Automated 5' nuclease PCR assay for identification of Salmonella enterica

Temporal and spatial relationships of CrAssphage and enteric viral and bacterial pathogens in wastewater in North Carolina

Enteric disease remains one of the most common concerns for public health, particularly when it results from human exposure to surface and recreational waters contaminated with wastewater. Characterizing the temporal and spatial variation of enteric pathogens prevalent in wastewater is critical to develop approaches to mitigate their distribution in the environment. In this study, we aim to characterize pathogen variability and test the applicability of the human-associated wastewater indicator crAssphage as an indicator of enteric viral and bacterial pathogens. We conducted weekly samplings for 14 months from four wastewater treatment plants in North Carolina, USA. Untreated wastewater samples were processed using hollow fiber ultrafiltration, followed by secondary concentration methods. Adenovirus, norovirus, enterovirus, Salmonella, Shiga toxin 2 (stx2), Campylobacter, and crAssphage were measured by quantitative polymerase chain reaction (qPCR) and reverse transcriptase (rt)-qPCR. Our results revealed significant correlations between crAssphage and human adenovirus, enterovirus, norovirus, Salmonella, and Campylobacter (p<0.01). Pathogens and crAssphage concentrations in untreated wastewater showed distinct seasonal patterns, with peak concentrations of crAssphage and viral pathogens in fall and winter, while bacterial pathogens showed peaked concentrations in either winter (Campylobacter), fall (Salmonella), or summer (stx2). This study enhances the understanding of crAssphage as an alternative molecular indicator for both bacterial and viral pathogens. The findings of this study can also inform microbial modeling efforts for the prediction of the impact of wastewater pathogens on surface waters due to increased flooding events and wastewater overflows associated with climate change.

Dissemination of antimicrobial-resistant isolates of Salmonella spp. in wild boars and its relationship with management practices

Antimicrobial resistance (AMR) is a global concern and controlling its spread is critical for the effectiveness of antibiotics. Members of the genus Salmonella are broadly distributed, and wild boar may play an important role in its circulation between peri-urban areas and the environment, due to its frequent interactions both with livestock or human garbage. As the population of these animals is rising due to management on certain hunting estates or the absence of natural predators, the aim of the present work is to identify the mechanisms of AMR present and/or expressed in Salmonella spp. from wild boar populations and to determine the possible role of management-related factors applied to different game estates located in central Spain. The detection of Salmonella spp. was carried out in 121 dead wild boar from 24 game estates, and antimicrobial resistance traits were determined by antibiotic susceptibility testing and screening for their genetic determinants. The effects of feeding supplementation, the proximity of livestock, the existence of a surrounding fence and the density of wild boar on the AMR of the isolates were evaluated. The predominant subspecies and serovar found were S. enterica subsp. enterica (n = 69) and S. choleraesuis (n = 33), respectively. The other subspecies found were S. enterica subsp. diarizonae, S. enterica subsp. salamae and S. enterica subsp. houtenae. AMR was common among isolates (75.2%) and 15.7% showed multi drug resistance (MDR). Resistance to sulphonamides was the most frequent (85.7%), as well as sul1 which was the AMR determinant most commonly found. Plasmids appeared in 38.8% of the isolates, with IncHI1 being the replicon detected with the highest prevalence. The AMR of the isolates increased when the animals were raised with feeding supplementation and enclosed by fences around the estates.

Evaluation of the different methods to detect Salmonella in poultry feces samples

Salmonella is one of the most common causes of foodborne outbreaks and infection worldwide. The gold-standard detection method of Salmonella is cultivation. There is a need to investigate rapid and accurate processes with time-consuming cultivation. The study evaluated different approaches to detect Salmonella in poultry feces samples. Poultry farm feces samples from 21 cities in Iran were collected from January 2016 to December 2019. Microbiological cultures, serological assays, and multiplex PCR (m-PCR) were used to detect and characterize Salmonella spp. isolates. Serological assays and m-PCR were used to determine the serogroups A, B, C1, C2, D1, E, H, and FliC. The m-PCR was used to detect seven Salmonella serovars, and a Chi-square test was performed to compare the discriminatory power of the methods. Of 2300 poultry feces samples, 173 (7.5%) and 166 (7.2%) samples were detected as Salmonella spp. by cultivation and m-PCR, respectively. The sensitivity of the molecular method was equal to cultivation at 0.96 (CI = 95%). Assessment of H antigenic subgroups showed the same for both m-PCR and serological tests. Therefore, the matching rate of the two methods for detecting all H antigenic subgroups was 100%. Thus, the relationship between the results obtained from both methods was significant in the contingency table test (P < 0.01). The PCR-based approach confirmed the detection of Salmonella in a shorter period (24-36 h) compared to the conventional microbiological approach (3-8 days).

Multiplex PCR method for the detection of human norovirus, Salmonella spp., Shigella spp., and shiga toxin producing Escherichia coli in blackberry, coriander, lettuce and strawberry

A multiplex PCR method was developed for the simultaneous detection of murine norovirus (MNV-1) as a surrogate for human norovirus (HuNoV) GI and GII, Salmonella spp., Shigella spp., and Shiga toxin producing Escherichia coli (STEC) in fresh produce. The toxicity of the glycine buffer on bacterial pathogens viability was evaluated. The growth of each of the three pathogens (previously stressed) was evaluated at 35 and 41.5 °C in modified buffered peptone water (mBPW) and trypticase soy broth (TSB), supplemented with vancomycin, novobiocin and brilliant green at two concentration levels. The selected conditions for simultaneous enrichment were: 41.5 °C/mBPW/supplemented with 8 ppm vancomycin, 0.6 ppm novobiocin and 0.2 ppm brilliant green. The pathogens and aerobic plate count (APC) growth was evaluated in the enrichment of lettuce, coriander, strawberry and blackberry under the best enrichment conditions. Starting from 1 to 10 CFU/mL, Salmonella reached from 7.63 to 8.91, Shigella 6.81 to 7.76 and STEC 7.43 to 9.27 log CFU/mL. The population reached for the APC was 5.11-6.56 log CFU/mL. Simultaneous detection by PCR was done using designed primers targeting invA, ipaH, stx1 and stx2 genes, and MNV-1. The detection sensitivity was 10-100 PFU for the MNV-1 and 1-10 CFU for each pathogenic bacteria. This protocol takes 6 h for MNV-1 and 24 h for Salmonella spp., Shigella spp., and STEC detection from the same food portion. In total, 200 samples were analyzed from retail markets from Queretaro, Mexico. Two strawberry samples were positive for HuNoV GI and one lettuce sample was positive for STEC. In conclusion, the method developed in this study is capable of detecting HuNoV GI and GII, Salmonella spp., Shigella spp and STEC from the same fresh produce sample.

