In a very long time after its first discovery by a Bavarian pediatrician in the late 19th century, Escherichia coli was recognized as a harmless bacterial species and as a normal flora in the gastrointestinal tract of warm-blooded animals and reptiles. However, several highly adapted commensal clones were found to have the ability to acquire specific virulence attributes and become highly virulent and even frequently deadly pathogens. Now, it is known that a spectrum of human and animal intestinal and extraintestinal diseases is associated with pathogenic E. coli, and several categories of E. coli pathotypes, including enteropathogenic E. coli, enterohemorrhagic E. coli, enterotoxigenic E. coli, enteroaggregative E. coli, enteroinvasive E. coli, diffusely adherent E. coli, uropathogenic E. coli, meningitis/sepsis-associated E. coli, and an additional animal pathotype, known as avian pathogenic E. coli, have been well described. This chapter focuses on these E. coli pathotypes, their clinical features, pathogenesis, epidemiology, and diagnosis.

Enteroviruses and rhinoviruses are small, nonenveloped RNA viruses in the family Picornaviridae. The viral genome consists of a single-stranded, positive-sense RNA genome of approximately 7.5 kilobases. The genus Enterovirus contains 15 species of morphologically identical viruses that share similar virion structure, genomic organization, and replication strategies. Of these, seven enterovirus species (Enterovirus A to D and Rhinovirus A to C) are known to cause human disease. Enteroviruses and rhinoviruses contribute to a wide variety of clinical traits, presenting as mild illness to severe respiratory and neurological complications requiring hospitalization and, in some instances, resulting in death. Clinical syndromes associated with enterovirus and rhinovirus infection include respiratory illness, acute and chronic cardiac disease, hand-foot-mouth disease, herpangina, myositis, pleurodynia, eye infections, aseptic meningitis, encephalitis, and acute flaccid paralysis. In this chapter, the virological and genomic features of enteroviruses and rhinoviruses, as well as the epidemiology, clinical manifestations, diagnosis, and treatment of enteroviral infections, with focus on nonpolio enteroviruses and diseases, are reviewed.

Thousands of bacterial genomes have been sequenced, analyzed, and applied for different purposes. This chapter starts with the introduction of bacterial genomes, genome sequencing methods, and subsequent genetic annotation. Pan-genome and phylogeny analyses allow us to analyze many genomes simultaneously. Many tools have been developed to support the analysis of bacterial protein features, such as subcellular location and adhesin probability. Proteome-wide analysis of these features allows us to further predict vaccine antigen candidates and virulence factors, which is also the foundation of reverse vaccinology. Bacterial whole genome sequences have also been used in various applications such as genomic diagnosis, epidemiology, host–microbiome interaction and pathogenesis studies. Data FAIRness and ontology are required to support heterogeneous data standardization and integration.

Rotavirus is a leading cause of severe diarrhea and child mortality, especially in low-middle income countries. Although introduction of WHO-prequalified rotavirus vaccines into national immunization programs of more than 110 countries has substantially increased vaccination coverage, at the global level, rotavirus vaccination coverage remains low at around 50%. Further implementation of rotavirus immunization programs is expected to prevent additional pediatric deaths related to rotavirus diarrhea. New low-cost rotavirus vaccines that have received the WHO prequalification recently will augment rotavirus vaccine supply and help overcome economic barriers toward the increasing adoption of rotavirus vaccination programs.

Dental caries is an infectious disease that causes tooth demineralization and the formation of cavities. The etiology of caries is multifactorial, involving host factors such as salivary components, diet factors such as the availability of fermentable carbohydrates, and opportunistic pathogens in a polymicrobial community. The gram-positive facultative anaerobe Streptococcus mutans is the most well-studied cariogenic organism. This organism has three key virulence characteristics: biofilm formation via extracellular polymers, acid tolerance, and acid production. Extracellular glucans derived from dietary sugar serve as a reserve food supply, and together with adhesins specific for salivary pellicle components, allow retention on the tooth surface. S. mutans can rapidly transport and ferment a variety of dietary carbohydrates, producing organic acids, primarily lactic acid, and tolerate acidic conditions via a variety of mechanisms that maintain the cytoplasm at an optimal pH. These factors contribute to the acidification of the biofilm microenvironment, which demineralizes the enamel, dentin, and cementum of teeth. However, there are a myriad of other microorganisms in the oral cavity, many of which are acidogenic and acid-tolerant. As a result, S. mutans does not act alone, but rather interacts with other organisms in a concerted polymicrobial action to contribute caries.

Capsules are the outmost structures of bacterial and fungal cells. Capsules protect microbial cells from immune recognition and phagocytosis during infection of mammalian hosts. With the exception of the poly-γ-glutamate (PGA) capsule of Bacillus anthracis, other known capsules are all composed of polysaccharides. Certain bacterial species (e.g., B. anthracis and Streptococcus pyogenes) produce only one capsule structure, whereas many others express capsule variants with great biochemical, structural and immunogenic diversity within the same species. The genes for capsule synthesis are typically clustered in a single locus of the bacterial chromosome. The number of genes associated with capsule synthesis range from one in serotype 37 S. pneumoniae to as many as 22 in serotype 16A S. pneumoniae. Different bacterial species can share similar genes or mechanisms for capsule synthesis, reflecting horizontal gene transfer and recombination events. The expression of the capsule genes is often regulated by multiple mechanisms under changing environmental conditions. Finally, the immunogenic properties of capsular polysaccharides have been employed to develop vaccines against several encapsulated pathogens. The capsule biosynthesis pathway is also considered as a promising target for novel antimicrobials.

