14, 127–138. N. Engl. Peptostreptococcaceae family was 1.56% overall and within the family the only identified member was the genus Clostridioides, positively correlated with the presence of Akkermansia that may be predictive of the presence of a CDI. MH performed the sequencing experiments. This reduction of diversity could be associated with the bacterial dysbiosis linked to CDI. MH and JE drafted the manuscript. Figure 1. doi: 10.1016/j.humic.2016.10.003, Lagier, J.-C., Million, M., Hugon, P., Armougom, F., and Raoult, D. (2012). (2016). All patients were reported to be CDI positive as they were positive for GDH antigen and the gene encoding toxin B (tcdB), but negative for the C. difficile ribotype 027 test. (2018) also reported similar figures; Enterobacteriaceae was the most abundant bacterial family and the abundance of Lachnospiraceae was also very low. That was true in our study for at least four patients who were infected by Klebsiella, Campylobacter, Staphylococcus, or Escherichia. Heat map showing the distribution and relative abundance of members of the Peptostreptococcaceae family grouped (in rows) within the different samples (in columns). However, our findings showed Bacteroidaceae, Lachnospiraceae, and Enterobacteriaceae to be the most abundant families, along with a higher abundance of Enterococcaceae. Clostridium difficile, a Gram-positive, spore-forming anaerobic bacillus, was first described in 1935, 1 but it was not associated with antibiotic-related diarrhea until the late 1970s. Citefast is a FREE APA, MLA and Chicago citation generator. In the last decade, the frequency and severity of C. difficile infection has been increasing worldwide to become one of the most common hospital-acquired infections. However, Firmicutes was more prevalent in 13 samples and Proteobacteria in three. Clinical Practice Guidelines for Clostridium difficile Infection • CID 2018:XX (XX XXXX) • 3 cases per 1000 patient admissions for CO-HCFA) in pedi-atric patients as for adults (good practice recommendation). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. We truncated reverse reads to 240 bp using the “–p-trunc-len-r” option implemented in the dada2 plugin due to decreased quality scores of the sequences at the end of the reverse reads. difficile, serotyping ofSalmonella spp., ribotyping and MLST ofC. Leffler, D. A., and Lamont, J. T. (2015). Microbiol. Softw. Follow the basic format for "Footnote or Endnote" and "Corresponding Bibliographical Entry" that are exemplified above, omitting author and/or editor names and beginning respective entries with the … coli, C. perfringens, andC. J. Med. Segregation of the samples into clusters, showed differences, as Bacteroidaceae and Lachnospiraceae were the most abundant families in cluster B (potentially associated to less severe CDI), whereas Enterobacteriaceae and Enterococcaceae were the most abundant in Cluster A, potentially associated with immune suppression, previous use of aggressive antibiotherapy, severe diarrhea, and a high incidence of recurrence. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. PubMed® comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Gut microbiota and Clostridium difficile infections. Patients in cluster B had had a history of less aggressive antibiotherapy, less severe diarrhea, and only a small incidence of recurrence. Microbiol. Nosocomial acquisition of Clostridium difficile infection. Optimizing taxonomic classification of marker-gene amplicon sequences with qiime 2’s q2-feature-classifier plugin. A total of 3,477 ASVs were identified among all samples. Dis. In … Eur. There was a high abundance of Rikenellaceae (13.65 and 15.05%), Bacteroidaceae was reduced to approximately 30%, and C. difficile was also identified in the two samples. Most of the patients in this cluster were either immunosuppressed (transplant patients) or immunocompromised (cancer patients), with a history of aggressive antibiotherapy. However, the main alpha diversity indices, such as the Chao richness estimator, and the Shannon and Simpson diversity indices were 134.32 ± 80.6, 4.01 ± 1.25, and 0.86 ± 0.12, respectively, indicating that the observed reduced alpha diversity was true, and not a sequencing artifact. One gram of feces were diluted in 25 mL of distilled water and centrifuged at 8000 rpm for 10 min. doi: 10.3390/toxins8050134, Hensgens, M. P. M., Goorhuis, A., Dekkers, O. M., van Benthem, B. H. B., and Kuijper, E. J. Microbiol. 