The Impact of Overstocking and Negative Energy Balance on Quantitative Measurement of Non-typhoidal Salmonella in Periparturient Dairy Cattle

Stressful conditions in animal production facilities may exacerbate the fecal shedding and foodborne transmission of non-typhoidal Salmonella enterica subsp. enterica. Dairy cows are reservoirs of this zoonotic microorganism, and its prevalence has roughly doubled in the past decade on dairy farms in United States. Dairy cows are commonly overstocked at the feed bunk, and stressors placed on the animal prior to parturition may exacerbate Salmonella shedding. However, no studies have evaluated the impact of overstocking and metabolic stress on fecal concentrations of the pathogen. Therefore, we conducted a field trial with 120 multiparous dairy cows randomized into one of four treatment groups with different stocking densities at the feed bunk during the periparturient period as follows: US, understocked from −60 to −1 DRC; OS, overstocked from −60 to −1 DRC; USOS, understocked from −60 to −26 DRC/overstocked from −25 to −1 DRC; and OSUS, overstocked from −60 to −26 DRC/ understocked from −25 to −1 DRC. Fecal and blood samples were collected at four time points relative to calving. qPCR assays were used to quantify Salmonella invA gene and total bacterial community from fecal samples, and a subset of isolates recovered from fecal bacterial culture were characterized using pulsed field gel electrophoresis and serotyping. Serum non-esterified fatty acids (NEFA) were measured as a metabolic stress indicator using an immunoassay. Multivariable analyses were performed to test if changes in Salmonella concentrations were associated with stocking density, energy balance, or days relative to calving. From fecal isolates, three Salmonella serovars were identified, S. Cerro; Kentucky; Meleagridis. Concentrations of Salmonella increased as cows approached calving. Higher stocking densities at the feed bunk did not impact total bacterial community or NEFA; however, cows in the overstocked groups had higher Salmonella fecal concentrations. Further, cows with higher NEFA concentrations after calving had a higher likelihood of detection of Salmonella. Future farm interventions should aim to reduce environmental and metabolic stress during the periparturient period to decrease the dissemination of Salmonella to cattle, the environment, and humans.

Genomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises

A type of monophasic group B Salmonella enterica with the antigenic formula 4,12:a:- (“Fulica-like”) has been described as associated with harbour porpoises (Phocoena phocoena), most frequently recovered from lung samples. In the present study, lung tissue samples from 47 porpoises found along the Swedish coast or as bycatch in fishing nets were analysed, two of which were positive for S. enterica. Pneumonia due to the infection was considered the likely cause of death for one of the two animals. The recovered isolates were whole genome sequenced and found to belong to sequence type (ST) 416 and to be closely related to ST416/ST417 porpoise isolates from UK waters as determined by core-genome MLST. Serovars Bispebjerg, Fulica and Abortusequi were identified as distantly related to the porpoise isolates, but no close relatives from other host species were found. All ST416/417 isolates had extensive loss of function mutations in key Salmonella pathogenicity islands, but carried accessory genetic elements associated with extraintestinal infection such as iron uptake systems. Gene ontology and pathway analysis revealed reduced secondary metabolic capabilities and loss of function in terms of signalling and response to environmental cues, consistent with adaptation for the extraintestinal niche. A classification system based on machine learning identified ST416/417 as more invasive than classical gastrointestinal serovars. Genome analysis results are thus consistent with ST416/417 as a host-adapted and extraintestinal clonal population of S. enterica, which while found in porpoises without associated pathology can also cause severe opportunistic infections.

Detection and differentiation of Salmonella Enteritidis and Salmonella Typhimurium by multiplex quantitative PCR from different poultry matrices

1. The aim of this study was to develop a multiplex quantitative polymerase chain reaction (qPCR) based molecular diagnostic kit for rapid diagnosis of Salmonella enterica serovar Enteritidis and S. enterica serovar Typhimurium serotypes, which are frequently isolated worldwide from poultry samples.2. Detection and discrimination of S. Enteritidis and S. Typhimurium were performed by targeting the sdf and the STM4492 (putative cytoplasmic protein) gene, respectively. The invA (invasion protein) gene was used to detect Salmonella spp. as a target gene, since it is considered a standard. In this study, a total of 200 bacterial strains (178 Salmonella spp. strains and 22 other genera) were used to test the specificity and sensitivity of the developed kit. The limit of detection (LOD) of the assays was determined to be 10⁰-10¹ cfu/25 g from chicken meat samples artificially contaminated by litter and 10⁰-10¹ cfu/ml for cloacal swab samples.3. The multiplex qPCR results were 100% compatible with conventional serotyping results while the specificity and sensitivity values were 100%. These findings indicated that the newly developed multiplex qPCR technique can provide an alternative method to conventional serotyping of S. Enteritidis and S. Typhimurium in laboratories lacking adequate infrastructure.

Prevalence, virulence factor and antimicrobial resistance analysis of Salmonella Enteritidis from poultry and egg samples in Iran

Background

Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the most common serovars, associated with human salmonellosis. The food-borne outbreak of this bacterium is mainly related to the consumption of contaminated poultry meat and poultry products, including eggs. Therefore, rapid and accurate detection, besides investigation of virulence characteristics and antimicrobial resistance profiles of S. Enteritidis in poultry and poultry egg samples is essential. A total of 3125 samples (2250 poultry and 875 poultry egg samples), sent to the administrative centers of veterinary microbiology laboratories in six provinces of Iran, were examined for Salmonella contamination, according to the ISO 6579 guideline. Next, duplex PCR was conducted on 250 presumptive Salmonella isolates to detect invA gene for identification of the genus Salmonella and sdf gene for identification of S. Enteritidis. Subsequently, the S. Enteritidis isolates were examined for detection of important virulence genes (pagC, cdtB, msgA, spaN, tolC, lpfC, and spvC) and determination of antibiotic resistance patterns against nalidixic acid, trimethoprim-sulfamethoxazole, cephalothin, ceftazidime, colistin sulfate, and kanamycin by the disk diffusion method.

Results

Overall, 8.7 and 2.3% of poultry samples and 6.3 and 1.3% of eggs were contaminated with Salmonella species and S. Enteritidis, respectively. The invA and msgA genes (100%) and cdtB gene (6.3%) had the highest and the lowest prevalence rates in S. Enteritidis isolates. The spvC gene, which is mainly located on the Salmonella virulence plasmid, was detected in 50.8% of S. Enteritidis isolates. The S. Enteritidis isolates showed the highest and the lowest resistance to nalidixic acid (87.3%) and ceftazidime (11.1%), respectively. Unfortunately, 27.0% of S. Enteritidis isolates were multidrug-resistant (MDR).

Conclusion

The rate of contamination with Salmonella in the poultry and egg samples, besides the presence of antimicrobial resistant and MDR Salmonella isolates harboring the virulence genes in these samples, could significantly affect food safety and subsequently, human health. Therefore, continuous monitoring of animal-source foods, enhancement of poultry farm control measures, and limiting the use of antibiotics for prophylactic purposes in food producing animals, are essential for reducing the zoonotic risk of this foodborne pathogen for consumers and also choosing effective antibiotics for the treatment of salmonellosis.

