Validation of a PCR-based method for detection of food-borne thermotolerant campylobacters in a multicenter collaborative trial

Campylobacter presence on Dutch broiler farms and associated risk factors

Campylobacter is the most reported zoonotic pathogen in humans in the European Union. Poultry is a major source of human infection with Campylobacter. Although many studies are done on the presence of Campylobacter in broilers and theoretically effective control measures are known, their relative importance at broiler farms remains poorly understood. Therefore, the aim of this study was to investigate the presence of Campylobacter on selected broiler farms in the Netherlands, to determine the moment of introduction, and associated risk factors. A longitudinal study on 25 broiler farms was carried out between June 2017 and December 2020. Fecal samples were collected weekly from 43 broiler houses. In total 497 flocks were sampled. Putative variables on flock and farm characteristics for a risk factor analysis were gathered through questionnaires. Risk factors associated with the presence of Campylobacter in a broiler flock were determined using regression models. In total 30% of the flocks included in the study were positive for Campylobacter. Factors associated with presence of Campylobacter at slaughter age included: season, mowing lawns and presence of agricultural side activities. While summer/autumn and mowing lawns were associated with an increase in Campylobacter presence in flocks, the farmer having agricultural side activities other than poultry production was associated with a decrease. Analysis of the age at which flocks first tested Campylobacter positive revealed that slower growing breeds became positive on average 1 wk later compared to regular growers. This study revealed a delayed introduction of Campylobacter in slower grower vs. regular grower broiler flocks reared indoors. In addition, it confirmed importance of season as major risk factor. The relevance of mowing and preceding positive flocks as risk factors needs further investigation.

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

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

PCR-assisted impedimetric biosensor for colibactin-encoding pks genomic island detection in E. coli samples

A fast PCR-assisted impedimetric biosensor was developed for the selective detection of the clbN gene from the polyketide synthase (pks) genomic island in real Escherichia coli samples. This genomic island is responsible for the production of colibactin, a harmful genotoxin that has been associated with colorectal cancer. The experimental protocol consisted of immobilizing the designated forward primer onto an Au electrode surface to create the sensing probe, followed by PCR temperature cycling in blank, positive, and negative DNA controls. Target DNA identification was possible by monitoring changes in the system’s charge transfer resistance values (R_ct) before and after PCR treatment through electrochemical impedance spectroscopy (EIS) analysis. Custom-made, flexible gold electrodes were fabricated using chemical etching optical lithography. A PCR cycle study determined the optimum conditions to be at 6 cycles providing fast results while maintaining a good sensitivity. EIS data for the DNA recognition process demonstrated the successful distinction between target interaction resulting in an increase in resistance to charge transfer (R_ct) percentage change of 176% for the positive DNA control vs. 21% and 20% for the negative and non-DNA-containing controls, respectively. Results showed effective fabrication of a fast, PCR-based electrochemical biosensor for the detection of pks genomic island with a calculated limit of detection of 17 ng/μL.

Environmental monitoring of waterborne Campylobacter: evaluation of the Australian standard and a hybrid extraction-free MPN-PCR method

Campylobacter is the leading agent of diarrheal disease worldwide. This study evaluates a novel culture-PCR hybrid (MPN-PCR) assay for the rapid enumeration of Campylobacter spp. from estuarine and wastewater systems. To first evaluate the current, culture-based, Australian standard, an inter-laboratory study was conducted on 69 subsampled water samples. The proposed Most-Probable Number (MPN)-PCR method was then evaluated, by analysing 147 estuarine samples collected over a 2 year period. Data for 14 different biological, hydrological and climatic parameters were also collated to identify pathogen-environment relationships and assess the potential for method specific bias. The results demonstrated that the intra-laboratory performance of the MPN-PCR was superior to that of AS/NZS (σ = 0.7912, P < 0.001; κ = 0.701, P < 0.001) with an overall diagnostic accuracy of ~94%. Furthermore, the analysis of both MPN-PCR and AS/NZS identified the potential for the introduction of method specific bias during assessment of the effects of environmental parameters on Campylobacter spp. numbers.

Evaluation of anatomically designed flocked rectal swabs for molecular detection of enteric pathogens in children admitted to hospital with severe gastroenteritis in Botswana

Two-hundred eighty matched bulk stool and anatomically designed flocked rectal swab samples were collected from children admitted to the hospital with acute diarrhea in Botswana. Their parents were asked about the acceptability of the swab collection method compared with bulk stool sampling. All samples underwent identical testing with a validated 15-target (9 bacterial, 3 viral, and 3 parasite) commercial multiplex PCR assay. The flocked swabs had a 12% higher yield for bacterial pathogen targets (241 versus 212; P = 0.003) compared with that of stool samples, as well as similar yields for viral targets (110 versus 113; P = 0.701) and parasite targets (59 versus 65; P = 0.345). One hundred sixty-four of the flocked swab-stool pairs were also tested with separate laboratory-developed bacterial and viral multiplex assays, and the flocked rectal swabs had a performance that was similar to that seen with commercial assay testing. Almost all parents/guardians found the swabs acceptable. Flocked rectal swabs significantly facilitate the molecular diagnosis of diarrheal disease in children.

Evaluation of MeningoFinder, a novel multiplex ligation-dependent probe amplification assay for simultaneous detection of six virus species causing central nervous system infections

A multiplex ligation-dependent probe amplification assay for simultaneous detection of six virus species was developed and tested on clinical cerebrospinal fluid (CSF) samples. The assay, termed MeningoFinder, showed an accordance of 97%, concordance of 96%, interlaboratory sensitivity of 90%, and interlaboratory specificity of 94% compared to PCRs.

