Microbial Pathogenesis: Mechanism and Recent Updates on Microbial Diversity of Pathogens

Abstract

Microorganisms or microbes are microscopic organisms that are found all around the globe and are too small to be seen by naked eyes. Microorganisms have a wide range of applications. They help to digest food, fasten the decay and decomposition processes, and produce macromolecules of industrial and commercial importance. They also help in environmental bioremediation and production of biofuels. Microorganisms are highly diversified in the environment ranging from single-celled to multicellular microscopic beings. They are classified as bacteria, archaea, fungi, protozoa, algae, and virus. Some of these also negatively impact our lives. They are pathogens and cause various diseases in humans, animals, and plants and also damage products and surfaces. Microorganisms produce various virulence factors, such as exoenzymes and toxins, which are responsible for causing diseases and invading host immune system. The pathogens enter into human body through various entry portals in the body after which they adhere to the receptors present on host cells. They damage host cells by either secreting biochemicals or by changing the morphology of host cells. This results in abnormal functioning of host cells which might even lead to death of cell or sometimes death of host too. Among these various classes of microbial diversity, pathogenic microorganisms constitute only a small portion, but they have high genetic diversity. A deep study of diversity of pathogens helps in understanding evolution and taxonomy of pathogens better along with their pathogenicity. This chapter focuses on the diversity of microorganisms and their subdivisions which affect plants, animals, and humans both positively and negatively. Moreover, the mechanisms by which various microorganisms cause pathogenesis in humans are also explained in this chapter along with the current scenario on different species of microbial pathogens.

3.1 Diversity of Microorganisms

Microorganisms or microbes are microscopic organisms that are found all around the globe. They are too small to be seen by naked eyes. Microorganisms have a wide range of applications. They help to digest food, fasten the decay and decomposition processes, and produce macromolecules of industrial and commercial importance. They also help in environmental bioremediation and production of biofuels. Some of the microorganisms also negatively impact our lives. They are pathogens and cause various diseases in humans, animals, and plants and also damage products and surfaces. Microbes are classified as bacteria, archaea, fungi, protozoa, algae, and virus.

3.2 Bacteria

All bacteria are unicellular organisms. They are classified as prokaryotes as they lack well-defined nucleus. They are found in varied environments including inside human gut, ocean, and soil. Relationship of human and bacteria is complex. They not only help humans in metabolism of food or fermentation of various food products, but they also cause diseases which at some cases may be lethal too. Typically, they have a length of 0.5–5 micrometers. According to their cellular shapes, they can be classified as bacilli (rod shaped, e.g., Bacillus, Clostridium, Propionibacterium, Corynebacterium), cocci (spherical or round shaped, e.g., Streptococcus, Staphylococcus, Micrococcus), spirilla (spiral shaped, e.g., Spirillum, Campylobacter, Helicobacter, Borrelia), and vibrio (comma or curved rod shaped). Unlike eukaryotic cells, they lack nucleus and membrane-bound organelles, such as mitochondria and endoplasmic reticulum. They have a cell wall made up of peptidoglycan and contain a circular chromosome in the cytoplasm. They can be classified as Gram-positive and Gram-negative on the basis of their cell wall composition. The presence of peptidoglycan layer in the bacterial cell wall binds strongly to a violet dye (crystal violet) and stains the cell purple. This dye is not retained in the Gram-negative bacterial cells, and hence their staining depends upon the secondary red-colored dye (safranin) used. Bacillus, Clostridium, Lactobacillus, Mycobacterium, Staphylococcus, Streptococcus, and Streptomyces are few genera of Gram-positive bacteria. The Gram-negative bacteria include Acinetobacter, Campylobacter, Enterobacter, Escherichia, Pseudomonas, and Shigella, most of which are pathogenic. On the basis of utilization of gaseous oxygen, they are categorized as aerobic (that live in the presence of oxygen), anaerobic (that live without oxygen), and facultative (that live with or without oxygen) and autotrophs or heterotrophs according to the way they obtain energy.

Multiplication of most bacteria is by binary fission wherein the parent bacterial cell grows in size, copies its DNA, and splits into two identical daughter cells. Another form of asexual reproduction occurring in bacteria is budding. Here, an organism develops as a bud which is pinched off as it matures. The process of horizontal gene transfer introduces variations in the bacterial genome. This occurs by transformation, transduction, and conjugation. In bacterial transformation, the cells take up short fragments of DNA from surrounding environment and integrate into their genome. Transduction also integrates DNA from environment by viruses called bacteriophage and transfers the DNA. Conjugation involves physical contact between two bacteria (known as donor and recipient) for transfer of genetic material.

Apart from their pathogenicity and contaminant in food, bacteria have a varied range of applications. In food industries, they are used for the fermentation of bread and production of yoghurt, cheese, and organic acids in pickles and vinegar. They are also exploited for the production of organic acids, enzymes, alcohols, acetones, and pharmaceutical products like human insulin, growth hormones, and vitamins. Bacteria present in the gut of cattle secrete cellulase that helps in the digestion of cellulose. Because of their specificity, few species of bacteria have also been used as an alternative to pesticides in pest control. Apart from these applications, they have the ability to digest pollutants and recycle them to energy and nutrients or to less toxic products.