Selected Instrumental Techniques Applied in Food and Feed: Quality, Safety and Adulteration Analysis

This review presents an overall glance at selected instrumental analytical techniques and methods used in food analysis, focusing on their primary food science research applications. The methods described represent approaches that have already been developed or are currently being implemented in our laboratories. Some techniques are widespread and well known and hence we will focus only in very specific examples, whilst the relatively less common techniques applied in food science are covered in a wider fashion. We made a particular emphasis on the works published on this topic in the last five years. When appropriate, we referred the reader to specialized reports highlighting each technique's principle and focused on said technologies' applications in the food analysis field. Each example forwarded will consider the advantages and limitations of the application. Certain study cases will typify that several of the techniques mentioned are used simultaneously to resolve an issue, support novel data, or gather further information from the food sample.

Development of novel visual detection methodology for Salmonella in meat using saltatory rolling circle amplification

AIM

The aim of this study was to develop a saltatory rolling circle amplification (SRCA) assay for rapid, simple and visual detection of Salmonella in meat.

METHODS AND RESULTS

Saltatory rolling circle amplification assay was established using simple PCR primers targeting the invA gene of Salmonella enterica. The specificity of the SRCA assay was determined using 28 Salmonella and 15 non-Salmonella strains. The analytical sensitivity of the developed SRCA, conventional and real-time PCR assays were 70 fg, 7 pg and 700 fg S. enterica DNA per tube, respectively. The limit of detection (LoD) of the SRCA assay was 40 CFU per gram of meat without enrichment and 4 CFU per gram after including 6 h brief enrichment step. The detection limits of 40 CFU per gram and 4 CFU per gram of meat were achieved within 165 min and 9 h, respectively (including DNA extraction). To assess the real-world relevance of the SRCA assay, it was used to screen Salmonella from the field pork samples (n = 82). The same samples were also tested with culture (ISO 6579: 2002) method, conventional and real-time PCR assays. Using the developed assay with 6-h enrichment step, it could give accurate results as that of the culture method.

CONCLUSIONS

The results of this study showed that the SRCA assay is a rapid, simple, sophisticated equipment-free and user-friendly method for accurate detection of Salmonella in meat foods. To our information, this is the first study to deploy SRCA assay for screening foods for Salmonella.

SIGNIFICANCE AND IMPACT OF THE STUDY

The developed SRCA assay is cost-effective, easy-to-perform and equipment-free; therefore, it has the potential to replace other molecular detection methods for regular screening of Salmonella in foods in field laboratories.

Efficacy of a Salmonella enterica serovar Abortusovis (S. Abortusovis) inactivated vaccine in experimentally infected gestating ewes

Salmonella enterica serovar Abortusovis (S. Abortusovis) infection is one of the most important causes of infectious late-term abortion as well as birth of weak lambs in sheep in many countries throughout the world. Implementation of protocols based on the application of effective vaccines is one of the most effective approaches for controlling this disease, but variable efficacy has been reported, possibly related to factors associated with the host, the vaccine, the parameters used for determining efficacy and the challenge protocols. In this context, a new commercial inactivated vaccine (INMEVA; Laboratorios Hipra S.A., Spain) was evaluated in 20 control and 17 vaccinated gestating ewes, subcutaneously challenged at 90 days of gestation with 5 × 10⁶ colony-forming units (cfu) of a wild strain of S. Abortusovis. Incidence of reproductive failures, bacterial vaginal excretion (by real time PCR), and lamb survival were evaluated as indicators of the vaccine's level of protection. Moreover, humoral response (by ELISA test in serum samples) was studied. Vaccination was showed to be safe under the study conditions. Vaccine efficacy was demonstrated in two different ways: i) it significantly decreased the percentage of abortions [29.4% (5/17) in the vaccinated group compared to the control group (65%; 13/20)] and ii) there was a significant reduction of the overall vaginal excretion in the sampling period (3.05 log cfu/mL ± 0.84 in the vaccinated group vs. 5.68 ± 0.67 in the control group). Given these results, the vaccine evaluated can be considered as an effective alternative for controlling S. Abortusovis infection in ovine flocks.

Direct detection of Salmonella from poultry samples by DNA isothermal amplification

1. Salmonellosis is one of the most important diseases in public health and it is usually associated with poultry product consumption. This study aimed to validate rapid methods to detect Salmonella spp. from poultry samples. 2. A DNA isothermal amplification method, previously developed for other matrices, was applied for the specific detection of Salmonella spp. from various samples, including poultry tissues, drag and boot swabs, faeces and feed. A new procedure was validated with Salmonella spp. serotypes and isolates from other enteric bacterial species, as well as naturally contaminated poultry samples. 3. The study demonstrated the successful development and implementation of a procedure, including a DNA isothermal amplification method, for the detection of Salmonella spp. directly from tissues, drag and boot swabs, faeces and feed. The whole procedure can be performed in less than 24 hours and it has been successfully used in a veterinary diagnostic laboratory.

A Simple Assay to Assess Salmonella enterica Persistence in Lettuce Leaves After Low Inoculation Dose

Salmonella enterica is an enterobacterium associated with numerous foodborne illnesses worldwide. Leafy greens have been a common vehicle for disease outbreaks caused by S. enterica. This human pathogen can be introduced into crop fields and potentially contaminate fresh produce. Several studies have shown that S. enterica can survive for long periods in the plant tissues. Often, S. enterica population does not reach high titers in leaves; however, it is still relevant for food safety due to the low infective dose of the pathogen. Thus, laboratory procedures to study the survival of S. enterica in fresh vegetables should be adjusted accordingly. Here, we describe a protocol to assess the population dynamics of S. enterica serovar Typhimurium 14028s in the leaf apoplast of three cultivars of lettuce (Lactuca sativa L.). By comparing a range of inoculum concentrations, we showed that vacuum infiltration of a bacterium inoculum level in the range of 3.4 Log CFU ml^–1 (with a recovery of approximately 170 cells per gram of fresh leaves 2 h post inoculation) allows for a robust assessment of bacterial persistence in three lettuce cultivars using serial dilution plating and qPCR methods. We anticipate that this method can be applied to other leaf–human pathogen combinations in an attempt to standardize the procedure for future efforts to screen for plant phenotypic variability, which is useful for breeding programs.

Improving Quantitative Power in Digital PCR through Digital High-Resolution Melting

Applying digital PCR (dPCR) technology to challenging clinical and industrial detection tasks has become more prevalent because of its capability for absolute quantification and rare target detection. However, practices learned from quantitative PCR (qPCR) that promote assay robustness and wide-ranging utility are not readily applied in dPCR. These include internal amplification controls to account for false-negative reactions and amplicon high-resolution melt (HRM) analysis to distinguish true positives from false positives. Incorporation of internal amplification controls in dPCR is challenging because of the limited fluorescence channels available on most machines, and the application of HRM analysis is hindered by the separation of heating and imaging functions on most dPCR systems. We use a custom digital HRM platform to assess the utility of HRM-based approaches for mitigation of false positives and false negatives in dPCR. We show that detection of an exogenous internal control using dHRM analysis reduces the inclusion of false-negative partitions, changing the calculated DNA concentration up to 52%. The integration of dHRM analysis enables classification of partitions that would otherwise be considered ambiguous "rain," which accounts for up to ∼3% and ∼10% of partitions in intercalating dye and hydrolysis probe dPCR, respectively. We focused on developing an internal control method that would be compatible with broad-based microbial detection in dPCR-dHRM. Our approach can be applied to a number of DNA detection methods including microbial profiling and may advance the utility of dPCR in clinical applications where accurate quantification is imperative.

