Simultaneous Identification of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari with SmartCycler-Based Multiplex Quantitative Polymerase Chain Reaction.

BACKGROUND: Consumption of Campylobacter contaminated food or water is a leading cause of human acute gastroenteritis. Campylobacter jejuni, Campylobacter coli, and Campylobacter lari account for over 95% of total Campylobacter infections. A multiplex quantitative polymerase chain reaction (qPCR) for simultaneous identification of C. jejuni, C. coli, and C. lari was developed for use with the SmartCycler II system. MATERIALS AND METHODS: We evaluated and combined previously described primers and probes for Campylobacter detection, designed a new internal amplification control, and optimized the multiplex qPCR for the detection of C. jejuni, C. coli, and C. lari. RESULTS: This method was 100% specific when tested against a panel of 32 target Campylobacter strains and 31 non-Campylobacter reference strains. Furthermore, there was no cross-reactivity with seven strains from four nontarget Campylobacter species. The amplification efficiency of each target in this multiplex qPCR was over 90%, and each coefficient of linearity was greater than 0.99. With artificially mixed genomic DNA, this method detected as few as two, three, and two genome copies of C. jejuni, C. coli, and C. lari, respectively. This method was also able to detect these three Campylobacter species in artificially contaminated milk with a sensitivity of five spiked cells of each target per reaction. CONCLUSION: The three Campylobacter targets were simultaneously identified using artificially mixed genomic DNA and spiked raw milk. This SmartCycler-based multiplex qPCR is a rapid, specific, and sensitive method to identify C. jejuni, C. coli, and C. lari.

Developing a competency framework for U.S. state food and feed testing laboratory personnel.

A competency-based training curriculum framework for U.S. state food and feed testing laboratories personnel is being developed by the International Food Protection Training Institute (IFPTI) and three partners. The framework will help laboratories catalog existing training courses/modules, identify training gaps, inform training curricula, and create career-spanning professional development learning paths, ensuring consistent performance expectations and increasing confidence in shared test results. Ultimately, the framework will aid laboratories in meeting the requirements of ISO/IEC 17025 (2005) international accreditation and the U.S. Food Safety Modernization Act (U.S. Public Law 111-353). In collaboration with the Association of Food and Drug Officials, the Association of Public Health Laboratories, and the Association of American Feed Control Officials, IFPTI is carrying out the project in two phases. In 2013, an expert panel of seven subject matter experts developed competency and curriculum frameworks for five professional levels (entry, mid-level, expert, supervisor/manager, and senior administration) across four competency domains (technical, communication, programmatic, and leadership) including approximately 80 competencies. In 2014 the expert panel will elicit feedback from peers and finalize the framework.

Analysis of toxic metals in seafood sold in New York state by inductively coupled plasma mass spectrometry and direct combustion analysis.

Concentrations of 12 metals (As, Be, Cd, Cr, Pb, Mo, Ni, Tl, Th, U, V, Hg) were determined in samples of fish and lobster obtained from various stores and markets in New York State. The seafood samples were chosen based on their popularity as a food source and the potential of the species to contain high levels of mercury based on past research results. A total of 177 fish and lobster samples were initially analyzed using combustion for Hg. The samples were then reanalyzed for several elements using microwave digestion followed by inductively coupled plasma mass spectrometry. The detection limits were as follows: 20 ng/g for Th, U, and Hg; 100 ng/g for Be, Cd, V, and As; and 300 ng/g for Cr, Mo, Tl, Pb, and Ni. Twenty-two samples had mercury concentrations greater than the 1,000 ng/g limit set by the Commission of the European Communities. The highest Cd concentration (511 ng/g) was found in a lobster. This level is greater than the 500 ng/g limit set by the Commission of the European Communities. All levels of As, Cd, Cr, Pb, and Ni were below the U.S. Food and Drug Administration action levels for these metals in crustaceans and shellfish. The highest average mercury level (1,190 ng/g) was found in swordfish. The highest average arsenic level (13,400 ng/g) was found in monkfish. Inductively coupled plasma mass spectrometry with microwave digestion was demonstrated to be a very effective technique for analyzing fish and lobster for Hg and other toxic metals.

Prevalence and molecular diversity of Listeria monocytogenes in retail establishments.