Yersinia enterocolitica is a common foodborne pathogen causing a zoonotic disease called yersiniosis in humans characterized by acute gastroenteritis and sometimes more serious conditions such as sepsis. Y. enterocolitica comprises a biochemically heterogeneous group with the ability to survive and grow at refrigeration temperature, which has considerable significance for food manufacturing and storage practice. Transimitted mainly via fecal–oral route, Y. enterocolitica-induced gastroenteritis is self-limiting. However, antimicrobial therapy is recommended for affected patients with sepsis or underlying immune disorders. Whole-genome sequencing and comparative genomics have identified several virulence factors related to pathogenicity on the genomes and pYV plasmids of three Y. enterocolitica strains, and the pathogenic mechanisms of Y. enterocolitica associated with these virulence factors have been clarified. Further examination of Y. enterocolitica microbiology, genomics, and epidemiology will be necessary for identification of new targets for improved treatment and prevention of this emerging foodborne pathogen.

The genus Pasteurella sensu stricto only includes the type species of the genus, Pasteurella multocida, and the species Pasteurella canis, Pasteurella stomatis, Pasteurella dagmatis, and Pasteurella oralis. These species are closely related according to 16S rRNA gene and conserved housekeeping protein sequence phylogeny. Other species are unrelated to P. sensu stricto even though they are validly named Pasteurella. The species excluded from the P. sensu stricto and labeled with the genus name in brackets are only described briefly: [Pasteurella] aerogenes, [Pasteurella] bettyae, [Pasteurella] caballi, [Pasteurella] caecimuris, [Pasteurella] langaaensis, [Pasteurella] mairii, [Pasteurella] skyensis, and [Pasteurella] testudinis. Members of P. sensu stricto are coccobacilli or rods, 0.3–1.0µm in diameter and 1.0–2.0µm in length, they are gram-negative, nonmotile, nonacid fast, and endospores are not formed. Growth is aerobic to microaerophilic or facultatively anaerobic. The metabolism is chemoheterotrophic with both oxidative and fermentative types of metabolism. The electron transport system is cytochrome-based with oxygen, nitrate, or fumarate as the terminal electron acceptor. Nitrate reductase is produced. Members of the genus are normally oxidase-positive, and the alkaline phosphatase and the catalase tests are positive. The optimum growth temperature of members of Pasteurella is 35°C–37°C. Members of the genus produce acid from (+)-d-glucose, (+)-d-galactose, (-)-d-fructose, (+)-d-mannose, and sucrose. There is no acid production from adonitol, meso-inositol, (+)-l-rhamnose, and (-)-l-sorbose. Members of the genus have a DNA GC content (mol%) of 36.8–43.5. In human beings, members of Pasteurella are mainly isolated from wound infections inflicted by animals. In this respect, members of the genus are zoonotic, since the main habitat of the genus Pasteurella is the oral cavity and respiratory tract of vertebrates including both mammals and birds. In animals, typical infections associated with P. multocida are hemorrhagic septicemia in cattle and buffaloes, fowl cholera in poultry, atrophic rhinitis in pigs, and snuffles in rabbits.

The genus Borrelia comprises two major groups of spirochetes with at least 43 validated species. The first group contains Borrelia species within the Borrelia burgdorferi sensu lato complex, which is transmitted by the hard Ixodes ticks and is associated with Lyme disease or Lyme borreliosis. The second group of spirochetes includes Borrelia species transmitted mainly by soft ticks Argasidae with a few exceptions and is associated with human relapsing fever (RF). The genus Borrelia possesses several genetic and phenotypic characteristics that are unique among prokaryotes. Borrelia species exist in nature in enzootic cycles primarily involving ticks and a wide range of animal and bird hosts. Both B. burgdorferi and RF borreliae have a linear chromosome of approximately 910kb and multiple linear and circular plasmids in a single cell. In this chapter, the general phenotypic and genetic features of Borrelia and associated clinical disease and diagnosis are discussed with a focus on their genome and molecular characteristics.

Parasites are a large group of eukaryotic organisms classified in the kingdoms Protozoa (flagellates and amoebae), Chromista (ciliates, sporozoa/apicomplexa, Blastocystis, and Pythium), and Animalia (helminths [roundworms, tapeworms, flukes, thorny-headed worms, and ringed worms] and arthropods [mites and ticks; lice, flies and fleas; and tongue worms]). In general, protozoa, chromists, and helminths reside mostly within the host, either intercellularly or intracellularly, and are considered as endoparasites, whereas arthropods dwell on the surface of the host and are considered as ectoparasites. However, exceptions to these rules exist. For example, ringed worms (e.g., leeches) in the phylum Platyhelminthes are blood-sucking ectoparasites, and tongue worms in the phylum Arthropoda are endoparasites, highlighting the need to further clarify their taxonomic status. Intracellular parasites often rely on a third organism (i.e., carrier or vector) for transmission to the host. Furthermore, some parasites spend their entire life in the host (e.g., Enterobius), and others may undergo free-living and parasitic stages during their life cycle (e.g., Strongyloides). The diversity, abundance, and adaptability of parasites offer continuing challenges for their identification, treatment, and prevention.