The transmission route used by many bacterial pathogens of clinical importance includes a step outside the host; thereafter refer to as the non-clinical environment. Obvious examples include food-borne and water-borne pathogens and also pathogens that are transmitted by hands or aerosols. In the non-clinical environment, pathogens have to cope with the presence of toxic compounds, sub-optimal temperature, starvation, presence of competitors and predators. In addition to virulence factors, pathogens must have genetic factors directed at resisting harmful conditions in the non-clinical environment. Many intracellular pathogens, such as Legionella, Salmonella, Yersinia and Mycobacterium, have the ability to infect and replicates inside amoeba, once outside the mammalian host, while other produce spores, such as Bacillus and Clostridium, or enter a viable but non-culturable state (VBNC) or other form of persistence state. For the pathogen, a genetic dilemma arises between the necessity to survive outside the host and the need to cope with the host defenses and establish an infection; however this dilemma is relieved when the virulence factors also mediate survival in the non-clinical environment as well. Many virulence factors used by pathogens to infect mammalian hosts are useful in the non-clinical environment, including type 3 and type 4 secretion systems, toxins, iron chelating systems and others. Those systems are used to counteract predation by amoeba and invertebrates and acquire iron in the highly competitive non-clinical environment. Therefore, many of the virulence systems used in the mammalian host context are also of importance outside of it and a better understanding of these system and their associated benefit is likely to provide a better understanding of the evolutionary pathway leading to virulence. Furthermore, genetic systems mediating persistence in the non-clinical environment are involved in the establishment of chronic infection. In addition, for many pathogens that are transmitted to the mammalian host from the external environment, high survival and replication in the non-clinical environment mean a better chance to successfully be transmitted to the host and to colonize it. Better knowledge of the ecology of bacterial pathogens in the non-clinical environment is likely to result in a better control of transmission routes and a decrease in the burden of infectious diseases. The primary goal of this research topic is to provide the reader with an overview of the strategy used by bacterial pathogens to survive and replicate outside the host and to present some of the latest research on the relationship between non-clinical environment and bacterial pathogens.
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