Use of a LightCycler gyrA mutation assay for identification of ciprofloxacin-resistant Campylobacter coli

A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars

The species Arcobacter cryaerophilus is found in many food products of animal origin and is the dominating species in wastewater. In addition, it is associated with cases of farm animal and human infectious diseases,. The species embraces two subgroups i.e., 1A (LMG 24291^T = LMG 9904^T) and 1B (LMG 10829) that can be differentiated by their 16S rRNA-RFLP pattern. However, some authors, on the basis of the shared intermediate levels of DNA-DNA hybridization, have suggested abandoning the subgroup classification. This contradiction indicates that the taxonomy of this species is not yet resolved. The objective of the present study was to perform a taxonomic evaluation of the diversity of A. cryaerophilus. Genomic information was used along with a Multilocus Phylogenetic Analysis (MLPA) and phenotypic characterization on a group of 52 temporally and geographically dispersed strains, coming from different types of samples and hosts from nine countries. The MLPA analysis showed that those strains formed four clusters (I–IV). Values of Average Nucleotide Identity (ANI) and in silico DNA-DNA Hybridization (isDDH) obtained between 13 genomes representing strains of the four clusters were below the proposed cut-offs of 96 and 70%, respectively, confirming that each of the clusters represented a different genomic species. However, none of the evaluated phenotypic tests enabled their unequivocal differentiation into species. Therefore, the genomic delimited clusters should be considered genomovars of the species A. cryaerophilus. These genomovars could have different clinical importance, since only the cluster I included strains isolated from human specimens. The discovery of at least one stable distinctive phenotypic character would be needed to define each cluster or genomovar as a different species. Until then, we propose naming them “A. cryaerophilus gv. pseudocryaerophilus” (Cluster I = LMG 10229^T), “A. cryaerophilus gv. crypticus” (Cluster II = LMG 9065^T), “A. cryaerophilus gv. cryaerophilus” (Cluster III = LMG 24291^T) and “A. cryaerophilus gv. occultus” (Cluster IV = LMG 29976^T).

Prevalence of Genetic Determinants and Phenotypic Resistance to Ciprofloxacin in Campylobacter jejuni from Lithuania

Recently, the number of reports on isolation of ciprofloxacin resistant Campylobacter jejuni has increased worldwide. The aim of this study was to determine the prevalence of resistance to ciprofloxacin and its genetic determinants among C. jejuni isolated from humans (n = 100), poultry products (n = 96) and wild birds (n = 96) in Lithuania. 91.4% of the C. jejuni isolates were phenotypically resistant to ciprofloxacin. DNA sequence analyses of the gyrA gene from 292 isolates revealed that a change in amino acid sequence, Thr86Ile, was the main substition conferring resistance to ciprofloxacin. This change was significantly associated with isolates from poultry products (P < 0.05) and humans (P < 0.05). A total of 26.7% of C. jejuni isolates from human (n = 47), poultry products (n = 30) and wild bird (n = 1), had a mutation from Ser at position 22, and six had an additional mutation from Ala at position 39. Eight isolates from poultry and two isolates from human, corresponding to 67.0% of isolates with MICs ≥128 μg/ml, showed missense mutations Thr86Ile (ACA → ATA) and Ser22Gly (AGT → GGT) together, whereas isolates without these mutations showed lower MIC values (from 4 to 64 μg/ml). Two hundred forty-five C. jejuni isolates showed one or more silent mutations, and 32.4% of examined isolates possessed six silent mutations. In addition to the ciprofloxacin resistant isolates harboring only Thr86Ile point mutation (110 isolates), the current study identified resistant isolates (n = 101) harboring additional point mutations (Ser22Gly, Ala39Ser, Arg48Lys, Thr85Ala Ala122Ser, Glu136Asp, Vall49Ile), and strains (n = 57) having only Glu136Asp point mutation. The study highlight the potential public health problem with elevated ciprofloxacin resistance in Campylobacters from poultry meat, wild birds and humans, and the need for extensive surveillance enabling to follow changes of antimicrobial resistance development in this species.

