The genome of Clostridium difficile 5.3
© Darling et al.; licensee BioMed Central Ltd. 2014
Received: 23 December 2013
Accepted: 1 February 2014
Published: 24 February 2014
Clostridium difficile is the leading cause of infectious diarrhea in humans and responsible for large outbreaks of enteritis in neonatal pigs in both North America and Europe. Disease caused by C. difficile typically occurs during antibiotic therapy and its emergence over the past 40 years is linked with the widespread use of broad-spectrum antibiotics in both human and veterinary medicine.
We sequenced the genome of Clostridium difficile 5.3 using the Illumina Nextera XT and MiSeq technologies. Assembly of the sequence data reconstructed a 4,009,318 bp genome in 27 scaffolds with an N50 of 786 kbp. The genome has extensive similarity to other sequenced C. difficile genomes, but also has several genes that are potentially related to virulence and pathogenicity that are not present in the reference C. difficile strain.
Genome sequencing of human and animal isolates is needed to understand the molecular events driving the emergence of C. difficile as a gastrointestinal pathogen of humans and food animals and to better define its zoonotic potential.
KeywordsClostridium difficile 5.3 Genome Sequencing
Clostridium difficile is a Gram-positive, spore-forming bacterium that over the last 40 years has emerged from obscurity to become a leading gastrointestinal pathogen in hospital environments . The clinical features of disease range from non-haemorrhagic watery diarrhea to fatal episodes of pseudomembranous colitis and toxic megacolon. C. difficile disease is also community-acquired with incidence rates increasing . In the past decade C. difficile has caused widespread outbreaks of neonatal diarrhea in piglets raising concerns that it may have a food-borne etiology. One porcine strain of C. difficile is frequently isolated from human cases of C. difficile disease in human in Europe, underscoring its zoonotic potential .
Non-toxigenic strains of Clostridium difficile have been isolated from patients with diarrhoeal disease . Recent studies showing that nontoxigenic strains are capable of blocking colonisation and prevent disease caused by toxigenic strains indicates that much remains to be learned about virulence factors that play important roles in colonization of the gastrointestinal tract . Here we report the sequence of nontoxigenic C. difficile strain 5.3 isolated from a patient with diarrhoea. The clinical presentation of this patient was of suspected Clostridium difficile infection. This was confirmed at the pathology laboratory with the isolation of only non-toxigenic C. difficile.
Isolation and DNA preparation
Clostridium difficile 5.3 originated from a faecal sample submitted from a female patient with the clinical symptomology of C. difficile infection. From the faecal sample 100 μ l of sample was added to cooked meat medium (TM0102 Oxoid Australia) and incubated anaerobically using the anoxomat system (MART Microbiology B.B., The Netherlands) at 37C for 24 hours. From here 200 μ l of the culture was transferred aseptically into a centrifuge tube and centrifuged at 10,000 rpm for 5 mins. The supernatant was discarded and the pellet resuspended in 1 ml of absolute ethanol and incubated at room temperature with periodic inversion for two hours.
A pellet was recovered by centrifuging at 10,000 rpm for 5 mins, the ethanol was discarded and the pellet resuspended in 100 μ l of brain heart infusion broth and spread plated onto Clostridium difficile selective agar (CC-BHIA + Taurocholate, PP2362 Oxoid Australia) and incubated anaerobically at 37 C for 24 hours. All plates were examined for colonies that morphologically represented C. difficile, from each plate colonies were selected and subcultured onto CC-BHIA + Taurocholate until pure cultures were achieved.
DNA was extracted from pure cultures by taking a single colony into 2 ml of brain heart infusion agar and incubating anaerobically at 37 C for upto 48 hours. The bacterial suspension was then vortexed and the DNA extracted using the DNeasy Blood and Tissue Kit (Qiagen, 69581) using the manufacturers instructions for the extraction of gram positive bacteria and the use of lysozyme.
DNA was quantified using qubit flourimetry and 0.5 ng gDNA was used as input to the Illumina Nextera XT library preparation protocol. Tagmentation of Genomic DNA, and PCR amplification of tagged DNA were performed as per manufacturer’s instructions. However the “PCR Clean-Up” and “Library Normalization” steps were omitted and size selection was instead performed by running balanced and pooled samples in a one percent agarose gel and excising the 600 bp to 1200 bp region of interest. The DNA was then purified from the agarose using Promega’s Wizard SV Gel and PCR Clean-Up System. Finally, an Agilent 2100 Bioanalyzer, with a High Sensitivity DNA Kit, was used to quantitate the pooled DNA library before loading onto the MiSeq with 23 other multiplexed samples. Paired-end 300 nt reads were generated using MiSeq V3 chemistry.
Assembly and annotation
The genome was assembled using a version of the A5 pipeline  called A5-miseq  that has been revised to process reads up to 500 nt long. Briefly, A5-miseq consists of five stages: (1) read quality filtering and error correction, (2) contig assembly, (3) permissive draft scaffolding, (4) misassembly detection, and (5) conservative scaffolding. The revised A5 pipeline uses a new version of idba_ud that uses read pairing information, and that has been modified to accept reads up to 500 nt long and to construct de Bruijn graphs with k-mers up to 500 nt. These modifications provide substantial improvements in assembly contiguity.
The genome was annotated with the RAST annotation system using FigFAM release 70 .
A5-miseq includes a quality checking step that detects putative misassemblies by identifying clusters of read pairs that map to disjoint locations in the assembled genome. This method did not detect any putative misassemblies.
Comparison of the gene content between C. difficile 5.3 and the finished C. difficile 630 reference genome identified 105 annotated gene functions predicted to be present only in C. difficile 5.3. In particular, genes related to metal resistance, bacitracin resistance, colicin resistance, drug efflux, and several phage-related genes are present only in C. difficile 5.3. These genes may contribute to the pathogenic phenotype of C. difficile 5.3. A full list of these genes has been provided in Additional file 1.
Improved efficiency of the clinical genomics pipeline will enable fine-scale epidemiological monitoring of Clostridium difficile outbreaks.
Availability of supporting data
The draft genome assembly has been submitted to NCBI and assigned accession PRJNA232267. Genome annotations are available from the RAST web server under accession 6666666.54620 when logged in with username guest, password guest. The Illumina sequence reads have been deposited to the Short Read Archive and under accession SRX396630.
Rapid annotation using subsystem technology
Andrew and Aaron’s Awesome Assembly
This work was supported by a collaboration between the NSW Department of Primary Industries and the ithree institute.
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