Detection of Campylobacter spp. in chicken fecal samples by real-time PCR

Campylobacter species, Salmonella serotypes and ribosomal RNA-based fecal source tracking in the Kokemäki River watershed

Fecal contamination of surface water compromises the usability of surface water for drinking water production due to an increase in human health risks. In this study, we collected surface water samples for two years from the Kokemäki River (Finland). The downstream river stretch is used for feeding production of artificial ground water for a major drinking water treatment plant. The prevalence of Campylobacter species and Salmonella serotypes together with fecal source identifiers targeting general, human, gull, swine, and ruminant were evaluated at 16 sampling sites throughout the studied watershed. We detected Campylobacter spp. from all 16 sampling sites with Campylobacter jejuni and Campylobacter lari as the most detected species. Salmonella spp. was detected in 10 out of 16 sampling sites, with Salmonella Typhimurium being the most common serovar. Regarding spatial variation in the hygienic quality of surface water, the upstream area (urban proximity) and downstream area (agricultural proximity) had higher microbial loads than the middle section of the study area. Samples taken in fall and spring had higher microbial loads than summer and winter samples. The lower ratio of rRNA to rRNA-gene (rDNA) of studied microbes in the winter than in other seasons may indicate low metabolic activity of bacterial targets during winter. The number of gulls, swine, and cattle in the catchment area concorded with the number of fecal source identifiers in the surface water. Further, the prevalence of gull-specific source identifier agreed with the detection of C. coli, C. lari, and S. Typhimurim, whereas the prevalence of swine- and ruminant-specific source identifiers agreed with the detection of C. jejuni and C. coli. Thus, fecal source identifiers are shown to be important tools for monitoring zoonotic pathogens affecting microbial quality of surface water. Further, variation in fecal loads indicates such variation in health risks related to surface water use.

A Bacteriophage Protein-Based Impedimetric Electrochemical Biosensor for the Detection of Campylobacter jejuni

Campylobacter jejuni is a common foodborne pathogen found in poultry that can cause severe life-threatening illnesses in humans. It is important to detect this pathogen in food to manage foodborne outbreaks. This study reports a novel impedimetric phage protein-based biosensor to detect C. jejuni NCTC 11168 at 100 CFU/mL concentrations using a genetically engineered receptor-binding phage protein, FlaGrab, as a bioreceptor. The electrochemical impedance spectroscopy (EIS) technique was employed to measure changes in resistance upon interaction with C. jejuni. The sensitivity of the phage protein-immobilized electrode was assessed using the various concentrations of C. jejuni NCTC 11168 ranging from 102-109 colony forming units (CFU)/mL). The change transfer resistance of the biosensor increased with increasing numbers of C. jejuni NCTC 11168 cells. The detection limit was determined to be approximately 103 CFU/mL in the buffer and 102 CFU/mL in the ex vivo samples. Salmonella enterica subsp. enterica serotype Typhimurium-291RH and Listeria monocytogenes Scott A were used as nontarget bacterial cells to assess the specificity of the developed biosensor. Results showed that the developed biosensor was highly specific toward the target C. jejuni NCTC 11168, as no signal was observed for the nontarget bacterial cells.

Foodborne pathogenic bacteria in wild European hedgehogs (Erinaceus europaeus)

BACKGROUND

European hedgehogs (Erinaceus europaeus) are widely distributed across Europe. They may play an important role by spreading zoonotic bacteria in the environment and to humans and animals. The aim of our work was to study the prevalence and characteristics of the most important foodborne bacterial pathogens in wild hedgehogs.

RESULTS

Faecal samples from 148 hospitalised wild hedgehogs originating from the Helsinki region in southern Finland were studied. Foodborne pathogens were detected in 60% of the hedgehogs by PCR. Listeria (26%) and STEC (26%) were the most common foodborne pathogens. Salmonella, Yersinia, and Campylobacter were detected in 18%, 16%, and 7% of hedgehogs, respectively. Salmonella and Yersinia were highly susceptible to the tested antimicrobials. Salmonella Enteritidis and Listeria monocytogenes 2a were the most common types found in hedgehogs. All S. Enteritidis belonged to one sequence type (ST11), forming four clusters of closely related isolates. L. monocytogenes was genetically more diverse than Salmonella, belonging to 11 STs. C. jejuni ST45 and ST677, Y. pseudotuberculosis O:1 of ST9 and ST42, and Y. enterocolitica O:9 of ST139 were also found.

CONCLUSIONS

Our study shows that wild European hedgehogs should be considered an important source of foodborne pathogens, and appropriate hygiene measures after any contact with hedgehogs and strict biosecurity around farms are therefore important.

Role of Maternal Antibodies in the Protection of Broiler Chicks against Campylobacter Colonization in the First Weeks of Life

Thermophilic Campylobacter species are the most common cause of bacterium-mediated diarrheal disease in humans globally. Poultry is considered the most important reservoir of human campylobacteriosis, but so far, no effective countermeasures are in place to prevent the bacterium from colonizing broiler flocks. This study investigated maternal antibodies' potential to offer protection against Campylobacter in broiler chicks via a field trial and an immunization trial. In the field trial, breeder flocks with high and low anti-Campylobacter antibody levels in the yolk were selected based on serological screening. Offspring were subsequently monitored for maternal antibodies and Campylobacter prevalence during early life. Although maternal antibodies declined rapidly in the serum of broilers, offspring from flocks with lower anti-Campylobacter antibody levels seemed to be more susceptible to colonization. In the immunization trial, breeders from a seropositive breeder flock were vaccinated with an experimental bacterin or subunit vaccine. Immunization increased antibody levels in the yolk and consequently in the offspring. Elevated maternal antibody levels were significantly associated with reduced Campylobacter susceptibility in broilers at 2 weeks old but not at 1 and 3 weeks old. Overall, the protective effect of maternal immunity should be cautiously considered in the context of Campylobacter control in broilers. Immunization of breeders may enhance resistance but is not a comprehensive solution.

Design of dot-blot hybridization assay for simultaneous detection of Campylobacter jejuni and Campylobacter coli: a preliminary study

Objectives

Campylobacters are a major cause of gastroenteritis worldwide. These are fastidious in culture and false negative results are seen in many clinical laboratories. Among molecular methods, the dot-blot technique is widely used for a variety of purposes, especially diagnostics. So, the authors aimed to detect C. jejuni and C. coli simultaneously using a dot-blot assay.

Methods

After evaluating the bioinformatics studies, a cadF-conserved fragment was selected for the design of primers and probe. DNAs from standard strains and a recombinant plasmid, prepared in this study, were used to assess the technique. The specificity of the method was also surveyed using DNAs from other enteric bacteria. The limit of detection was evaluated by recombinant plasmid and different concentrations of the designed probe.

Results

A 95-bp fragment of cadF was selected, and in silico analysis studies showed that it is conserved between both species. Also, the non-specific annealing of the primers and probe with other bacteria was not seen theoretically. The technique with recombinant plasmid as well as DNAs of standard strains created black spots on the membrane, confirming that the probe was correctly synthesized. No non-specific reactions with other bacterial species were observed (specificity=100%). The limit of detection of the test was determined to be 50 µg/ml.

Conclusions

This is the first study to simultaneously detect two important pathogens in the Campylobacter genus and was able to detect C. jejuni and C. coli with acceptable sensitivity and specificity.

Reducing Campylobacter colonization in broilers by active immunization of naive broiler breeders using a bacterin and subunit vaccine

Campylobacter is the main cause of human gastroenteritis worldwide, with 50 to 80% of the cases related to consumption of poultry products. Maternal antibodies (MAB) from commercial breeder flocks may protect their progeny against infection during the first few weeks of life. We here studied the prevalence of Campylobacter antibody titers in broiler breeder flocks and to which extent immunization of broiler breeders increases maternal anti-Campylobacter titers in their progeny and protects the offspring against Campylobacter colonization. Two vaccines were used: a bacterin mix of 13 Campylobacter strains and a subunit vaccine comprising 6 immunodominant Campylobacter antigens. All sampled on-farm breeder flocks were positive for anti-Campylobacter antibodies, yet in some breeder flocks only very low titers were detected. Vaccination of SPF broiler breeder flocks with both subunit and bacterin vaccines resulted in a prolonged presence of anti-Campylobacter antibodies in the serum and intestinal mucus of chicks. These bacterin- or subunit vaccine-induced MAB conferred protection against Campylobacter colonization in chicks until 7 and 21 d of age, respectively, but only at a low challenge dose (102.5 cfu). The concentration of MAB in the mucus is probably too low to sufficiently capture Campylobacter when higher challenge doses are used. In conclusion, vaccinating broiler breeders protects their offspring against Campylobacter colonization under low pathogen exposure conditions.

