Using SeqSphere+ for the rapid development of clone-specific screening assays from WGS data
In a just published study SeqSphere+ was used for the rapid development of clone-specific screening assays (probe-based real-time PCR or high-resolution melting curve analysis) and compared to other available tools (Microbiol Spectr. 2022 Oct 17: e0303622).
New core genome MLST (cgMLST) for four species published
SeqSphere+ was used to establish, evaluate, and publish four species cgMLST schemes, i.e., Mycobacterium abscessus (PubMed), Burkholderia mallei (PubMed and PubMed), Brucella spp. (PubMed), Serratia marcescens (in press). All five schemes are available for all SeqSphere+ users and the community via cgMLST.org.
SeqSphere+ Version 8.2 released that is freely available to customers
This is a minor update that addresses the potential log4j server vulnerability. In addition this update features an improved NCBI SRA FASTQ download and a faster retrieval of samples for comparison tables. We strongly recommend to all users to install this update.
Ridom SeqSphere+ Potential log4j Vulnerability (CVE-2021-44228)
On Friday December 10 morning a new exploit in log4j Java logging framework was reported, that can be trivially exploited. This vulnerability is caused by a new feature introduced in log4j 2.x versions where a specific string embedded in messages logged by log4j would be interpreted by log4j to connect to remote sites and even execute code directly. The vulnerability, also called log4shell was assumed not to impact SeqSphere+ as the software ships only with an older version of log4j (version 1.2).
However, as it is more recently under discussion that this older log4j version might also be occasionally affected under certain specific configurations, we recommend to all our customers to update to version 8.2 or to install this patch that removes potentially critical classes from log4j version 1.2 but does not change the SeqSphere version..
New functionality for a SeqSphere+ Consortium
New functionality for a SeqSphere+ Consortium that allows several SeqSphere+ users each with their own installation to share a minimum agreed upon amount of data (e.g., for [supra]national/regional genomic surveillance or in the framework of a funded project, etc.) while the original and complete data remain locally.
SeqSphere+ Version 8.0 released that is freely available to customers
This is a major update that features most prominently a new sample QC overview function, recursive similarity searches, early warning alerts (detecting and noting of sample clusters), and local single linkage clustering (allows to build a ‘nomenclature’ based just on own samples). Furthermore, the opening of large comparison tables has been substantially accelerated and it is now possible to search in those tables for gene and product annotations. Finally, a number of smaller improvements and several bug-fixes are part of this release.
NimaGen and Ridom cordially invited to a joint-webinar entitled
'Complete and Convenient Wet- and e-Lab Workflow for SARS-CoV-2 Surveillance Sequencing'
NimaGen explained its one-step solution EasySeq™ SARS-CoV-2 WGS kit that utilizes Reverse Complement PCR (RC-PCR) for WGS library preparation with just a single PCR reaction for both amplicon generation and indexing. This drastically simplified protocol can reduce hands on time for library prep by up to 80% compared with other methods currently being used for the WGS of SARS-CoV-2.
Ridom demonstrated its SeqSphere+ software with the recently released SARS-CoV-2 plug-in. Once configured the software can automatically analyze SARS-CoV-2 tiled amplicon raw read data with virtually no user intervention. The PANGO lineage is determined, and sequences and metadata can be batch-uploaded and imported from GISAID. Furthermore, a multiple FASTA export is implemented for visualization of own data in a global phylogenetic context with Nextstrain.
See Recording of the Webinar...
From version 7.5 onwards SeqSphere+ supports starting from Illumina raw reads the analysis of SARS-CoV-2 tiled amplicon (e.g., ARTIC, AmpliSeq, EasySeq RC-PCR, or CleanPlex) data. The generated FASTA files can be analyzed by two task templates: The SARS-CoV-2 all ORFs task template separates the genomic sequence into subsequences matching the different open reading frames (ORFs). In addition, the task template queries the ORFs for notable mutations (e.g., S:N501Y). The SARS-CoV-2 Pangolin task template determines from the genomic FASTA file a PANGO lineage (e.g., B.1.1.7). Sequences and metadata can be batch-uploaded and imported from GISAID. Furthermore, a multiple FASTA export is implemented for visualization of own data in global context with Nextstrain’s web app Nextclade.
Information on how to update.
