Negative Fecal Samples Research Articles

Comparison of Mini-FLOTAC, Flukefinder® and sedimentation techniques for detection and quantification of Fasciola hepatica and Calicophoron daubneyi eggs using spiked and naturally infected bovine faecal samples

BackgroundFasciolosis (Fasciola hepatica) and paramphistomosis (Calicophoron daubneyi) are two important infections of livestock. Calicophoron daubneyi is the predominant Paramphistomidae species in Europe, and its prevalence has increased in the last 10–15 years. In Italy, evidence suggests that the prevalence of F. hepatica in ruminants is low in the southern part, but C. daubneyi has been recently reported at high prevalence in the same area. Given the importance of reliable tools for liver and rumen fluke diagnosis in ruminants, this study evaluated the diagnostic performance of the Mini-FLOTAC (MF), Flukefinder® (FF) and sedimentation (SED) techniques to detect and quantify F. hepatica and C. daubneyi eggs using spiked and naturally infected cattle faecal samples.MethodsBriefly, negative bovine faecal samples were artificially spiked with either F. hepatica or C. daubneyi eggs to achieve different egg count levels: 10, 50 and 100 eggs per gram (EPG) of faeces. Moreover, ten naturally infected cattle farms from southern Italy with either F. hepatica and/or C. daubneyi were selected. For each farm, the samples were analysed individually only with MF technique and as pools using MF, FF and SED techniques. Bayesian latent class analysis (LCA) was used to estimate sensitivity and accuracy of the predicted intensity of infection as well as the infection rate in the naturally infected farms.ResultsThe outcome of this study showed that the highest number of eggs (F. hepatica and C. daubneyi) recovered was obtained with MF, followed by FF and SED in spiked infected samples at 50 and 100 EPG, while at lower infection levels of 10 EPG, FF gave the best results. Moreover, the sensitivity for all the techniques included in the study was estimated at > 90% at infection levels > 20 EPG for both F. hepatica and C. daubneyi eggs. However, MF was the most accurate of the three techniques evaluated to estimate fluke infection intensity. Nevertheless, all three techniques can potentially estimate infection rate at farm level accurately.ConclusionsOptimization and standardization of techniques are needed to improve the FEC of fluke eggs.Graphical

Verification of accuracy of qPCR method for intravital diagnostics of Macrorhabdus ornithogaster in avian droppings

The objective of this study was to verify the accuracy of the quantitative PCR (qPCR) method for in vivo detection of Macrorhabdus ornithogaster. A total of 100 faecal and gastric mucosa samples from avian cadavers were investigated, using cytological and qPCR techniques (budgerigars, Fischer’s lovebirds, red-crowned parakeets, scarlet-chested parrots, eastern rosellas, domestic canaries, zebra finches, white Java sparrow). Using qPCR, the probability of detecting positive samples of droppings was significantly higher than in the faecal smear microscopy (P < 0.01). Cytology detected the presence of Macrorhabdus ornithogaster in 34 faecal samples, whereas qPCR detected 54 positive samples. In all 46 qPCR negative faecal samples, gastric smear qPCR was performed and also yielded negative results. Gastric smear qPCR was also performed in 20 cadavers where faecal qPCR has detected the presence of Macrorhabdus ornithogaster and in all samples confirmed the positive result. This verifies the accuracy of faecal sample qPCR for intravital diagnostics. Overall, the faecal qPCR technique appears to be extremely reliable, as it made it possible to detect all infected individuals, including those with negative stool or gastric cytology.

Comparative evaluation of various in-house protocols on diagnostic performance for paratuberculosis IS900 PCR.

Paratuberculosis is a worldwide endemic infectious disease of ruminants that results in high economic losses. Public health concerns are also being raised with human Crohn's disease. Therefore, control is becoming priority for governments. Control is largely dependent on "Test and Cull" or "Test and Segregate" policy. Hence, it is critical to assure the infection before making the decision. Commercial kits are costly especially in view of resource limited areas. Present study analyzed the performance various in house DNA isolation methods and PCR master mix combinations to optimize a protocol for confirmation of paratuberculosis bacilli shedding in feces. Present study included five protocols of fecal DNA isolation (chemical, bio-chemical, physio-chemical and physical) and three reaction mixes (based on Qiagen, Genei and Thermo 2X master mixes) in nine different combinations using additives and tested their performance for IS900 PCR. Spiked fecal samples were used to select the best combination of DNA isolation method and PCR master mix (PRM). Selected combination was used to test reference (positive and negative) fecal samples and field samples. Findings revealed that combination physical method of DNA isolation and Genei based PRM (with additives; betaine DMSO and BSA) had lowest limit of detection. Sensitivity was 83% and specificity was 100% in comparison to fecal culture. High prevalence (23%) was reported for paratuberculosis on field samples. Optimized protocol has acceptable sensitivity and can easily be adopted in resource-limited laboratories. High prevalence of paratuberculosis needs immediate implementation of the control strategies.