3.2.1 Bacterial Pathogenesis

Pathogenic bacteria attach themselves to receptors present on host cells by adhesin. Adhesin is a protein or glycoprotein and is present on the surface of pathogens. Adhesins are present on the surface of pathogenic bacteria, fungi, virus, and protozoa. Examples of bacterial adhesins are type I fimbriae present on enterotoxigenic Escherichia coli (causing traveler’s disease) that help in attachment of bacteria to intestinal epithelial cells of host. Type IV pili on Neisseria gonorrhoeae help in its attachment to host urethral epithelial cell and cause gonorrhea. Streptococcus mutans produce adhesin P1 and attached to host teeth causing dental caries. Streptococcus pyogenes (causative agent of strep throat) produces F-protein and attaches to respiratory epithelial cells. N-Methylphenylalanine pili are produced by Vibrio cholerae and attach to intestinal epithelial cells causing cholera.

Patients who have bacteria present and multiplying in blood can get septic shock where the blood of the person decreases. This results in insufficient supply of oxygen and nutrients to cells and organism. Some bacteria also produce toxins which results in low blood pressure. Bacteria can also cause excessive swelling by release of many pro-inflammatory molecules from immune cells. They cause increased permeability of blood vessels which allows fluid to escape the bloodstream and enter tissues causing edema.

Exoenzymes are extracellular enzymes that help pathogen invade host cells and tissues. For example, Hyaluronidase S produced by Staphylococcus aureus, Clostridium perfringens, and Streptococcus pyogenes degrade hyaluronic acid present as intracellular cement in tissues. This increases the permeability of pathogens inside the tissue layers. Phospholipase C is also an exoenzyme produced by Bacillus anthracis. This enzyme degrades membrane of phagosomes which leads to escape of bacteria into cytoplasm. Collagenase produced by Clostridium perfringens degrades collagen present in connective tissue and promotes its spread to other cells. C. perfringens then multiply in blood and use toxins and phospholipase to cause lysis and necrosis. After the death of host cells, the organism ferments carbohydrates of muscles to produce gas. This results in necrosis of tissue with gas known as gas gangrene.

Pathogenic bacteria also produce biological poison called as toxins which invade the host by damaging tissues. They can be classified as endotoxins or exotoxins. An example of bacterial endotoxin is lipopolysaccharide (LPS) present on the outer membrane of Gram-negative bacteria. Lipid A is the lipid component of endotoxin and is highly conserved among Gram-negative pathogen. The Gram-negative pathogenic bacteria release endotoxin when the cells die during infection by pathogens. This results in disruption of host cell membrane. Lipid A triggers inflammatory response in host. The inflammatory response caused by low concentration of endotoxin in body is effective to defend against pathogens, whereas excessive inflammatory response due to high concentration of endotoxin can result in drop in blood pressure, multiple organ failure, and death of host. They are stable at high temperature (121 °C for 15 min) to get inactivated.

Exotoxins are produced by both Gram-positive and Gram-negative bacteria. Exotoxins are target specific and interact with specific receptors present on specific cells and cause cellular damage. They are inactivated at temperatures above 41 °C due to the presence of protein in them. Even small concentration of exotoxins is lethal. Exotoxins can be classified as intracellular targeting, membrane disrupting, and superantigens. The intracellular-targeting exotoxins consist of two subunits: A and B. The B subunit binds to specific receptors present on host cell, whereas the A toxin is responsible for interfering with the specific cellular activity. Examples of intracellular-targeting exotoxins are tetanus, botulinum, diphtheria, and cholera toxins. Membrane-disrupting toxins disrupt cell membrane by either degrading the phospholipid bilayer of cell membrane in host cells or by forming pores. Examples of membrane-disrupting toxins are hemolysins, leukocidins, and streptolysins. Superantigens trigger an excessive stimulation of immune cells to secrete cytokines known as cytokine storm. This results in a strong immune response and inflammation that may cause low blood pressure, high fever, multiple organ failure, and death. Examples of superantigen exotoxins are toxic shock syndrome toxin, streptococcal mitogenic exotoxins, and streptococcal pyrogenic toxins.

Bacteria produce a number of virulence factors to evade the immune system of host cells, especially phagocytosis. Capsules produced by many bacteria are used for the adhesion of bacteria to host cells. They also prevent ingestion of bacteria by phagocytes. In addition to this, the capsules increase the size of bacterial cells making them difficult to be engulfed by immune cells. Example of capsule-producing bacterium is Streptococcus pneumoniae. Pathogenic bacteria also produce protease. These proteases cleave and digest antibodies, thereby preventing phagocytosis and killing of bacteria. Some other virulence factors are M-protein and mycolic acid.

M-protein is present in fimbriae of Streptococcus sp. This protein alters the surface of Streptococcus and blocks binding of complement molecules. As complement molecules assist in phagocytosis, the binding of M-protein inhibits the process of phagocytosis, thereby evading the host immune system. Mycolic acid is a waxy substance present on the cell envelope of Mycobacterium tuberculosis. When the pathogen is engulfed by the phagocytes present in lungs, the mycolic acid coat helps the bacteria in resisting the killing of pathogen in phagolysosome.