The other Campylobacters: Not innocent bystanders in endemic diarrhea and dysentery in children in low-income settings

Background

Campylobacter is one of the main causes of gastroenteritis worldwide. Most of the current knowledge about the epidemiology of this food-borne infection concerns two species, C. coli and C. jejuni. Recent studies conducted in developing countries and using novel diagnostic techniques have generated evidence of the increasing burden and importance of other Campylobacter species, i.e. non-C. coli/jejuni. We performed a nested case-control study to compare the prevalence of C. coli/jejuni and other Campylobacter in children with clinical dysentery and severe diarrhea as well as without diarrhea to better understand the clinical importance of infections with Campylobacter species other than C. coli/jejuni.

Methodology/Principal findings

Our nested case-control study of 439 stool samples included dysenteric stools, stools collected during severe diarrhea episodes, and asymptomatic stools which were systematically selected to be representative of clinical phenotypes from 9,160 stools collected during a birth cohort study of 201 children followed until two years of age. Other Campylobacter accounted for 76.4% of the 216 Campylobacter detections by qPCR and were more prevalent than C. coli/jejuni across all clinical groups. Other Campylobacter were also more prevalent than C. coli/jejuni across all age groups, with older children bearing a higher burden of other Campylobacter. Biomarkers of intestinal inflammation and injury (methylene blue, fecal occult test, myeloperoxidase or MPO) showed a strong association with dysentery, but mixed results with infection. MPO levels were generally higher among children infected with C. coli/jejuni, but Shigella-infected children suffering from dysentery recorded the highest levels (26,224 ng/mL); the lowest levels (10,625 ng/mL) were among asymptomatic children infected with other Campylobacter. Adjusting for age, sex, and Shigella infection, dysentery was significantly associated with C. coli/jejuni but not with other Campylobacter, whereas severe diarrhea was significantly associated with both C. coli/jejuni and other Campylobacter. Compared to asymptomatic children, children suffering from dysentery had a 14.6 odds of C. coli/jejuni infection (p-value < 0.001, 95% CI 5.5–38.7) but were equally likely to have other Campylobacter infections–odds ratio of 1.3 (0.434, 0.7–2.4). Children suffering from severe diarrhea were more likely than asymptomatic children to test positive for both C. coli/jejuni and other Campylobacter–OR of 2.8 (0.034, 1.1–7.1) and 1.9 (0.018, 1.1–3.1), respectively. Compared to the Campylobacter-free group, the odds of all diarrhea given C. coli/jejuni infection and other Campylobacter infection were 8.8 (<0.001, 3.0–25.7) and 2.4 (0.002, 1.4–4.2), respectively. Eliminating other Campylobacter in this population would eliminate 24.9% of the diarrhea cases, which is almost twice the population attributable fraction of 15.1% due to C. coli/jejuni.

Conclusions/Significance

Eighty-seven percent of the dysentery and 59.5% of the severe diarrhea samples were positive for Campylobacter, Shigella, or both, emphasizing the importance of targeting these pathogens to limit the impact of dysentery and severe diarrhea in children. Notably, the higher prevalence of other Campylobacter compared to C. coli/jejuni, their increasing burden during early childhood, and their association with severe diarrhea highlight the importance of these non-C. coli/jejuni Campylobacter species and suggest a need to clarify their importance in the etiology of clinical disease across different epidemiological contexts.

Campylobacter is a major public health concern in developed and developing countries. C. coli and C. jejuni have long been considered to be the major disease-causing species, and clinical microbiologic approaches target these two species. However, less selective diagnostic approaches have shown the increasing importance of other Campylobacter species (i.e. non-C. coli/jejuni). Our case-control study investigated the association between diarrhea, C. coli/jejuni, and other Campylobacter among 439 stool samples from 201 children in peri-urban communities in Loreto, Peru. Three quarters of the 216 Campylobacter detections were associated with other Campylobacter, whose prevalence increased with age and was greater than that of C. coli/jejuni in all age and clinical groups (dysentery, severe diarrhea, and asymptomatic). Despite their lower prevalence, C. coli/jejuni were more strongly associated with higher levels of myeloperoxidase, clinical dysentery, and the presence of leukocytes and blood in the stool compared to other Campylobacter. Other Campylobacter were equally likely as C. coli/jejuni to be detected in severe diarrhea cases–odds ratio of 1.9 (p-value = 0.018, 95% CI 1.1–3.1) and 2.8 (0.034, 1.1–7.1), respectively. Removing C. coli/jejuni in this population would eliminate 15.1% of diarrhea compared to 24.9% if other Campylobacter were eliminated.