378, 2535–2536. Remarkably, patients who tested positive for the binary toxin gene did not show severe diarrhea. The Gram-positive, spore-forming anaerobe, Clostridioides difficile (formerly Clostridium difficile and Peptoclostridium difficile; Yutin and Galperin, 2013) is an asymptomatic component of the healthy intestinal microbiota of approximately 2–7% of healthy human adults and up to 70% of healthy newborns (McFarland et al., 1989; Lees et al., 2016). Infect. doi: 10.1038/nature09944, Bokulich, N. A., Kaehler, B. D., Rideout, J. R., Dillon, M., Bolyen, E., Knight, R., et al. Rev. ESD stands for Enfants en Situation Difficile (French: Children in Difficult Circumstances). Libraries were sequenced on a MiSeq platform at the University of Burgos, leading to 300-bp, paired-end reads. (2018). Lopetuso, L. R., Petito, V., Graziani, C., Schiavoni, E., Paroni Sterbini, F., Poscia, A., et al. 14, 1208–1219. In conclusion, our findings show that a reduction in Bacteroides is a clear disadvantage for healthy gut microbiota and can result in a worse CDI prognosis, including severe diarrhea and a high incidence of recurrence. In a recent study of more than 80 patients, the most abundant bacterial family was Enterobacteriaceae (>30%) and the five most abundant families (Enterobacteriaceae, Lachnospiraceae, Bacteroidaceae, Porphyromonadaceae, and Ruminococcaceae) represented less than 50% of the bacterial diversity (Staley et al., 2018). The immune system protects the host from pathogenic organisms (bacteria, viruses, fungi, parasites). New treatment strategies are needed. The editor and reviewers' affiliations are the latest provided on their Loop research profiles and may not reflect their situation at the time of review. Among all samples Bacteroidaceae 31.01%, Enterobacteriaceae 9.82%, Lachnospiraceae 9.33%, Tannerellaceae 6,16%, and Ruminococcaceae 5.64%, were the most abundant families. The DNA concentration was determined using a Qubit®fluorimeter (Invitrogen). (2013). Bacteroidaceae was the most abundant family along all samples, followed by Enterobacteriaceae. Oral antibiotics such as metronidazole, vancomycin and fidaxomicin are therapies of choice for Clostridium difficile infection. Arbitrarily primed polymerase chain reaction (AP-PCR) was used to determine strain identity of C. difficile isolates recovered on our oncology ward, at an incidence rate of 0.84%. Best. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. 1 The organism is acquired from an exogenous source and given certain conditions can induce disease. How is Enfants en Situation Difficile (French: Children in Difficult Circumstances) abbreviated? The clostridial phylogeny in the phylum Firmicutes has recently been reconsidered and, among other reassignments of the taxa, it has been suggested that C. difficile and its close relatives, C. paradoxum and C. sticklandii, be reclassified within the family Peptostreptococcaceae in the order Clostridiales as a tentative solution to resolve various taxonomical problems (Yutin and Galperin, 2013). Generate references, bibliographies, in-text citations and title pages quickly and accurately. ESPD stands for Enfants En Situation Particulièrement Difficile (French). The individuals in this study clearly belonged to enterotype 1, with a high abundance of Bacteroides (31.01% overall). Here, we characterized the gut microbiota from the feces of 57 patients with diarrhea from nosocomial and community-acquired CDI. 3. Correlation matrix of the relative abundance of genera above 1% abundance (significance level = 0.05). Google Scholar Citations lets you track citations to your publications over time. Four other bacterial families had an overall relative abundance of over 5%: Enterobacteriaceae 9.82%, Lachnospiraceae 9.33%, Tannerellaceae 6.16%, and Ruminococcaceae 5.64%. Only patient MS1496 was finally successfully treated with fidaxomicin, because of multiple recurrences. Culture-based studies suggest that all healthy adults share most of the same gut bacterial species, whereas culture-independent sequencing studies have revealed vast microbial diversity (more than 1,000 species), that varies highly over time and among the population. Dis. Check out our other citation guides on MLA 8 and Harvard referencing. In contrast, cluster B was compact (Figure 2) and contained most of the samples (79.24% of the patients), suggesting that this group may represent the general CDI scenario. Rev. doi: 10.1007/s10096-016-2639-3. This citation style was created by the American Psychological Association. The immune system is always active, carrying out surveillance, but its activity is enhanced if an individual becomes infected. Microbiol. Demultiplexed paired-end fastq files were processed using QIIME2 pipeline version 2018.6 (Caporaso et al., 2010) and dada2 (Callahan et al., 2016) and feature-table (McDonald et al., 2012) plugins were used for quality filtering of the reads, merging of the paired ends, chimera removal, and assignation of amplicon sequence variants (ASV). Acquisition of C. difficile appears to be from the environment rather than maternal sources. Yutin, N., and Galperin, M. Y. Samples were rarefied to 17,520 reads per sample for beta-diversity analysis to reduce the bias due to different sequencing depths (only sample MS1498 was excluded from beta-diversity analysis). ; this inpatient was immunocompromised and aggressive therapy, including broad-spectrum