Some bacteria also exploit the natural mechanism of the host cells by producing certain virulence factors. Coagulase, produced by Staphylococcus aureus, exploits the mechanism of blood clotting in host. The release of coagulase into the bloodstream results in clot formation without damaging blood vessels. This clot coats bacteria in fibrin and prevents the bacteria from getting exposed to immune cells in bloodstream. Kinases, another virulence factor, have effects opposite to coagulase. Kinases convert plasminogen to plasmin which digests fibrin clot. Kinases digest the clot and release trapped pathogens in clot to escape. Examples of kinases as virulence factors are streptokinase and staphylokinase produced by Streptococcus pyogenes and Staphylococcus aureus, respectively.

Another mechanism by which pathogens evade the immune system of host is antigenic variation. In this method, the surface proteins of pathogens are altered so that they are not recognized by host immune system, for example, variation of VlSE protein in Borrelia burgdorferi (causative agent of Lyme disease) and type IV pili in Neisseria gonorrhoeae (causative agent of gonorrhea).

3.2.2 Diseases Caused by Pathogenic Bacteria in Humans

Human body contains more number of bacterial cells than human cells themselves. Many species of bacteria are either harmless or beneficial to human being, whereas only a few species of pathogenic bacteria exist. The pathogenic bacteria are troublesome due to the generation of strains which show resistance to antimicrobial agents. Generally, the infections from these bacteria are nosocomial, that is, the infections of these multidrug-resistant strains originate from hospitals (Fair and Tor 2014). Few of such pathogenic bacterial strains are discussed below.

3.2.2.1 Enterococcus faecalis

Enterococcus faecalis is normally present in the gut of human beings but can cause serious human infections such as bacteremia, endocarditis, urinary tract infections, and wound infections. Among these infections, urinary tract infections are the most common and cause around 110,000 cases every year. The infections by E. faecalis are hospital-acquired infections and affect hospitalized people as they have weak immune system. The people at high risk of E. faecalis infections are those that have undergone surgery or undergoing cancer treatment, dialysis or HIV/AIDS patients and those who have received organ transplant or had root canal. The bacteria cause infections when they enter human body through wounds, blood, or urine. These infections are difficult to treat as the organism is resistant to multiple antibiotics. The intravascular and urinary tract catheter devices harbor E. faecalis, and hence their use also leads to spread of infection. The common infections caused by E. faecalis are bacteremia (infection of blood), endocarditis (infection of endocardium, heart’s inner lining), urinary tract infections (infections of the bladder, urethra, and kidneys), wound infections (infection through open cut, especially during surgery), periodontitis (infection of gum found in people who had root canal), and meningitis (inflammation of membranes surrounding the brain and spinal cord) (Kau et al. 2005).

3.2.2.2 Enterococcus faecium

Enterococcus faecium is a Gram-positive bacterium inhabiting the intestinal tract of humans (Fisher and Phillips 2009). It causes infections of the skin, urinary tract, and endocardium in humans (Arias and Murray 2012) and has been found to be associated with infections in ventilators, urinary drainage catheters, and central lines of medical intensive care units. It is one of the leading cause of multidrug-resistant enterococcal infections (Hidron et al. 2008). The vancomycin-resistant enterococci (VRE) were first detected in the late 1980s in hospitals in the USA, and since then, they have spread to Europe and worldwide making their treatment difficult (Werner et al. 2008). The World Health Organization has included vancomycin-resistant E. faecium in a list of antibiotic-resistant bacteria as a high-priority pathogen (Tacconelli et al. 2018). Germany experienced increased rates of VRE infections of the blood and urinary tract in intensive care units between 2007 and 2016 (Higuita and Huycke 2014; Remschmidt et al. 2018; Markwart et al. 2019).

3.2.2.3 Escherichia coli

Escherichia coli colonizes the gastrointestinal tract of humans in few hours after birth where they coexist with the host as commensals. They generally do not cause any disease but infect immunocompromised individuals or when the normal gastrointestinal barriers are breached. E. coli contains different disease-causing pathogens. They affect cell signaling, mitochondrial function, cytoskeletal function, mitosis, and protein synthesis in eukaryotes. They cause diverse disease in humans such as diarrhea to severe dysentery, cystitis or pyelonephritis in the urinary tract, hemorrhagic colitis, meningitis, and septicemia (Donnenberg and Whittam 2001; Kaper et al. 2004).

3.2.2.4 Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogenic bacterium that affects immunocompromised individuals and causes severe pulmonary disease. P. aeruginosa also results in neutropenia, severe burns, or cystic fibrosis (Lyczak et al. 2000). It is a leading pathogen for nosocomial infection. P. aeruginosa has been found in cystic fibrosis, pulmonary infections, burn wounds, urinary tract infections, and medical equipment, such as ventilators, inhalers, respirators, dialysis equipment, vaporizers, and anesthesiology equipment, and from toilet and sinks (Gales et al. 2001). Along with these infections, it also causes gastrointestinal infections; skin infections such as external otitis, folliculitis, and dermatitis; bacteremia; soft tissue infections; respiratory system infections in patients with cystic fibrosis; and bone and joint infections (Tacconelli et al. 2002; Gellatly and Hancock 2013; Alhazmi 2015; Azam and Khan 2019).

3.2.2.5 Staphylococcus aureus

Staphylococcus aureus causes skin infections, pneumonia, bone infections, heart valve infections, bacteremia, infective endocarditis, osteoarticular infections, soft tissue infections, pleuropulmonary infections, and device-related infections. These infections can be from mild to serious. These bacteria infect catheters that are inserted through the skin into the blood vessel or medical implants. The bacteria cause bacteremia by traveling through the bloodstream and infect heart valves and bones. Staphylococcus aureus also produce toxins that cause staphylococcal food poisoning, scalded skin syndrome, or toxic shock syndrome. Toxic shock syndrome progresses rapidly and causes rash, fever, low blood pressure, and multiple organ failure (Tong et al. 2015; Eswari and Yadav 2019).