C. difficile cgMLST scheme updated (version 2.0)
In 2018 Bletz et al. published [PubMed] the first version of a C. difficile cgMLST scheme. This scheme is one of our very few schemes that was optimized for the de novo assembler SPAdes. End of 2019 Eyre et al. reported [PubMed] about reproducibility issues when using this scheme and re-sequencing and assembling with SPAdes the same samples. Indeed, we could verify in our recent de novo assembler evaluation such problems especially when SPAdes assemble regions with very low local coverage. Therefore, we introduced with the recent update to SeqSphere+ version 7 remapping of reads and consensus calling (with a minimum base coverage of 5 required to call a non-ambiguous base) as a ‘polishing’ step for SPAdes assembly contigs. Furthermore, herewith we update the C. difficile cgMLST scheme that is now optimized for the SKESA assembler with targets removed that were either not present in 95% of all samples when compared to a sample collection with the world-wide most prevalent ribotypes or especially problematic for SPAdes assemblies. Thereby, the total number of core genome targets was reduced from 2,270 to 2,147.
Only the new version 2.0 of the C. difficile cgMLST scheme will be available for download from the Task Template Sphere and shown at cgMLST.org starting from now on. To prevent confusion between old and new scheme Cluster Types (CT), the new scheme starts with CT 5000. However, if the old scheme was already downloaded, it will remain functional at least until the end of this year.
SeqSphere+ Version 7.0 released that is freely available to customers
This is a major update that features most prominently support for virulence profiling for 54 species with medical importance by using VFDB data, E. coli O- and H-antigen serotyping, and antimicrobial resistance gene finding by using the new AMRFinderPlus tool (supports all species except M. tuberculosis; requires Linux or WSL). Furthermore, a number of important QC and performance improvements have been implemented, e.g., remapping of reads to SPAdes and SKESA assemblies or support for the fast BWA-MEM mapping algorithm. Finally, a number of smaller improvements and several bug-fixes are part of this release.
IS26-Mediated Transfer of blaNDM-1 as the Main Route of Resistance Transmission During a
Polyclonal, Multispecies Outbreak in a German Hospital
SeqSphere+ was instrumental to analyze a multi-species hospital outbreak with clonal-, plasmid-, and potential mobile genetic element-transmission (Front Microbiol 10: 2817, 2019).
Core genome MLST (cgMLST) scheme for Salmonella enterica evaluated and made public at cgMLST.org
SeqSphere+ was used to evaluate a cgMLST scheme for Salmonella enterica. PLEASE NOTE: This cgMLST scheme uses exactly the same loci and reference gene sequences as the EnteroBase S. enterica cgMLST v2 scheme. However, the SeqSphere+ allele calling procedure is slightly different and the cgMLST.org allele numbering is independent from and not compatible with the EnteroBase allele nomenclature.
SeqSphere+ Version 6.0 released that is freely available to customers
This is a major update that features most importantly a number of QC improvements, e.g., read data quality and adapter content control, trimming of Illumina adapters, and assessment of paired-end library insert sizes. QC issues are highlighted in the procedure tab of each sample. In addition the specification of project specific default epidemiological and procedure metadata fields for comparison tables is supported now. - Furthermore, for Windows 10/Windows Server 2019 (with installed Windows Subsystem for Linux) and Linux CLIENT users only we support the new super fast NCBI SKESA de novo assembler. In addition, we support a contamination check, automatic project choosing for a multiple species run, and import of Illumina sequencing run details (InterOp files). Finally, smaller improvement and several bug-fixes are part of this release.
Novel core genome MLST (cgMLST) scheme for Enterococcus faecalis published
SeqSphere+ was used to establish and evaluate a cgMLST scheme for Enterococcus faecalis (JCM ahead of print, 2019).
Novel core genome MLST (cgMLST) scheme for Clostridium difficile published
SeqSphere+ was used to establish and evaluate a cgMLST scheme for Clostridium difficile (JCM 56: e01987-17, 2018).
SeqSphere+ Version 5.0 released that is freely available to customers
This is a major update that features most importantly an improved cgMLST.org functionality, i.e., anonymized sample submission to cgMLST.org and the possibility to withdraw already submitted samples was added. In addition, the search similar samples in database function was improved (possibility now to limit the search by place and time) and the speed of searches was vastly enhanced. Furthermore, the database size will reduce to about 50% of the previous size by internal conversions and compressions. Finally, smaller improvement, renaming of functions/commands (most importantly ‘Cluster Type’ was renamed into ‘Complex Type’ and minimum spanning tree ‘Complexes’ into ‘Clusters’), and several bug-fixes are part of this release.