Characterization of the emerging zoonotic pathogen Arcobacter thereius by whole genome sequencing and comparative genomics

Four Arcobacter species have been associated with human disease, and based on current knowledge, these Gram negative bacteria are considered as potential food and waterborne zoonotic pathogens. At present, only the genome of the species Arcobacter butzleri has been analysed, and still little is known about their physiology and genetics. The species Arcobacter thereius has first been isolated from tissue of aborted piglets, duck and pig faeces, and recently from stool of human patients with enteritis. In the present study, the complete genome and analysis of the A. thereius type strain LMG24486T, as well as the comparative genome analysis with 8 other A. thereius strains are presented. Genome analysis revealed metabolic pathways for the utilization of amino acids, which represent the main source of energy, together with the presence of genes encoding for respiration-associated and chemotaxis proteins. Comparative genome analysis with the A. butzleri type strain RM4018 revealed a large correlation, though also unique features. Furthermore, in silico DDH and ANI based analysis of the nine A. thereius strains disclosed clustering into two closely related genotypes. No discriminatory differences in genome content nor phenotypic behaviour were detected, though recently the species Arcobacter porcinus was proposed to encompass part of the formerly identified Arcobacter thereius strains. The report of the presence of virulence associated genes in A. thereius, the presence of antibiotic resistance genes, verified by in vitro susceptibility testing, as well as other pathogenic related relevant features, support the classification of A. thereius as an emerging pathogen.

Antimicrobial resistance in campylobacter: susceptibility testing methods and resistance trends

Most Campylobacter infections are self-limiting but antimicrobial treatment (e.g., macrolides, fluoroquinolones) is necessary in severe or prolonged cases. Susceptibility testing continues to play a critical role in guiding therapy and epidemiological monitoring of resistance. The methods of choice for Campylobacter recommended by the Clinical and Laboratory Standards Institute (CLSI) are agar dilution and broth microdilution, while a disk diffusion method was recently standardized by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Macrolides, quinolones, and tetracyclines are among the common antimicrobials recommended for testing. Molecular determination of Campylobacter resistance via DNA sequencing or PCR-based methods has been performed. High levels of resistance to tetracycline and ciprofloxacin are frequently reported by many national surveillance programs, but resistance to erythromycin and gentamicin in Campylobacter jejuni remains low. Nonetheless, variations in susceptibility observed over time underscore the need for continued public health monitoring of Campylobacter resistance from humans, animals, and food.

Detection of gyrA and gyrB mutations in Clostridium difficile isolates by real-time PCR

Fluoroquinolone (FQ)-resistance in Clostridium difficile has been associated with mutations in the quinolone-resistance determining region (QRDR) of gyr genes. In particular, the majority of resistant clinical isolates show mutations in codon 82 of gyrA or in codon 426 of gyrB. A real-time PCR method was developed to identify these mutations in FQ-resistant C. difficile strains. Twenty-one clinical isolates, selected as representative of the different gyr alleles known up to date, and 20 clinical isolates with unknown behavior towards FQs were used to validate the method. Each mutation was detected by real-time amplification followed by hybridization with two fluorescent probes designed with the sequence complementary to the wild-type sequences of gyr genes. The melting peak analysis of the probe-PCR product hybrid was performed on a LightCycler (Roche Diagnostic). Single and multiplex assays were performed with the same reaction conditions. In both cases, isolates showing mutations in gyr sequences had a well distinguished T(m) compared to that of isolates showing wild-type genes or silent mutated codons in the nucleotide region covered by probes. The results obtained indicate that this real-time PCR assay is a rapid, reproducible and accurate screening method of the predominant mutations determining FQ-resistance in C. difficile strains.