3.2.2.6 Clostridioides d ifficile

Clostridioides difficile is a bacterium that causes diarrhea and colitis which can lead to serious bowel problems. C. difficile was discovered in 1935, but the antibiotic-associated diarrhea was not recognized until 1978. The widespread use of antibiotic clindamycin in the 1970s led to a rise in the infections of C. difficile. The broad-spectrum antibiotics increased the C. difficile epidemic in the next 20 years. The feces of patients infected with C. difficile contain bacterial spores, which when transferred to another person’s gastrointestinal tract through contaminated food or hands come to life. Normally, the bacteria remain dormant and do not develop any illness. But when good bacteria of the stomach are knocked down by antibiotics, C. difficile grows and multiplies. The bacteria produce toxins in the colon which injures the lining of the colon and causes diarrhea and inflammation. Generally, they affect those who have been taking broad-spectrum antibiotics or medication (proton pump inhibitor) to reduce amount of stomach acid, had surgery of the digestive tract, have weak immune system, are 65 years old, or have inflammatory bowel disease, kidney disease, or cancer. It causes around half a million infections in the USA every year with the recurrence of 1 in 6 patients in 2–8 weeks.

3.2.2.7 Streptococcus pneumoniae

Streptococcus pneumoniae causes pneumococcal disease which causes pneumonia, otitis, sinusitis, meningitis, and bacteremia. The bacteria mainly colonize mucosal surfaces of the upper respiratory tract of humans. Normally 27–65% of children and < 10% of adults are carriers of S. pneumoniae, which causes invasive inflammatory disease when it enters the bloodstream. Pneumococcal disease is common in low- and middle-income countries where availability of pneumococcal vaccine is less. Pneumococcal disease is common in dry season with tropical climate, whereas in temperate climate, it is more common during winter and early spring. In 2017, S. pneumoniae was included in the list of 12 priority pathogens by WHO (Dion and Ashurst 2020; Weiser et al. 2018).

3.2.2.8 Acinetobacter baumannii

Acinetobacter baumannii is the leading pathogen responsible for nosocomial infections among patients in intensive care units. A. baumannii leads to approximately 9% of hospital-acquired infections and can cause post-surgical urinary tract and respiratory tract infections in hospitalized patients. The major route of transmission of bacteria is via the hands of hospital staff. Acinetobacter results in mild-to-severe infections and can also be fatal. The severity of disease also depends on the site of infection and immune response of the individual (Joly-Guillou 2005; Lee et al. 2017).

3.2.2.9 Klebsiella pneumoniae

Klebsiella pneumoniae is an opportunistic pathogen which is found in the skin, mouth, and intestines. Klebsiella spp. affect immunocompromised individuals who suffer from diabetes mellitus or chronic pulmonary obstruction. K. pneumoniae is the most important infection-causing pathogen of Klebsiella spp. K. pneumoniae causes pyogenic liver abscess, necrotizing fasciitis, meningitis, severe pneumonia, endophthalmitis, soft tissue infections, septicemia, and urinary tract infections. The transmission of K. pneumoniae is via the hands of hospital staff and medical devices as K. pneumoniae forms biofilms on endotracheal tubes and catheters which causes infections in patients (Schroll et al. 2010). The hospital-acquired outbreaks of K. pneumoniae are generally caused by multidrug-resistant Klebsiella spp., the extended-spectrum β-lactamase (ESBL) producers. Klebsiella spp. account for approximately 8% of hospital-acquired infections in Europe and the USA. In the USA, Klebsiella is the eighth most important nosocomial infectious pathogen and causes around 3–7% of all hospital-acquired infections (Horan et al. 1988; Schaberg et al. 1991; Podschun and Ullmann 1998; Li et al. 2014).

3.2.2.10 Neisseria gonorrhoeae

Neisseria gonorrhoeae is an obligate pathogen that infects mucosal surfaces of the pharynx, female and male reproductive tracts, conjunctiva, and rectum. Asymptomatic infections in female reproductive tract can also result in serious infections which might affect the fallopian tube. The infections of reproductive tracts can also lead to inflammatory response causing pelvic inflammatory disease (PID). The infection causes scarring of tubes, occlusion of oviduct, and loss of ciliated cells. This can lead to infertility and problems during pregnancy and can also cause chronic pelvic pain (Lenz and Dillard 2018).

3.2.2.11 Mycobacterium tuberculosis

Even though the vaccine for tuberculosis has been used worldwide, it accounts for one of the highest mortalities among infectious diseases. Multidrug-resistant Mycobacterium tuberculosis is resistant to treatment of first-line anti-TB drugs such as rifampin and isoniazid, while resistance to second-line medications results in generation of extensively drug-resistant TB (XDR-TB). Almost 25% of people in the world are infected with Mycobacterium tuberculosis, but the disease results when the bacteria become active in individuals. The individuals with compromised immune system, old people, diabetics, and HIV patients are more prone to activation of M. tuberculosis. The year 2014 experienced around 9.6 million new TB cases with 2.96 cases per 100,000 people in the USA, whereas 1.5 million people died of it. Year 2016 resulted in 600,000 new cases of TB with 240,000 deaths, out of which multidrug-resistant strains accounted for 4.1% of all new TB cases. The major cases of multidrug-resistant Mycobacterium tuberculosis occurred in India, China, South America, former Soviet Union, and southern region of Africa (Smith 2003).

