Civilization factors are responsible for the increasing of human exposure to mycobacteria from environment, water, and food during the last few decades. Urbanization, lifestyle changes and new technologies in the animal and plant industry are involved in frequent contact of people with mycobacteria. Type 1 diabetes is a multifactorial polygenic disease; its origin is conditioned by the mutual interaction of genetic and other factors. The environmental factors and certain pathogenetic pathways are shared by some immune mediated chronic inflammatory and autoimmune diseases, which are associated with triggers originating mainly from Mycobacterium avium subspecies paratuberculosis, an intestinal pathogen which persists in the environment. Type 1 diabetes and some other chronic inflammatory diseases thus pose the global health problem which could be mitigated by measures aimed to decrease the human exposure to this neglected zoonotic mycobacterium.

Mycobacteria in drinking water and in the water of swimming pools, whirlpools, hydrotherapy facilities and aquaria contribute significantly to human exposure to triggers of immune regulated chronic inflammatory and autoimmune diseases. Technological elements of water distribution systems, especially their inner surface, taps, shower heads and blind spots where sediments settle, affect the number of mycobacteria in the water. The review presents the possibilities of using analytical instruments for rapid determination of mycobacteria and for their typing as an alternative to classical culture and a method of monitoring specific nucleic acid sequences by polymerase chain reaction (PCR). Information about the use of flow cytometry (FCM), matrix-assisted laser desorption ionisation time-of-flight (MALDI-TOF) spectrometry, Raman and infrared (IR) spectroscopy and biosensors are presented.