Ecology of Pathogens and Antibiotic-resistant Bacteria in Environments: Challenges and Opportunities

Abstract

Various bacteria can cause human diseases. They spread directly from person to person or indirectly via various environmental matrixes, such as food and water. Major food-and waterborne pathogens include Campylobacter, Listeria, Salmonella, Shigella, Shiga toxin-producing Escherichia coli, Salmonella, Yersinia, and Vibrio (31). Most of these pathogens spread through the fecal-oral route. Their primary hosts include humans, farm animals (e.g., cows, pigs, and chickens), and wildlife (e.g., deer, birds). These hosts contribute to the spread of pathogens. For example, geese and other birds are known to harbor diverse Campylobacter (29, 40, 59) and Salmonella spp. (40). However, some of these pathogens also survive for long periods of time and even grow in environments such as water, soil, sediment, and algae (13, 22, 32), in many cases in association with or by forming biofilms (35, 36, 52). Since difficulties are associated with detecting various pathogens in a timely manner, the microbial quality of food and water has been monitored using so-called fecal indicator bacteria (FIB), such as E. coli and enterococci (22, 24). Although their primary habitats are the gastrointestinal tracts of warmblooded animals (18, 49), some FIB strains are more adapted to soil or other environments (22, 24, 37). Moreover, alternative FIB, such as Bacteroides, have been used to identify the occurrence of pathogens and their potential sources of contamination (28, 59). However, poor correlations have been reported between pathogen and FIB concentrations (23, 58), which limits the use of FIB for predicting the occurrence of pathogens. Some opportunistic pathogens, including Mycobacterium avium and Legionella pneumophila, are not of a fecal origin. These opportunistic pathogens use environments such as water distribution systems (11, 14, 15) and showerhead biofilms (12) as their primary habitats, and occasionally infect humans to cause diseases. Furthermore, various environmental bacteria have been reported as emerging pathogens. Among these, Arcobacter spp. are of great interest because this genus is frequently and abundantly detected in many wastewater treatment plants (10, 50). This genus is phylogenetically closely related to Campylobacter, but is metabolically more versatile and can grow at relatively low temperatures and with a wider range of O 2 concentrations (9). Some members of Arcobacter have also been reported to form symbiotic relationships with protists (16). A better understanding of the ecology of these environmental pathogens is essential for preventing their occurrence and spread (39, 47).

A High-Throughput Microfluidic Quantitative PCR Platform for the Simultaneous Quantification of Pathogens, Fecal Indicator Bacteria, and Microbial Source Tracking Markers

“…High-throughput quantitative PCR is a powerful method to quantify multiple genes of interest for many samples (Ishii, 2019). When microfluidic technology is used to dispense and mix reagents and samples for high-throughput qPCR, it is called microfluidic qPCR (MFQPCR).…”

High-Throughput Microfluidic Quantitative PCR Platform for the Simultaneous Quantification of Pathogens, Fecal Indicator Bacteria, and Microbial Source Tracking Markers

“…High-throughput quantitative PCR is a powerful method to quantify multiple genes of interest for many samples . When microfluidic technology is used to dispense and mix reagents and samples for high-throughput qPCR, it is called microfluidic qPCR (MFQPCR).…”

Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission

“…The environment is a known reservoir for both opportunistic pathogens and antimicrobial resistant (AMR) bacteria ( Ishii, 2019 ). It is important to investigate environmental microbial populations as prominent extended-spectrum β-lactamases (ESBLs), quinolone resistance genes and carbapenemases originated from marine and soil bacterium and have subsequently entered clinical isolates through horizontal gene transfer (HGT) ( Poirel et al., 2005 ; Wyres and Holt, 2018 ), as well as identifying potential infection transmission pathways ( Ishii, 2019 ).…”