As our understanding of Listeria monocytogenes transmission in retail and deli operations is limited, we conducted a cross-sectional study of L. monocytogenes contamination patterns in 121 retail establishments, using testing of food and environmental samples and subtype analysis (ribotyping) of L. monocytogenes isolates. Seventy-three (60%) establishments had at least one sample that tested positive for L. monocytogenes; 5 (2.7%) of the 183 food and 151 (13.0%) of the 1,161 environmental samples tested positive for L. monocytogenes, including 125 (16.7%) and 26 (6.3%) of non-food contact and food contact surface samples, respectively. Thirty-two EcoRI ribotypes were identified among the 156 L. monocytogenes isolated. Twenty-seven establishments had two or more L. monocytogenes with the same ribotype within a given establishment, including 9 establishments where isolates from 3 to 5 samples had the same ribotype. In 5 of 7 establishments where follow-up sampling was conducted 8 to 19 months after the initial sampling, isolates with the same ribotype were obtained in both samplings; persistence of a given strain was also confirmed by pulsed-field gel electrophoresis. Our data indicate that (i) L. monocytogenes is regularly found in some retail environments; (ii) L. monocytogenes strains are often widely distributed in retail, indicating cross-contamination and dispersal; (iii) L. monocytogenes can persist in retail environments for more than 1 year; and (iv) a number of L. monocytogenes subtypes isolated at retail are common among human listeriosis cases. We also identified specific contamination patterns in retail establishments, providing critical information for the development of L. monocytogenes control strategies.

Strategic use of state and local regulatory and public health surveillance resources to address the growing demand for food safety oversight in the United States.

Although considerable progress has been made, federal food safety oversight in the United States has not overcome challenges posed by a decentralized, rapidly expanding food supply network. To complement limitations of federal measures, we believe that state-based food safety regulatory and surveillance systems should be better leveraged and integrated. A strengthened national food safety program would include implementation of uniform standards of food inspection and testing, reciprocal acceptance of state and federal inspection and laboratory findings, and systematic, timely sharing of data on pathogens recovered from contaminated foods and from ill persons.

Whole Genome Sequencing and Multiplex qPCR Methods to Identify Campylobacter jejuni Encoding cst-II or cst-III Sialyltransferase.

Campylobacter jejuni causes more than 2 million cases of gastroenteritis annually in the United States, and is also linked to the autoimmune sequelae Guillan-Barre syndrome (GBS). GBS often results in flaccid paralysis, as the myelin sheaths of nerve cells are degraded by the adaptive immune response. Certain strains of C. jejuni modify their lipooligosaccharide (LOS) with the addition of neuraminic acid, resulting in LOS moieties that are structurally similar to gangliosides present on nerve cells. This can trigger GBS in a susceptible host, as antibodies generated against C. jejuni can cross-react with gangliosides, leading to demyelination of nerves and a loss of signal transduction. The goal of this study was to develop a quantitative PCR (qPCR) method and use whole genome sequencing data to detect the Campylobacter sialyltransferase (cst) genes responsible for the addition of neuraminic acid to LOS. The qPCR method was used to screen a library of 89 C. jejuni field samples collected by the Food and Drug Administration Pacific Northwest Lab (PNL) as well as clinical isolates transferred to PNL. In silico analysis was used to screen 827 C. jejuni genomes in the FDA GenomeTrakr SRA database. The results indicate that a majority of C. jejuni strains could produce LOS with ganglioside mimicry, as 43.8% of PNL isolates and 46.9% of the GenomeTrakr isolates lacked the cst genes. The methods described in this study can be used by public health laboratories to rapidly determine whether a C. jejuni isolate has the potential to induce GBS. Based on these results, a majority of C. jejuni in the PNL collection and submitted to GenomeTrakr have the potential to produce LOS that mimics human gangliosides.

Long-term persistence of multi-drug-resistant Salmonella enterica serovar Newport in two dairy herds.