Quantifying Enteropathogen Contamination along Chicken Value Chains in Maputo, Mozambique: A Multidisciplinary and Mixed-Methods Approach to Identifying High Exposure Settings

BACKGROUND

Small-scale poultry production is widespread and increasing in low- and middle-income countries (LMICs). Exposure to enteropathogens in poultry feces increases the hazard of human infection and related sequela, and the burden of disease due to enteric infection in children < 5 y in particular is substantial. Yet, the containment and management of poultry-associated fecal waste in informal settings in LMICs is largely unregulated.

OBJECTIVES

To improve the understanding of potential exposures to enteropathogens carried by chickens, we used mixed methods to map and quantify microbial hazards along production value chains among broiler, layer, and indigenous chickens in Maputo, Mozambique.

METHODS

To map and describe the value chains, we conducted 77 interviews with key informants working in locations where chickens and related products are sold, raised, and butchered. To quantify microbial hazards, we collected chicken carcasses (n = 75 ) and fecal samples (n = 136 ) from chickens along the value chain and assayed them by qPCR for the chicken-associated bacterial enteropathogens C. jejuni/coli and Salmonella spp.

RESULTS

We identified critical hazard points along the chicken value chains and identified management and food hygiene practices that contribute to potential exposures to chicken-sourced enteropathogens. We detected C. jejuni/coli in 84 (76%) of fecal samples and 52 (84%) of carcass rinses and Salmonella spp. in 13 (11%) of fecal samples and 16 (21%) of carcass rinses. Prevalence and level of contamination increased as chickens progressed along the value chain, from no contamination of broiler chicken feces at the start of the value chain to 100% contamination of carcasses with C. jejuni/coli at informal markets. Few hazard mitigation strategies were found in the informal sector.

DISCUSSION

High prevalence and concentration of C. jejuni/coli and Salmonella spp. contamination along chicken value chains suggests a high potential for exposure to these enteropathogens associated with chicken production and marketing processes in the informal sector in our study setting. We identified critical control points, such as the carcass rinse step and storage of raw chicken meat, that could be intervened in to mitigate risk, but regulation and enforcement pose challenges. This mixed-methods approach can also provide a model to understand animal value chains, sanitary risks, and associated exposures in other settings. https://doi.org/10.1289/EHP11761.

Research Note: Detection of Campylobacter spp. in chicken meat using culture methods and quantitative PCR with propidium monoazide

Globally, Campylobacter spp. are prominent causative agents of food-borne gastroenteritis. These pathogens are commonly detected using conventional culture methods; however, culture methods are unable to detect viable but nonculturable (VBNC) bacteria. Currently, the detection rate of Campylobacter spp. on chicken meat does not correlate with the seasonal peak of human campylobacteriosis. We hypothesized that this may be due to the presence of undetectable VBNC Campylobacter spp. Therefore, we previously established a quantitative PCR assay using propidium monoazide (PMA-qPCR), which can detect viable Campylobacter cells. In this study, PMA-qPCR was conducted to detect viable Campylobacter spp. in chicken meat, and the detection rates of PMA-qPCR and the culture method throughout all 4 seasons were compared. A total of 105 chicken meat samples (whole legs, breast fillets, and livers) were screened for the presence of Campylobacter spp. using both PMA-qPCR and the conventional culture method. The detection rates of the 2 methods did not differ significantly; however, the positive and negative samples were not always consistent. Detection rates in March were significantly lower compared to months with the highest detection rates. These results suggest that, to increase the detection rate of Campylobacter spp., the 2 methods should be used in parallel. In this study, PMA-qPCR could not detect VBNC Campylobacter spp. effectively in C. jejuni-spiked chicken meat. Further studies using improved viability-qPCR should be performed to describe the impact of the VBNC state of Campylobacter spp. on the detection of this bacterium in chicken meat.

Rapid and sensitive detection of gram-negative bacteria using surface-immobilized polymyxin B

Although detection of gram-negative bacteria (GNB) in body fluids is important for clinical purpose, traditional gram staining and other recently developed methods have inherent limitations in terms of accuracy, sensitivity, and convenience. To overcome the weakness, this study proposed a method detecting GNB based on specific binding of polymyxin B (PMB) to lipopolysaccharides (LPS) of GNB. Fluorescent microscopy demonstrated that surface immobilized PMB using a silane coupling agent was possible to detect fluorescent signal produced by a single Escherichia coli (a model GNB) cell. Furthermore, the signal was selective enough to differentiate between GNB and gram-positive bacteria. The proposed method could detect three cells per ml within one hour, indicating the method was very sensitive and the sensing was rapid. These results suggest that highly multifold PMB binding on each GNB cell occurred, as millions of LPS are present on cell wall of a GNB cell. Importantly, the principle used in this study was realized in a microfluidic chip for a sample containing E. coli cells suspended in porcine plasma, demonstrating its potential application to practical uses. In conclusion, the proposed method was accurate, sensitive, and convenient for detecting GNB, and could be applied clinically.

Monitoring within-farm transmission dynamics of antimicrobial-resistant Campylobacter in dairy cattle using broth microdilution and long-read whole genome sequencing

Campylobacter jejuni and Campylobacter coli are important foodborne zoonotic pathogens and cause for concern due to the increasing trend in antimicrobial resistance. A long-run surveillance study was conducted in animals from different age groups in five dairy cattle farms to investigate the within-farm diversity and transmission dynamics of resistant Campylobacter throughout time. The resistance phenotype of the circulating isolates (170 C. jejuni and 37 C. coli) was determined by broth microdilution and a selection of 56 isolates were whole genome sequenced using the Oxford-Nanopore long-fragment sequencing technology resulting in completely resolved and circularized genomes (both chromosomes and plasmids). C. jejuni was isolated from all farms while C. coli was isolated from only two farms, but resistance rates were higher in C. coli than in C. jejuni and in calves than in adult animals. Some genotypes (e.g. ST-48, gyrA_T86I/tet(O)/blaOXA-61 in farm F1; ST-12000, aadE-Cc/tet(O)/blaOXA-489 in F4) persisted throughout the study while others were only sporadically detected. Acquisition of extracellular genes from other isolates and intracellular mutational events were identified as the processes that led to the emergence of the resistant genotypes that spread within the herds. Monitoring with Oxford Nanopore Technologies sequencing helped to decipher the complex molecular epidemiology underlying the within-farm dissemination of resistant Campylobacter.

Adapted method for rapid detection and quantification of pathogen Campylobacter jejuni from environmental water samples

Building on a previously developed workflow for rapid and sensitive pathogen detection by qPCR, this work has established a sample treatment strategy that produces consistent quantification efficiencies (QEs) for Campylobacter jejuni against a complex and highly variable sample matrix from a suburban river. The individual treatments most effective at minimizing the inhibitory effects of the sample matrix were pH buffering with HEPES (50 mM, pH 5.7) and addition of the surfactant Tween 20 (2% v/v). Unexpectedly, sample acidification (pH 4-5) resulting from the use of aged Tween 20 that had undergone partial hydrolysis, appeared to play a key role in enhancing QE. This effect could be replicated by direct pH adjustment with dilute hydrochloric acid and may be linked to the solubilization and removal of inhibitory particles at an acidic pH. While the effectiveness of each individual treatment method varied, a combined treatment of either HEPES buffer + Tween 20, or direct pH adjustment + Tween 20, consistently produced QEs of 60%-70% and up to 100%, respectively, over a sampling period of one year. The consistency and scalability of this workflow make it a suitable alternative to culture-based ISO methods for detecting Campylobacter spp.