Antimicrobial resistant Escherichia coli in Scottish wild deer: Prevalence and risk factors

Antimicrobial resistance (AMR) is a recognised threat to global health. Obtaining data on the prevalence of AMR in environmental bacteria is key to understanding drivers and routes of transmission. Here, 325 Shiga toxin negative deer faecal samples—gathered from across the Scottish mainland—were screened for the presence of AMR Escherichia coli and investigated for potential risk factors associated with AMR occurrence. E. coli with resistance to antimicrobials of clinical health concern, including carbapenems and 3rd generation cephalosporins, were targeted. Ninety-nine percent of samples yielded E. coli, and the prevalence of resistant E. coli at the level of faecal samples was 21.8% (n = 71) for tetracycline, 6.5% (n = 21) for cefpodoxime, 0.3% for ciprofloxacin (n = 1), with no recorded resistance to meropenem. Potential risk factors for tetracycline and cefpodoxime resistance were investigated. The presence of broadleaved woodlands was significantly associated with both AMR phenotypes, which may relate to land use within or around such woodlands. Associated risk factors varied across resistance phenotype and deer species, with proximity or density of horses an indicator of significantly decreased and increased risk, respectively, or tetracycline and cefpodoxime resistance in E. coli from roe deer, but not from red deer. Distance from wastewater treatment plants was a significant risk factor for tetracycline resistance in E. coli from red deer but not from roe deer. Data indicated that AMR E. coli can occur in wild deer populations that are not directly exposed to the selective pressure exerted by antimicrobial treatment. Overall, resistance to critically important antimicrobials was found to be low in the studied population, suggesting no immediate cause for concern regarding human health. Utilising existing culling frameworks, wild deer in Scotland could function well as a sentinel species for the surveillance of AMR in the Scottish environment.

Gut Microbiome Profiles in Colonizations with the Enteric Protozoa Blastocystis in Korean Populations.

The influence of unicellular eukaryotic microorganisms on human gut health and disease is largely unexplored. Blastocystis species commonly colonize the gut, but their clinical significance and ecological role are unclear. We evaluated the effect of Blastocystis colonization on the fecal microbiota of Koreans. In total, 39 Blastocystis-positive and -negative fecal samples were analyzed. The fecal microbiome was assessed by targeting the V3–V4 region of the bacterial 16S ribosomal gene. Bacterial diversity was greater in the Blastocystis-positive than in the Blastocystis-negative group. The bacterial community structure and phylogenetic diversity differed according to the presence of Blastocystis. The mean proportions of Faecalibacterium species and Ruminococcaceae were larger in the Blastocystis-positive group, and that of Enterococcus species was larger in the Blastocystis-negative group. Linear discriminant analysis showed that Faecalibacterium, Prevotella 9, Ruminococcaceae UCG-002, Muribaculaceae, Rikenellaceae, Acidaminococcaceae, Phascolarctobacterium, and Ruminococcaceae UCG-005 were highly enriched in the Blastocystis-positive group, whereas Enterococcus hirae, Enterococcus faecalis, Enterococcus durans, Enterococcaceae, Lactobacillales, and Bacilli were highly abundant in the Blastocystis-negative group. Overall, our results enlighten the notion that Blastocystis colonization is associated with a healthy gut microbiota.