OBJECTIVE: To evaluate the association between maintaining joint hospital and maternity pens and persistence of multi-drug-resistant (MDR) Salmonella enterica serovar Newport on 2 dairy farms. DESIGN: Observational study. SAMPLE POPULATION: Feces and environmental samples from 2 dairy herds. PROCEDURE: Herds were monitored for fecal shedding of S enterica Newport after outbreaks of clinical disease. Fecal and environmental samples were collected approximately monthly from pens housing sick cows and calving cows and from pens containing lactating cows. Cattle shedding the organism were tested serially on subsequent visits to determine carrier status. One farm was resampled after initiation of interventional procedures, including separation of hospital and maternity pens. Isolates were characterized via serotyping, determination of antimicrobial resistance phenotype, detection of the CMY-2 gene, and DNA fingerprinting. RESULTS: The prevalence (32.4% and 33.3% on farms A and B, respectively) of isolating Salmonella from samples from joint hospital-maternity pens was significantly higher than the prevalence in samples from pens housing preparturient cows (0.8%, both farms) and postparturient cows on Farm B (8.8%). Multi-drug-resistant Salmonella Newport was isolated in high numbers from bedding material, feed refusals, lagoon slurry, and milk filters. One cow excreted the organism for 190 days. Interventional procedures yielded significant reductions in the prevalences of isolating the organism from fecal and environmental samples. Most isolates were of the C2 serogroup and were resistant to third-generation cephalosporins. CONCLUSIONS AND CLINICAL RELEVANCE: Management practices may be effective at reducing the persistence of MDR Salmonella spp in dairy herds, thus mitigating animal and public health risk.

Genome sequencing and annotation of a Campylobacter coli strain isolated from milk with multidrug resistance.

As the most prevalent bacterial cause of human gastroenteritis, food-borne Campylobacter infections pose a serious threat to public health. Whole Genome Sequencing (WGS) is a tool providing quick and inexpensive approaches for analysis of food-borne pathogen epidemics. Here we report the WGS and annotation of a Campylobacter coli strain, FNW20G12, which was isolated from milk in the United States in 1997 and carries multidrug resistance. The draft genome of FNW20G12 (DDBJ/ENA/GenBank accession number LWIH00000000) contains 1, 855,435 bp (GC content 31.4%) with 1902 annotated coding regions, 48 RNAs and resistance to aminoglycoside, beta-lactams, tetracycline, as well as fluoroquinolones. There are very few genome reports of C. coli from dairy products with multidrug resistance. Here the draft genome of FNW20G12, a C. coli strain isolated from raw milk, is presented to aid in the epidemiology study of C. coli antimicrobial resistance and role in foodborne outbreak.

Antimicrobial resistance of commensal Escherichia coli from dairy cattle associated with recent multi-resistant salmonellosis outbreaks.

The use of antimicrobial drugs in livestock is suspected to contribute to bacterial antimicrobial resistance (AR) development. Dairy farms experiencing recent outbreaks of salmonellosis involving multi-resistant (MR) Salmonella strains were compared to control farms with respect to AR among bovine commensal E. coli isolates. For most antimicrobials tested, the percentage of AR E. coli isolated from salmonellosis-affected farms was significantly higher than that from control farms. Calf E. coli from both case and control farms had greater levels of AR than cow isolates. Commensal E. coli isolates from case farms and calves tended to more frequently be MR. These data are consistent with the existence of higher antimicrobial selection pressure on farms with recent salmonellosis outbreaks, however, the directionality of the relationship remains to be elucidated. An improved understanding of the epidemiology of AR bacteria in livestock production, both at the herd and molecular level, is essential to mitigate risk to public health and food safety.

Feedstuffs as a vehicle of cattle exposure to Escherichia coli O157:H7 and Salmonella enterica.

Feed has been reported as a vehicle for transmission of Salmonella enterica in cattle and several lines of evidence suggest that feed can be a vehicle for transmitting Escherichia coli O157:H7 as well. To show whether microbial contamination of feeds could contribute to the populations of S. enterica and E. coli O157:H7 on a farm, we compared isolates from feed samples to bovine fecal isolates from the same farm using pulsed-field gel electrophoresis (PFGE). Four of 2365 component feed samples (0.2%) and 1 of 226 feed mill samples (0.4%) were positive for E. coli O157:H7. Twenty of 2405 (0.8%) component feed samples and none of 226 feed mill samples were positive for Salmonella. PFGE profiles from E. coli O157:H7 isolated from a component feed sample closely resembled that from a fecal isolate collected later from the same farm, and a similar observation was made of a Salmonella Tyhpimurium isolate from component feed on another farm. There were indistinguishable PFGE profiles from component feed Salmonella Tyhpimurium DT104 isolates and fecal isolates from the same farm. These results provide evidence for a role of cattle feed in transmission of E. coli O157:H7; S. enterica; cattle-bacteria.