antimicrobials, corticoids, and antifungal medicines, was used. (B) Distribution of the patients according to the number of previous hospital admissions (1, 2, or more than 3 previous hospital admissions). doi: 10.1371/journal.pone.0081330, Staley, C., Kaiser, T., Vaughn, B. P., Graiziger, C. T., Hamilton, M. J., Rehman, T. U., et al. There were two clusters (A and B) that described 38.9% of the variability in the x-axis. doi: 10.1111/1462-2920.12173, Keywords: CDI, Clostridioides difficile, diarrhea, microbiota, bacterial, 16S rRNA, Citation: Hernández M, de Frutos M, Rodríguez-Lázaro D, López-Urrutia L, Quijada NM and Eiros JM (2019) Fecal Microbiota of Toxigenic Clostridioides difficile-Associated Diarrhea. The richness of the microbiota composition was also reduced; although the microbiota composition associated with CDI is still unclear, we observed limited variability and a microbiota characteristic of the presence of C. difficile, independent of the severity of the disease. In addition to the different profiles of the bacterial communities, the previous medical interventions, prognoses, and recurrences were different between the two groups. 56, 1108–1116. Amplicon Sequence Variants (ASVs) were obtained instead and represent much higher taxonomic resolution than OTUs, as single-nucleotide differences over the sequenced gene region are taken into account (Callahan et al., 2017). Bacteroidaceae was the most abundant family overall (31.01%). A change in microbiota composition and a decrease in the richness of bacterial species within individuals with diarrhea and a positive diagnosis of C. difficile is to be expected because, although the gut microbiota stabilizes early in life (during the first 3 years), severe interventions, such as antibiotic administration, or diseases can lead to dysbiosis. EMPeror: a tool for visualizing high-throughput microbial community data. infections . 2.Conduct surveillance for HO-CDI for inpatient pediatric Plotting was carried out in the R environment4, using ggplot2 (Wickham, 2016) and reshape2 (Wickham, 2007) packages. J. Clin. Together with Bacteroidaceae, these five bacterial families represented almost two thirds of the bacterial diversity. We analyzed only samples from patients with diarrhea and a positive diagnosis for C. difficile. Euro Surveill. The 16S rRNA profiling data sequenced in this study were deposited in the Sequence Read Archive of the National Center for Biotechnology Information database under the following study accession number: PRJNA493204. Wellington: Ministry of Health and Ministry for Primary Industries. Diversity of Clostridium difficile PCR ribotypes in Europe: results from the European, multicentre, prospective, biannual, point-prevalence study of Clostridium difficile infection in hospitalised patients with diarrhoea (EUCLID), 2012 and 2013. Shankar, V., Hamilton, M. J., Khoruts, A., Kilburn, A., Unno, T., Paliy, O., et al. Microbiome 6:90. doi: 10.1186/s40168-018-0470-z, Callahan, B. J., McMurdie, P. J., and Holmes, S. P. (2017). DADA2: high-resolution sample inference from Illumina amplicon data. Background . (2016) characterized 24 patients, of whom 12 were suspected of having an initial episode of CDI (not recurrent CDI). 3 citations < Page 1/1. A phylogenetic tree was built using alignment (Katoh and Standley, 2013) and phylogeny (Price et al., 2010) plugins. In most of these infections, the use of antibiotics was a major contributing factor leading to the illness . This is the first time that QIIME2 has been used to analyze the gut microbiota associated with CDI, and, different from previous studies, sequences are not clustered together into “Operational Taxonomic Units” (OTUs) using a certain dissimilarity threshold (generally 97 or 99% similarity). 15, 2631–2641. Sample multiplexing, library purification, and sequencing were carried out as described in the “16S Metagenomic Sequencing Library Preparation” guide by Illumina. View all In our study, samples MS0223 and MS1753 exhibited an abnormal expansion of the family Prevotellaceae (16.50% and 32.25%, respectively). (2012). The inner ring indicates a community origin (there were two patients with no previous admission not shown in the figure) and the outer ring, nosocomial or healthcare-in-a-nursing home origin of the infection. We found a higher average abundance of Bacteroidetes (46.51% in the samples) than in previous studies, followed by 34.70% for Firmicutes and 13.49% for Proteobacteria. In our study, we were able to segregate the samples into clusters in which these two aspects were highly relevant. Metadata of the 57 patients studied. C. difficile TcdA — information from the Consortium for Functional Glycomics on one of the major virulence factors from C. difficile If anyone thinks any of these meet WP:EL then say so. Stool samples were initially tested for the presence of both glutamate dehydrogenase (GDH) and toxins A and B by the lateral flow assay C.Diff Quik Chek Complete assay (Techlab). In addition, some C. difficile strains may also produce a binary toxin, called C. difficile transferase (CDT), with a potential role in the pathogenesis of the bacterium (Di Bella et al., 2016). Front. A total of 7,474,887 reads survived the quality filtering process (108,239 ± 53,034 reads/sample). Although Lachnospiraceae are common inhabitants of the healthy human and mammalian gut microbiota (Lagier et al., 2012), they are highly sensitive to antimicrobial chemotherapy. All subjects gave written informed consent in accordance with the Declaration of Helsinki. Two clusters A (full black) and B (dot lane) were observed. (2013). 