Origin and evolution of community-acquired Staphylococcus aureus USA300 clone
SeqSphere+ was instrumental in helping to elucidate the origin and evolution of community-acquired Staphylococcus aureus ST8 (Proc Natl Acad Sci U S A. 2017 Nov 20. pii: 201702472).
Novel core genome MLST (cgMLST) scheme for Acinetobacter baumannii published
SeqSphere+ was used to establish and evaluate a cgMLST scheme for Acinetobacter baumannii (PLoS One 12: e0179228, 2017).
High interlaboratory reproducibility and accuracy of NGS based bacterial genotyping in a ring trial
SeqSphere+ was used in an international bacterial genomic typing ring trial with high reproducibility and accuracy (JCM 55: 908, 2017).
Real time genome sequencing with SeqSphere+ of resistant bacteria provides precision infection control in an institutional setting
The increasing prevalence of multidrug-resistant (MDR) bacteria is a serious global challenge. In a just published study (J. Clin. Microbiol. 54: 2874, 2016) it was prospectively analyzed whether bacterial whole-genome sequencing (WGS) for real-time MDR surveillance is technical feasible, returns actionable results, and is cost-beneficial. WGS was applied to all MDR isolates of four species (methicillin-resistant Staphylococcus aureus [MRSA], vancomycin-resistant Enterococcus faecium, MDR Escherichia coli, and MDR Pseudomonas aeruginosa) at the University Hospital Muenster, Muenster, Germany, a tertiary care hospital with 1,450 beds, during two 6-month intervals. More than 1,200 isolate WGS data were analyzed automatically with the Ridom SeqSphere+ tool. Turnaround times (TAT) were measured, and total costs for sequencing per isolate were calculated. After cancelling prior policies of preemptive isolation of patients harboring certain Gram-negative MDR bacteria in risk areas, the second interval was conducted. During interval I, 645 bacterial isolates were sequenced. From culture, TATs ranged from 4.4 to 5.3 days, and costs were €202.49 per isolate. During interval II, 550 bacterial isolates were sequenced. Hospital-wide transmission rates of the two most common species (MRSA and MDR E. coli) were low during interval I (5.8% and 2.3%, respectively) and interval II (4.3% and 5.0%, respectively). Cancellation of isolation of patients infected with non-pan-resistant MDR E. coli in risk wards did not increase transmission. Comparing sequencing costs with avoided costs mostly due to fewer blocked beds during interval II, €200,000 in excess was saved. Real-time microbial WGS in our institution was feasible, produced precise actionable results, helped to monitor transmission rates that remained low following a modification in isolation procedures, and ultimately saved costs.
Meningococcal disease: identification of a sexually transmitted variant
A study elucidates the mechanisms of the emergence of an outbreak of meningococcal disease in men who have sex with men (MSM).
SeqSphere+ Version 3.1 released that is freely available to customers
This is a maintenance release with a number of smaller improvements and bug fixes (e.g., EBI ENA submission works now again after EBI has changed some details of the API; proxy support for SRA download). Most important the cgMLST Target Definer and our NCBI Genome Browser now support bacteria with multiple chromosomes. In addition draft genomes can be now chosen if really needed in the Target Definer as reference genomes. All NCBI codon translation tables are now properly supported on various places in the SeqSphere+ software. Furthermore, export of core and/or accessory genome gene concatenated SNPs in FASTA file format is now supported. Finally, also export of trees in publication ready EMF format that immediately can be read by e.g. MS PowerPoint is now implemented. For a full list of version changes invoke the SeqSphere+ menu command Help | About.
SeqSphere+ version 3.0 released that is freely available to customers with GIS & epi-curve functionality and SRA interface
Most important we have now implemented geographical information system (GIS) and epi-curve functionality for visualization of the four dimensions place, time, ‘person’, and type. Furthermore, a convenient download of NCBI complete and draft genomes and raw reads from the Sequence Read Archive (SRA) has been realized. Finally, a first version of sample reports has been incorporated as major new feature. In addition, bug-fixes and many smaller usability enhancements are part of this release.
Novel core-genome MLST typing scheme for Listeria monocytogenes presents prospects for a standardized,
portable and expandable typing method based on whole genome sequencing.
