pathogens and potential for colonization in the gastrointestinal tract has to be considered with these types of production systems. The gastrointestinal tract microbial composition and function of birds grown and maintained in alternative poultry operations may differ depending on diets, breed, and age of bird. Dietary variety and foraging behavior are potential influential factors on bird nutrition. The gastrointestinal tract microbiomes of birds raised under alternative poultry production systems are now being characterized with next-generation sequencing to identify individual microbial members and assess the impact of different factors on the diversity of microbial populations. In this review, the gastrointestinal tract microbiota contributions to free-range or pasture-raised broiler and egg layer production systems, subsequent applications, and potential future directions will be discussed.

Prevalence and risk factors associated with Campylobacter spp. and Salmonella enterica in livestock raised on diversified small-scale farms in California

Diversified farms are operations that raise a variety of crops and/or multiple species of livestock, with the goal of utilising the products of one for the growth of the other, thus fostering a sustainable cycle. This type of farming reflects consumers' increasing demand for sustainably produced, naturally raised or pasture-raised animal products that are commonly produced on diversified farms. The specific objectives of this study were to characterise diversified small-scale farms (DSSF) in California, estimate the prevalence of Salmonella enterica and Campylobacter spp. in livestock and poultry, and evaluate the association between farm- and sample-level risk factors and the prevalence of Campylobacter spp. on DSSF in California using a multilevel logistic model. Most participating farms were organic and raised more than one animal species. Overall Salmonella prevalence was 1.19% (95% confidence interval (CI95) 0.6-2), and overall Campylobacter spp. prevalence was 10.8% (CI95 = 9-12.9). Significant risk factors associated with Campylobacter spp. were farm size (odds ratio (OR)10-50 acres: less than 10 acres = 6, CI95 = 2.11-29.8), ownership of swine (OR = 9.3, CI95 = 3.4-38.8) and season (ORSpring: Coastal summer = 3.5, CI95 = 1.1-10.9; ORWinter: Coastal summer = 3.23, CI95 = 1.4-7.4). As the number of DSSF continues to grow, evaluating risk factors and management practices that are unique to these operations will help identify risk mitigation strategies and develop outreach materials to improve the food safety of animal and vegetable products produced on DSSF.

Microbiological Parameters in the Primary Production of Berries: A Pilot Study

The primary production of fresh soft fruits was considered to be a suspected critical point for the contamination of frozen berries that were responsible for the large 2013⁻2014 Hepatitis A virus (HAV) outbreak in Europe. In this study, an Italian berries’ production area was studied for its agro-technical characteristics, and the fresh fruits were analyzed for the presence of enteric viruses (HAV and Norovirus (NoV) genogroup I and genogroup II (GGI and GGII)), the enumeration of hygienic quality parameters, and the prevalence of bacterial pathogens. A total of 50 producers were sampled, who specialized in the exclusive or shared cultivation of berries. Escherichia coli was detected in two blackberry samples, whereas HAV and Norovirus were not detected. The samples were negative for Salmonella spp., Listeria monocytogenes, and Shiga toxin-producing Escherichia coli (STEC). The farms’ attributes were not associated with positive samples, apart from the presence of E. coli and the aerobic mesophilic bacteria for blackberry that were statistically correlated. In blueberries, the high aerobic mesophilic count could likely be associated with the resistance of the outer layer to handling. However, the two pathogens (Salmonella spp. and STEC) and the targeted viruses (HAV, NoV GGI and GGII) were not detected, highlighting the low risk of foodborne pathogens and viral contamination at the primary production stage of the berry food chain in the area considered in this pilot study.

Identifying and modeling meteorological risk factors associated with pre-harvest contamination of Listeria species in a mixed produce and dairy farm

This study sought to investigate the prevalence of Listeria species (including L. monocytogenes) in a mixed produce and dairy farm and to identify specific meteorological factors affecting Listeria spp. presence. Environmental samples were collected monthly from locations within the mixed farm over 14months and were analyzed for Listeria spp. Meteorological factors were evaluated for their association with the presence of Listeria spp. by using logistic regression (LR) and random forest (RF). The developed LR model identified wind speed and precipitation as significant risk factors (P<0.05), indicating higher wind speed at day 2 prior to sampling and higher average precipitation over the previous 25days before sampling increased the probability of isolation of Listeria spp. from the mixed farm. Results from RF revealed that average wind speed at day 2 prior to sampling and average precipitation in the previous 25days before sampling were the most important factors influencing the presence of Listeria spp., which supported the findings from LR. These findings indicate that the occurrence of Listeria spp. was influenced by wind speed and precipitation, suggesting run-off and wind-driven dust might be possible routes of pathogen transmission in mixed farms. The developed LR and RF models, with robust predictive performances as measured by the area under the receiver operating characteristic curves, can be used to predict Listeria spp. contamination risk in a mixed farm under different weather conditions and can help with the evaluation of farm management practices and the development of control strategies aimed at reducing pre-harvest microbial contamination in a mixed farming system.