Genomic Characterization and Wetland Occurrence of a Novel Campylobacter Isolate from Canada Geese

Populations of resident, non-migratory Canada geese are rapidly increasing. Canada geese are known to transmit viral and bacterial diseases, posing a possible threat to human health. The most prevalent pathogens vectored by geese are Campylobacter species, yet the current understanding of the identity and virulence of these pathogens is limited. In our previous study, we observed a high prevalence of Campylobacter spp. in the Banklick Creek wetland—a constructed treatment wetland (CTW) located in northern KY (USA) used to understand sources of fecal contamination originating from humans and waterfowl frequenting the area. To identify the types of Campylobacter spp. found contaminating the CTW, we performed genetic analyses of Campylobacter 16s ribosomal RNA amplified from CTW water samples and collected fecal material from birds frequenting those areas. Our results showed a high occurrence of a Campylobacter canadensis-like clade from the sampling sites. Whole-genome sequence analyses of an isolate from Canada goose fecal material, called MG1, were used to confirm the identity of the CTW isolates. Further, we examined the phylogenomic position, virulence gene content, and antimicrobial resistance gene profile of MG1. Lastly, we developed an MG1-specific real-time PCR assay and confirmed the presence of MG1 in Canada goose fecal samples surrounding the CTW. Our findings reveal that the Canada goose-vectored Campylobacter sp. MG1 is a novel isolate compared to C. canadensis that possesses possible zoonotic potential, which may be of human health concern.

Simultaneous Detection of Salmonella spp. and Quantification of Campylobacter spp. in a Real-Time Duplex PCR: Myth or Reality?

In Europe, there is a process hygiene criterion for Salmonella and Campylobacter on broiler carcasses after chilling. The criterion gives indicative contamination values above which corrective actions are required by food business operators. The reference methods for verifying compliance with the criterion for Salmonella and Campylobacter are international standards EN ISO 6579-1 (2017) and EN ISO 10272-2 (2017), respectively. These methods are time-consuming and expensive for food business operators. Therefore, it would be advantageous to simultaneously detect Salmonella spp. and quantify Campylobacter in the same analysis, using the same sample after the pre-enrichment step for Salmonella recovery. A duplex PCR for Salmonella detection and Campylobacter spp. enumeration was developed. Considering the method as a whole, the LOD and LOQ for Campylobacter enumeration were slightly over the limit of 3 log CFU/g set by the process hygiene criterion. A comparison of the duplex PCR method developed with the ISO method on artificially contaminated bacterial suspensions and on naturally contaminated samples demonstrated a good correlation of the results for Campylobacter enumeration when the duplex PCR was performed on samples taken before or after the pre-enrichment step, but revealed a slight bias with a large standard deviation resulting in widely spaced limits of agreement.

Effects of DNA extraction methods on the real time PCR quantification of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari in chicken feces and ceca contents

Polymerase chain reaction (PCR) method was coupled with a DNA extraction to enumerate Campylobacter spp. from poultry gastrointestinal tract samples. Three experiments were conducted that included: 1) Development of a DNA standard curve related to bacterial DNA primers; 2) Design of a cell/genomic DNA extraction protocol to isolate Campylobacter spp. DNA from complex samples such as poultry feces; and 3) Comparison of PCR quantification to standard plate count methodology. The standard curve using primers for Campylobacter spp. was created for DNA extracted from environmental isolates with a linear range (R² > 0.95) and with a high specificity for C. coli and C. jejuni recovered from poultry, swine and laboratory isolates. A 2-step extraction process of bacterial DNA from poultry feces was developed in which the cells were first concentrated using a gradient-centrifugation step followed by comparison of 4 DNA extraction methods. Two commercial DNA extraction methods (Zymo Research Quick DNA, and Invitrogen magnetic separation), a traditional phenol-chloroform DNA extraction method using proteinase K to inactivate DNAses, and an in-house isolation method for DNA extraction based on chaotropic salts were used. The middle gradient layer recovered 89% to 98% of the bacteria cells from the sample, with recovery dependent upon the Campylobacter genus. The 4 DNA extractions methods recovered 112 to 302 ug/nL of DNA. Finally, the qPCR and standard plate methods were highly correlated for enumerating Campylobacter spp. in the 2.0 to 8.0-log CFU range. Analyses of the results from this study demonstrate that the combination of the standard curve for Campylobacter spp. DNA primers, the gradient cell concentration method and DNA extraction techniques with qPCR can be used to enumerate Campylobacter spp. from poultry samples with findings similar those of traditional plate count methodology.

A One Health real-time surveillance system for nowcasting Campylobacter gastrointestinal illness outbreaks, Norway, week 30 2010 to week 11 2022

BackgroundCampylobacter is a leading cause of food and waterborne illness. Monitoring and modelling Campylobacter at chicken broiler farms, combined with weather pattern surveillance, can aid nowcasting of human gastrointestinal (GI) illness outbreaks. Near real-time sharing of data and model results with health authorities can help increase potential outbreak responsiveness.AimsTo leverage data on weather and Campylobacter on broiler farms to build a risk model for possible human Campylobacter outbreaks and to communicate risk assessments with health authorities.MethodsWe developed a spatio-temporal random effects model for weekly GI illness consultations in Norwegian municipalities with Campylobacter monitoring and weather data from week 30 2010 to 11 2022 to give 1-week nowcasts of GI illness outbreaks. The approach combined a municipality random effects baseline model for seasonally-adjusted GI illness with a second model for peak deviations from that baseline. Model results are communicated to national and local stakeholders through an interactive website: Sykdomspulsen One Health.ResultsLagged temperature and precipitation covariates, as well as 2-week-lagged positive Campylobacter sampling in broilers, were associated with higher levels of GI consultations. Significant inter-municipality variability in outbreak nowcasts were observed.ConclusionsCampylobacter surveillance in broilers can be useful in GI illness outbreak nowcasting. Surveillance of Campylobacter along potential pathways from the environment to illness such as via water system monitoring may improve nowcasting. A One Health system that communicates near real-time surveillance data and nowcast changes in risk to health professionals facilitates the prevention of Campylobacter outbreaks and reduces impact on human health.

Monitoring of Campylobacter jejuni in a chicken infection model by measuring specific volatile organic compounds and by qPCR

Campylobacter is one of the leading bacterial foodborne pathogens worldwide. Poultry is the host species with this pathogen with the highest clinical impact. Flocks become colonised with Campylobacter, which leads to contamination of product entering the food-chain. Rapid and reliable Campylobacter detection methods could support controls to minimize the risks of contamination within the food-chain, which would easier enable the implementation of a logistical slaughter schedule or other control options. The present study evaluates current and emerging C. jejuni detection technologies on air samples in a unique study set-up of pre-defined C. jejuni prevalences. Both non-invasive detection technologies on air samples by subsequent measuring of volatile organic compounds (VOCs) or by qPCR detected the C. jejuni presence and could additionally distinguish between the number of present C. jejuni-positive birds in the study set-up. Nevertheless, electrostatic air samplers diagnosed fewer birds as C. jejuni-positive compared to the cultivation-based method. By measuring the VOCs, it was possible to detect the presence of two positive birds in the room. This apparent high sensitivity still needs to be verified in field studies. Techniques, such as these promising methods, that can facilitate C. jejuni surveillance in poultry flocks are desirable to reduce the risk of infection for humans.

Temporal dynamics of Campylobacter and Arcobacter in a freshwater lake that receives fecal inputs from migratory geese

Migratory geese could influence the microbiological water quality; however, their impacts on pathogen dynamics remain largely unknown. In this study, we analyzed the population dynamics of Campylobacter and Arcobacter group bacteria (AGB) in a freshwater lake in Japan over two years. The bacteria were quantified by using both culture-dependent and -independent methods. The potential sources of these bacteria were examined by a high-throughput flaA sequencing approach. Campylobacter was abundantly detected both by culture-dependent and -independent methods in the lake, especially when migratory geese were present in the lake. High-throughput flaA sequencing suggests that geese were the likely source of Campylobacter in the lake. The viable population of Campylobacter exceeds the concentrations that can potentially cause 10^-4 infections per person per year when water is used to grow fresh vegetables. The occurrence of AGB, on the other hand, was not directly related to the population of migratory geese. AGB were not detected in geese fecal samples. Diverse AGB flaA genotypes occurred in the lake over multiple seasons. Our results suggest that AGB likely comprise a part of the indigenous microbial population of the lake and grow in response to high nutrient, warm temperature, and low dissolved oxygen concentrations in the lake. Geese therefore can indirectly impact the AGB population by providing nutrients to cause eutrophication and lower the dissolved oxygen concentration. Since geese travel long-distance and disperse their fecal microbiota and nutrients to wide areas, they may have significant impacts on water quality and public health.