The high co-existence rate of Blastocystis and Dientamoeba fragilis in human faecal samples and the analysis of demographic and clinical findings

Aim: Blastocystis and Dientamoeba fragilis (D. fragilis) are among the most common protozoon species in human faecal samples. The cross-sectional studies have reported the frequencies in a variety of populations. However, we have very limited information about the co-existence rate of those protozoans. The study aimed to compare D. fragilis frequency in Blastocystis positive and negative faecal samples in order to determine the co-existence rate. The secondary objective was to analyse demographic characteristics and gastrointestinal (GI) symptoms in relation to both infections.&#x0D; Material and Method: In the present study, we defined a study group that included 100 Blastocystis positive faecal samples and a control group that included 100 Blastocystis negative samples. The frequency of D. fragilis in samples was determined with a PCR assay specific to the small-subunit ribosomal RNA (SS rRNA) gene. A positive control of D. fragilis was used and the samples with amplification of the expected size (863 bp) were considered as positive. In addition to the statistical comparison of frequencies, the descriptive and clinical findings of cases were analysed retrospectively with Pearson chi-square or ANOVA tests. &#x0D; Results: The frequency of D. fragilis was 21% in Blastocystis positive group and it was 10% in Blastocystis negative group. There was statistically significant difference in terms of D. fragilis positivity between the groups (p 0.05). &#x0D; Conclusion: Our study highlighted the high co-existence of D. fragilis and Blastocystis in human faecal samples. A possible explanation for this finding may be the faecal-oral transmission of these protozoans. In addition, analysis of clinical findings was supported common asymptomatic colonisation of Blastocystis and D. fragilis.

Evaluation of three commercial PCR kits for the direct detection of Mycobacterium avium subsp. paratuberculosis (MAP) in bovine faeces

Mycobacterium avium subsp. paratuberculosis which is more commonly referred to as MAP is the causative agent of Johnes’s disease in ruminants. While cultivation of MAP from faecal samples remains the reference standard diagnostic test for the disease, faecal culture is expensive, slow and not widely available in Ireland. The current study evaluated three commercial kits that combine both DNA extraction and real-time PCR amplification of specific targets for direct MAP detection in cattle faeces.In total, 100 positive samples were tested which consisted of 25 high shedders, 25 medium shedders, 25 low shedders and 25 very low shedders. Also included were 100 negative faecal samples obtained from two Irish herds known to be free of Johne’s disease. The kits evaluated in this study showed significant differences in identifying MAP DNA from animals shedding various concentrations of the bacterium. Kit C had the highest specificity, followed by kits B and A. Sensitivity in kits A, B and C was 73.5%, 81% and 93%, respectively, and specificity was 99%, 97% and 100%, respectively. Sensitivity decreased with lower concentrations of MAP in faeces but this was more significant for kits A and B than for kit C. The results of this study demonstrate that PCR can provide an accurate and rapid detection of MAP faecal shedding and kit C was selected for further evaluation of the role of PCR in the confirmation of animal infection in cattle.

Enhanced sensitivity and fast turnaround time in laboratory diagnosis for bovine paratuberculosis in faecal samples

Bovine paratuberculosis (Johne's disease in cattle) is caused by the pathogen Mycobacterium avium subsp. paratuberculosis (MAP) and is a widespread chronic bacterial infectious disease in cattle. Due to the peculiarities of the pathogen, detection of MAP in faeces remains difficult.DNA extraction and real-time PCR for detection of MAP in bovine faeces (direct PCR) have been refined and feasible procedures for rapid, sensitive and automatable detection of the pathogen agent have been developed. Accordingly, in a first step we tested 20 faecal samples using two MAP complete kits (DNA extraction kits based on magnetic beads combined with real-time PCR assays) and six other DNA extraction kits for faeces. MAP-specific DNA was detected by real-time PCR assays. Cultivation of MAP on the solid medium HEYM and in the liquid medium M7H9C served as reference standards.The two complete kits detected significantly more MAP-DNA positive samples than the other procedures applied (p < 0.04). Ct values of 37 and 38 served as cut-off for the respective real-time PCR assays calculated on the basis of standard curves and droplet digital PCR (ddPCR).In a second step, the two MAP complete kits were employed for a comprehensive study including 107 positive and 50 negative faecal samples which had been previously tested on HEYM cultivation. The MAP complete kits yielded sensitivity values of 86% and 89% and specificity values of 100% compared to cultivation of MAP in the liquid medium M7H9C. In detail, cultivation of MAP in M7H9C detected the pathogen in 97% and 100% of the samples tested after an incubation period of six and twelve weeks, respectively. However, the cultivation of MAP on HEYM succeeded in only 74% after twelve weeks of incubation. In all these solid culture positive samples, MAP was also detected using the two complete kits.Additionally, the impact of repeated freezing and thawing of samples on re-cultivation of MAP was tested using 20 faecal samples and resulted in a reduction to 75% and 25% of bacterial growth when using liquid medium M7H9C and solid medium HEYM, respectively.The results of this study show that complete kits with refined automatable protocols for DNA extraction in combination with real-time PCR assays for detection of MAP can compete with sensitive cultivation of the pathogen in liquid medium.

