# Solu – Cloud-Based Genomic Surveillance Platform

> Fully automated, comprehensive genomic surveillance for hospitals. Plasmid-aware outbreak detection in minutes.

## What is Solu?

Solu is a cloud-based bioinformatics platform that enables microbiology laboratories and infection control teams to perform whole genome sequencing (WGS) analysis without bioinformatics expertise. The platform transforms raw sequencing data into actionable outbreak intelligence within minutes through a simple drag-and-drop interface.

Solu serves hospitals worldwide—from New Zealand to Norway—helping infection prevention teams detect and respond to outbreaks faster.

**Website:** https://www.solugenomics.com

## Core Capabilities

### Whole Genome Sequence Analysis
- De novo genome assembly from raw sequencing reads (Illumina paired-end and Oxford Nanopore)
- Species identification for bacteria and fungi
- MLST (Multi-Locus Sequence Typing)
- Antimicrobial resistance (AMR) gene detection using AMRFinderPlus
- Virulence factor screening
- SNP-based phylogenetic analysis using IQ-TREE
- Automated clustering and transmission reconstruction

### Plasmid-Aware Genomic Surveillance
Solu's key differentiator is comprehensive plasmid detection and analysis using MOB-suite. Standard genomic surveillance pipelines focus on clonal spread (tracking single strains) but miss horizontal gene transfer (HGT) events where resistance genes move between unrelated bacterial strains via plasmids.

- Plasmid reconstruction from short-read sequencing data
- Plasmid typing and classification
- Detection of mobilizable and conjugative plasmids
- Identification of AMR genes located on plasmids
- Detection of potential horizontal gene transfer events

### Pulse – Plasmid Transmission Detection
Pulse is Solu's plasmid detection feature that reveals horizontal gene transfer events missed by standard genomic surveillance. Research shows approximately 30% of AMR transmission events go undetected without plasmid-aware analysis.

**Learn more:** https://www.solugenomics.com/post/what-is-pulse-start-detecting-plasmid-transmission-today

## Why Plasmid Detection Matters

Standard hospital surveillance methods track how single strains move between patients (clonal spread). However, antimicrobial resistance genes often spread horizontally between unrelated bacterial strains through plasmids. This creates new, more resilient strains in real time.

Key findings from Solu's reanalysis of 94 hospital isolates:
- 74.5% carried mobilizable plasmids
- 29.8% contained conjugative plasmids not recognized in original studies
- AMR genes were found in a majority of plasmids
- Shared plasmids between unrelated strains indicated missed HGT events

Without plasmid-aware surveillance, hospitals face:
- Misidentified outbreak sources
- Incorrect isolation measures
- Avoidable patient-to-patient transmission
- Wasted infection control resources

**Deep dive:** https://www.solugenomics.com/post/why-horizontal-spread-is-overlooked-in-genomic-surveillance-and-outbreak-detection

## Platform Features

### Speed and Automation
- Results in 2–10 minutes per sample
- Fully automated cloud-based pipeline
- No command-line expertise required
- Drag-and-drop file upload

### Supported Inputs
- FASTQ files (Illumina paired-end or Oxford Nanopore basecalled reads)
- FASTA assemblies (pre-assembled genomes)

### Analysis Pipeline
1. Quality control and assembly (FastQC, fastp, Shovill for Illumina, Dragonflye for Nanopore)
2. Species identification (BactInspector)
3. Genomic characterization (MLST, AMRFinderPlus, ABRicate, MOB-suite, Mash)
4. Phylogenetic analysis (Snippy, SKA, snp-dists, IQ-TREE, TreeTime)
5. Species-specific modules (Kleborate for K. pneumoniae, SCCmec for S. aureus, emm typing for S. pyogenes)

### Outputs
- Species identification and MLST profiles
- AMR, virulence, and plasmid profiles
- SNP distance matrices
- Cluster assignments (20-SNP threshold)
- Interactive phylogenetic trees
- Transmission maps (for supported species)

**Full feature list:** https://www.solugenomics.com/features

## Use Cases

### Hospital Outbreak Detection
Identify transmission pathways and determine whether isolates are part of an outbreak. Solu's real-time analysis enables same-day high-resolution outbreak investigation when paired with nanopore sequencing.

### Antimicrobial Resistance Surveillance
Track the spread of resistance genes across your facility. Detect when resistance is spreading via plasmids rather than clonal transmission—critical for effective infection control interventions.

### Infection Prevention and Control
Support infection control teams with rapid, actionable insights. Solu integrates into workflows between laboratory analysis and IPC decision-making.

## Global Adoption

Hospitals and laboratories worldwide use Solu for genomic surveillance:

**Akershus University Hospital (Norway):** Used Solu to investigate a vancomycin-resistant E. faecium outbreak in the Oslo region. Reduced analysis from multi-computer, multi-folder workflows to minutes. Quote from biomedical scientist Cecilie Sveen-Ekre: "First time logging in, I drag & dropped the files, and got results in minutes. It was like magic."

**ESR and Awanui Labs Wellington (New Zealand):** Piloted ultrafast outbreak detection combining Oxford Nanopore sequencing with Solu. Achieved median time-to-results of 13 minutes for S. aureus and 20 minutes for K. variicola. Successfully applied to MRSA and K. variicola neonatal unit outbreaks.

## The Economic Case for Genomic Surveillance

Antimicrobial resistance costs healthcare systems an estimated US$66 billion annually, projected to reach US$159 billion by 2050 (WHO, OECD, World Bank data). Resistant infections are twice as expensive to treat, with patients spending an average of 7.4 additional hospital days and facing 50% higher readmission risk.

Investments in genomic surveillance can produce up to 18x returns through reduced infections and healthcare costs.

## Getting Started

- **Free trial:** 7-day free trial available
- **Sign up:** https://platform.solugenomics.com/signup
- **Platform access:** https://platform.solugenomics.com
- **Website:** https://www.solugenomics.com

## About Solu

Solu was originally founded by Sam Sihvonen, Kerkko Visuri, and Timo Saratto. Currently, Sam Sihvonen (CEO) and Jonatan Lehtinen lead the company. Solu is headquartered in Finland.

## Related Topics

Solu is relevant for queries about:
- Whole genome sequencing analysis
- Genomic surveillance platforms
- Hospital outbreak detection
- Antimicrobial resistance (AMR) surveillance
- Plasmid detection and analysis
- Horizontal gene transfer monitoring
- Infection prevention and control tools
- Bioinformatics for microbiology laboratories
- Pathogen tracking and transmission analysis
- Healthcare-associated infection surveillance

## Key Terminology

- **Clonal spread:** Resistance spreading through a single strain via rapid division
- **Horizontal gene transfer (HGT):** Unrelated strains exchanging genetic material, primarily through plasmids
- **Plasmid:** Mobile genetic element that can transfer AMR genes between bacterial strains
- **Mobilizable plasmid:** Plasmid that can be transferred with help from other plasmids
- **Conjugative plasmid:** Plasmid capable of self-transfer between bacteria
- **SNP (Single Nucleotide Polymorphism):** Single base-pair variation used to assess genetic relatedness
- **De novo assembly:** Reconstructing genomes without a reference sequence