Molecular diagnostics of Salmonella and Campylobacter in human/animal fecal samples remain feasible after long-term sample storage without specific requirements

Rapid advances in the development of sequencing technologies, numbers of commercial providers and diminishing costs have made DNA-based identification and diagnostics increasingly accessible to doctors and laboratories, eliminating the need for local investments in expensive technology and training or hiring of skilled technicians. However, reliable and comparable molecular analyses of bacteria in stool samples are dependent on storage and workflow conditions that do not introduce post-sampling bias, the most important factor being the need to keep the DNA at a stable detectable level. For that reason, there may remain other prohibitively costly requirements for cooling or freezing equipment or special chemical additives.

This study investigates the diagnostic detectability of Salmonella and Campylobacter DNA in human, pig and chicken stool samples, stored at different temperatures and with different preservation methods. Stool samples were spiked with 10⁶ CFU/mL of both Salmonella and Campylobacter strains stored at −20 °C, 5 °C and 20 °C (Room temperature, RT) and treated with either RNAlater, EDTA or Silica/ethanol. DNA was extracted at 9 different time points within 30 days and quantified by Qubit (total DNA) and qPCR (Salmonella and Campylobacter DNA). We found no statistically significant differences among the different preservation methods, and DNA from both species was easily detected at all time points and at all temperatures, both with and without preservation. This suggests that infections by these bacteria can be diagnosed and possibly also analysed in further detail simply by taking a stool sample in any suitable sealed container that can be transported to laboratory analysis without special storage or preservation requirements. We briefly discuss how this finding can benefit infection control in both developed and developing countries.

Effects of Zinc Source and Enzyme Addition on the Fecal Microbiota of Dogs

Supplemental zinc from organic sources has been suggested to be more bioavailable than inorganic ones for dog foods. However, the bioavailability of zinc might be affected by dietary constituents such as phytates. The present study aimed to evaluate the effects of two zinc sources (zinc sulfate and zinc proteinate) and the addition of a multi-enzymatic complex from the solid-state fermentation of Aspergillus niger on end-products of fecal fermentation and fecal microbiota of adult Beagles fed a high-phytate diet. The experimental design consisted of three 4 × 4 Latin Squares with a 2 × 2 factorial arrangement of treatments (n = 12 Beagles), with four periods and four diets: zinc sulfate without (IZ) or with (IZ +) enzyme addition, and zinc proteinate without (OZ) or with (OZ +) enzyme addition. Enzyme addition significantly affected Faith’s phylogenetic diversity index, whereas zinc source did not affect either beta or alpha diversity measures. Linear discriminant analysis effect size detected nine taxa as markers for organic zinc, 18 for inorganic source, and none for enzyme addition. However, with the use of a negative binomial generalized linear model, further effects were observed. Organic zinc was associated with a significantly higher abundance of Firmicutes and lower Proteobacteria and Bacteroidetes, although at a genus level, the response varied. The DNA abundance of Clostridium cluster I, Clostridium cluster XIV, Campylobacter spp., Ruminococcaceae, Turicibacter, and Blautia was significantly higher in dogs fed IZ and IZ + diets. Higher abundance of genus Lactobacillus was observed in dogs fed enzyme-supplemented diets. End-products of fecal fermentation were not affected by zinc source or enzymes. An increase in some taxa of the phyla Actinobacteria and Firmicutes was observed in feces of dogs fed organic zinc with enzyme addition but not with inorganic zinc. This study fills a gap in knowledge regarding the effect of zinc source and enzyme addition on the fecal microbiota of dogs. An association of zinc bioavailability and bacteria abundance is suggested, but the implications for the host (dog) are not clear. Further studies are required to unveil the effects of the interaction between zinc sources and enzyme addition on the fecal microbial community.

Impact of the gut microecology on Campylobacter presence revealed by comparisons of the gut microbiota from chickens raised on litter or in individual cages

Background

Poultry is the major reservoir of Campylobacter that contributes to human campylobacteriosis and threatens food safety. Litter contact has been linked to Campylobacter colonization, but the gut microecological impact underlying this link remains not fully clear. Here, we sought to investigate the impact of the gut microecology on the presence of Campylobacter by examining the microbiota in the duodenum, jejunum, ileum, ceca, and feces from chickens raised on commercial litter and in individual cages at 0–57 days of age.

Results

Through litter contact, the presence of Campylobacter was found to benefit from microecological competition among Lactobacillus, Helicobacter, and genera that are halotolerant and aerobic or facultatively anaerobic in the upper intestine, such as Corynebacterium and Brachybacterium. The presence was also promoted by the increased abundance in obligate anaerobic fermentation microbes, especially members of the orders Clostridiales and Bacteroidales. The longitudinal analysis supported the vertical or pseudo-vertical transmission but suggested that colonization might occur immensely at 7–28 days of age. We observed a host genetic effect on the gut microecology, which might lead to increased heterogeneity of the microecological impact on Campylobacter colonization.

Conclusions

The findings advance the understanding of the gut microecological impact on Campylobacter presence in the chicken gut under conditions of litter contact and suggest that manipulations of the gut microecology, as well as the microbes identified in the Campylobacter association networks, might be important for the development of intervention strategies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02353-5.

Enrichment Free qPCR for Rapid Identification and Quantification of Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis in Chicken Meat Samples by a New Couple of Primers

Campylobacter is the main cause of bacterial foodborne disease and poultry meat is the principal source of human infections. Rapid methods for Campylobacter detection are urgently needed to decrease high bacterial prevalence in poultry products. In this study, we developed new primers, CampyPFw and CampyPRv, that target the 16S-23S rRNA genes of Campylobacter jejuni, C. coli, C. lari and C. upsaliensis. The primers were tested on positive and negative reference strains in pure cultures and in inoculated poultry meat samples before their application in real-time PCR (qPCR) protocol for analyzing chicken meat samples. In parallel, the samples were tested by using the ISO 10272-1:2006 method. The qPCR protocol based on CampyPFw and CampyPRv showed good sensitivity, with the limit of detection of 4.6 × 10² cells/mL in chicken samples without enrichment steps.

Combined Loop-Mediated Isothermal Amplification Assays for Rapid Detection and One-Step Differentiation of Campylobacter jejuni and Campylobacter coli in Meat Products

A loop-mediated isothermal amplification (LAMP) assay system was established, allowing rplD gene-based simultaneous detection of Campylobacter jejuni and Campylobacter coli in enriched meat products. Additionally, one-step differentiation of target species on agar plates was enabled by cdtC gene- and gyrA gene-based duplex LAMP. Both the rplD and cdtC–gyrA LAMP assays amplified the target sequences in all 62 C. jejuni and 27 C. coli strains used for determining inclusivity and revealed 100% exclusivity toward 85 tested non-target species. Throughout the entire experiments, C. jejuni and C. coli strains were 100% distinguishable by melting curves of cdtC and gyrA LAMP products. After 24-h enrichment, the rplD LAMP assay reliably detected initial inoculation levels of 10–100 CFU/g in artificially contaminated minced meat. Investigation of naturally contaminated meat samples revealed a diagnostic accuracy of 95% toward real-time PCR and 94.1% toward the standard culture method applying the 24-h incubation period. Diagnostic sensitivity and specificity, and positive and negative predictive values were 89.8, 100, 100, and 91.2%, respectively, when measured against real-time PCR, and 89.6, 98.1, 97.7, and 91.2%, respectively, when measured against the standard culture method. After 48-h enrichment, the detection limit of the rplD LAMP assay improved to initial inoculation levels of 1–10 CFU/g in artificially contaminated minced meat. Applying the 48-h incubation period on naturally contaminated meat samples resulted in 100% concordant results between rplD LAMP, real-time PCR, and the standard culture method. The established LAMP assay system was proved to be suitable for rapid meat sample screening. Furthermore, it constitutes a promising tool for investigating other Campylobacter sources and could therefore make a valuable contribution to protect consumers from foodborne illness.

The diversity of Campylobacter spp. throughout the poultry processing plant

Campylobacteriosis is the leading food-borne disease in developed countries, and poultry are a major source for human infection. The diversity of Campylobacter on chicken carcasses during processing may lead to isolates that are able to survive abattoir processing. This has important implications for public health and adds a further layer to the complexity of the epidemiology of campylobacteriosis. The diversity of the Campylobacter spp. populations on broiler carcasses was studied at three different stages of processing (post-bleed, post-scald and post-chill) in three UK processing plants, using the pulsed-field gel electrophoresis (PFGE) KpnI enzyme. One hundred and sixty Campylobacter strains from 3 processing plants were identified as C. jejuni (92.3%) with 27 PFGE subtype profiles recovered from carcasses at the post-bleed point. Change in populations was identified when carcasses move towards the end of poultry processing. Seven C. jejuni genotypes were able to survive the scalding tank stage process, and 5 genotypes surviving the entire poultry process. Confirmation by PFGE gives information on the genotypic profiles of C. jejuni on chicken carcasses and how they change according to the temperatures exposed to during processing. Diversity within C. jejuni populations produces genotypes that adapt to tolerate the processing environment, and these may be capable of causing human disease. Understanding more about the genotypes that survive the processing will have important implications for public health.

