The Fecal Bacteria

In studies of environmental quality, there are several different groups of bacteria frequently used as fecal indicators. The most widely applied approach is to use the group represented by the family Enterobacteriaceae (coliforms and fecal coliforms). Fecal indicators other than Escherichia coli, include members of the genus Enterococcus (formally fecal streptococci) and the anaerobic bacteria Clostridium perfringens, Bifidobacteria, and some members of the genus Bacteroides. Due to their widespread use as indictors of the quality of water and other environments, this chapter covers the phylogeny, taxonomy, and physiology of the key fecal indicator bacteria. E. coli and K. pneumoniae are specifically classified as fecal coliforms. The major set of phenotypic characteristics defining the Enterobacteriaceae family include the following: small gram-negative rods, facultative but preferring aerobic metabolism, oxidase negative, catalase positive, can reduce nitrates to nitrites, do not require Na+ for growth, can ferment D-glucose, and contain enterobacterial common antigens. Originally, classification of coliform bacteria was based on fermentation of sucrose and dulcitol, production of indole and acetylmethylcarbinol, and gelatin liquefaction. Functionally, enterococci are divided into five groups based on their ability to produce acid from mannitol and sorbose, and hydrolyze arginine. Bacteroides spp. are present in much greater numbers than E. coli, and can account for up to 30% of the total fecal isolates, with the most common species being B. vulgatus, B. distasonis, and B. thetaiotaomicron.

This chapter talks about the distribution of the major indicator bacteria, Escherichia coli, Enterococcus spp., and a variety of anaerobes (including Clostridium perfringens, Bifidobacteria spp., and members of the Bacteroidales) in humans, in domesticated animals and birds, and in undomesticated animal hosts. Enterococci are gram-positive bacteria ubiquitously found in the gastrointestinal (GI) tracts of animals, birds, and humans, as well as in soil and water. Enterococci are widely distributed among undomesticated mammals and birds, reptiles, and insects. Culture-independent analyses of total fecal bacterial microflora have been conducted with swine and equine samples using 16S rRNA gene libraries prepared from fecal DNA extracts and universal PCR primers for eubacterial 16S rRNA genes. A study by Fogarty and Voytek confirmed the presence of Bacteroidales in the feces of deer (Cervus sp.) inhabiting Virginia and West Virginia. In this study, feces were collected from 21 individual deer and extracted DNA was amplified with primers capable of amplifying 16S rRNA DNA from members of the Bacteroidales group. Fecal indicator bacteria shed by humans and domestic animals are subject to profound alteration of their abundance and characteristics by anthropogenic effects of antibiotic use and waste treatment.

Early studies that examined the survival of fecal indicator bacteria (FIB) in water and their potential impact on water quality were focused on the influence of point source (sewage) contamination and dilution in the nearshore coast. Wave action is one of the primary means by which Escherichia coli and other enteric bacteria may be transported from distant source water to beach sand. Alderisio and DeLuca found that the potential impact of fecal coliforms from bird feces is not only related to the numbers and types of birds, but also to the duration and time of day that the birds roost on the surface water and their defecation rates. Microbial occurrence, survival, and growth in natural environments such as soil, sediments, and water are influenced by various physical, chemical, and biological factors, the extent of which may vary by environment. A section in the chapter addresses how environmental factors, such as temperature, moisture, predation, and competition, influence the population dynamics of FIB in the environment. A number of complex and often interrelated physical processes control the levels of FIB in nearshore waters including turbulent diffusion and dispersion, alongshore transport, dilution, advection, sedimentation, and resuspension. These physical processes control the distribution of FIB in recreational water, which influences estimates of nearshore beach water quality.

This chapter provides a basic review of deterministic and empirical statistical modeling and their application for predicting microbiological surface water quality. The key to deterministic model development is the conceptualization of the various processes affecting fate and transport of fecal bacteria in the environment. Several different types of deterministic models have been applied to fecal bacteria in surface waters. A simplified conceptual model for fecal bacteria in surface water is presented. The chapter describes various processes that affect the fate and transport of fecal indicator bacteria (FIB) in surface waters and provide examples of their mathematical parameterization. The movement of bacteria from one water parcel to another occurs because of advection, diffusion, and dispersion. Advection is the movement of bacteria with water. In surface waters, velocities must be measured using flow meters to gain insight into the importance of advection. Kinetic models have been used extensively to model particle aggregation in surface waters, but have not yet been applied to the study of fecal bacteria-particle interactions in surface waters. There are four steps in the development of a statistical model. First, appropriate predictors must be selected to be used as independent variables in the model. Second, the statistical method must be chosen (e.g., multiple linear regression, partial least squares regression, random forests). Third, the model must be trained, or developed. Finally, the model must be validated using an independent data set.

This chapter examines the available information concerning prevalence, survival, and, ultimately, fate of enteric bacterial pathogens in different environments and under various conditions. The bacterial pathogens discussed in this chapter are those known to have a water-based or water-mediated transmission route between the environment and humans. Animal contamination, especially by bird flocks, is believed to be a primary source of campylobacters in remote water environments and Campylobacter jejuni has been consistently isolated from wild bird populations. Sand in particular appears capable of supporting significant populations of enterococci, especially when compared to water. It is clear that enterococci are capable of multiplication under simulated environmental conditions; however, whether these types of conditions are ever naturally present in the environment is debatable. Studies suggest that Salmonella is capable of surviving for extended periods in the environment, especially within soil and livestock waste. The presence of bacteria in the environment is essentially dependent on two factors: loading and survival. Pathogenic Vibrio spp. are also clearly capable of persistence and growth within the aquatic environment. Many of the studies examining characteristics of enteric pathogens in the environment have focused on the presence of these organisms in aquatic environments and water supplies, perhaps because this is viewed as the most likely vector for human infection. Recent studies have presented novel, molecular-based approaches to detection or quantification of certain enteric pathogens.

Enterococcus, Bifidobacterium, and coliphages have been proposed as fecal indicator bacteria for foods, but to this date E. coli continues to be used as the preferred indicator of fecal contamination. Although there is significant controversy whether the term "fecal indicator"; can be applied unequivocally to any of the groups of microorganisms discussed in this chapter, presently, most microbiologists agree on the value of testing some of them as general indicators of the quality and hygiene of foods. The characteristic IMViC profile of E. coli and other Enterobacteriaceae classified as coliforms is provided in the chapter. Investigators often compared the usefulness of coliforms and enterococci as indicators of safety in foods. The term coliphages is used to refer to specific types of viruses or bacteriophages that are capable of infecting enteric bacteria and, specifically, E. coli. The rationale for the use of a fecal indicator microorganism is ultimately to signify the potential presence of pathogenic microorganisms. The distribution of fecal food-borne pathogens in animals is quite diverse. Although some bacteria have the unique ability to colonize the intestine of many different animal species, others are confined to a single or few species. The presence of other food-borne pathogens, such as Staphylococcus aureus, is also tolerated in some foods, but for the most part the use of pathogenic bacteria as indicator microorganisms is not encouraged. With the advent of novel, rapid, sensitive, and specific genomic and metabolomictechniques, better alternatives may be soon be discovered.