Prevalence, distribution, and diversity of Listeria monocytogenes in retail environments, focusing on small establishments and establishments with a history of failed inspections.

Despite growing concerns about cross-contamination of ready-to-eat foods with Listeria monocytogenes, our knowledge about the ecology and transmission of L. monocytogenes in retail establishments has remained limited. We conducted a cross-sectional study to characterize the prevalence, distribution, and subtype diversity of L. monocytogenes in 120 New York State retail deli establishments that were hypothesized to present an increased risk for environmental L. monocytogenes contamination (i.e., small establishments and establishments with a history of failed New York State Agriculture and Markets inspections). Analysis of these data along with previously reported data for 121 predominantly larger retail establishments in New York State identified establishment size, geographic location, and inspection history as significant predictors of L. monocytogenes presence and prevalence. The odds of an establishment being L. monocytogenes positive were approximately twice as high for large establishments, establishments located in New York City, or establishments with poor inspection history (as compared with establishments without these attributes), even though correlation between location and inspection history complicated interpretation of results. Within an establishment, L. monocytogenes was significantly more prevalent on nonfood contact surfaces than on food contact surfaces; prevalence was particularly high for floors and in floor drains, sinks, the dairy case, and milk crates. L. monocytogenes subtype diversity differed between sites, with lineage I isolates significantly associated with nonfood contact surfaces and lineage II isolates significantly associated with food contact surfaces. Isolates belonging to the same ribotype were often found dispersed across multiple sites within an operation.

Quantitative risk assessment of listeriosis due to consumption of raw milk.

The objectives of this study were to estimate the risk of illness for raw milk consumers due to Listeria monocytogenes in raw milk sold by permitted dealers, and the risk for people on farms who consume raw milk. Three scenarios were evaluated for raw milk sold by dealers: raw milk purchased directly from bulk tanks, from on-farm stores, and from retail. To assess the effect of mandatory testing of raw milk by regulatory agencies, the number of listeriosis cases per year was compared where no raw milk testing was done, only a screening test to issue a permit was conducted, and routine testing was conducted and milk was recalled if it was L. monocytogenes positive. The median number of listeriosis cases associated with consumption of raw milk from bulk tanks, farm stores, and retail for an intermediate-age population was 6.6 × 10(-7), 3.8 × 10(-5), and 5.1 × 10(-5) cases per year, respective ly. In populations with high susceptibility, the estimated median number of cases per year was 2.7 × 10(-7) (perinatal, i.e., pregnant women and their fetuses or newborns) and 1.4 × 10(-6) (elderly) for milk purchased from bulk tanks, 1.5 × 10(-5 ) (perinatal) and 7.8 × 10(-5) (elderly) for milk from farm stores, and 2.1 × 10(-5) (perinatal) and 1.0 × 10(-4) (elderly) for milk from retail. For raw milk consumed on farms, the median number of listeriosis cases was 1.4 × 10(-7) cases per year. A greater risk of listeriosis was associated with consumption of raw milk obtained from retail and farm stores as compared with milk obtained from bulk tanks. This was likely due to additional time-temperature combination steps in the retail and farm store models, which increased the chances for growth of L. monocytogenes in raw milk. A close relationship between prevalence of L. monocytogenes in raw milk and the values of disease incidence was observed. Hence, a reduction in the number of cases per year in all populations was observed when a raw milk-testing program was in place, especially when routine testing and recalling of milk was conducted.

Rectoanal junction colonization of feedlot cattle by Escherichia coli O157:H7 and its association with supershedders and excretion dynamics.