A Systematic Review of Campylobacter jejuni Vaccine Candidates for Chickens

Campylobacter jejuni infection linked to the consumption of contaminated poultry products is one of the leading causes of human enteric illness worldwide. Vaccination of chickens is one of the potential strategies that could be used to control C. jejuni colonization. To date, various C. jejuni vaccines using potential antigens have been evaluated, but a challenge in identifying the most effective formulation is the wide variability in vaccine efficacies reported. A systematic review was undertaken to compare C. jejuni vaccine studies. Based upon specific selection criteria eligible papers were identified and included in the analysis. Vaccine efficacy reported from different C. jejuni antigens, vaccine types, and vaccination regimens reported in these papers were reviewed. Our analysis shows that total outer membrane proteins and cysteine ABC transporter substrate-binding protein were among the most efficacious vaccine antigen candidates reported. This review also highlights the importance of the need for increased consistency in the way C. jejuni vaccine studies in poultry are designed and reported in order to be able to undertake a robust comparison of C. jejuni vaccine candidates.

Comparative decay of culturable faecal indicator bacteria, microbial source tracking marker genes, and enteric pathogens in laboratory microcosms that mimic a sub-tropical environment

Enteric pathogens can be present in drinking water catchments due to several point and non-point sources of faecal contamination. Pathogen and contaminant signatures will decay due to environmental stresses, such as temperature, Ultra Violet (UV) radiation, salinity, and predation. In this study, we determined the decay of the culturable faecal indicator bacterium (FIB) Escherichia coli (E. coli), two sewage-associated marker genes (Bacteroides HF183 and crAssphage CPQ_056), and enteric pathogens (Campylobacter spp., human adenovirus 40/41, and Cryptosporidium parvum) in two freshwater laboratory microcosms using culture-based, quantitative PCR (qPCR) and vital dye (determine the fraction of viable Cryptosporidium oocysts) assays. Freshwater samples from the Lake Wappa and Lake Wivenhoe (Australia) were seeded with untreated sewage and C. parvum oocysts, and their declining concentrations were measured over a 28-day period. Moreover, 16S rRNA amplicon sequencing was also undertaken to determine the change/shift in sewage-associated bacterial communities using SourceTracker. Overall, culturable E. coli and the HF183 marker gene decayed significantly (p < 0.05) faster than did the qPCR measured enteric pathogens suggesting that the absence of culturable FIB or qPCR HF183 in water samples may not indicate the absence of pathogens. The decay of crAssphage was similar to that of HAdV 40/41 and other pathogens tested, suggesting crAssphage may be a better surrogate for enteric viruses in sub-tropical catchment waters. The decay rates were greater at 25 °C compared to 15 °C, suggesting that FIB and pathogens persist longer in the winter season compared to summer. Overall decay rates of the tested microorganisms in this microcosm study suggest that sub-tropical conditions, especially temperature, have a negative impact on the persistence of tested microorganisms. Sewage-associated bacterial communities also showed similar patterns. Based on the results, which showed differences in simulated summer and winter temperatures for pathogen decay, corresponding management options and treatment need to be adjusted accordingly to minimize human health risks effectively.

Verification of Bacteroidales 16S rRNA markers as a complementary tool for detecting swine fecal pollution in the Yangtze Delta

To correctly assess and properly manage the public health risks associated with exposure to contaminated water, it is necessary to identify the source of fecal pollution in a watershed. In this study, we evaluated the efficacy of our two previously developed real time-quantitative PCR (qPCR) assays for the detection of swine-associated Bacteroidales genetic markers (gene 1-38, gene 3-53) in the Yangtze Delta watershed of southeastern China. The results indicated that the gene 1-38 and 3-53 markers exhibited high accuracy (92.5%, 91.7% conditional probability, respectively) in detecting Bacteroidales spp. in water samples. According to binary logistic regression (BLR), these two swine-associated markers were well correlated (P < 0.05) with fecal indicators (Escherichia coli and Enterococci spp.) and zoonotic pathogens (E. coli O157: H7, Salmonella spp. and Campylobacter spp.) in water samples. In contrast, concentrations of conventional fecal indicator bacteria (FIB) were not correlated with zoonotic pathogens, suggesting that they are noneffective at detecting fecal pollution events. Collectively, the results obtained in this study demonstrated that a swine-targeted qPCR assay based on two Bacteroidales genes markers (gene 1-38, gene 3-53) could be a useful tool in determining the swine-associated impacts of fecal contamination in a watershed.

Performance of the QIAstat-Dx Gastrointestinal Panel for Diagnosing Infectious Gastroenteritis

Detection and identification of enteropathogens that cause infectious gastroenteritis are essential steps for appropriate patient treatment and effective isolation precautions. Several syndrome-based tests have recently become available, with the gastrointestinal panel (GIP) assay on the QIAstat-Dx as the most recent addition to the syndromic testing landscape.

Detection and identification of enteropathogens that cause infectious gastroenteritis are essential steps for appropriate patient treatment and effective isolation precautions. Several syndrome-based tests have recently become available, with the gastrointestinal panel (GIP) assay on the QIAstat-Dx as the most recent addition to the syndromic testing landscape. The QIAstat-Dx GIP assay offers simultaneous testing for 24 bacterial, viral, and parasitic enteropathogens using a single test that reports the results in 70 min. In this study, we compared the performance of the GIP assay to laboratory-developed real-time PCR assays (LDTs), using 172 prospectively and retrospectively collected fecal samples from patients suspected to have infectious gastroenteritis. The GIP assay detected 97/107 enteropathogens (91%) that were detected by LDTs, and the overall agreement of results increased to 95% when excluding discrepant results with cycle threshold (C_T) values of >35. Further, the GIP assay detected 42 additional enteropathogens that were not detected, or tested, by LDTs. These included 35 diarrheagenic Escherichia coli targets for which the clinical relevance is unclear for most. The main advantage of the QIAstat-Dx system compared to other syndromic testing systems is the ability to generate C_T values that could help with the interpretation of results. However, compared to LDTs, the GIP assay is limited by flexibility and high-throughput testing. In conclusion, the GIP assay offers an easy, sample-to-answer workflow with a rapid detection of the most common enteropathogens and therefore has the potential to direct appropriate therapy and infection control precautions.

Research Note: Lyophilization of hyperimmune egg yolk: effect on antibody titer and protection of broilers against Campylobacter colonization

Oral administration of antibodies is a promising strategy against various infectious diseases. Previously, it was demonstrated that passive immunization by providing hyperimmune egg yolk through the feed reduces Campylobacter jejuni colonization in broilers. Campylobacteriosis is the most commonly reported bacterial foodborne zoonosis worldwide, and poultry products are the number one origin of these bacteria for human infection. To date, no effective control measures exist to limit Campylobacter colonization in the chicken's intestinal tract. Here, the effect of lyophilization of hyperimmune egg yolk on protection of broilers against C. jejuni was investigated. During an in vivo trial, broiler chickens were prophylactically given feed with lyophilized hyperimmune or non-immunized egg yolk powder starting from day 1 after hatch. At day 11, broilers were inoculated with C. jejuni according to a seeder model. Five days later, all broilers were euthanized and cecal content was examined for C. jejuni colonization. No decrease in C. jejuni colonization was found. The freeze-drying resulted in a 16-fold decrease of the antibody titer in the yolk powder compared to the fresh yolks, presumably caused by structural changes in the antibodies. In conclusion, applying freeze-dried hyperimmune egg yolk failed to protect broilers against C. jejuni colonization, possibly because lyophilization affected the antibodies' functionality.