3.2.2.12 Helicobacter pylori

Helicobacter pylori infect approximately half of the world’s population. H. pylori can colonize human body lifelong, if not treated. Medical conditions associated with H. pylori include chronic active gastritis and peptic ulcers and gastrointestinal diseases, duodenal ulcer, gastric mucosa-associated lymphoid tissue lymphoma, and gastric adenocarcinoma. Hence H. pylori can also be referred to as bacterial carcinogen. H. pylori infections prevail highly in Latin American countries and have low prevalence in the USA and Japan (Kusters et al. 2006; Calvet et al. 2013; Kao et al. 2016).

3.2.2.13 Campylobacter spp.

Campylobacter jejuni is transmitted via contaminated food or water and causes foodborne diarrhea and acute human enterocolitis even at low doses. The organism has also been linked with the development of Guillain-Barré syndrome (GBS), a neurological disorder. C. jejuni adheres to enterocytes in the gut and induces diarrhea by production of toxins (cytotoxins and enterotoxins) (Wallis 1994; Van Vliet and Ketley 2001).

3.2.2.14 Salmonella

Salmonella is one of the most common foodborne pathogens. In severe cases, it can also lead to chronic enterocolitis. Salmonella enterica is highly pathogenic among all strains of Salmonella. It accounts for approximately 93.8 million foodborne illness with 155,000 deaths every year. The mortality rate of Salmonella infections is due to the prevalence of multidrug-resistant strains of Salmonella (D’Aoust 1991; Eng et al. 2015).

3.2.2.15 Haemophilus influenzae

The problem with Haemophilus influenzae, causal organism of H. influenzae type B (Hib) disease, is an increase in the number of antibiotic-resistant strains of the organism. The nontypeable strains of H. influenzae (NTHi) live within biofilms and hence induce otitis media which is a bacterial infection of the middle ear (Harrison and Mason 2015).

3.2.2.16 Shigella spp.

Shigella is a common bacterial pathogen isolated from patients suffering with diarrhea. Shigellosis is an acute intestinal infection which can result in watery diarrhea to severe inflammatory bacillary dysentery. This can be accompanied by fever, abdominal cramps, and stools containing blood and mucus. These diseases can severely affect immunocompromised patients. The world encounters about 5–15% of diarrheal cases due to Shigella with approximately 1.1 million deaths, majority of which are children below the age of 5 years. The continuous increase in the incidence of shigellosis has become a global health problem which is yet to be solved (Schroeder and Hilbi 2008; Organization 2017).

3.3 Archaea

The domain Archaea was not recognized until the twentieth century, but in the late 1970s, a new group of microorganisms were discovered based on their differences with bacteria. Archaea are prokaryotic cells that are different from bacteria as they lack peptidoglycans in their cell wall but consist of ether-linked lipids termed as pseudopeptidoglycan. They comprise approximately 20% of the earth’s biomass. They inhabit extreme environmental conditions such as hot springs and deep-sea well with temperatures over 100 °C and in extremely acidic or alkaline water; digestive tracts of cattle producing methane; anoxic conditions, such as muds of marshes and bottom of ocean; and underground petroleum deposits.

The archaeans use different inorganic substances as energy sources like sulfur, hydrogen gas, and carbon dioxide. Some of them also use sunlight by absorbing it using their light-sensitive membrane pigment, bacteriorhodopsin. The pigment reacts with sunlight and pumps protons out of the membrane. These protons flow back inside and are used in the synthesis of adenosine triphosphate (ATP) which is the energy source of cells. Bacteriorhodopsin exhibits similarity to rhodopsin, a light-detecting pigment found in vertebral retina.

3.3.1 Classification of Archaea

Archaea are classified as crenarchaeota, euryarchaeota, and korarchaeota. Crenarchaeota consists of microorganisms that can tolerate extreme temperature and acidic conditions. They can be further divided as thermophiles, mesophiles, and psychrophiles. Thermophiles inhabit extremely hot temperatures and can grow and reproduce at 100 °C or higher. They inhabit hot springs, volcanic openings, and acidic soils (Eswari et al. 2019; Dhagat and Jujjavarapu 2020). Mesophiles live in neither hot nor cold conditions with a temperature range from 20 °C to 40 °C. They are mostly used in fermentation processes requiring room temperature. Psychrophiles grow and reproduce at extremely low temperatures ranging from −20 °C to 10 °C. They are found in deep ocean water, high altitude, snowfields, and Arctic and alpine soil.

Euryarchaeota are methane-producing and salt-loving archaea and are categorized into methanogens and halophiles. They are the only life forms that can utilize carbon as electron acceptor and perform cellular respiration. Methanogens break down complex carbon molecules into methane during digestion, which leads to their degradation. They play an important role in sewage treatment plants and carbon cycle and are present in the stomach of cows where they help in the breakdown of sugars in grass which are generally not digested by eukaryotes. Halophiles, on the other hand, thrive in extremely salty or saline environments. They generally inhabit places such as Dead Sea and Great Salt Lake where salt concentration is five times higher than oceans. Korarchaeota is the oldest lineage of archaebacteria. They consist of genes found in both crenarchaeota and euryarchaeota and also genes different from both groups. They are not abundantly present in nature, and their presence is restricted to high-temperature hydrothermal vents.

