Nevin Manimala Statistics

Bacteria spatial tracking in Urban Park soils with MALDI-TOF Mass Spectrometry and Specific PCR

BioData Min. 2023 Jan 14;16(1):1. doi: 10.1186/s13040-022-00318-6.


Urban parks constitute one of the main leisure areas, especially for the most vulnerable people in our society, children, and the elderly. Contact with soils can pose a health risk. Microbiological testing is a key aspect in determining whether they are suitable for public use. The aim of this work is to map the spatial distribution of potential dangerous Enterobacteria but also bioremediation useful (lipase producers) isolates from soils in an urban park in the area of Valencia (Spain). To this end, our team has collected 25 samples of soil and isolated 500 microorganisms, using a mobile application to collect information of the soil samples (i.e. soil features, temperature, humidity, etc.) with geolocation. A combined protocol including matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing PCR has been established to characterize the isolates. The results have been processed using spatial statistical techniques (using Kriging method), taking into account the number of isolated strains, also proving the reactivity against standard pathogenic bacterial strains (Escherichia coli, Bacillus cereus, Salmonella, Pseudomonas and Staphylococcus aureus), and have increased the number of samples (to 896 samples) by interpolating spatially each parameter with this statistical method. The combined use of methods from biology and computer science allows the quality of the soil in urban parks to be predicted in an agile way, which can generate confidence in its use by citizens.

PMID:36639651 | DOI:10.1186/s13040-022-00318-6

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