Salmonella serotype assignment by sequencing analysis of intergenic regions of ribosomal RNA operons

Salmonella laboratorial detection is usually carried out by bacteriological culture and serological methods. Salmonella isolates are then classified into more than 2,650 serotypes with different somatic (O) and flagellar (H) antigenic combinations. More recently, DNA analysis methods were developed and applied for the identification of Salmonella serotypes, including intergenic spacer regions (ISRs) that separates DNA-encoding ribosomal subunits (rRNA gene) in Salmonella genomes. The present study aimed to evaluate the nucleotide diversity of the ISRs in 2 rRNA operons (rrnB and rrnH) for the assignment of Salmonella serotypes. A total of 63 Salmonella isolates (bacterial cultures) from 21 serotypes were obtained in the period of 2014 to 2017. DNA was extracted, and PCRs were used to detect the genus Salmonella and 4 important serotypes: Enteritidis, Gallinarum, Heidelberg, and Typhimurium. ISRs of the operons rrnB and rrnH were amplified by PCR and then sequenced. All sequence results were submitted to BLASTn search and were aligned in comparison to 72 Salmonella reference nucleotide sequences. The results demonstrated that 60 (95.2%) samples returned a sequence of the same serotype (determined by the traditional serological procedure) after searching in BLASTn and/or in the alignment with the reference sequences for both operons (rrnB and rrnH). These PCR-sequencing procedures had a general agreement index of 0.792 based on the Kappa analysis, 98.7% sensitivity value, 100% specificity, and 98.4% accuracy. Three different phylogenetic trees were generated from the alignments with the sequences of rrnH, rrnB, and rrnH plus rrnB and isolates clustered in specific branches according to the serotypes.

Prevalence and genomic characteristics of zoonotic gastro-intestinal pathogens and ESBL/pAmpC producing Enterobacteriaceae among Swedish corvid birds

Introduction: Wild birds pose a potential threat to animal and human health by spreading infectious diseases. In the present study, we studied the occurrence of bacterial zoonotic pathogens as well as enterobacteria with transferrable antimicrobial resistance genes among Swedish corvids. Materials and methods: Intestines from 66 jackdaws, crows, rooks and magpies from the vicinity of livestock farms at 14 locations in 7 counties were analysed by direct culture or PCR screening followed by culture. Isolates were investigated by whole-genome sequencing. Results and discussion: Campylobacter jejuni were detected in 82% and Yersinia in 3% of the birds. ESBL-producing E. coli were found in one sample (2%) and carried bla CTX-M-55. No Enterobacteriaceae with transferable carbapenem resistance were identified. No Salmonella or E. coli O157:H7 were found, but PCR analysis for enterohaemorrhagic E. coli virulence genes revealed 35% positive samples for intimin, 9% for verotoxin 1 and 17% for verotoxin 2. C. jejuni isolates from corvids were compared to previously published isolates from Swedish sources by multi-locus sequence typing based on genome sequences. All corvid C. jejuni isolates formed a cluster, intermingled with human and chicken isolates. Our results indicate that C. jejuni is ubiquitous among Swedish corvid birds, with sporadic transmission to poultry and humans.

Multiplex touchdown PCR assay to enhance specificity and sensitivity for concurrent detection of four foodborne pathogens in raw milk

AIMS

The aim of this study was to develop a multiplex touchdown PCR (multiplex TD-PCR) for rapid and simultaneous detection of four major foodborne pathogens to avoid mispriming and unwanted production during gene amplification. Touchdown PCR is the modified form of standard PCR, which enhances specificity, sensitivity.

METHODS AND RESULTS

For this reason, a multiplex TD-PCR assay with a pre-enrichment step was developed to detect four foodborne pathogens namely Escherichia coli O157:H7, Listeria monocytogenes, Staphylococcus aureus, and Salmonella enterica serovar Enteritidis in pure culture and raw milk samples. The results showed that this protocol can eliminate the unwanted band or reduce significantly. The detection sensitivity of the single and multiplex TD-PCR was one cell per ml in pure culture. Furthermore, the detection limit of multiplex TD-PCR was one cell per 25 ml for artificially contaminated raw milk. We obtained similar results for detection of aforementioned pathogens in raw milk, after comparing the multiplex TD-PCR method with the traditional culture, except in one or two samples.

CONCLUSIONS

Hence, the proposed multiplex TD-PCR method could be confirmed as an effective way for rapid optimization of PCR reactions to increase specificity, sensitivity during gene amplification.

SIGNIFICANCE AND IMPACT OF THE STUDY

Hence, due to its simplicity, cost-effectiveness and being time-saving, it seems that this method is reasonable and economical for rapid optimization of PCR reactions.

Molecular detection of Salmonella serovars Enteritidis, Heidelberg and Typhimurium directly from pre-enriched poultry samples

1. Salmonella is one of the most important pathogens in public health and it is usually associated with food-borne diseases. Salmonella serovars Enteritidis and Typhimurium are widespread in the world with outbreaks frequently associated with consumption of poultry products; furthermore, there is an increasing public health concern with the wide dissemination of the serovar Heidelberg in poultry flocks. 2. The aim of the experiment was to develop and to validate rapid methods to detect Salmonella serovars Enteritidis, Typhimurium, and Heidelberg by real-time PCRs and test isolates from pre-enriched poultry samples. 3. Three real-time PCRs were developed and used in combination to detect the serovars Enteritidis, Typhimurium and Heidelberg. These assays were validated by the analysis of 126 Salmonella isolates, eight other enteric bacterial species and 34 naturally contaminated poultry samples after pre-enrichment with buffered peptone water (BPW). 4. Real-time PCRs detected the isolates of the most important poultry serovars (Enteritidis, Typhimurium and Heidelberg) with 100% inclusivity and exclusivity in each assay. The PCR identified monophasic variants of the serovars Typhimurium and Heidelberg. All PCRs were validated in detecting these specific serovars directly from pre-enriched poultry samples. The whole analytical procedure was performed in less than 24 h in a veterinary diagnostic laboratory.