Multidrug resistant Clostridium difficile ribotype 027 in southwestern Virginia, 2007 to 2013

The excess from fecal samples submitted to a centralized laboratory in Roanoke, Virginia for routine C. difficile testing was used for this research study. We tested all samples, including any formed samples usually not assayed in diagnostic laboratories. Our first aim was to rank ribotypes by their frequency. Between 2007 and 2013, fluoroquinolone resistant 027 (027FQR), a multi-drug resistant ribotype, was 32% of 3118 Clostridium difficile isolates and the most common of 128 ribotypes. 027FQR was in 45% of cytotoxin positive but only 17% of cytotoxin negative fecal samples (p = 0.001) and 34% of unformed but only 21% of formed stool samples (p = 0.001), strong associations with features of symptomatic infection. Conversely, 014/020 (10% of isolates, third most common ribotype) was more often in unformed than formed stools (14% versus 9%; p = 0.002) and in cytotoxin negative than cytotoxin positive samples (11% versus 8%, p = 0.01). Fecal lactoferrin levels, an indication of intestinal inflammation, were significantly higher with 027FQR than with 014/020 infections (median 308 versus 26 ng/mL, p = 0.02). 027FQR fecal bioburdens and toxin levels were significantly higher than their 014/020 equivalents (median 104.1 versus 103.2/g feces, p = 0.01; median TcdA 58.7 versus 1.3 ng/g feces, p = 0.04; median TcdB 43.4 versus 0.3 ng/g feces, p = 0.001). Binary toxin was present in 40% of 027FQR positive samples but none of the 014/020 or non-toxigenic C. difficile positive samples. 027FQR made no more TcdA/cell than did 014/020 (p = 0.7) but did make close to significantly more TcdB/cell (p = 0.08).

BaiCD gene cluster abundance is negatively correlated with Clostridium difficile infection.

BackgroundClostridium difficile infection (CDI) is a major cause of hospital-acquired diarrhea. Secondary bile acids were shown to confer resistance to colonization by C. difficile. 7α-dehydroxylation is a key step in transformation of primary to secondary bile acids and required genes have been located in a single bile acid-inducible (bai) operon in C. scindens as well as in C. hiranonis, two Clostridium sp. recently reported to protect against C. difficile colonization.AimTo analyze baiCD gene abundance in C. difficile positive and negative fecal samples.Material & methodsA species-specific qPCR for detecting baiCD genes was established. Fecal samples of patients with CDI, asymptomatic toxigenic C. difficile colonization (TCD), non-toxigenic C. difficile colonization (NTCD), of C. difficile negative (NC) patients, and of two patients before and after fecal microbiota transplantation (FMT) for recurrent CDI (rCDI) were tested for the presence of the baiCD genes.ResultsThe prevalence of the baiCD gene cluster was significantly higher in C. difficile negative fecal samples than in samples of patients diagnosed with CDI (72.5% (100/138) vs. 35.9% (23/64; p<0.0001). No differences in baiCD gene cluster prevalence were seen between NC and NTCD or NC and TCD samples. Both rCDI patients were baiCD-negative at baseline, but one of the two patients turned positive after successful FMT from a baiCD-positive donor.ConclusionFecal samples of CDI patients are less frequently baiCD-positive than samples from asymptomatic carriers or C. difficile-negative individuals. Furthermore, we present a case of baiCD positivity observed after successful FMT for rCDI.

P872 BaiCD gene abundance is negatively correlated with Clostridium difficile infection

