Comparison of Established PCR Assays for Accurate Identification of Campylobacter jejuni and Campylobacter coli

Evaluation of a rapid fluorescence immunoassay for detecting Campylobacter antigens in stool samples

BACKGROUND

The species most frequently causing campylobacteriosis are Campylobacter jejuni and Campylobacter coli, followed by Campylobacter fetus, Campylobacter upsaliensis, and Campylobacter lari. Although polymerase chain reaction (PCR) can be used to detect Campylobacter DNA in stool samples, PCR assays are often validated for C. jejuni and C. coli only, and coproculture results can take several days to receive. For laboratories that do not have access to PCR technology, rapid antigen tests can be of the utmost importance for early diagnosis of the disease. We evaluated the performance of the Sofia Campylobacter Fluorescence Immunoassay (SCFIA) for rapid detection of Campylobacter antigens in stool.

METHODS

In total, 94 frozen and 205 fresh stool specimens were included in retrospective and prospective evaluations, respectively. The linearity of the assay and its limit of detection for different Campylobacter species was evaluated using serial dilutions. Cross reactivity to phylogenetically related species was also investigated. The PCR results from the BD MAX Enteric Panel were considered the gold standard.

RESULTS

The sensitivity of the SCFIA was 97.87% and 96.88% in retrospective and prospective evaluations, respectively. The specificity was 98.84%. The assay exhibited high linearity in serial dilutions for C. coli, C. jejuni, C. armoricus, C. ornithocola, C. lari, and C. upsaliensis, with correlation coefficients of 0.991-0.999, whereas C. fetus was not detected. No cross-reactivity was detected for Aliarcobacter butzleri, Helicobacter cinaedi, or Helicobacter pullorum. The minimum concentration for a positive result at the assay-specific cut-off was 4-17 million CFU/mL. The limit of detection ranged from 106 to 107 CFU/mL.

CONCLUSION

SCFIA results are highly correlated with PCR results, with no cross-reactivity with phylogenetically related species. The linear correlation between fluorescence and CFU/mL results was strong. The assay's ability to detect antigens of various Campylobacter species can aid early diagnosis. However, the inability to detect C. fetus must be considered.

Expression of recombinant Omp18 and MOMP of Campylobacter jejuni and the determination of their suitability as antigens for serological diagnosis of campylobacteriosis in animals

Background and Aim

Campylobacteriosis causes gastrointestinal tract lesions in adults and children and may result in severe complications. The primary sources of infection are infected animals and animal products. Immunochemical methods effectively diagnose intestinal infections but require highly specific antigens to detect their antibodies. This study aimed to obtain two recombinant immunogenic antigens of Campylobacter jejuni, an outer membrane protein with a molecular weight of 18 kDa (Omp18) and the major outer membrane protein (MOMP) with a molecular weight of 45 kDa, and evaluate their suitability for the serological diagnosis of campylobacteriosis using immunochromatographic assay (ICA).

Materials and Methods

The C. jejuni Omp18 and MOMP gene sequences were synthesized de novo (Macrogen, Korea) and cloned into the pET32 expression plasmid. Using these genetic constructs, electrocompetent cells of the Escherichia coli BL21 strain were transformed and cultured under various conditions. Antigens were purified and refolded using metal affinity chromatography. The properties of the purified proteins were studied by western blotting, liquid chromatography with tandem mass spectrometry, and enzyme-linked immunosorbent assay (ELISA).

Results

We developed two recombinant E. coli BL21 cells producing rOmp18 and Recombinant MOMP (rMOMP) antigens with molecular weights of 36 and 64 kDa, respectively. Amino acid sequence analysis of the obtained antigens showed complete homology with the reference sequences in the PubMed NCBI database. Western blotting using positive-control sera demonstrated the specificity of the recombinant antigens. The results of ELISA with 94 bovine sera showed the interaction of recombinant antigens with specific antibodies.

Conclusion

The obtained rOmp18 and rMOMP antigens can detect antibodies in the serum of infected or recovered animals and can be used to develop ICA.

Agents of Campylobacteriosis in Different Meat Matrices in Brazil

We aimed to identify the prevalence of thermophilic species of Campylobacter in meats of different species available on the Brazilian commercial market and to determine the genetic diversity, antimicrobial resistance and virulence potential of the isolates. A total of 906 samples, including chicken, beef and pork carcasses and chicken and beef livers, were purchased in retail outlets, and prevalences of 18.7% (46/246), 3.62% (5/138), 10.14% (14/138), 3.62% (5/138) and 4.47% (11/132), respectively, were identified, evidencing the dissemination of genotypes in the main producing macro-regions. Of all isolates, 62.8% were classified as multidrug resistant (MDR), with resistance to amoxicillin-clavulanate (49.4%), tetracycline (51.8%) and ciprofloxacin (50.6%) and co-resistance to macrolides and fluoroquinolones (37.1%). Multivirulent profiles were identified mainly in isolates from chicken carcasses (84.8%), and the emergence of MDR/virulent strains was determined in pork isolates. All isolates except those from chicken carcasses showed a high potential for biofilm formation (71.4% luxS) and consequent persistence in industrial food processing. For chicken carcasses, the general virulence was higher in C. jejuni (54.3%), followed by C. coli (24%) and Campylobacter spp. (21.7%), and in the other meat matrices, Campylobacter spp. showed a higher prevalence of virulence (57.2%). The high rates of resistance and virulence reinforce the existence of strain selection pressure in the country, in addition to the potential risk of strains isolated not only from chicken carcasses, but also from other meat matrices.