Two of the other minor subdivisions of archaea are thaumarchaeota and nanoarchaeota. Thaumarchaeota are the most abundant and unique archaea. Initially, they were classified as “mesophilic crenarchaeota.” They are ammonia-oxidizing microorganisms present in soil, hot springs, acidic soils, and marine water. They are capable of surviving under low concentrations of ammonia. They aerobically oxidize ammonia to nitrate in a process termed as nitrification. They are autotrophic and help in carbon dioxide fixation. They consist of ammonia monooxygenases which belong to a family of copper-containing membrane-bound monooxygenases with a wide range of substrates. Some thaumarchaeota are also dependent on other bacteria or organic material for their survival. The strains belonging to thaumarchaeota have tetraether lipids with crenarchaeol which is a thaumarchaeota-specific core lipid (Pester et al. 2011; Stieglmeier et al. 2014).

Nanoarchaeota are very small obligate parasites or symbionts belonging to the Archaea domain. They inhabit terrestrial hot springs, marine thermal vents, and mesophilic hypersaline environments (Hohn et al. 2002; Casanueva et al. 2008), and thus these microorganisms are capable of surviving in a wide range of temperature and geochemical environments (Munson-McGee et al. 2015). The only genus belonging to this phylum is Nanoarchaeum. The optimal environmental conditions of these small coccoids are pH 6.0 and salinity of 2%. Nanoarchaeum equitans is a hyperthermophile which can survive temperatures up to 90 °C. It is found to be associated with its host Ignicoccus hospitalis which is a marine hyperthermophilic crenarchaeon. It is incapable of synthesizing its own amino acids, lipids, and nucleotides but obtains them from its host cells. It is the smallest known archaeal parasite with a diameter of 400 nm without any contribution to the environment. Due to the lack of its ability to metabolize inorganic compounds, it inhabits places rich in carbon dioxide, hydrogen, and sulfur.

3.3.2 Pathogenicity in Archaea

The ability of archaea to act as a pathogen is still not clear, but the mechanism of pathogenesis of archaea may be linked to the following factors. Archaea are present in the gut of human body, and they have high access opportunity to colonize hosts. Methanogens are present in human colon (Miller et al. 1982), vagina (Belay et al. 1990), and subgingival area (Bonelo et al. 1984; Belay et al. 1988; Kulik et al. 2001). They require anaerobic environments for their growth and hence exist in sites in human body where anaerobic bacteria flourish.

Some archaea consist of unique flagella which show structural similarity to type IV pili (adhesin) of bacteria rather than the bacterial flagella (Thomas et al. 2001). Archaea also produce Tad-like proteins which are involved in fibril formation and help the archaea adhere to the surface of host cells. For example, Pyrodictium produces a network of flagellum-like filaments which helps connect other Pyrodictium cells. The role of these structures is not clear but might help in host-microbe adhesion or microbe-microbe interaction within a host.

Archaea, especially methanogens, have also been shown to cause disease in syntropy. Syntropy involves cooperation of two or more microorganisms for the consumption of a substrate which cannot be catabolized alone by either of the microbial species (Madigan et al. 2000). This also makes the process energy-efficient. Syntropy between anaerobic microbial community of deep periodontal pockets leads to periodontal disease. In this condition, the hydrogen atoms produced by secondary fermenters are consumed by methanogens (Carlsson 2000). Lack of methanogenic population compared to sulfate-reducing bacteria in human intestine leads to increase in toxic levels of hydrogen sulfide. This is the main reason for ulcerative colitis, a kind of inflammatory bowel disease in humans (Levine et al. 1996).

The structure of cell wall of archaea differs from bacteria and eukarya. The cell walls of archaea lack murein, and their lipids are made up of branched phytanyl chains which are attached to glycerol backbones via ether bonds. This is in contrast to bacteria and eukarya where the fatty acyl chains are ester-linked. They also lack lipopolysaccharides. The unique polar lipids of archaea can be incorporated into liposomes, forming archaeosomes which act as potent immune adjuvants in vitro and in vivo (Krishnan et al. 2000). Archaeosomes activate antigen-presenting cells by increasing expression of major histocompatibility complex class II and costimulatory molecules and induce strong antigen-specific response similar to lipopolysaccharides (Krishnan et al. 2001). This shows that the archaeal polar lipids are specifically recognized by the human immune system.

It is not known till date whether archaea have specific mechanism to evade human immune system. The paracrystalline cell surface S-layer present in archaea may play a role in evading immune response. It is proposed that the acquisition of virulence factors by archaea might be due to lateral gene transfer between bacteria and archaea over evolutionary period, but the evidence for the same is not available.

Methanogens are present in anaerobic environments in human body where other disease-causing endogenous anaerobic microflorae are present. These anaerobic microflorae are responsible for bite wounds, genitourinary and gastrointestinal surgery, malignancy, and aspiration. As methanogens colonize alimentary canal in humans, they may be attributed to anaerobic microbial infection. Methanobrevibacter smithii is a dominant methanogen present in human colon and has been found to be more in the fecal samples of patients with diverticulosis than normal humans.