Clostridium difficile infection (CDI) poses an increased risk to patients with inflammatory bowel disease. Preconditions are colonisation with C. difficile, but also a breakdown of the colonisation resistance, of which secondary bile acids are believed to constitute a decisive component. 7α-dehydroxylation is one of the key steps in primary to secondary bile acid transformation, and required genes have been located in a single bile acid inducible (baiCD) operon in C. scindens as well as in C. hiranonis. The prevalence of these species in human fecal samples—particularly with regard to samples tested positive for C. difficile—and in the setting of fecal microbiota transfer (FMT) in CDI patients has not been studied. A species-specific qPCR for detection of baiCD in C. scindens and C. hiranonis was established. Fecal samples of patients with CDI, toxigenic C. difficile colonisation (TCD), non-toxigenic C. difficile colonisation (NTCD), of C. difficile negative (NC) patients, and of two patients before and after fecal microbiota transfer (FMT) for recurrent CDI (rCDI) were tested for the presence of the baiCD gene cluster. In NC samples, the prevalence of the baiCD gene cluster was significantly higher than in CDI samples, with 72.5% (100/138) vs. 35.9% (23/64; p < 0.0001), respectively. No differences were seen between NC compared with NTCD samples or TCD samples. Both rCDI patients were baiCD negative at baseline, but one patient turned positive after successful FMT from a baiCD positive donor. BaiCD/16S rDNA ratio calculation showed no significant difference between the relative abundances in both groups (NC vs. CDI; p = 0.3244). The median of the NC group was 0.006% (IQR 0.0005%-0.376%) and for the CDI group 0.009% (IQR 0.0002%-7.8%). In addition, stool consistency did not measurably influence the relative abundance of bacterial species in this context of complex microbial communities. BaiCD gene positive species are reduced in fecal samples of patients with C. difficile infection as compared with asymptomatic carriers or C. difficile negative fecal samples. Furthermore, we present a case of baiCD gene positivity observed after successful fecal microbiota transfer for recurrent CDI.

Comparison of different commercial DNA extraction kits and PCR protocols for the detection of Echinococcus multilocularis eggs in faecal samples from foxes

Effective and sensitive methods for the molecular detection of Echinococcus multilocularis in faecal samples of final hosts are crucial for the prevention and control of human alveolar echinococcosis and for studies on the epidemiology of the parasite. Little is known about the suitability of commercial test kits for isolating DNA of E. multilocularis from fox faeces and the performance of standard Polymerase Chain Reaction (PCR) protocols in relation to the quality of DNA extracted by these kits.We compared four different kits: ZR Faecal DNA MiniPrep™ (Zymo Research), FastDNA® SPIN Kit for Soil (MP Biomedicals), QIAamp® Fast DNA Stool Mini Kit (QIAGEN) and NucleoSpin® Soil Kit (Macherey-Nagel) for the extraction of DNA from E. multilocularis eggs present in faeces of foxes. Negative faecal samples were spiked with 600, 300, 150, 75, 37, 18, 9, 5 or 2 E. multilocularis eggs, and each egg concentration was tested 10 times with each of the DNA extraction kits. Each extracted DNA sample was amplified using three PCR protocols: i. conventional PCR (cPCR, Platinum®Taq, Invitrogen), ii. qPCR with the iQ™ Supermix (Bio-Rad) and iii. qPCR with the QuantiTect® Multiplex-Master Mix (QIAGEN).The highest analytical sensitivities for molecular detection of E. multilocularis eggs in spiked fox faeces were observed when combining either the QIAamp® Fast DNA Stool Mini Kit or the ZR Faecal DNA MiniPrep™ kit with the qPCR using the QuantiTect® Multiplex-Master Mix (Sensitivities 97% and 94%, respectively). Combinations including the remaining test kits (NucleoSpin® Soil Kit and FastDNA® SPIN Kit for Soil) showed a markedly lower analytical sensitivity for PCR examinations.The results of the present study indicate that it is of utmost importance to select suitable DNA extraction kits in combination with robust PCR methods or reagents to achieve acceptable analytical sensitivity in the molecular detection of E. multilocularis eggs in fox faecal samples.

Presence of Toxocara Eggs on the Hairs of Dogs from Southwest Nigeria

The close contact between dogs and humans poses a high risk of exposure to Toxocara canis eggs which can lead to Visceral Larva Migrans (VLM) syndrome. The aim of the study was to assess whether the hair of domestic dog in Nigeria was contaminated with eggs of T. canis, a zoonotic parasite. Samples of hair from 267 dogs of different ages comprising local and exotic breeds were collected from the neck, back and anal regions between April 2015 and February 2016 at Ile –Ife and Ibadan, Southwest Nigeria. Eggs were recovered from the hair using a previously standardised detection method. Eggs were found on the hair of 48 (18.0%) dogs. A total of 188 T. canis eggs were recovered from the hair of infected dogs. None of the eggs found were embryonated. 62.5% of the infected were under one year of age. As no domestic dogs which were positive from hair samples had negative faecal samples, this indicates that the presence of T. canis eggs in hair is probably due to self-contamination. As T. canis eggs were found on the hair of domestic dogs, direct contact with dogs may be a potential risk factor for transmission of T. canis eggs to humans.