Prevalence of Salmonella spp. in tonsils, mandibular lymph nodes and faeces of wild boar from Spain and genetic relationship between isolates

The importance of wild boars as game species in Spain is well known. Their feeding habits and intrusive behaviour, together with a progressively wider spreading of populations, increases the interactions of these animals with livestock and humans. Considering that wild boars could have a potential role in the transmission of certain pathogens as salmonellae, the aims of this study were to determine the prevalence of Salmonella spp. in wild boars hunted in central-western Spain, the occurrence of this pathogen in tonsils, mandibular lymph nodes and faeces (as markers for transmission risk), and to define the phylogenetic relationships among isolated strains, in order to investigate the circulation pathways of bacteria among tissues, animals and estates. Samples from 1,041 hunted wild boars were analysed for the presence of Salmonella spp. by bacteriological culture. Isolates were confirmed by PCR and serotyped in the Spanish national reference laboratory. The genetic relationships between strains were determined by PFGE. The results showed a 7.7% of positive animals (81 wild boars), being tonsils the organ most frequently colonised by Salmonella spp. (18.7%), followed by lymph nodes (5.1%) and faecal samples (2.9%). Serovars Enteritidis and Newport were the most frequent amongst the 34 different serovars obtained. The pulsed-field gel electrophoresis (PGFE) analysis showed a great genetic diversity, with serovars that exhibited different pulsotypes when isolated from different estates and multiple serovars in the same estate. In conclusion, this study reveals the importance of wild boars as carriers and possible transmitters of virulent and/or antimicrobial-resistant clones of Salmonella spp. to livestock and humans.

Salmonella isolates from urine cultures: serotypes and antimicrobial resistance in hospital settings

This study investigated the serotypes and antimicrobial resistance of Salmonella isolates in urine cultures from 38 hospitalized patients. Nine serotypes were detected, and a large proportion was Typhimurium and Enteritidis. The strains presented resistance to 11 different antibiotics. Thirteen isolates (11 from serotype Typhimurium) exhibited multidrug resistance.

Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia

Water borne diarrheal pathogens might accumulate in river water and cause contamination of drinking and irrigation water. The La Paz River basin, including the Choqueyapu River, flows through La Paz city in Bolivia where it is receiving sewage, and residues from inhabitants, hospitals, and industry. Using quantitative real-time PCR (qPCR), we determined the quantity and occurrence of diarrheagenic Escherichia coli (DEC), Salmonella enterica, Klebsiella pneumoniae, Shigella spp. and total enterobacteria in river water, downstream agricultural soil, and irrigated crops, during one year of sampling. The most abundant and frequently detected genes were gapA and eltB, indicating presence of enterobacteria and enterotoxigenic E. coli (ETEC) carrying the heat labile toxin, respectively. Pathogen levels in the samples were significantly positively associated with high water conductivity and low water temperature. In addition, a set of bacterial isolates from water, soil and crops were analyzed by PCR for presence of the genes blaCTX-M, blaKPC, blaNDM, blaVIM and blaOXA-48. Four isolates were found to be positive for blaCTX-M genes and whole genome sequencing identified them as E. coli and one Enterobacter cloacae. The E. coli isolates belonged to the emerging, globally disseminated, multi-resistant E. coli lineages ST648, ST410 and ST162. The results indicate not only a high potential risk of transmission of diarrheal diseases by the consumption of contaminated water and vegetables but also the possibility of antibiotic resistance transfer from the environment to the community.

Fluorescent S1 nuclease assay utilizing exponential strand displacement amplification

We devise a simple, label-free S1 nuclease activity assay by exploiting target-induced inhibition of exponential strand displacement amplification (eSDA).

Outbreaks of antimicrobial resistant Salmonella Choleraesuis in wild boars piglets from central-western Spain

Salmonella enterica serovar Choleraesuis is the aetiological agent of swine paratyphoid being a highly invasive zoonotic pathogen. Wild boar natural populations are experiencing a demographical expansion as well as some farms are breeding this species to release for hunting with management sometimes identical to that of domestic pigs, including supplementation, grouping, and antibiotic treatments. This situation increases the chance of contact between wild boars and livestock, and potentially induces stress, with different sanitary consequences. The present work aims to describe the clinical features of recent outbreaks caused by S. Choleraesuis in wild boar from central-western Spain, as well as the antimicrobial resistance and phylogenetic relationships of isolates involved. 28 strains of S. Choleraesuis were isolated from 28 different wild boars belonging to 10 different game states located in central western Spain and submitted to the Clinical Veterinary Hospital (CVH) of the University of Extremadura. Samples were taken from different organs and cultured according to the ISO 6579:2002 procedure. Suspicious colonies were identified by PCR and antimicrobial resistance was evaluated by disc diffusion susceptibility test and the presence of the main resistance genes as well as 18 plasmid replicons frequently found among the Enterobacteriaceae was verified by PCR. Pulsed field gel electrophoresis was applied to determine the genetic relationship between isolates. The outbreaks under study were characterized by high mortality (35%-84%) and a septicaemic presentation. S. Choleraesuis was isolated from all the wild boars analysed, and 26 of the 28 isolates presented resistance to at least one antibiotic. The predominant resistances found were against sulphonamide, streptomycin, tetracycline, and doxicicline and sul1, strA-strB, and tetA were the most prevalent resistance genes among isolates. 10 strains carried FIIA, FIB+H/1 or FIIA+H/1 plasmids. PFGE classified the isolates into four different profiles, grouped into two clusters. This results show that prevention against S. Choleraesuis must be considered in the sanitary programs of the wild boar breeders.

Fate of bacterial indicators and Salmonella in biofilm developed on ultrafiltration membranes treating secondary effluents of domestic wastewater

The fate of representative indicator and pathogenic bacteria on ultrafiltration (UF)-membrane surfaces treating secondary wastewater effluent, as well as their reaction to common biofouling-removal techniques was investigated. Field-condition experiments showed that the number of heterotrophic bacteria, fecal coliforms, E. coli and Salmonella on membrane surface increased rapidly and continuously until the end of the experiment, reaching 9, 6.5, 6, and 2.4 logs, respectively. Similar results were obtained under controlled laboratory conditions. However, the increase in the bacterial numbers was dependent on the supply of fresh wastewater. Quantitative real-time PCR verified the behavior of attached E. coli cells, although the numbers were 1–2 logs higher compared to the standard culture-based method. The number of attached bacteria was positively correlated to increases in DNA and protein content and negatively correlated to the membrane flux. In-situ membrane cleaning using sodium hypochlorite significantly reduced the number of attached bacteria. However, the effect was temporary and affected bacterial cell cultivability rather than viability. Taken together, these findings suggest that, under the studied conditions, indicator and pathogenic bacteria can initiate rapid biofilm development, persist on UF membrane surfaces, and survive membrane cleaning with sodium hypochlorite.

Increasing prevalence and dissemination of invasive nontyphoidal Salmonella serotype Typhimurium with multidrug resistance in hospitalized patients from southern Brazil

Introduction

Aim

Methods

Results

Conclusion

Distribution of enteropathogenic Yersinia spp. and Salmonella spp. in the Swedish wild boar population, and assessment of risk factors that may affect their prevalence

BACKGROUND

Pure Eurasian wild boars and/or hybrids with domestic pigs are present in the wild on most continents. These wild pigs have been demonstrated to carry a large number of zoonotic and epizootic pathogens such as Salmonella spp., Yersinia enterocolitica and Y. pseudotuberculosis. Wild boar populations throughout Europe are growing and more and more wild boar meat is being consumed, the majority within the homes of hunters without having passed a veterinary inspection. The aim of this study was to investigate if factors such as population density, level of artificial feeding, time since establishment of a given population, and the handling of animal by-products from slaughtered animals could influence the presence of these pathogens in the wild boar.