In ovo vaccination of broilers against Campylobacter jejuni using a bacterin and subunit vaccine

Campylobacter jejuni and Campylobacter coli originating from poultry meat have been the most important causes of foodborne bacterial gastroenteritis in the European Union since 2005. In-feed application of maternal antibodies from vaccinated hens was shown to confer protection of broilers against Campylobacter infection. Here, it was investigated if these vaccines can be used to protect broilers against Campylobacter infection after in ovo vaccination. Embryos were immunized in ovo at day 18 with a bacterin or a subunit vaccine and at 19 D post hatch, these birds were inoculated with C. jejuni according to a seeder model. Quantification of C. jejuni in the broilers cecal content showed that the in ovo vaccinated birds were not protected against C. jejuni infection. Quantification of blood anti-Campylobacter antibody titers did not show any induction of Campylobacter-specific serological response in the vaccinated birds, which may explain the lack of protection in the vaccinated chicks.

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.

Prevalence, Persistence, and Antimicrobial Resistance of Campylobacter spp. from Eggs and Laying Hens Housed in Five Commercial Housing Systems

Husbandry practices for laying hens in commercial egg production is a topic of interest from a social, economic, and regulatory standpoint. Animal welfare concerns regarding the use of conventional cages have arisen and consumer perceptions of hen welfare have led to a higher demand for cage-free eggs. The aim of this study was to assess the impact of housing systems on prevalence, persistence, and antimicrobial resistance (AMR) of Campylobacter from laying hens and shell eggs. A total of 425 samples were collected over a 10-month period from the North Carolina Layer Performance and Management Test and Campylobacter isolates were identified by serological, biochemical, and molecular tests. Genetic variability was evaluated using pulsed-field gel electrophoresis (PFGE) and AMR testing was performed. Prevalence of Campylobacter spp. ranged from 11.1% in the enrichable cages to 19.7% in the conventional systems. A greater prevalence of Campylobacter was found in the fecal swab samples from free-range birds compared with those of birds housed in the more intensive housing systems (p > 0.05). Overall, 72 isolates were confirmed as Campylobacter spp. by PCR. More than 90% of the isolates (n = 66) were identified as Campylobacter jejuni, followed by Campylobacter coli (n = 6). C. jejuni isolates displayed high levels of resistance to tetracycline (67%). Genetic variability of Campylobacter was high, with more than 20 PFGE patterns identified. Pattern "a" comprised 42% of isolates from all housing systems and was also the most persistent. This study suggests that housing systems of laying hens used for commercial shell egg production may impact the rate of Campylobacter shedding by layers. Isolation rates and tetracycline resistance levels of this pathogen are still of concern, emphasizing the need for well-implemented biosecurity measures on the farm.

Quantification of Microbial Source Tracking and Pathogenic Bacterial Markers in Water and Sediments of Tiaoxi River (Taihu Watershed)

Taihu Lake is one of the largest freshwater lakes in China, serving as an important source of drinking water; >60% of source water to this lake is provided by the Tiaoxi River. This river faces serious fecal contamination issues, and therefore, a comprehensive investigation to identify the sources of fecal contamination was carried out and is presented here. The performance of existing universal (BacUni and GenBac), human (HF183-Taqman, HF183-SYBR, BacHum, and Hum2), swine (Pig-2-Bac), ruminant (BacCow), and avian (AV4143 and GFD) associated microbial source tracking (MST) markers was evaluated prior to their application in this region. The specificity and sensitivity results indicated that BacUni, HF183-TaqMan, Pig-2-Bac, and GFD assays are the most suitable in identifying human and animal fecal contamination. Therefore, these markers along with marker genes specific to selected bacterial pathogens were quantified in water and sediment samples of the Tiaoxi River, collected from 15 locations over three seasons during 2014 and 2015. Total/universal Bacteroidales markers were detected in all water and sediment samples (mean concentration 6.22 log10 gene copies/100 ml and 6.11 log10 gene copies/gram, respectively), however, the detection of host-associated MST markers varied. Human and avian markers were the most frequently detected in water samples (97 and 89%, respectively), whereas in sediment samples, only human-associated markers were detected more often (86%) than swine (64%) and avian (8.8%) markers. The results indicate that several locations in the Tiaoxi River are heavily polluted by fecal contamination and this correlated well with land use patterns. Among the five bacterial pathogens tested, Shigella spp. and Campylobacter jejuni were the most frequently detected pathogens in water (60% and 62%, respectively) and sediment samples (91% and 53%, respectively). Shiga toxin-producing Escherichia coli (STEC) and pathogenic Leptospira spp. were less frequently detected in water samples (55% and 33%, respectively) and sediment samples (51% and 13%, respectively), whereas E. coli O157:H7 was only detected in sediment samples (11%). Overall, the higher prevalence and concentrations of Campylobacter jejuni, Shigella spp., and STEC, along with the MST marker detection at a number of locations in the Tiaoxi River, indicates poor water quality and a significant human health risk associated with this watercourse. GRAPHICAL ABSTRACTTracking fecal contamination and pathogens in watersheds using molecular methods.

Prevalence and antimicrobial resistance of Campylobacter from antibiotic-free broilers during organic and conventional processing

Campylobacter is one of the leading cause of foodborne illness in the US and worldwide, especially linked to poultry and poultry products. In recent years, the increasing popularity of organic chicken products and chickens raised without antibiotics (RWA) has resulted in more companies adopting organic and antibiotic-free production and processing methods; however, it is not evident what effect these practices have on pathogens such as Campylobacter. The purpose of this study was to determine the effects of RWA and organic methods on the prevalence and antimicrobial resistance (AMR) of Campylobacter. Samples were collected from a processing facility that used organic and conventional methods to process RWA broilers. Samples included fecal grab samples from incoming birds, carcass rinses at important steps throughout processing, and environmental samples including equipment swabs, water samples, and air samples. Samples were analyzed for prevalence of Campylobacter by enrichment, and populations of presumptive Campylobacter were quantified. Isolates collected in this study were analyzed for AMR according to the National Antimicrobial Resistance Monitoring System (NARMS) protocol. Results showed that organic birds had a lower prevalence (P < 0.05) of Campylobacter and lower populations of presumptive Campylobacter during early processing steps, but no differences (P > 0.05) between organic and conventional birds were seen post-chill, with the exception of a lower prevalence in post-water-chill organic birds. These observations show that organic methods can be associated with lower initial Campylobacter levels than conventional methods, although appropriate processing interventions result in similar Campylobacter populations post-chill, regardless of processing method. Prevalence of AMR Campylobacter in chickens at slaughter suggest that raising birds without the use of antimicrobials may not be effective in reducing the incidence of AMR Campylobacter in chicken.

Developments in Rapid Detection Methods for the Detection of Foodborne Campylobacter in the United States

The accurate and rapid detection of Campylobacter spp. is critical for optimal surveillance throughout poultry processing in the United States. The further development of highly specific and sensitive assays to detect Campylobacter in poultry matrices has tremendous utility and potential for aiding the reduction of foodborne illness. The introduction and development of molecular methods such as polymerase chain reaction (PCR) have enhanced the diagnostic capabilities of the food industry to identify the presence of foodborne pathogens throughout poultry production. Further innovations in various methodologies, such as immune-based typing and detection as well as high throughput analyses, will provide important epidemiological data such as the identification of unique or region-specific Campylobacter. Comparable to traditional microbiology and enrichment techniques, molecular techniques/methods have the potential to have improved sensitivity and specificity, as well as speed of data acquisition. This review will focus on the development and application of rapid molecular methods for identifying and quantifying Campylobacter in U.S. poultry and the emergence of novel methods that are faster and more precise than traditional microbiological techniques.

Altered fecal bacterial composition correlates with disease activity in inflammatory bowel disease and the extent of IL8 induction

PURPOSE OF THE STUDY

In this study we investigated the presence and relative abundance of important genera of the gut microbiota in IBD patients and their role in induction of IL8 in a cell culture model.

PATIENTS AND METHODS

Stool samples of IBD patients and healthy controls were collected and relative diversity of thirteen bacterial families was measured using quantitative real-time PCR assay. Moreover, filtrate of the stool samples was used for treatment of HT-29 cell line to analyze involvement of diversity of the fecal bacterial communities in the extent of IL8 induction.

RESULTS

Bacteroides, Faecalibacterium prausnitzii, Prevotella spp., and Methanobrevibacterium were significantly less abundant in IBD patients (UC, N = 22; CD, N = 7) compared with control group (N = 29). Increase in relative amounts of Haemophilus, Streptococcus spp., and H. pylori were detected in IBD patients, which was not statistically significant. Relative decrease in amount of Bacteroides spp., Faecalibacterium prausnitzii, and Prevotella spp. were found in UC patients with disease activity score greater than 4; however, higher levels of Streptococcus and Haemophilus were detected in the patients who were at flares. A relationship between the reduction of Haemophilus spp. and higher BMI was shown in IBD patients. Expression of IL8 was significantly higher in the treated cells by the fecal inoculates of IBD patients. Increase in relative amounts of Enterobacteriacea showed a correlation with the higher level of IL8 induction in both groups.