Report of an outbreak of Clostridium difficile infection caused by ribotype 053 in a neurosurgery unit.

We describe an outbreak of Clostridium difficile infection (CDI) with ribotype 053, a possible hypervirulent strain that causes outbreaks, in a neurosurgical unit. The outbreak was investigated by creating a timeline of all toxin positive patients with root cause analysis, supplemented with ribotyping results, hand hygiene and environmental audits. There were five cases of CDI, three caused by ribotype 053 indicating transmission. These included a short period of ward closure to allow enhanced cleaning, including use of vaporised hydrogen peroxide, isolation of infected patients, reinforcement of hand hygiene, education of all staff on C. difficile, reduction of shared bay occupancy from six to four, and addressing staffing levels. The patients with ribotype 053 all had long inpatient stays and had required several courses of broad-spectrum antibiotics for aspiration pneumonia. They also required enteral feeding, which can cause diarrhoea, and during long inpatient stays they had multiple toxin negative faecal samples making clinical diagnosis of CDI difficult. Hence they were not isolated promptly, leading to transmission. This is the first reported outbreak of C. difficile ribotype 053 in the UK and highlights the unique aspects of an outbreak in neurosurgical patients.

New multiplex PCR method for the simultaneous diagnosis of the three known species of equine tapeworm

Although several techniques exist for the detection of equine tapeworms in serum and feces, the differential diagnosis of tapeworm infection is usually based on postmortem findings and the morphological identification of eggs in feces. In this study, a multiplex polymerase chain reaction (PCR)-based method for the simultaneuos detection of Anoplocephala magna, Anoplocephala perfoliata and Anoplocephaloides mamillana has been developed and validated. The method simultaneously amplifies hypervariable SSUrRNA gene regions in the three tapeworm species in a single reaction using three pairs of primers, which exclusively amplify the internal transcribed spacer 2 (ITS-2) in each target gene. The method was tested on three types of sample: (a) 1/10, 1/100, 1/500, 1/1000, 1/2000 and 1/5000 dilutions of 70ng of genomic DNA of the three tapeworm species, (b) DNA extracted from negative aliquots of sediments of negative control fecal samples spiked with 500, 200, 100, 50 and 10 eggs (only for A. magna and A. perfoliata; no A. mamillana eggs available) and (c) DNA extracted from 80, 50, 40, 30, 10 and 1 egg per 2μl of PCR reaction mix (only for A. magna and A. perfoliata; no A. mamillana eggs available). No amplification was observed against the DNA of Gasterophilus intestinalis, Parascaris equorum and Strongylus vulgaris. The multiplex PCR method emerged as specific for the three tapeworms and was able to identify as few as 50 eggs per fecal sample and as little as 0.7ng of control genomic DNA obtained from the three species. The method proposed is able to differentiate infections caused by the two most frequent species A. magna or A. perfoliata when the eggs are present in feces and is also able to detect mixed infections by the three cestode species.

Detection of Torque teno sus virus in diarrheic piglet fecal samples positive or negative for porcine group A rotavirus

Association of Torque teno sus virus (TTSuV) and porcine group A rotavirus (PoRVA) was evaluated in PoRVA-positive or PoRVA-negative diarrheic piglet fecal samples. Molecular TTSuV detection was 40.4% (21/52) and 53.3% (49/92) in PoRVA-positive and -negative fecal samples, respectively. No association (P = .19) was observed between TTSuV and PoRVA diarrhea.

Is there any value in measuring faecal calprotectin in Clostridium difficile positive faecal samples?