RESULTS

In total, 90 wild boars from 30 different populations in Sweden were sampled and analysed using a protocol combining pre-cultivation and PCR-detection. The results showed that 27% of the sampled wild boars were positive for Salmonella spp., 31% were positive for Y. enterocolitica and 22% were positive for Y. pseudotuberculosis. In 80% of the sampled populations, at least one wild boar was positive for one of these enteropathogens and in total, 60% of the animals carried at least one of the investigated enteropathogens. The presumptive risk factors were analysed using a case-control approach, however, no significant associations were found.

CONCLUSION

Human enteropathogens are commonly carried by wild boars, mainly in the tonsils, and can thus constitute a risk for contamination of the carcass and meat during slaughter. Based on the present results, the effect of reducing population densities and number of artificial feeding places might be limited.

Presence and Persistence of Salmonella in Water: The Impact on Microbial Quality of Water and Food Safety

Salmonella ranks high among the pathogens causing foodborne disease outbreaks. According to the Centers for Disease Control and Prevention, Salmonella contributed to about 53.4% of all foodborne disease outbreaks from 2006 to 2017, and approximately 32.7% of these foodborne Salmonella outbreaks were associated with consumption of produce. Trace-back investigations have suggested that irrigation water may be a source of Salmonella contamination of produce and a vehicle for transmission. Presence and persistence of Salmonella have been reported in surface waters such as rivers, lakes, and ponds, while ground water in general offers better microbial quality for irrigation. To date, culture methods are still the gold standard for detection, isolation and identification of Salmonella in foods and water. In addition to culture, other methods for the detection of Salmonella in water include most probable number, immunoassay, and PCR. The U.S. Food and Drug Administration (FDA) issued the Produce Safety Rule (PSR) in January 2013 based on the Food Safety Modernization Act (FSMA), which calls for more efforts toward enhancing and improving approaches for the prevention of foodborne outbreaks. In the PSR, agricultural water is defined as water used for in a way that is intended to, or likely to, contact covered produce, such as spray, wash, or irrigation. In summary, Salmonella is frequently present in surface water, an important source of water for irrigation. An increasing evidence indicates irrigation water as a source (or a vehicle) for transmission of Salmonella. This pathogen can survive in aquatic environments by a number of mechanisms, including entry into the viable but nonculturable (VBNC) state and/or residing within free-living protozoa. As such, assurance of microbial quality of irrigation water is critical to curtail the produce-related foodborne outbreaks and thus enhance the food safety. In this review, we will discuss the presence and persistence of Salmonella in water and the mechanisms Salmonella uses to persist in the aquatic environment, particularly irrigation water, to better understand the impact on the microbial quality of water and food safety due to the presence of Salmonella in the water environment.

New York City House Mice (Mus musculus) as Potential Reservoirs for Pathogenic Bacteria and Antimicrobial Resistance Determinants

House mice (Mus musculus) thrive in large urban centers worldwide. Nonetheless, little is known about the role that they may play in contributing to environmental contamination with potentially pathogenic bacteria. Here, we describe the fecal microbiome of house mice with emphasis on detection of pathogenic bacteria and antimicrobial resistance genes by molecular methods. Four hundred sixteen mice were collected from predominantly residential buildings in seven sites across New York City over a period of 13 months. 16S rRNA sequencing identified Bacteroidetes as dominant and revealed high levels of Proteobacteria A targeted PCR screen of 11 bacteria, as indicated by 16S rRNA analyses, found that mice are carriers of several gastrointestinal disease-causing agents, including Shigella, Salmonella, Clostridium difficile, and diarrheagenic Escherichia coli Furthermore, genes mediating antimicrobial resistance to fluoroquinolones (qnrB) and β-lactam drugs (bla_SHV and bla_ACT/MIR) were widely distributed. Culture and molecular strain typing of C. difficile revealed that mice harbor ribotypes associated with human disease, and screening of kidney samples demonstrated genetic evidence of pathogenic Leptospira species. In concert, these findings support the need for further research into the role of house mice as potential reservoirs for human pathogens and antimicrobial resistance in the built environment.IMPORTANCE Mice are commensal pests often found in close proximity to humans, especially in urban centers. We surveyed mice from seven sites across New York City and found multiple pathogenic bacteria associated with febrile and gastrointestinal disease as well as an array of antimicrobial resistance genes.

Manure management and public health: Sanitary and socio-economic aspects among urban livestock-keepers in Cambodia

Livestock manure is a valuable source of nutrients for crop production, but can also pose a public health hazard and have negative environmental impacts. This study investigated manure management practices among urban and peri-urban livestock keepers in Cambodia, to identify risk behaviours and socio-economic aspects associated with the handling of manure. A survey including 204 households was conducted, using a structured questionnaire with questions on demographics, socio-economic characteristics and household practices related to manure management. Faecal samples were obtained from pig pens and pig manure storage units for analysis of the potential zoonotic pathogens Salmonella enterica (Polymerase Chain Reaction (PCR)), Ascaris suum and Trichuris suis (McMaster flotation technique). The survey revealed a difference in management between cattle and pig manure. Cattle manure was most commonly used as fertiliser for crop production (66%) (p<0.001), whereas pig manure was most commonly dumped in the environment (46%) (p<0.001). Logistic regression models showed that households with a lower socio-economic position were more likely to dump pig manure (p<0.001), with scarcity of agricultural land (p<0.001) and lack of carts for transportation of manure (p<0.01) being identified as contributing factors. Salmonella enterica was detected in 9.7% of manure samples, while Ascaris suum and Trichuris suis were detected in 1.6% and 2.4% of the samples, respectively. The results presented in this study indicate that manure management by urban and peri-urban households may pose a public health threat and an environmental hazard. There is evidently a need for further knowledge support to the livestock keepers to promote good management practices.

Fate of Manure-Borne Pathogens during Anaerobic Digestion and Solids Separation

Anaerobic digestion can inactivate zoonotic pathogens present in cattle manure, which reduces transmission of these pathogens from farms to humans through the environment. However, the variability of inactivation across farms and over time is unknown because most studies have examined pathogen inactivation under ideal laboratory conditions or have focused on only one or two full-scale digesters at a time. In contrast, we sampled seven full-scale digesters treating cattle manure in Wisconsin for 9 mo on a biweekly basis ( = 118 pairs of influent and effluent samples) and used real-time quantitative polymerase chain reaction to analyze these samples for 19 different microbial genetic markers. Overall, inactivation of pathogens and fecal indicators was highly variable. When aggregated across digester and season, log-removal values for several representative microorganisms-bovine , -like CowM3, and bovine polyomavirus-were 0.78 ± 0.34, 0.70 ± 0.50, and 0.53 ± 0.58, respectively (mean ± SD). These log-removal values were up to two times lower than expected based on the scientific literature. Thus, our study indicates that full-scale anaerobic digestion of cattle manure requires optimization with regard to pathogen inactivation. Future studies should focus on identifying the potential causes of this suboptimal performance (e.g., overloading, poor mixing, poor temperature control). Our study also examined the fate of pathogens during manure separation and found that the majority of microbes we detected ended up in the liquid fraction of separated manure. This finding has important implications for the transmission of zoonotic pathogens through the environment to humans.