A collaborative study on a Nordic standard protocol for detection and enumeration of thermotolerant Campylobacter in food (NMKL 119, 3. Ed., 2007)

A Nordic standard protocol for detection and enumeration of thermotolerant Campylobacter in food has been elaborated (NMKL 119, 3. Ed., 2007). Performance and precision characteristics of this protocol were evaluated in a collaborative study with participation of 14 laboratories from seven European countries. The laboratories performed qualitative, semi-quantitative and quantitative analyses on samples of chicken meat, cut lettuce, and milk artificially inoculated with different concentrations including blank duplicates of one strain of Campylobacter coli (SLV-271) and one strain of Campylobacter jejuni (SLV-542). Expected concentrations (95% C.I.) (cfu g(-1) or ml(-1)) of both strains in matrices were 0.6-1.4 and 23-60 for qualitative detection, and 0.6-1.4; 23-60; and 420-1200 for semi-quantitative detection. For quantitative determination, the expected concentrations of C. jejuni/C. coli were 420-1200/580-1100; 2100-6000/6300-11,000; and 4100-11,000/53,000-97,000 cfu g(-1) or ml(-1). The qualitative and semi-quantitative techniques resulted in comparable detection. The overall specificity and sensitivity of the detection techniques was 98.6% (95% C.I.: 95.1-99.8%) and 82.8% (C.I.: 78.4-86.6%), respectively. The sensitivity was not influenced by food matrix (P=0.359), but was significantly lower for C. coli compared to C. jejuni (P=0.007) and for concentrations below 1.4 cfu g(-1) (P<0.001). The detection techniques were therefore only considered satisfactory for detection of Campylobacter concentrations above approximately 25 cfu g(-1) for all matrices tested, which was supported by calculation of values for accordance, concordance, and concordance odds ratio. No statistical difference was found between enumerations obtained by the semi-quantitative and quantitative techniques for comparable concentrations of Campylobacter (420-1200 cfu g(-1) or cfu ml(-1)) (P=0.104). Both techniques underestimated concentrations of thermotolerant Campylobacter in milk. The semi-quantitative technique estimated low inoculation levels of Campylobacter more correctly than the high inoculation levels. Counts obtained on the two selective plating media, Abeyta-Hunt-Bark agar added to it 0.1% triphenyl tetrazolium chloride and modified charcoal cephoperazone desoxycholate agar were not significantly different (P=0.143). Expressed as an absolute difference between log(10)-transformed results, the overall values for repeatability (r) and reproducibility (R) were r=log(10) 0.43 and R=log(10) 1.99, respectively. By omitting results from laboratories with high level of variability in results, R was reduced to log(10) 1.88. We suggest that the poor detection of low numbers, the underestimation in milk samples, and the large variation between laboratories can be explained by the general difficulties in handling Campylobacter. In conclusion, NMKL 119, 3. Ed., 2007, is regarded as an acceptable protocol for detection of thermotolerant Campylobacter at concentrations above 25 cfu g(-1) and also for enumeration of thermotolerant Campylobacter in chicken meat.

Campylobacters as zoonotic pathogens: a food production perspective

Campylobacters remain highly important zoonotic pathogens worldwide which infect an estimated 1% of the population of Western Europe each year. Certain campylobacters are also important in infections of animals, particularly of the reproductive tract, and some are involved in periodontal disease. This paper focuses, however, on the two species which are most important in food-borne infections of humans, Campylobacter (C.) jejuni and C. coli. Infection with these campylobacters is serious in its own right but can also have long-term sequelae such as reactive arthritis and Guillain-Barré syndrome. The pathogens are ubiquitous in nature and in domestic animals and, as a consequence, are found frequently in the environment and on many raw foods, of both plant and animal origin and bacterial numbers can be very high on certain key foods like raw poultry meat. Although all commercial poultry species can carry campylobacters, the risk is greater from chicken because of the high levels of consumption. Campylobacters are relatively 'new' zoonotic pathogens as routine culture from clinical specimens only became possible in the late 1970s. As a consequence there is much that still needs to be understood about the behaviour and pathogenicity of these highly important bacteria. In particular, and from a food industry/food safety perspective, it is important to better understand the behaviour of C. jejuni and C. coli in the food production environment, and how this affects their ability to survive certain food production processes. There is a belief that campylobacters are much more sensitive to hostile conditions than either salmonellas or Escherichia coli. Much of data to support this view have been derived from laboratory experiments and may not fully represent the natural situation. Studies are showing that campylobacters may be more robust than previously thought and thus may represent a greater challenge to food safety. We recommend that research is undertaken to better understand how campylobacters behave in the food chain and how responses to relevant conditions affect their ability to survive processing and their virulence. There is also a need to better understand the reasons why campylobacters are capable of frequent change, particularly in the expression of surface antigens.

Diagnostic PCR: validation and sample preparation are two sides of the same coin

Increased use of powerful PCR technology for the routine detection of pathogens has focused attention on the need for international validation and preparation of official non-commercial guidelines. Bacteria of epidemiological importance should be the prime focus, although a "validation infrastructure" once established could easily be adapted for PCR-based detection of viruses and parasites. The aim of standardization should be the widespread adoption of diagnostic PCR for routine pathogen testing. European experience provides the impetus for realization of this vision through preparation of quantitative reference DNA material and reagents, production of stringent protocols and tools for thermal cycler performance testing, uncomplicated sample preparation techniques, and extensive ring trials for assessment of the efficacy of selected matrix/pathogen detection protocols.