Feedlot cattle were observed for fecal excretion of and rectoanal junction (RAJ) colonization with Escherichia coli O157:H7 to identify potential "supershedders." RAJ colonization and fecal excretion prevalences were correlated, and E. coli O157:H7 prevalences and counts were significantly greater for RAJ samples. Based on a comparison of RAJ and fecal ratios of E. coli O157:H7/E. coli counts, the RAJ appears to be preferentially colonized by the O157:H7 serotype. Five supershedders were identified based on persistent colonization with high concentrations of E. coli O157:H7. Cattle copenned with supershedders had significantly greater mean pen E. coli O157:H7 RAJ and fecal prevalences than noncopenned cattle. Cumulative fecal E. coli O157:H7 excretion was also significantly higher for pens housing a supershedder. E. coli O157:H7/E. coli count ratios were higher for supershedders than for other cattle, indicating greater proportional colonization. Pulsed-field gel electrophoresis analysis demonstrated that isolates from supershedders and copenned cattle were highly related. Cattle that remained negative for E. coli O157:H7 throughout sampling were five times more likely to have been in a pen that did not house a supershedder. The data from this study support an association between levels of fecal excretion of E. coli O157:H7 and RAJ colonization in pens of feedlot cattle and suggest that the presence of supershedders influences group-level excretion parameters. An improved understanding of individual and population transmission dynamics of E. coli O157:H7 can be used to develop preslaughter- and slaughter-level interventions that reduce contamination of the food chain.

Comparison of cultures from rectoanal-junction mucosal swabs and feces for detection of Escherichia coli O157 in dairy heifers.

Fecal culture for Escherichia coli O157:H7 was compared to rectoanal mucosal swab (RAMS) culture in dairy heifers over a 1-year period. RAMS enrichment culture was as sensitive as fecal culture using immunomagnetic separation (IMS) (P = 0.98, as determined by a chi-square test). RAMS culture is less costly than fecal IMS culture and can yield quantitative data.

Increasing prevalence of Campylobacter jejuni in feedlot cattle through the feeding period.

The prevalence of Campylobacter jejuni in commercial feedlot cattle was monitored throughout the feeding period by repeated bacteriologic culture of feces. Fecal pats (n = 10) in 20 feedlot pens were sampled at 2-weeks interval beginning at entry into the feedlot and continuing until slaughter. The least-squares mean C. jejuni prevalence increased from 1.6% at the first sampling to 61.3% at the final sampling just prior to slaughter. Diverse C. jejuni pulsed-field gel electrophoresis macrorestriction profiles (MRP) were identified among the cattle isolates, but five prevalent MRP and minor variants accounted for >80% of all typed isolates. Chlorination of the water supplied to the water troughs of half of the pens did not affect C. jejuni prevalence in the cattle. Overall, the least-squares mean C. jejuni prevalences were 45.6 and 43.6% in chlorinated and nonchlorinated feedlot pens, respectively. The results of this study demonstrate apparent transmission of C. jejuni among feedlot cattle during the feeding period, unaffected by water chlorination, resulting in a high prevalence of C. jejuni excretion by cattle approaching slaughter.

Multidrug-resistant Salmonella Typhimurium in four animal facilities.

In 1999 and 2000, 3 state health departments reported 4 outbreaks of gastrointestinal illness due to Salmonella enterica serotype Typhimurium in employees, clients, and client animals from 3 companion animal veterinary clinics and 1 animal shelter. More than 45 persons and companion animals became ill. Four independent investigations resulted in the testing of 19 human samples and >200 animal samples; 18 persons and 36 animals were culture-positive for S. Typhimurium. One outbreak was due to multidrug-resistant S. Typhimurium R-type ACKSSuT, while the other 3 were due to multidrug-resistant S. Typhimurium R-type ACSSuT DT104. This report documents nosocomial transmission of S. Typhimurium and demonstrates that companion animal facilities may serve as foci of transmission for salmonellae between animals and humans if adequate precautions are not followed.

Prevalence of Fecal Salmonella Shedding by Cull Dairy Cattle Marketed in Washington State.