Molecular and phylogenetic analyses of Salmonella Gallinarum trace the origin and diversification of recent outbreaks of fowl typhoid in poultry farms

Fowl typhoid (FT) and pullorum disease (PD) are two important poultry infections caused by Salmonella enterica subsp. enterica serotype Gallinarum (S. Gallinarum). S. Gallinarum strains are adapted to birds and classified into biovars Gallinarum (bvGA) and Pullorum (bvPU) as they are the causative agent of FT and PD, respectively. In Brazil, FT/PD outbreaks have been reported along the last 50 years, but there was a recent increase of FT field reports with the suspicion it could be due to virulence reversion of the attenuated live vaccine SG9R. In this study, we applied molecular biology assays and phylogenetic methods to detect and investigate S. Gallinarum isolates from commercial poultry flocks in order to understand the evolutionary history and origin of the recent FT outbreaks in Brazil. S. Gallinarum isolates were obtained from thirteen different poultry flocks with clinical signs of FT/PD from 2013 to 2015. These isolates were serotyped, tested with three specific PCR (for the detection of bvGA, bvPU and live vaccine strain SG9R) and submitted to sequencing of a variable genome region (ISR analysis). The complete genome of one bvGA strain (BR_RS12) was also compared to other S. Gallinarum complete genomes (including other two Brazilian ones: bvGA 287/91 and bvPU FCVA198). PCR detected all thirteen isolates as S. Gallinarum (eight bvGA and five bvPU), none positive for SG9R strain. ISR analysis revealed that all eight bvGA isolates showed exactly the same nucleotide sequences with 100% similarity to reference strains, while two patterns were observed for bvPU. Genome phylogeny demonstrated distinct clades for bvGA and bvPU, with the bvGA clade showing a clear subdivision including three genomes: SG9R vaccine, the respective SG9 parent strain and one SG9R revertant field isolate (MB4523). The evolutionary rate of the total S. Gallinarum genome was calculated at 6.15×10^-7 substitutions/site/year, with 2.8 observed substitutions per year per genome (1 SNP per 4292 bases). Phylodynamics analysis estimated that at least two introductions of S. Gallinarum bvGA happened in Brazil, the first in 1885 and the second in 1950. The Brazilian bvGA genomes 287/91 and BR_RS12 analyzed here were related to the early and the late introductions, respectively. In conclusion, these results indicate the occurrence of S. Gallinarum strains associated with FT outbreaks that have been circulating for more than 50 years in Brazil and are not originated from virulence reversion of the SG9R vaccine.

A study on prevalence of microbial contamination on the surface of raw salad vegetables

The present work evaluates the microbiological quality of raw salad vegetables (RSV) consumed in Dhanbad city, India. A total of 480 samples of 8 different raw salad vegetables from local market were examined for overall microbial quality in terms of aerobic mesophilic, psychrotrophic counts, yeast, mould and total coliform levels. E. coli O157:H7, Listeria monocytogenes and Salmonella sp. were detected by real-time polymerase chain reaction (qPCR) subsequent to isolation. Results showed that all the samples were found positive for total coliform; however, E. coli was detected in 16.7% of the total samples. Pathogenic microorganisms such as E. coli O157:H7, L. monocytogenes and Salmonella spp. were detected in 1.3, 3.5 and 4.0%, respectively, of the total samples. However, pathogens were not detected in any of the cabbage samples. The Exiguobacterium sp. (Strain ISM SP 2014) was detected in the spinach sample while studying the bacterial contamination, reported for the first time on the surface of RSV. The 16S rRNA gene sequencing showed less than 92% similarity with sequences available in the public domain.

Microbial Quality, Safety, and Pathogen Detection by Using Quantitative PCR of Raw Salad Vegetables Sold in Dhanbad City, India

Consumption of ready-to-eat fresh vegetables has increased worldwide, with a consequent increase in outbreaks caused by foodborne pathogens. In the Indian subcontinent, raw fresh vegetables are usually consumed without washing or other decontamination procedures, thereby leading to new food safety threats. In this study, the microbiological quality and pathogenic profile of raw salad vegetables was evaluated through standard protocols. In total, 480 samples (60 each of eight different salad vegetables) of cucumber, tomato, carrot, coriander, cabbage, beetroot, radish, and spinach were collected from different locations in Dhanbad, a city famous for its coal fields and often called the "Coal Capital of India." The samples were analyzed for total plate count, total coliforms, Escherichia coli , E. coli O157:H7, Listeria monocytogenes , and Salmonella spp. Incidences of pathogens were detected through quantitative PCR subsequent to isolation. Results showed that 46.7% (for total plate counts) and 30% (for total coliforms) of samples were unacceptable for consumption per the Food Safety and Standards Authority of India. Pathogenic microorganisms were detected in 3.7% of total samples. E. coli O157:H7 was detected in three samples of spinach (2) and beetroot ( 1 ); L. monocytogenes was detected in 14 samples of spinach ( 8 ), tomato ( 3 ), cucumber ( 2 ), and radish ( 1 ); and Salmonella spp. were detected in 16 samples of spinach ( 7 ), tomato ( 3 ), beetroot ( 2 ), cucumber ( 2 ), carrot ( 1 ), and radish ( 1 ). Pathogens were not detected in any of the cabbage and coriander samples.

Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial source tracking (MST) markers, developed to determine potential sources of fecal contamination, can also be resuspended from bed sediments. The primary objective of this study was to predict occurrence of waterborne pathogens in water and streambed sediments using a simple statistical model that includes traditionally measured FIB, environmental parameters and source allocation, using MST markers as predictor variables. Synoptic sampling events were conducted during baseflow conditions downstream from agricultural (AG), forested (FORS), and wastewater pollution control plant (WPCP) land uses. Concentrations of FIB and MST markers were measured in water and sediments, along with occurrences of the enteric pathogens Campylobacter, Listeria and Salmonella, and the virulence gene that carries Shiga toxin, stx2. Pathogens were detected in water more often than in underlying sediments. Shiga toxin was significantly related to land use, with concentrations of the ruminant marker selected as an independent variable that could correctly classify 76% and 64% of observed Shiga toxin occurrences in water and sediment, respectively. FIB concentrations and water quality parameters were also selected as independent variables that correctly classified Shiga toxin occurrences in water and sediment (54%-87%), and Salmonella occurrences in water (96%). Relationships between pathogens and indicator variables were generally inconsistent and no single indicator adequately described occurrence of all pathogens. Because of inconsistent relationships between individual pathogens and FIB/MST markers, incorporating a combination of FIB, water quality measurements, and MST markers may be the best way to assess microbial water quality in mixed land use systems.