The excretion of breath methane can be linked to the methane production by methanogenic bacteria present inside a host (Bond Jr et al. 1971). The concentration of breath methane increases in patients with precancerous condition than in healthy patients (Haines et al. 1977; Piqué et al. 1984). This might be due to the use of laxatives and enemas (Karlin et al. 1982). It is still not clear whether the excretion of methane increases after the development of diseases or the increase in methanogenic population leads to disease development (Eckburg et al. 2003).

3.3.3 Pathogenic Archaea

Not many reports have been available till date that focus on pathogenic species of archaea. Due to the presence of archaea in subgingival area, they have been mostly linked with diseases of oral cavity. The most common disease of oral cavity caused by archaea is periodontitis which is an infection and inflammation of periodontal tissue. It is caused by a mixed culture of oral microorganisms consisting of Gram-negative anaerobes, Gram-positive bacteria, spirochetes, and methanogenic archaea (Socransky 2002; Wade 2011). Methanobrevibacter oralis and species of Methanobacterium, Methanosarcina, and Thermoplasmata are some of the archaeal species that inhabit periodontal pocket and gingival sulcus and cause periodontitis, whereas M. oralis and Synergistes sp. are responsible for causing apical periodontitis (Maeda et al. 2013).

3.4 Fungi

Fungi are eukaryotic, multicellular organisms with cell wall made up of chitin. They consist of mushroom, molds, mildews, rusts, smuts, and yeasts. They may be free-living present in soil or water, have symbiotic relationship with plants, or are parasites. They are decomposers, that is, they absorb organic matter from dead material present in environment and thus play an important part in recycling the nutrients back to the soil. Some fungi, known as mycorrhizae, are present as symbionts with plants. They live in the roots of plants and affect their growth by supplying essential nutrients to them. Fungi are also source of some antibiotic drugs and foods such as morels, mushrooms, and truffles and are also required in the fermentation of beer, champagne, and bread. Some fungi can even harm hosts and are responsible for causing many diseases in plants and animals. Fungi, being eukaryotes, share chemical and genetic similarity with animals which makes the fungal diseases difficult to treat. Fungal diseases in plants might lead to severe damage to crops.

Fungi can be single-celled, for example, yeasts, or multicellular, wherein cells are arranged in the form of characteristic filaments called hyphae. These filamentous tubes called hyphae help fungi in absorbing nutrients. A group of hyphae is called as mycelium. They can either be well structured, for example, in mushroom, or tangled and unstructured, e.g., in molds. Dimorphic fungi exist in the form of yeast and hyphae. The reproduction of fungi is by the release of spores. They can be found in any habitat but live mostly in soil or on plants rather than in aquatic bodies.

3.4.1 Fungal Classification

Fungi are further classified into five phyla, namely, Chytridiomycota, Zygomycota, Glomeromycota, Ascomycota, and Basidiomycota. Chytridiomycota or chytrids are aquatic and microscopic organisms. They move with the help of flagella, are asexual, and produce motile spores. They are present in various environments, such as in the Arctic and high-elevation soils. They have the ability to grow under anaerobic conditions with a variety of pH ranges. Their morphology is different from other groups as they have zoospores with single flagellum at the posterior end. These zoospores are produced in zoosporangia. The zoosporangium of Chytridiomycota is a sac-like structure which results in the production of zoospores. One of the examples of chytrids, Batrachochytrium dendrobatidis, has the ability to cause fungal infection in frogs. They burrow under the skin of frogs and have been found to kill two-thirds of frogs in South and Central America.

Zygomycetes (singular Zygomycota) are terrestrial microorganisms that consume dead and decaying animal matter and plant detritus. They are also responsible for contaminating food, such as Rhizopus stolonifer, which is a bread mold. The phylum Zygomycota consists of approximately 900 species which consists of 1% of the true fungi. The mycelium of zygomycetes is a large cell with many nuclei as their hyphae are not separated by septa. Their reproduction is asexual through non-motile endospores formed in sporangia, sporangiola, or merosporangia and sexual by forming zygospores in zygosporangia. Zygomycetous fungi are saprotrophs or parasites or cause diseases in plants, fungi, animals, and humans. Some zygomycetous fungi, known as mycorrhizae, also form mutualistic relation with plants.

Glomeromycota consists of almost half of the fungi present in soil and is often associated with plants as mycorrhizae. They obtain sugar from plants and help the plants by dissolving minerals in soil which the plants take up as nutrients. This is done with the help of specialized structures called as arbuscules which help in the exchange of nutrients. Glomeromycota also reproduce asexually.

Ascomycota or ascomycetes comprise the largest phylum of fungi. They consist of both single-celled and multicellular fungi. Their reproduction is majorly asexual with the help of conidia, but some of them produce sexual spores in reproductive sacs known as asci. Some of the microorganisms belonging to this group are Aspergillus nidulans, Laboulbeniales, Monascus, Pezizomycotina, Verticillium, and yeast. Ascomycetes have commercial importance. Aspergillus oryzae are used for the fermentation of rice. Morels and truffles are used as gourmet delicacies. Yeasts are used in fermentation of wine, brewing, and baking. They are also pathogens of plants and animals and cause various infections like ringworm, ergotism, and athlete’s foot, which may also lead to death. Pneumonia caused by fungi also poses threat to AIDS patients. Ascomycetes may also live inside humans, such as Candida albicans, which exists in the respiratory, gastrointestinal, and female reproductive tracts. They are capable of producing poisonous secondary metabolites making the crops unfit for consumption. They also infest and destroy the crops.