On nine occasions over a 1-year period, cull dairy cattle (n = 1,289) at four saleyards and one abattoir in Washington State were surveyed for salmonellae shedding by bacterial culture of duplicate rectal swabs, 251 single fecal samples and duplicate rectal swabs, and 225 mesenteric lymph node and duplicate rectal swabs. Using parallel selective enrichment and brilliant green media, salmonellae were isolated from six cattle, from rectal swabs only, and consisted of five isolates of Salmonella typhimurium and one of Salmonella dublin . In the two rectal swab- positive cattle for which mesenteric nodes were also sampled, 1-g samples of the nodes were negative. The rate of fecal shedding of cull dairy cattle marketed in Washington State as detected by this methodology is estimated to be 4.6 per 1,000 head (95% confidence interval of 1.9 to 10.6) and is expected to be no higher than 9.2 per 1,000 head if larger fecal samples were used. Based on antibiograms and plasmid profiles, none of the six isolates matched any of the 280 previously characterized isolates of the same serotypes obtained from human salmonellosis cases 2 years previously by the State health department. Four of the five S. typhimurium isolates matched three of 215 S. typhimurium isolates obtained from bovine submissions to the State's animal disease diagnostic laboratory and by a field animal disease investigation unit. The S. dublin isolate matched 17 of the 165 S. dublin isolates in those submissions. In this State, swab sampling of cull dairy cows at the point of first market concentration does not appear to be an efficient method of detecting salmonellae- infected dairy herds.

Comparison of shiga-toxigenic Escherichia coli prevalences among dairy, feedlot, and cow-calf herds in Washington State.

Shiga-toxigenic Escherichia coli (STEC) strains were isolated from 7.4% of 1,440 fecal and farm environmental samples. Shiga toxin gene and STEC prevalences were significantly associated with animal production type and season. A range of serogroups were identified. Nine percent of isolates possessed all three principal virulence markers: stx(2), eae, and ehx.

Survival of Salmonella enterica in freshwater and sediments and transmission by the aquatic midge Chironomus tentans (Chironomidae: Diptera).

Survival of a nalidixic acid-resistant strain of Salmonella enterica serovar Typhimurium mr-DT-104 in water and sediments was tested using artificially contaminated aquaria. Water samples remained culture positive for salmonella for up to 54 days. Sediment samples were culture positive up to 119 days. In addition, potential mechanisms for spreading salmonella in the environments by chironomid larvae and adults were tested. We evaluated the acquisition of mr-DT-104 by chironomids from contaminated aquatic sediments and subsequent spread to uncontaminated sediments. Larval chironomids raised in contaminated sediments became culture positive, and the bacteria were carried over to adults after emergence. Contamination of clean sediments by chironomid larvae was not demonstrated. These findings clearly suggest that mr-DT-104 serovar organisms can survive in aquatic sediments for at least several months. Uptake of salmonellae by chironomid larvae and adults suggests that they are possible vectors of mr-DT-104 in both aquatic and terrestrial environments, although the role of larval defecation in movement of bacteria to new sediments was not demonstrated.

Rectoanal mucosal swab culture is more sensitive than fecal culture and distinguishes Escherichia coli O157:H7-colonized cattle and those transiently shedding the same organism.

Enrichment and direct (nonenrichment) rectoanal mucosal swab (RAMS) culture techniques were developed and compared to traditional fecal culture for the detection of Escherichia coli O157:H7 in experimentally infected and naturally infected cattle. Holstein steers (n = 16) orally dosed with E. coli O157:H7 were sampled after bacterial colonization starting 15 days postinoculation. Enrichment RAMS cultures (70.31% positive) were more sensitive than enrichment fecal cultures with 10 g of feces (46.88% positive) at detecting E. coli O157:H7 (P < 0.01). Holstein bull calves (n = 15) were experimentally exposed to E. coli O157:H7 by penning them with E. coli O157:H7-positive calves. Prior to bacterial colonization (1 to 14 days postexposure), enriched fecal cultures were more sensitive at detecting E. coli O157:H7 than enriched RAMS cultures (P < 0.01). However, after colonization (40 or more days postexposure), the opposite was true and RAMS culture was more sensitive than fecal culture (P < 0.05). Among naturally infected heifers, enriched RAMS or fecal cultures were equally sensitive (P = 0.5), but direct RAMS cultures were more sensitive than either direct or enriched fecal cultures at detecting E. coli O157:H7 (P < 0.01), with 25 of 144, 4 of 144, and 10 of 108 samples, respectively, being culture positive. For both experimentally and naturally infected cattle, RAMS culture predicted the duration of infection. Cattle transiently shedding E. coli O157:H7 for <1 week were positive by fecal culture only and not by RAMS culture, whereas colonized animals (which were culture positive for an average of 26 days) were positive early on by RAMS culture. RAMS culture more directly measured the relationship between cattle and E. coli O157:H7 infection than fecal culture.