Markers of intestinal inflammation have been proposed for inclusion in Clostridium difficile diagnostic algorithms. Faecal calprotectin (f-Cp), a sensitive marker of intestinal inflammation, was evaluated for utility in C. difficile diagnosis in the hospital setting. One hundred and twenty C. difficile positive and 99 C. difficile negative faecal samples of hospital-acquired diarrhoea were analysed for f-Cp using a quantitative ELISA. C. difficile positivity was confirmed using ELISAs for either toxins (n = 45) or glutamate dehydrogenase (GDH) with toxin gene confirmation (n = 75). Non-parametric ANOVA (Kruskal-Wallis) was used for data analysis. C. difficile positive samples had higher (P<0.05) median (interquartile range) f-Cp levels; 336 µg g(-1) (208-536) for toxin and 249 µg g(-1) (155-498) for GDH and toxin gene positive compared with 106 µg g(-1) (46-176) for C. difficile and culture-negative faecal samples. Five C. difficile positive samples were f-Cp negative (<50 µg g(-1)). A f-Cp concentration >50 µg g(-1) was 96 % sensitive and 26 % specific for C. difficile, with area under the ROC curve of 0.82. There is no role for f-CP alone in predicting C. difficile infection in hospital-acquired diarrhoea due to its low specificity.

Development of Three PCR Assays for the Differentiation between Echinococcus shiquicus, E. granulosus (G1 genotype), and E. multilocularis DNA in the Co-Endemic Region of Qinghai-Tibet plateau, China

To investigate echinococcosis in co-endemic regions, three polymerase chain reaction (PCR) assays based on the amplification of a fragment within the NADH dehydrogenase subunit 1 (ND1) mitochondrial gene were optimized for the detection of Echinococcus shiquicus, Echinococcus granulosus G1, and Echinococcus multilocularis DNA derived from parasite tissue or canid fecal samples. Specificity using parasite tissue-derived DNA was found to be 100% except for E. shiquicus primers that faintly detected E. equinus DNA. Sensitivity of the three assays for DNA detection was between 2 and 10 pg. Ethanol precipitation of negative PCR fecal samples was used to eliminate false negatives and served to increase sensitivity as exemplified by an increase in detection from 0% to 89% of E. shiquicus coproDNA using necropsy-positive fox samples.

Development of an untargeted metabolomics method for the analysis of human faecal samples using Cryptosporidium-infected samples

Faecal metabolite profiling, though in its infancy, allows for investigation of complex metabolic interactions between gastrointestinal infections or diseases and host health. In the present study, we describe a faecal metabolite extraction method for untargeted gas chromatography–mass spectrometry (GC–MS) analysis using Cryptosporidium positive and negative human faecal samples. The extraction method takes into account the varying faecal consistencies and quantities received for clinical diagnosis. Optimisation was carried out using different extraction solvents and on three different faecal quantities to determine the minimum amount of faecal sample required. The method was validated by untargeted GC–MS analysis on 8 Cryptosporidium positive and 8 Cryptosporidium negative human faecal samples, extracted using the optimised conditions. The method showed good extraction reproducibility with a relative standard deviation of 9.14%. Multivariate analysis of the GC–MS generated dataset showed distinct differences between profiles of Cryptosporidium positive and Cryptosporidium negative samples. The most notable differences included changes in amino acid, nitrogen and energy metabolism, demonstrating the association of infection with Cryptosporidium and altered permeability of the small intestine.

Rapid detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini eggs in human fecal samples using a duplex real-time fluorescence resonance energy transfer PCR and melting curve analysis

We developed a single step duplex real-time fluorescence resonance energy transfer (FRET) PCR merged with melting curve analysis for the fast detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini eggs in human fecal samples. Two species of mitochondrial NADH dehydrogenase subunit 2 (nad2) DNA elements, the 165-bp nad2 product of C. sinensis and the 209-bp nad2 product of O. viverrini, were amplified by species-specific primers, and the fluorescence melting curve analyses were generated from hybrid of amplicons and two pairs of species-specific fluorophore-labeled probes. By their different fluorescence channels and melting temperatures, both C. sinensis and O. viverrini eggs in infected human fecal samples were detected and differentiated with high (100%) sensitivity and specificity. Detection limit was as little as a single C. sinensis egg and two O. viverrini eggs in 100 mg of fecal sample. The assay could distinguish the DNA of both parasites from the DNA of negative fecal samples and fecal samples with other parasitosis, as well as from the well-defined genomic DNA of human leukocytes and other parasites. It can reduce labor time of microscopic examination and is not prone to carry over contamination of agarose electrophoresis. Our duplex real-time FRET PCR method would be useful to determine the accurate range of endemic areas and/or to discover the co-endemic areas of two liver flukes, C. sinensis and O. viverrini, in Asia. This method also would be helpful for the differential diagnosis of the suspected cases of liver fluke infections among travelers who had visited the endemic countries of those parasites.