Differential effects of temperature on natural transformation to erythromycin and nalidixic acid resistance in Campylobacter coli

Campylobacter jejuni and Campylobacter coli are naturally competent, but limited information exists on the impact of environmental conditions on transformation. In this study, we investigated the impact of temperature and microaerobic versus aerobic atmosphere on transformation of C. coli to erythromycin and nalidixic acid resistance. Frequency of transformation was not significantly different between microaerobic (5 to 10% CO(2)) and aerobic conditions. However, C. coli was transformed to erythromycin resistance at a significantly higher frequency at 42 degrees C than at 25 degrees C (P < 0.05), and few or no transformants were obtained at 25 degrees C. In contrast, transformation to nalidixic acid resistance was highly efficient at both 42 degrees C and 25 degrees C and was similar or, at the most, fourfold higher at 42 degrees C than at 25 degrees C. DNase I treatment experiments suggested that steps both prior and subsequent to internalization of DNA were influenced by temperature in the case of transformation of C. coli to erythromycin resistance. However, the moderately increased (fourfold) frequency of transformation to nalidixic acid resistance at 42 degrees C compared to that at 25 degrees C was exclusively associated with steps prior to DNA internalization. These findings suggest that transformation to erythromycin resistance may be significantly more frequent in the gastrointestinal tract of hosts such as poultry (at 42 degrees C) than in other habitats characterized by lower temperatures, whereas transformation to nalidixic acid resistance may be highly efficient both within and outside the animal hosts.

Genotyping of benzimidazole-resistant and dicarboximide-resistant mutations in Botrytis cinerea using real-time polymerase chain reaction assays

Botrytis cinerea, an economically important gray mold pathogen, frequently exhibits multiple fungicide resistance. A fluorescence resonance energy transfer-based real-time polymerase chain reaction assay has been developed to detect benzimidazole- and dicarboximide-resistant mutations. Three benzimidazole-resistant mutations-(198)Glu to Ala (E198A), F200Y, and E198K-in beta-tubulin BenA were detected using a single set of fluorescence-labeled sensor and anchor probes by melting curve analysis. Similarly, three dicarboximide-resistant mutations-I365S, V368F plus Q369H, and Q369P-in the histidine kinase BcOS1 were successfully distinguished. Unassigned melting profiles in BenA genotyping assay resulted in the identification of a new benzimidazole-resistant BenA E198V mutation. This mutation conferred resistance to carbendazim as do E198A and E198K mutations. The isolates with BenA E198V mutation showed a negative cross-resistance to diethofencarb, but to a lesser extent than the E198A mutants. A survey of 210 B. cinerea field isolates revealed that most of benzimidazole-resistant isolates possessed the E198V or E198A mutation in the BenA gene, and the I365S mutation in the BcOS1 gene was also frequently observed in Japanese isolates. However, benzimidazole-resistant isolates with BenA F200Y or E198K mutations, which confer the diethofencarb-insensitive phenotype, were rare. Our BenA and BcOS1 genotyping is a rapid and reliable method that is suitable for monitoring the fungicide-resistant field population.

Quantification and differentiation of Campylobacter jejuni and Campylobacter coli in raw chicken meats using a real-time PCR method

Campylobacter species are one of the most common causes of bacterial diarrhea in humans worldwide. The consumption of foods contaminated with two Campylobacter species, C. jejuni and C. coli, is usually associated with most of the infections in humans. In this study, a rapid, reliable, and sensitive multiplex real-time quantitative PCR was developed for the simultaneous detection, identification, and quantification of C. jejuni and C. coli. In addition, the developed method was applied to the 50 samples of raw chicken meat collected from retail stores in Korea. C. jejuni and C. coli were detected in 88 and 86% of the samples by real-time quantitative PCR and the conventional microbiological method, respectively. The specificity of the primer and probe sets was confirmed with 30 C. jejuni, 20 C. coli, and 35 strains of other microbial species. C. jejuni and C. coli could be detected with high specificity in less than 4 h, with a detection limit of 1 log CFU/ml by the developed real-time PCR. The average counts (log CFU per milliliter) of C. jejuni or C. coli obtained by the conventional methods and by the real-time PCR assay were statistically correlated with a correlation coefficient (R2) between 0.73 and 0.78. The real-time PCR assay developed in this study is useful for screening for the presence and simultaneous differential quantification of C. jejuni and C. coli.