EMA and EFSA Joint Scientific Opinion on measures to reduce the need to use antimicrobial agents in animal husbandry in the European Union, and the resulting impacts on food safety (RONAFA)

EFSA and EMA have jointly reviewed measures taken in the EU to reduce the need for and use of antimicrobials in food-producing animals, and the resultant impacts on antimicrobial resistance (AMR). Reduction strategies have been implemented successfully in some Member States. Such strategies include national reduction targets, benchmarking of antimicrobial use, controls on prescribing and restrictions on use of specific critically important antimicrobials, together with improvements to animal husbandry and disease prevention and control measures. Due to the multiplicity of factors contributing to AMR, the impact of any single measure is difficult to quantify, although there is evidence of an association between reduction in antimicrobial use and reduced AMR. To minimise antimicrobial use, a multifaceted integrated approach should be implemented, adapted to local circumstances. Recommended options (non-prioritised) include: development of national strategies; harmonised systems for monitoring antimicrobial use and AMR development; establishing national targets for antimicrobial use reduction; use of on-farm health plans; increasing the responsibility of veterinarians for antimicrobial prescribing; training, education and raising public awareness; increasing the availability of rapid and reliable diagnostics; improving husbandry and management procedures for disease prevention and control; rethinking livestock production systems to reduce inherent disease risk. A limited number of studies provide robust evidence of alternatives to antimicrobials that positively influence health parameters. Possible alternatives include probiotics and prebiotics, competitive exclusion, bacteriophages, immunomodulators, organic acids and teat sealants. Development of a legislative framework that permits the use of specific products as alternatives should be considered. Further research to evaluate the potential of alternative farming systems on reducing AMR is also recommended. Animals suffering from bacterial infections should only be treated with antimicrobials based on veterinary diagnosis and prescription. Options should be reviewed to phase out most preventive use of antimicrobials and to reduce and refine metaphylaxis by applying recognised alternative measures.

Excretion of infectious hepatitis E virus into milk in cows imposes high risks of zoonosis

Hepatitis E virus (HEV) represents the main cause of acute hepatitis worldwide. HEV infection in immunocompromised patients involves a high risk for the development of chronic hepatitis. Because HEV is recognized as a zoonotic pathogen, it is currently believed that swine is the primary reservoir. However, this is not sufficient to justify the strikingly high seroprevalence of HEV in both developing and Western countries. Thus, this study aimed to identify new zoonotic sources that bear a high risk of transmission to humans. We collected fecal, blood, and milk samples of cows in a typical rural region of Yunnan Province in southwest China, where mixed farming of domestic animals is a common practice. HEV RNA was quantified by quantitative real-time polymerase chain reaction, and the whole genome was sequenced. HEV infectivity was assessed in rhesus macaques. We found a high prevalence of active HEV infection in cows as determined by viral RNA positivity in fecal samples. Surprisingly, we discovered that HEV is excreted into milk that is produced by infected cows. Phylogenetic analysis revealed that all HEV isolates from cow/milk belong to genotype 4 and subtype 4h. Gavage with HEV-contaminated raw and even pasteurized milk resulted in active infection in rhesus macaques. Importantly, a short period of boiling, but not pasteurization, could completely inactivate HEV.

CONCLUSION

Infectious HEV-contaminated cow milk is recognized as a new zoonotic source that bears a high risk of transmission to humans; these results call attention to understanding and establishing proper measurement and control of HEV zoonotic transmission, particularly in the setting of mixed farming of domestic animals. (Hepatology 2016;64:350-359).

Ecological Dynamics of Campylobacter in Integrated Mixed Crop-Livestock Farms and Its Prevalence and Survival Ability in Post-Harvest Products

This study investigated the ecological distribution of zoonotic bacterial pathogen, Campylobacter, in mixed crop-livestock (MCL) farms compared to conventional farms and their products at pre- and post-harvest levels. A total of 222 Campylobacter isolates were identified. At pre-harvest level, a total of 1287 samples from seven MCL farms, four conventional poultry farms, four organic produce-only and five conventional produce-only farms from Maryland and the DC metropolitan area were analysed from 2012 to 2014. Campylobacter was detected in 11.16% and 3.6% of MCL and conventional farm samples, respectively, but none from produce-only farm samples. Tetracycline resistance was observed in 51.02% of MCL farm isolates but none among conventional farm isolates. For post-harvest analysis, a total of 1281 food products from seven farmers markets, three organic retail supermarkets and three conventional retail supermarkets were collected from the same area. Campylobacter was isolated in 87.5%, 71.43% and 33.33% of whole chicken carcasses in farmers markets, organic and conventional retail supermarkets, respectively. No Campylobacter was detected in post-harvest produce samples due in part to the inability of Campylobacter to survive in absence of sufficient water activity. Overall, this study reveals public health concerns regarding the MCL farm environment and their products that are sold in retail and farmers markets.