11, 2639–2643. Primers 7:16020. doi: 10.1038/nrdp.2016.20, Song, Y., Garg, S., Girotra, M., Maddox, C., von Rosenvinge, E. C., Dutta, A., et al. The information provided in the guide above follows the 6th edition (2009) of the manual. Finally, a relevant aspect that must be considered in clinical practice is the misdiagnosis of CDI, as patients with a stool sample that tests positive for C. difficile are usually diagnosed with CDI and subsequently treated as such. For each stool sample, 220 mg of feces was homogenized and total DNA extracted using the QIAamp DNA Stool Mini Kit (Qiagen), according to manufacturer’s instructions. Each citation style handles this situation a little bit differently! 9:3331. doi: 10.3389/fmicb.2018.03331. Gut microbiota in health, diverticular disease, irritable bowel syndrome, and inflammatory bowel diseases: time for microbial marker of gastrointestinal disorders. 28, 721–741. As expected, C. difficile was the most abundant species within both the order Clostridiales and the family Peptostreptococcaceae, and was identified in almost all samples. Nat. (2018). Human gut microbiota: repertoire and variations. Nat. Clostridium difficile (C. difficile) infections . Meaning of difficult. ASV assigned to the family Peptostreptococcaceae were extracted from the feature table and used to construct a heatmap using JColorGrid (Joachimiak et al., 2006). doi: 10.1093/nar/gks808, Knight, D. R., Elliott, B., Chang, B. J., Perkins, T. T., and Riley, T. V. (2015). New York, NY: Springer-Verlag. The clinical symptoms within this group included severe diarrhea and an uncertain prognosis, which in many cases was fatal, and the percentage of recurrences higher. J. JColorGrid: software for the visualization of biological measurements. Similarly, the trigger may be also the status of the immune system. doi: 10.1159/000477205, McDonald, D., Price, M. N., Goodrich, J., Nawrocki, E. P., DeSantis, T. Z., Probst, A., et al. C. difficile infection (CDI) is thus a toxin-mediated disease of the colon, with clinical symptoms that range from mild or self-limiting diarrhea to pseudomembranous colitis and life-threatening fulminant colitis (Leffler and Lamont, 2015; Smits et al., 2016). 38, 779–786. Clin. Infect. (2018). {{ U }}) while signing a reply, thx 12:01, 6 October 2013 (UTC) The protocol was approved by the CEIC with reference number CEIm PI128-18. 11 Reported C. difficile colonisation rates vary, and may be as high as 50% in neonates and 70% in infants <1 year of age. Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. Prevotellaceae is a family that can enzymatically disrupt mucosal barrier function and tends to be more abundant in intestinal biopsy samples isolated from patients with inflammatory bowel disease (IBD) (Nagao-Kitamoto et al., 2016). A positive correlation was observed between the Akkermansia and Clostridioides genera (C. difficile). Lancet Infect. 13 Thus, it remains controversial whether CDI can even be diagnosed in children <1 year of age. doi: 10.1371/journal.pone.0009490. Our study describes retrospective cohort treated with FMT at two major hospitals in Stockholm. (2018). However, the percentage of Bacteroides was lower among the most affected patients and in those with the worst evolution; a reduction in the abundance of this family to below 50% could be considered to be a marker for worsening of the clinical prognosis. However, given that C. difficile could be ruled out as the primary etiological agent for four patients, the percentage dropped to 20.75%. Figure 3. Antibiotherapy generally consisted of metronidazole and then vancomycin if the diarrhea persisted. Misdemeanor traffic … Res. The study consisted of an ecological analysis by high-throughput sequencing of the V3-V4 region of the 16S rRNA amplicons and evaluation of the association of the various ecological profiles with CDI risk factors. Clostridium difficile infection is currently one of the most important causes of infectious diarrhea in developed countries and the main cause in healthcare settings (Lagier, 2016). Predicting microbiota dynamics in individuals and determining whether changes in composition are associated with varying severity and outcomes of CDI will require determining whether such changes lead to the disease.