Campylobacter coli isolates derived from chickens in Senegal: Diversity, genetic exchange with Campylobacter jejuni and quinolone resistance

We used the multilocus sequence typing (MLST) method to study the genetic diversity of Campylobacter coli isolated from chickens in Senegal, and to check the presence of genetic exchange with Campylobacter jejuni. In addition, we assessed the resistance of the isolates to ciprofloxacin and nalidixic acid, and their gyrA sequences. MLST revealed a low level of diversity and the absence of lineages among C. coli isolates. In addition, an exchange of alleles with C. jejuni was found. Twenty percent of the ciprofloxacin-resistant isolates lacked mutations within the quinolone resistance-determining region (QRDR) of GyrA. There was no link between quinolone resistance and sequence type (ST).

Phenotypic and genotypic anti-microbial resistance profiles of campylobacters from untreated feedlot cattle and their environment

Anti-microbial resistance is an emerging public health issue. Farmed animals may act as reservoirs and potential sources of anti-microbial resistant Campylobacters. The aim of this study was to investigate the anti-microbial resistance profile of cattle and environmental Campylobacter isolates from normal untreated feedlot cattle, the role of the gyrA Thr-86-Ile mutation in ciprofloxacin-resistant Campylobacter jejuni isolates and the involvement of the tripartite CmeABC efflux system for multi-resistant C. jejuni isolates. The phenotypic anti-microbial resistance testing was carried out on 500 Campylobacter isolates (445 cattle isolates and 55 environmental isolates). In general, there was a higher level of anti-microbial resistance for the environmental isolates compared with the animal isolates, 45% of the animal isolates were resistant to one or more of the seven anti-microbials compared with 84% of the environmental isolates. The combined cattle and environmental Campylobacters had 34 (6.8%) isolates resistant to three or more of the seven anti-microbials tested on all isolates and 11 (2.2%) isolates were resistant to the seven anti-microbials. There was a substantial level of ciprofloxacin-resistant Campylobacters in both animal (8.5%) and environmental (21.8%) isolates. The gyrA Thr-86-Ile mutation was only present in five of 22 ciprofloxacin-resistant C. jejuni isolates investigated. No multi-drug-resistant associated mutation was detected in the CmeB or the CmeR regions investigated. In conclusion, our study observed a substantial level of Campylobacter anti-microbial resistance, highlighting the need for an active anti-microbial surveillance program for food animals in Ireland and the importance of the chosen sampling point can have on the findings of such a program.

Enumeration and identity of Campylobacter spp. in Italian broilers

Transmission of Campylobacter to humans has been prominently associated with mishandling or improperly preparing contaminated poultry carcasses. The number of organisms per carcass represents an important measure of human exposure to the agent. Therefore, we wished to estimate this public exposure over 1 yr among Italian broiler carcasses. We sampled 213 broiler carcasses from rinse water samples collected from a single slaughterhouse. Groups of carcasses had mean processed weights ranging from 1.2 to 2.7 kg. These were produced from 22 commercial broiler chicken flocks collected from 12 different farms, 3 of which were seasonally tested. Carcasses were rinsed with sterile water, and the rinse suspension was then serially diluted and spread-plated directly onto Campy-Cefex agar plates. One to 5 typical Campylobacter colonies per plate were identified by polymerase chain reaction as Campylobacter thermo-tolerant species. The overall estimated mean count per carcass in our study was 5.16 +/- 0.80 log10 cfu. This value increased in summer and autumn, as well as on carcasses collected from farms located > 100 km far from the slaughterhouse. A total of 678 Campylobacter colonies were identified by polymerase chain reaction. The majority of isolates were classified as Campylobacter jejuni (49.2%) or Campylobacter coli (47.5%). The overall number of C. jejuni was significantly higher on 1) carcasses weighing > 2 kg, 2) carcasses belonging to flocks with > 10,000 birds, and 3) carcasses collected from farms located > 100 km from the slaughterhouse. Moreover, among farms tested seasonally, C. jejuni was significantly greater than C. coli in winter. These data provide the first results of a continuing survey on Campylobacter loads and species identification from Italian broiler carcasses and represents an important baseline to estimate the human exposure to Campylobacter in Italy.