CONCLUSIONS

These results showed that changes in the fecal microbiota composition could affect disease activity, BMI, and IL8 induction.

A Constructed Wetland for Treatment of an Impacted Waterway and the Influence of Native Waterfowl on its Perceived Effectiveness

A constructed, variable-flow treatment wetland was evaluated for its ability to reduce microbial loads from the Banklick Creek, an impacted recreational waterway in Northern Kentucky. For this study, levels of traditional (Escherichia coli and enterococci measured by culture and molecular techniques) and alternative fecal indicators (infectious somatic and F+ coliphage, Clostridium spp. and Clostridium perfringens by culture), potential pathogens (molecular signal of Campylobacter spp.) as well as various microbial source tracking (MST) markers (human fecal marker HF183 and avian fecal marker GFD) were monitored during the summer and early fall through five treatment stages within the Banklick Creek Wetland. No difference in concentrations of traditional or alternative fecal indicators were observed in any of the sites monitored. Microbial source tracking markers were employed to identify sources of fecal contamination within the wetland. Human marker HF183 concentrations at beginning stages of treatment were found to be significantly higher (P value range: 0.0016-0.0003) than levels at later stages. Conversely, at later stages of treatment where frequent bird activity was observed, Campylobacter and avian marker (GFD) signals were detected at significantly higher frequencies (P value range: 0.024 to <0.0001), and both signals were strongly correlated (P = 0.0001). Our study suggests constructed wetlands are an effective means for removal of microbial contamination in ambient waters, but reliance on general fecal indicators is not ideal for determining system efficacy or assessing appropriate remediation efforts.

Comparison of the Filtration Culture and Multiple Real-Time PCR Examination for Campylobacter spp. From Stool Specimens in Diarrheal Patients

Campylobacter is one of the most common pathogens leading to the bacterial diarrheal illness. In order to set up one effective culture independent assay for the screen of the Campylobacter infection in the diarrheal patients, the quadruple real-time PCR method comparing to the culture based on the enriched filtration method which was recognized as the most effective isolation method was assessed for 190 stool samples from the diarrheal patients collected during the Foodborne Diseases Active Surveillance Network in Beijing. This multiple real-time PCR was designed to identify the Campylobacter genus, C. jejuni, C. coli, and C. lari simultaneously. With the enrichment culture method, 23 (12.1%, 23/190) Campylobacter isolates were obtained (20 C. jejuni and 3 C. coli), however, 31 samples (16.3%, 31/190) were detected positively with the real-time PCR (21 C. jejuni, 8 C. coli, and 2 Campylobacter genus only). With the comparison, the real-time-PCR method is more sensitive than the enrichment filtration method (16.3 vs. 12.1%, p = 0.021). Among the culture-positive samples, 95.7% (22/23) were detected positively by PCR which indicate the specificity of this method was higher. These two methods were consistent well (Kappa = 0.785, p < 0.05). Comparing to the culture methods, the result of the multiple real-time PCR method is sensitive, reliable and rapid. The present study indicated this multiple real-time PCR can be used both for the surveillance network and the preceding screen for bacteria isolation. This is first comparative study between the culture and multiple real-time PCR method for Campylobacter identification in stool specimens from the diarrheal patients.

Migratory birds along the Mediterranean – Black Sea Flyway as carriers of zoonotic pathogens

At the crossroad between Europe, Asia, and Africa, Bulgaria is part of the Mediterranean – Black Sea Flyway (MBSF) used by millions of migratory birds. In this study, bird species migrating through Bulgaria were investigated as carriers of zoonotic pathogens. In total, 706 birds belonging to 46 species were checked for the presence of various bacterial pathogens (Campylobacter, Yersinia, Salmonella, Listeria, Escherichia coli, Staphylococcus aureus, Francisella tularensis, Coxiella burnetii, Borrelia burgdorferi, and Brucella spp.). From 673 birds we investigated fecal samples, from the remaining 33, blood samples. We detected Campylobacter 16S rDNA gene in 1.3% of birds, but none were of pathogenic Campylobacter jejuni and Campylobacter coli species. Escherichia coli 16S rDNA gene was found in 8.8% of the birds. Out of 34 birds that transported Yersinia enterocolitica strains (5.05%), only 1 carried a pathogenic isolate. Three birds (0.4%) were carriers of nonpathogenic Salmonella strains. Four avian samples (0.6%) were positive for Listeria monocytogenes and 1 (0.15%) was positive for Brucella spp. None of the birds tested carried the tick-borne pathogens C. burnetii or B. burgdorferi sensu lato. Antibiotic-resistant strains were detected, suggesting that migratory birds could be reservoirs and spreaders of bacterial pathogens as well as antibiotic resistance genes.

Disinfection and removal of human pathogenic bacteria in arctic waste stabilization ponds

Wastewater stabilization ponds (WSPs) are commonly used to treat municipal wastewater in Arctic Canada. The biological treatment in the WSPs is strongly influenced by climatic conditions. Currently, there is limited information about the removal of fecal and pathogenic bacteria during the short cool summer treatment season. With relevance to public health, the objectives of this paper were to determine if treatment in arctic WSPs resulted in the disinfection (i.e., removal of fecal indicator bacteria, Escherichia coli) and removal of selected human bacterial pathogens from the treated effluent. The treatment performance, with focus on microbial removal, was assessed for the one-cell WSP in Pond Inlet (Nunavut [NU]) and two-cell WSP in Clyde River (NU) over three consecutive (2012-2014) summer treatment seasons (late June-early September). The WSPs provided a primary disinfection treatment of the wastewater with a 2-3 Log removal of generic indicator E. coli. The bacterial pathogens Salmonella spp., pathogenic E. coli, and Listeria monocytogenes, but not Campylobacter spp. and Helicobacter pylori, were detected in the untreated and treated wastewater, indicating that human pathogens were not reliably removed. Seasonal and annual variations in temperature significantly (p < 0.05) affected the disinfection efficiency. Improved disinfection and pathogen removal was observed for the two-cell system in Clyde River as compared to the one-cell system in Pond Inlet. A quantitative microbial risk assessment should be performed to determine if the release of low levels of human pathogens into the arctic environment poses a human health risk.

Monitoring of microbial dynamics in a drinking water distribution system using the culture-free, user-friendly, MYcrobiota platform

Drinking water utilities currently rely on a range of microbiological detection techniques to evaluate the quality of their drinking water (DW). However, microbiota profiling using culture-free 16S rRNA gene next-generation sequencing (NGS) provides an opportunity for improved monitoring of the microbial ecology and quality of DW. Here, we evaluated the utility of a previously validated microbiota profiling platform (MYcrobiota) to investigate the microbial dynamics of a full-scale, non-chlorinated DW distribution system (DWDS). In contrast to conventional methods, we observed spatial and temporal bacterial genus changes (expressed as operational taxonomic units - OTUs) within the DWDS. Further, a small subset of bacterial OTUs dominated with abundances that shifted across the length of the DWDS, and were particularly affected by a post-disinfection step. We also found seasonal variation in OTUs within the DWDS and that many OTUs could not be identified, even though MYcrobiota is specifically designed to reduce potential PCR sequencing artefacts. This suggests that our current knowledge about the microbial ecology of DW communities is limited. Our findings demonstrate that the user-friendly MYcrobiota platform facilitates culture-free, standardized microbial dynamics monitoring and has the capacity to facilitate the introduction of microbiota profiling into the management of drinking water quality.

