An apparatus in one embodiment comprises a distributed data processing system in which multiple processing devices communicate with one another over at least one network. The distributed data processing system is configured to obtain reads of biological samples of respective sample sources, with each of the biological samples containing genomic material from a plurality of distinct microorganisms within an environment of a corresponding one of the sample sources, and to perform distributed data analytics to characterize an actual or potential outbreak of at least one of a disease, an infection and a contamination that involves genomic material from multiple ones of the distinct microorganisms in one or more of the sample sources. Performing distributed data analytics illustratively comprises performing local analytics in respective ones of a plurality of data zones, and performing global analytics utilizing results of the local analytics performed in the respective data zones.