Development of a real-time fluorescence resonance energy transfer PCR to identify the main pathogenic Campylobacter spp

A simple real-time fluorescence resonance energy transfer (FRET) PCR, targeting the gyrA gene outside the quinolone resistance-determining region, was developed to identify Campylobacter jejuni and Campylobacter coli. These species were distinguished easily, as the corresponding melting points showed a difference of 15 degrees C. A second assay using the same biprobe and PCR conditions, but different PCR primers, was also developed to identify the less frequently encountered Campylobacter fetus. These assays were applied to 807 Campylobacter isolates from clinical specimens. Compared to phenotypic identification tests, the FRET assay yielded the same results for all except three of the isolates. Analysis by standard PCR and 16S rDNA sequencing demonstrated that two of these isolates were hippurate-negative C. jejuni strains, resulting in an erroneous phenotypic identification, while the third was an isolate of C. coli that contained a gyrA gene typical of C. jejuni, resulting in misidentification by the FRET assay. The FRET assay identified more isolates than standard PCR, which failed to yield amplification products with c. 10% of isolates. It was concluded that the FRET assays were rapid, reliable, reproducible and relatively cost-efficient, as they require only one biprobe and can be performed directly on boiled isolates.

Incidence and mechanism of ciprofloxacin resistance in Campylobacter spp. isolated from commercial poultry flocks in the United Kingdom before, during, and after fluoroquinolone treatment

Five commercial broiler flocks were treated with a fluoroquinolone for a clinically relevant infection. Fresh feces from individual chickens and environmental samples were cultured for campylobacters before, during, and weekly posttreatment until slaughter. Both Campylobacter jejuni and C. coli were isolated during all treatment phases. An increased proportion of quinolone-resistant strains was seen during treatment, and these strains persisted posttreatment. One quinolone-resistant isolate of each species, each serotype, and each phage type from each sample at all treatment phases was examined for its phenotype and mechanism of resistance. Two resistant phenotypes were isolated: Nal(r) Cip(r) and Nal(r) Cip(s). The majority (269 of 290) of fluoroquinolone-resistant isolates, whether they were C. jejuni or C. coli, had a mutation in gyrA that resulted in the substitution Thr-86-->Ile. The other gyrA mutations detected were Thr-86-->Ala (n = 17) and Asp-90-->Asn (n = 10). The genotypic variation, based on the silent mutations in gyrA identified by the denaturing high-performance liquid chromatography pattern and DNA sequencing, was used to supplement typing data and provided evidence for both the spread of preexisting resistant strains and the selection of spontaneous resistant mutants in treated flocks. Multidrug resistance was significantly (P < 0.01) associated with resistance to ciprofloxacin. Twenty-five percent (73 of 290) of ciprofloxacin-resistant isolates but only 13% (24 of 179) of susceptible isolates were resistant to three or more unrelated antimicrobial agents. In conclusion, quinolone-resistant campylobacters were isolated from commercial chicken flocks in high numbers following therapy with a veterinary fluoroquinolone. Most ciprofloxacin-resistant isolates had the GyrA substitution Thr-86-->Ile. Resistant isolates were isolated from the feces of some flocks up to the point of slaughter, which may have consequences for public health.