Persistence and Potential Viable but Non-culturable State of Pathogenic Bacteria during Storage of Digestates from Agricultural Biogas Plants

Despite the development of on-farm anaerobic digestion as a process for making profitable use of animal by-products, factors leading to the inactivation of pathogenic bacteria during storage of digestates remain poorly described. Here, a microcosm approach was used to evaluate the persistence of three pathogenic bacteria (Salmonella enterica Derby, Campylobacter coli and Listeria monocytogenes) in digestates from farms, stored for later land spreading. Nine samples, including raw digestates, liquid fractions of digestate and composted digestates, were inoculated with each pathogen and maintained for 40 days at 24°C. Concentrations of pathogens were monitored using culture and qPCR methods. The persistence of L. monocytogenes, detected up to 20 days after inoculation, was higher than that of Salmonella Derby, detected for 7-20 days, and of C. coli (not detected after 7 days). In some digestates, the concentration of the pathogens by qPCR assay was several orders of magnitude higher than the concentration of culturable cells, suggesting a potential loss of culturability and induction of Viable but Non-Culturable (VBNC) state. The potential VBNC state which was generally not observed in the same digestate for the three pathogens, occurred more frequently for C. coli and L. monocytogenes than for Salmonella Derby. Composting a digestate reduced the persistence of seeded L. monocytogenes but promoted the maintenance of Salmonella Derby. The effect of NH[Formula: see text]/NH3 on the culturability of C. coli and Salmonella Derby was also shown. The loss of culturability may be the underlying mechanism for the regrowth of pathogens. We have also demonstrated the importance of using molecular tools to monitor pathogens in environmental samples since culture methods may underestimate cell concentration. Our results underline the importance of considering VBNC cells when evaluating the sanitary effect of an anaerobic digestion process and the persistence of pathogens during the storage of digestates and subsequent land spreading.

Determining the 95% limit of detection for waterborne pathogen analyses from primary concentration to qPCR

The limit of detection (LOD) for qPCR-based analyses is not consistently defined or determined in studies on waterborne pathogens. Moreover, the LODs reported often reflect the qPCR assay alone rather than the entire sample process. Our objective was to develop an approach to determine the 95% LOD (lowest concentration at which 95% of positive samples are detected) for the entire process of waterborne pathogen detection. We began by spiking the lowest concentration that was consistently positive at the qPCR step (based on its standard curve) into each procedural step working backwards (i.e., extraction, secondary concentration, primary concentration), which established a concentration that was detectable following losses of the pathogen from processing. Using the fraction of positive replicates (n = 10) at this concentration, we selected and analyzed a second, and then third, concentration. If the fraction of positive replicates equaled 1 or 0 for two concentrations, we selected another. We calculated the LOD using probit analysis. To demonstrate our approach we determined the 95% LOD for Salmonella enterica serovar Typhimurium, adenovirus 41, and vaccine-derived poliovirus Sabin 3, which were 11, 12, and 6 genomic copies (gc) per reaction (rxn), respectively (equivalent to 1.3, 1.5, and 4.0 gc L(-1) assuming the 1500 L tap-water sample volume prescribed in EPA Method 1615). This approach limited the number of analyses required and was amenable to testing multiple genetic targets simultaneously (i.e., spiking a single sample with multiple microorganisms). An LOD determined this way can facilitate study design, guide the number of required technical replicates, aid method evaluation, and inform data interpretation.

Supplementation with Quaternary Benzo(c)phenanthridine Alkaloids Decreased Salivary Cortisol and Salmonella Shedding in Pigs After Transportation to the Slaughterhouse

The present study was aimed at evaluating the effect of herbal extracts supplementation, particularly quaternary-benzo(c)phenanthridine alkaloids (QBA), which have been previously demonstrated to have anti-inflammatory, antimicrobial, and immune-modulator effects. We investigated the role of QBA on stress response and Salmonella shedding in finishing pigs transported to the slaughterhouse. A total of 82 pigs were orally challenged with a Salmonella cocktail (day 0) containing Salmonella Meleagridis, Hartford, Bovismorbificans and Newport serovars and randomly assigned to three treatment groups after 2 wks (day [D] 14): T1, in-feed QBA; T2, in-feed and water-soluble QBA; CON, nonsupplemented). Pigs were transported to the slaughterhouse 2 weeks after intervention (D 28) and slaughtered after nearly 19 h (D 29). Saliva, fecal samples, and carcass swabs were collected from all pigs. Salivary cortisol, Salmonella shedding, and carcass contamination were measured. A high positive correlation (Spearman rank correlation coefficient range 0.82-0.93) between salivary cortisol and Salmonella shedding was found after transportation in all groups (p < 0.05). Only the CON group showed an increase in salivary cortisol after transportation (5.48 ng/mL; p < 0.0001) to concentrations that were higher than in T1 (2.73 ng/mL; p = 0.0002) and T2 (1.88 ng/mL; p < 0.0001). Salmonella prevalence and shedding decreased after transportation in pigs receiving the QBA intervention (p < 0.05), whereas the control group showed a significant increase in Salmonella shedding after transportation (p = 0.04). At D 28, pigs in T2 shed lower numbers of Salmonella as compared to T1 (1.3E + 02 CFU/mL versus 8E + 03 CFU/mL; p = 0.002). Additionally, carcass contamination by Salmonella was higher in the CON group than the treated groups (p = 0.01). The findings show QBA intervention was effective in reducing transportation stress of pigs, resulting in reduced Salmonella shedding and positively impacting animal welfare and pork safety.

An Improved Multiplex Real-Time SYBR Green PCR Assay for Analysis of 24 Target Genes from 16 Bacterial Species in Fecal DNA Samples from Patients with Foodborne Illnesses

Here, we developed a new version of our original screening system (Rapid Foodborne Bacterial Screening 24; RFBS24), which can simultaneously detect 24 genes of foodborne pathogens in fecal DNA samples. This new version (RFBS24 ver. 5) detected all known stx2 subtypes, enterotoxigenic Escherichia coli (STh genotype), and Vibrio parahaemolyticus (trh2), which were not detected by the original RFBS24 assay. The detection limits of RFBS24 ver. 5 were approximately 5.6 × 10(-2)-5.6 × 10(-5) (ng DNA)/reaction, significantly lower (10- to 100-fold) than those of the original RFBS24 for the 22 target genes analyzed here. We also tested the new assay on fecal DNA samples from patients infected with Salmonella, Campylobacter, or enterohemorrhagic E. coli. The number of bacterial target genes detected by RFBS24 ver. 5 was greater than that detected by RFBS24. RFBS24 ver. 5 combined with an Ultra Clean Fecal DNA Isolation Kit showed adequate performance (sensitivity and specificity 89% and 100%, respectively, for Salmonella spp. and 100% and 83%, respectively, for Campylobacter jejuni) in terms of rapid detection of a causative pathogen during foodborne-illness outbreaks. Thus, RFBS24 ver. 5 is more useful than the previous assay system for detection of foodborne pathogens and offers quick simultaneous analysis of many targets and thus facilitates rapid dissemination of information to public health officials.