A Cutoff Determination of Real-Time Loop-Mediated Isothermal Amplification (LAMP) for End-Point Detection of Campylobacter jejuni in Chicken Meat

Campylobacter jejuni is one of the leading causes of foodborne illness worldwide. C. jejuni is commonly found in poultry. It is the most frequent cause of contamination and thus resulting in not only public health concerns but also economic impacts. To test for this bacterial contamination in food processing plants, this study attempted to employ a simple and rapid detection assay called loop-mediated isothermal amplification (LAMP). The best cutoff value for the positive determination of C. jejuni calculated using real-time LAMP quantification cycle (Cq) was derived from the receiver operating characteristic (ROC) curve modeling. The model showed an area under curve (AUC) of 0.936 (95% Wald CI: 0.903–0.970). Based on Youden’s J statistic, the optimal cutoff value which had the highest sensitivity and specificity from the model was calculated as 18.07. The LAMP assay had 96.9% sensitivity, 95.8% specificity, and 93.9 and 97.9% positive and negative predictive values, respectively, compared to a standard culture approach for C. jejuni identification. Among all non-C. jejuni strains, the LAMP assay gave each of 12.5% false-positive results to C. coli and E. coli (1 out of 8 samples). The assay can detect C. jejuni at the lowest concentration of 103 CFU/mL. Our results suggest a preliminary indicator for the application of end-point LAMP assays, such as turbidity and UV fluorescence tests, to detect C. jejuni in field operations. The LAMP assay is an alternative screening test for C. jejuni contamination in food samples. The method provides a rapid detection, which requires only 9 min with a cutoff value of Cq. We performed the extraction of DNA from pure cultures and the detection of C. jejuni using the LAMP assay within 3 h. However, we were not able to reduce the time for the process of enrichment involved in our study. Therefore, we suggest that alternative enrichment media and rapid DNA extraction methods should be considered for further study. Compared to other traditional methods, our proposed assay requires less equipment and time, which is applicable at any processing steps in the food production chain.

New Developments in PCR-Based Diagnostics for Bacterial Pathogens Causing Gastrointestinal Infections-A Narrative Mini-Review on Challenges in the Tropics

The application of modern PCR approaches for the diagnosis of bacterial gastrointestinal pathogens is on the rise due to their rapidly available results combined with high sensitivity. While multiple studies describe the ongoing implementation of this technique for routine diagnostic purposes in laboratories in Western industrialized countries, reports on successful and also sustainable respective approaches in resource-poor tropical settings are still scarce. In order to shed light on potential reasons for this marked discrepancy, this narrative review summarizes identified challenges for the application of diagnostic PCR targeting bacterial gastrointestinal pathogens from stool samples in the tropics. The identified and discussed issues comprise the lack of generally accepted definitions for (1) minimum standards regarding sample acquisition, storage and transport time for diagnostic PCR analyses in the tropics, (2) nucleic acid extraction standards allowing an optimum detection of all types of pathogens which may be responsible for gastroenteritis in the tropics, (3) validation standards to ensure comparable quality of applied diagnostic assays, and (4) cut-offs for a reliable discrimination of infection and mere colonization in areas where semi-immunity due to repeated exposition associated with poor hygiene conditions has to be expected. Further implementation research is needed to solve those issues.

Evaluation of CAMPYLOBACTER QUIK CHEK™ rapid membrane enzyme immunoassay to detect Campylobacter spp. antigen in stool samples

Campylobacter spp. enteritis is the most frequent bacterial enteritis in both adults and children and is sometimes a source of severe complications. Its diagnosis by culture suffers from a lack of sensitivity and delays the result, preventing an early initiation of optimal antibiotic therapy in some cases. Our aim was to test a new rapid immuno-enzymatic method for Campylobacter spp. diagnosis in comparison to a composite reference standard (CRS). Stool samples from the French National Reference Center for Campylobacter and Helicobacter were tested with the CAMPYLOBACTER QUIK CHEK™ (Abbott). The CRS used to consider a case positive for Campylobacter spp. was a positive culture and, in case of a negative culture, a positive result obtained with both an ELISA and a molecular test. One hundred and eight stools were included: 53 were positive according to the CRS. If performed alone, culture would have missed 5 cases which the CAMPYLOBACTER QUIK CHEK™ detected. Finally, the CAMPYLOBACTER QUIK CHEK™ showed a sensitivity of 96.2% and a specificity of 94.5% and is relevant for clinical practice. Given the characteristics of the new method, it can be used as a screening method for Campylobacter spp. detection.

Comparison of two commercial and one in-house real-time PCR assays for the diagnosis of bacterial gastroenteritis

Introduction

The aim of the study was a comparative evaluation of in-house real-time PCR and commercial real-time PCR (Fast Track Diagnostics (FTD), ampliCube/Mikrogen) targeting enteropathogenic bacteria from stool in preparation of Regulation (EU) 2017/746 on in vitro diagnostic medical devices.

Methods

Both 241 stool samples from patients and 100 samples from German laboratory control schemes (“Ringversuche”) were used to comparatively assess in-house real-time PCR, the FTD bacterial gastroenteritis kit, and the ampliCube gastrointestinal bacterial panels 1&2 either with the in-house PCRs as gold standard and as a test comparison without gold standard applying latent class analysis. Sensitivity, specificity, intra- and inter-assay variation and Cohen’s kappa were assessed.

Results

In comparison with the gold standard, sensitivity was 75–100% for strongly positive samples, 20–100% for weakly positive samples, and specificity ranged from 96 to 100%. Latent class analysis suggested that sensitivity ranges from 81.2 to 100% and specificity from 58.5 to 100%. Cohen’s kappa varied between moderate and nearly perfect agreement, intra- and inter-assay variation was 1–3 to 1–4 Ct values.

Conclusion

Acceptable agreement and performance characteristics suggested replaceability of the in-house PCR assays by the commercial approaches.

DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables

The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.