Rapid detection and differentiation of pathogenic Campylobacter jejuni and Campylobacter coli by real-time PCR

A two-tube real-time assay, developed in a LightCycler, was used to detect, identify and differentiate Campylobacter jejuni and Campylobacter coli from all other pathogenic members of the family Campylobacteriaceae. In the first assay, continuous monitoring of the fluorescence resonance energy transfer (FRET) signal acquired from the hybridisation of two adjacent fluoroprobes, a specific FITC probe 5'-GTGCTAGCTTGCTAGAACTTAGAGA-FITC-3') and a universal downstream probe Cy5 (5'-Cy5-AGGTGITGCATGGITGTCGTTGTCG-PO(4)-3'), to the 681-base pair 16S rRNA gene amplicon target (Escherichia coli position 1024-1048 and 1050-1075, respectively) produced by the primer pair, F2 (ATCTAATGGCTTAACCATTAAAC, E. coli position 783) and Cam-Rev (AATACTAAACTAGTTACCGTC, E. coli position 1464), detected C. coli, C. lari and C. jejuni. As expected, a Tm of 65 degrees C was derived from the temperature-dependent probe DNA strand disassociation. In the second assay, an increase in fluorescence due to binding of the intercalating dye SYBR Green I to the DNA amplicons of the hippuricase gene (hipO) (produced by the primer pair hip2214F and hip2474R) was observed for C. jejuni but not for C. coli which lacks the hipO gene. A Tm of 85+/-0.5 and 56 degrees C determined from temperature-dependent dye-DNA disassociation identified C. jejuni and the non-specific PCR products, respectively, in line with our expectation. The two-tube assay was subsequently used to identify and differentiate the 169 Campylobacteriaceae isolates of animal, human, plant and bird origin held in our culture collection into C. coli (74 isolates), C. jejuni (86 isolates) and non-C. coli-C. jejuni (9 isolates). In addition, the method successfully detected C. jejuni, C. coli and C. lari from 24-h enrichment cultures initiated from 30 commercial chicken samples.

Identification of ciprofloxacin-resistant Campylobacter jejuni and analysis of the gyrA gene by the LightCycler mutation assay

A real-time PCR assay was developed to identify ciprofloxacin-resistant Campylobacter jejuni. Ciprofloxacin resistance in C. jejuni has been associated with a C-->T nucleotide point mutation occurring at the 86 codon of the gyrA gene. Other nucleotide substitutions have been identified in proximity to or at the same codon in the gyrA gene, but their role in ciprofloxacin resistance is still unknown. The LightCycler assay is based on the fluorescence resonance energy transfer technology using melting peak analysis of two fluorescent probes hybridized on PCR amplicons. This assay was used to detect the 86-codon mutation conferring ciprofloxacin resistance, as well as other nucleotides substitutions occurring within the same site in the gyrA gene. This gyrA mutation assay allows a rapid and reproducible screening method of ciprofloxacin resistant strains and was applied to C. jejuni strains isolated in Italy in 2000.

A real-time multiplexed PCR assay for rapid detection and differentiation of Campylobacter jejuni and Campylobacter coli

Campylobacter species are the leading agents of bacterial gastroenteritis worldwide. C. jejuni and C. coli together are responsible for more than 95% of all cases of Campylobacter-induced diarrheal disease in the United States. Detection of campylobacteria in clinical samples by conventional culture is problematic and slow due to their complex taxonomy, fastidious growth requirements, and biochemical inertness. The current study describes a rapid, sensitive, and specific real-time polymerase chain reaction (PCR) assay capable of detecting and differentiating C. jejuni (hippuricase gene, hipO) and C. coli (serine hydroxymethyltransferase gene, glyA) in a single reaction, directly from clinical isolates and human feces. The analytical specificity of the assay was demonstrated with a diverse range of Campylobacter species, related organisms, and other diarrhea-inducing bacterial pathogens. The analytical sensitivity of the multiplexed, PCR assay was 10 genome copies for both C. jejuni and C. coli. Following a rapid DNA extraction method (QIAGEN QIAamp DNA stool Mini Kit), the multiplexed PCR identified C. jejuni or C. coli in 100% of fecal samples containing 10(3) colony-forming units (CFU) per gram of feces. This assay represents the first real-time PCR method capable of detecting and differentiating C. jejuni and C. coli in a single reaction.