SeqSphere+ was used to establish and evaluate a cgMLST scheme for Listeria monocytogenes.(JCM 53: 2015)
Novel core-genome MLST typing scheme for Legionella pneumophilia presents prospects for a standardized,
portable and expandable typing method based on whole genome sequencing.
SeqSphere+ was used to establish and evaluate a cgMLST scheme for Legionella pneumophilia. (Eurosurveillance 20: 2015)
SeqSphere+ Version 2.3 with Raw Read Data Submission to EBI ENA Released
As more and more of our customers start using the software on a daily basis for routine surveillance tasks we laid great emphasis in implementing productivity enhancement features.
In more than 99% of all S. aureus samples the correct Spa type could be extracted by Ridom SeqSphere+ from WGS data
From 423 MRSA strains encoding 75 different spa types (with 2-19 repeats) the correct Spa type could be extracted in 99.1% from WGS data (250bp Nextera XT read pairs; SeqSphere+ analysis with incorporated Velvet assembly) (CMI 20: 2014).
Article in Press...
Review: WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories
Review 'WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare?' just published that includes Ridom SeqSphere+ among other tools. (Pathogens 3: 2014).
Whole genome based Mycobacterium tuberculosis surveillance: A standardized, portable, and expandable approach
A new study published in Journal Clinical Microbiology demonstrated that standardization of whole genome sequencing based (WGS) genotyping of the bacteria causing tuberculosis (TB) is possible, and can be used for improved tracing of pathogen transmission (JCM 52: 2014).
MRSA whole genome typing with Ridom SeqSphere+ and MLST+
Bacterial whole genome sequencing revisited: portable, scalable and standardized analysis for typing and detection of virulence and antibiotic resistance genes (JCM 52: 2014).
Listeria whole genome typing with Ridom SeqSphere+ and MLST+
Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011-2013. (CMI 20: 2014).
Life Technologies released App-note describing Ridom SeqSphere+
Life Technologies Corporation (NASDAQ: LIFE) just has released an App-note describing bacterial typing using the Ion PGM™ system and Ridom SeqSphere+ software.
Dag Harmsen discusses the advantage of benchtop sequencing for smaller laboratories
He believes that the afforability of benchtop sequencers, such as, the Ion PGM™ Sequencer is democratizing next generation sequencing, allowing smaller laboratories to compete with larger genome sequencing centers.
Play the Video...
Life Technologies Partners with Ridom and Releases SeqSphere+ Software to Speed and Simplify Bacterial Typing
Life Technologies Corporation announced that it is partnering with Ridom GmbH (Münster, Germany) to make SeqSphere+ whole genome bacterial typing software available for Ion Torrent users.
Update on next generation benchtop sequencing - Ridom SeqSphere+ software used for analysis
New study "Updating benchtop sequencing performance comparison" published in the Nature Biotechnology journal / MiSeq and PGM mature and affordable enough for soon application in routine epidemiologic surveillance for clinical and public health microbiology.
Rapid NGS for public health microbiology workshop
The in cooperation with PathoNGenTrace organized Workshop & Conference Rapid NGS for Public Health Microbiology was held successfully in Münster, Germany from March 4th to 8th 2013. About 80 participants from 20 countries attended the one day conference. 26 participants stayed for the whole week for a wet laboratory - Ion Torrent PGM and Illumina MiSeq bacterial whole genome sequencing - and computer class part (CLC Genomics Workbench, BIGSdb, Outbreaker, Ridom SeqSphere+ and CloVR).
Ridom celebrates 10-year anniversary
Founded January 2003 Ridom GmbH (Münster, Germany) celebrates its ten year anniversary. We are proud due to the loyal and continuous support of our customers to serve the clinical and public health microbiology community for such a long time. Stay another ten years with us and watch out for 'cool' new software products to be released soon.
Patho-NGen-Trace project With Ridom as consortium member started
The Patho-NGen-Trace project, proposed to the FP7 (Seventh Framework Programme for Research and Technological Development), has been started. The overall objective of Patho-NGen-Trace is to foster the development of new and widespread applications of Next Generation Sequencing (NGS) in clinical microbiology and disease surveillance, ranging from basic research to medical research, diagnostics, and pathogen genotyping. Major aim of Patho-NGen-Trace is to bring NGS from a basic research tool to a highly efficient technology for pathogen typing and diagnostics on the EU level.