Comparative effects of two multi-enzyme combinations and a Bacillus probiotic on growth performance, digestibility of energy and nutrients, disappearance of non-starch polysaccharides, and gut microflora in broiler chickens

The efficacy of two exogenous enzyme combinations and a multi-strain Bacillus probiotic (DFM) on the growth performance, nutrient digestibility, disappearance of non-starch polysaccharides (NSP) and gut microbial composition was investigated in broilers. One-day old Ross 308 chicks were assigned to 36 pens with 22 birds/pen and 6 pens/treatment (Experiment 1) or 36 cages with 8 birds/cage and 6 cages/treatment (Experiment 2). Treatment additives were added to nutritionally complete corn/soy based starter (d 1 to 21) and finisher (d 22 to 42) diets. Treatments included 1) a control diet containing 500 FTU/kg phytase (CTL), 2) CTL + xylanase (2,000 U/kg) and amylase (200 U/kg; XA), 3) CTL+XA + protease (4000 U/g; XAP), 4) CTL+DFM (150,000 cfu/g of 3 strains of Bacillus spp), 5) CTL+DFM+XA, and 6) CTL+DFM+XAP. Supplementation with DFM increased BW, BWG, and FI compared with the CTL (P < 0.05); XAP, but not XA, resulted in increased final BW, BWG and FI compared to the control (P < 0.05). XA and XAP improved apparent ileal digestibility (AID) of starch and fat on d 22 to 42 with XAP improving AME_n (by ∼82 kcal) compared with CTL birds (P < 0.01). DFM+XAP improved apparent ileal digestible energy (AIDE), AID of fat and starch on d 22 to 42, and additionally had a greater than additive effect on AIDE and AME_n. Supplementation with DFM+XAP reduced the ileal and total tract flow of insoluble arabinose and additionally total tract flow of soluble and insoluble xylose and total galactose (P < 0.05); similar effects of XA+DFM were not seen or were lower in magnitude, suggesting that the protease component plays an important role in increasing the availability of NSP for hydrolysis. Supplementation with DFM alone did not affect gut bacterial populations, but XA and XAP reduced numbers of Campylobacter species (by > 2.5 log cfu/g; P < 0.001) and Bacteroides (P < 0.02) in the cecum compared with CTL birds.

Improved simultaneous quantification of multiple waterborne pathogens and fecal indicator bacteria with the use of a sample process control

Quantitative polymerase chain reaction (qPCR) is now commonly used to detect fecal indicator bacteria (FIB) as well as pathogens in water samples. However, DNA loss during sample processing can cause underestimation of target genes. In this study, we created a sample process control strain (SPC) by genetically engineering a non-pathogenic, Gram-negative bacterium Pseudogulbenkiania sp. strain NH8B. The SPC strain, named NH8B-1D2, has a kanamycin-resistance gene inserted to one of the 23S rRNA genes. To specifically quantify the SPC strain, a new TaqMan qPCR assay was developed. To obtain the relationship between the DNA recovery efficiencies of various pathogens and those of the SPC strain, known amount of E. coli O157:H7, Salmonella Typhimurium, Campylobacter jejuni, or Listeria monocytogenes cells were co-spiked with the SPC strain to environmental water samples. The DNA recovery efficiencies were calculated by comparing the quantity of bacterial cells inoculated to water samples prior to filtration and DNA extraction, and those measured by qPCR. We then obtained the ratios in the recovery efficiencies between pathogens and SPC strain (RR_PATH/SPC). The RR_PATH/SPC values obtained using Oono pond water collected in Japan were used as a pathogen-specific constant to estimate the accurate concentrations of pathogens in water samples collected from Mississippi River in Minnesota. Estimated pathogen concentrations were not significantly different from the inoculated pathogen concentration, suggesting our normalization approach is useful to estimate the accurate concentrations of pathogens in environmental water samples. The qPCR assay targeting the SPC strains and FIB were incorporated into the microfluidic qPCR chip format (PBQ chip ver. 2); therefore, we can simultaneously quantify multiple pathogens, FIB, and the SPC strain in high throughput from many water samples. This new tool can be useful for water quality monitoring and risk assessment.

Quantification of pathogens and markers of fecal contamination during storm events along popular surfing beaches in San Diego, California

Along southern California beaches, the concentrations of fecal indicator bacteria (FIB) used to quantify the potential presence of fecal contamination in coastal recreational waters have been previously documented to be higher during wet weather conditions (typically winter or spring) than those observed during summer dry weather conditions. FIB are used for management of recreational waters because measurement of the bacterial and viral pathogens that are the potential causes of illness in beachgoers exposed to stormwater can be expensive, time-consuming, and technically difficult. Here, we use droplet digital Polymerase Chain Reaction (digital PCR) and digital reverse transcriptase PCR (digital RT-PCR) assays for direct quantification of pathogenic viruses, pathogenic bacteria, and source-specific markers of fecal contamination in the stormwater discharges. We applied these assays across multiple storm events from two different watersheds that discharge to popular surfing beaches in San Diego, CA. Stormwater discharges had higher FIB concentrations as compared to proximal beaches, often by ten-fold or more during wet weather. Multiple lines of evidence indicated that the stormwater discharges contained human fecal contamination, despite the presence of separate storm sewer and sanitary sewer systems in both watersheds. Human fecal source markers (up to 100% of samples, 20-12440 HF183 copies per 100 ml) and human norovirus (up to 96% of samples, 25-495 NoV copies per 100 ml) were routinely detected in stormwater discharge samples. Potential bacterial pathogens were also detected and quantified: Campylobacter spp. (up to 100% of samples, 16-504 gene copies per 100 ml) and Salmonella (up to 25% of samples, 6-86 gene copies per 100 ml). Other viral human pathogens were also measured, but occurred at generally lower concentrations: adenovirus (detected in up to 22% of samples, 14-41 AdV copies per 100 ml); no enterovirus was detected in any stormwater discharge sample. Higher concentrations of avian source markers were noted in the stormwater discharge located immediately downstream of a large bird sanctuary along with increased Campylobacter concentrations and notably different Campylobacter species composition than the watershed that had no bird sanctuary. This study is one of the few to directly measure an array of important bacterial and viral pathogens in stormwater discharges to recreational beaches, and provides context for stormwater-based management of beaches during high risk wet-weather periods. Furthermore, the combination of culture-based and digital PCR-derived data is demonstrated to be valuable for assessing hydrographic relationships, considering delivery mechanisms, and providing foundational exposure information for risk assessment.

Effects of dietary yeast cell wall on faecal bacteria and fermentation products in adult cats

This study evaluated the effects of increasing concentrations of spray-dried yeast cell wall (YCW) in diets for healthy adult cats on apparent nutrient digestibility and on bacterial composition and fermentation products in the stool. Fourteen cats with an average weight of 4.40 ± 1.05 kg and an average age of 6.2 ± 0.54 years were used and assigned to treatments in an unbalanced randomized block design (by experimental period) with two blocks and three or four cats per diet in each block. Treatments included: control (0% YCW), 0.2% YCW, 0.4% YCW and 0.6% YCW, totalling seven animals per experimental diet. We found that YCW did not affect body weight, nutrient and food intake, faecal production, faecal score, faecal pH or urine output (p > .05). Regarding faecal bacteria, we observed a linear reduction in Clostridium perfringens, a quadratic reduction in Escherichia coli, and linear increases in Bifidobacterium spp. and Lactobacillus spp. (p < .05) with the inclusion of YCW. Regarding the faecal short-chain fatty acid profile, butyrate, valerate, total biogenic amines, putrescine, cadaverine and histamine increased linearly (p < .05) with the inclusion of YCW. It was concluded that in healthy adult cats, consumption of YCW modulates the faecal bacterial populations, with an increased presence of beneficial bacteria and a reduction in some potentially pathogenic bacteria. It was concluded that YCW modulated the levels of fermentation products. There was an increase in fermentation products coming from carbohydrate metabolism, an important effect that can potentially benefit the intestinal health of cats. The consumption of YCW also increased the fermentation of nitrogen compounds, which have not yet been defined as deleterious or beneficial. The fermentability of carbohydrates and nitrogen compounds may be associated. Therefore, YCW may cause rapid fermentation of both classes of compounds by enhancing the fermentability of one class.

Potential for gulls to transport bacteria from human waste sites to beaches

Contamination of recreational beaches due to fecal waste from gulls complicates beach monitoring and may pose a risk to public health. Gulls that feed at human waste sites may ingest human fecal microorganisms associated with that waste. If these gulls also visit beaches, they may serve as vectors, transporting fecal microorganisms to the beach where they may subsequently contaminate sand and water. In this study, samples collected from landfills, treated wastewater storage lagoons, and public beaches demonstrated a spatial and temporal overlap of markers for gull and human-associated microorganisms. In addition, markers for gull, fecal indicator bacteria, and the human-associated marker, HF183, were detected in gull feces and cloacae samples. Further, HF183 was detected in cloacae samples from gulls that were documented by radio-telemetry traveling between human waste sites and public beaches. This study highlights the potential for gulls that visit human waste sites to disperse human-associated microorganisms in the beach landscape.