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Processed *Salmonella* Epidemiology Data
Synthetic Biology & Genetic Engineering
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About
Data on Salmonella enterica pathogen detection provides critical insights into bacterial strain characteristics, geographical spread, and associated antimicrobial resistance (AMR) genotypes. This resource is a processed version of a significantly larger original dataset, meticulously refined to ensure quality and readiness for immediate scientific investigation. Key processing steps included eliminating redundant duplicate rows, standardising data types, and strategically addressing missing values in vital fields such as location and strain information. This high-quality data product is suitable for direct application in public health, infectious disease monitoring, and microbial surveillance research.
Columns
The dataset consists of 14 columns, detailing various aspects of each microbial isolate. Key identifiers such as Isolate, BioSample, and AMR genotypes were validated to maintain consistency and reliability across the records. Other important fields include Strain data, the Location of isolation, and the Isolation type, which shows a split of approximately 72% clinical and 28% environmental/other sources. Time tracking is facilitated by the Create date column, which has been converted to a proper datetime format. Numerical attributes like Min-same and Min-diff were subjected to forward-filling to preserve data continuity.
Distribution
The product is available in CSV format, allowing immediate utilisation in standard data analysis environments like R or Python. The dataset spans 118.8 MB in size and contains approximately 419,000 valid records focused solely on the Salmonella enterica pathogen. This particular version has an expected update frequency of Never.
Usage
This data product is exceptionally well-suited for several critical research and operational applications:
- Epidemiological Studies: Analysing the movement and geographical distribution of Salmonella enterica strains and pinpointing potential outbreak origins based on SNP cluster data.
- Antimicrobial Resistance (AMR) Research: Investigating the occurrence and prevalence of resistance genotypes across different strains, which facilitates understanding of global AMR trends.
- Public Health Surveillance: Tracking pathogen diversity and evolutionary patterns over time, which supports timely interventions and policy generation.
- Environmental and Food Safety Analysis: Studying microbial isolates derived from environmental samples and food sources to improve established safety protocols.
Coverage
The data records span a wide time period, running from a minimum date of May 2010 up to a maximum date in August 2023. Geographically, the records originate from almost a thousand unique locations worldwide. The primary contributing regions include the USA (48%) and the United Kingdom (13%). Isolation data is heavily skewed towards clinical sources (72%).
License
Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Who Can Use It
- Microbiology and Epidemiology Researchers: For high-throughput analysis of strain lineage and geographic spread.
- Government Health Authorities: To enhance tracking and monitoring of infectious disease trends.
- Data Scientists: Needing high-integrity microbial data for predictive modelling and trend identification.
- Food and Environmental Safety Specialists: Requiring verified isolate data for risk assessment.
Dataset Name Suggestions
- Cleaned Salmonella enterica Pathogen Isolate Data
- AMR Genotype and Location Dataset for Salmonella
- Global Microbial Surveillance Records
- Processed Salmonella Epidemiology Data
Attributes
Original Data Source: Processed Salmonella Epidemiology Data
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Download Dataset in CSV Format
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