Basidiomycota produce sexual spores called basidiospores in club-shaped basidia. Because of these club-shaped bodies, basidiomycote or basidiomycetes are called as club fungi. Mushrooms, rusts, and smuts are some of the most common examples of basidiomycetes. Basidiomycota consists of edible fungi as well as some deadly toxins, such as Cryptococcus neoformans, which cause severe respiratory illness. The Basidiomycota also contributed to the ecosystem by degrading components of wood, especially lignin.

3.4.2 Mechanism of Fungal Pathogenesis

The virulence factors produced by pathogenic fungi are similar to the ones produced by pathogenic bacteria. But certain strains of fungi produce specific virulence factors. Candida albicans produce surface glycoproteins as adhesins which bind to phospholipids of endothelial and epithelial cells. Candida also produces exoenzymes, proteases, and phospholipases that help the pathogen to invade tissues. The proteases degrade keratin which is a structural protein found on epithelial cells. This increases the ability of fungi to invade host tissue. The phospholipase disrupts the host cell membrane leading to killing of host cells or pathogenic invasion of host tissue.

Claviceps purpurea is a pathogenic fungus that causes ergotism and grows on grains, such as rye. The fungus produces a mycotoxin (fungal toxin) called as ergot toxin, an alkaloid. The ergotism caused by ergot toxin is of two types: gangrenous and convulsive. The gangrenous ergotism occurs when the ergot toxin causes vasoconstriction. This results in improper blood flow to the extreme sites of the body leading to gangrene. The convulsive ergotism occurs when the ergot toxin targets the central nervous system. This results in mania and hallucinations. Cryptococcus which causes pneumonia and meningitis produces capsule as virulence factor. The capsule is made up of a polysaccharide, glucuronoxylomannan, and helps the pathogen resist phagocytosis than the non-capsulated strains.

The virulence factor produced by Aspergillus is a mycotoxin, aflatoxin. Aflatoxin can act both as a mutagen and as a carcinogen in host cells. It is responsible for development of liver cancer, and it can also cross blood-placental barrier (Wild et al. 1991). Aspergillus also produces gliotoxin which promotes virulence by inhibiting the function of phagocytic cells and pro-inflammatory response as well as by inducing host cells for self-destruction. Aspergillus produces two protease enzymes which help the pathogen to evade the immune system. Elastase degrades elastin protein present in the connective tissue of lungs. This leads to development of lung disease. Catalase, produced by Aspergillus, protects the pathogen from hydrogen peroxide which is produced by host immune system as a mechanism to destroy pathogens.

3.4.3 Diseases Caused by Pathogenic Fungi in Humans

Many fungal species cause disease in humans, animals, and plants. Fungal diseases have a serious impact on human health. Some of the most common fungal diseases affecting humans are enlisted here.

3.4.3.1 Adiaspiromycosis

It is a rare pulmonary infection caused by Chrysosporium parvum var. crescens (Emmonsia parva) due to inhalation of fungal spores (Buyuksirin et al. 2011; Anstead et al. 2012).

3.4.3.2 Aspergillosis

It is caused by various species of Aspergillus, especially A. fumigatus and A. flavus. It occurs in humans, animals, and birds. It might result in acute or chronic infections. Acute aspergillosis is associated with severely compromised immune patients. Patients with respiratory illness such as cystic fibrosis, asthma, tuberculosis, sarcoidosis, and chronic obstructive pulmonary disease are more susceptible to chronic infections of aspergillosis (Smith and Denning 2011; Denning et al. 2013; Denning et al. 2014; Warris et al. 2019).

3.4.3.3 Candidiasis

It is caused by different types of Candida with the most prominent being Candida albicans. It affects the mouth where it causes white patches on tongue, mouth, and throat and may lead to soreness. It also causes infections in vagina. Rare candidial infections might also become invasive and spread to other parts of the body (Andrews and Domonkos 1963).

3.4.3.4 Entomophthoromycosis

It is a rare fungal infection affecting immunocompromised patients and is dominant in tropical and subtropical regions. Depending on the affected tissue, it can be classified as basidiobolomycosis and conidiobolomycosis. Basidiobolomycosis is caused by Basidiobolus ranarum and occurs due to implantation of fungus into subcutaneous tissues of gluteal muscles, thighs, or torso. Conidiobolomycosis is caused by Conidiobolus coronatus and C. incongruous. It occurs when fungal spores enter nasal tissue, facial soft tissue, and paranasal sinuses (Gugnani 1992; Ribes et al. 2000). It is generally limited to rhinofacial area (Costa et al. 1991; El-Shabrawi et al. 2014).

3.4.3.5 Fungal Keratitis

It is an inflammation of eye’s cornea caused by species of Fusarium, Aspergillus, Candida, basidiomycetes, or Mucorales (Bongomin et al. 2017).

3.4.3.6 Lobomycosis

It is a chronic skin and subcutaneous mycosis caused by Lacazia loboi. It is endemic to the Americas and Amazon basin (Francesconi et al. 2014). This results in appearance of cutaneous lesions which might be ulcerated, keloid-like, nodular, or plaque-like and develop slowly (Rodríguez-Toro 1993; Elsayed et al. 2004).

3.4.3.7 Pneumocystis Pneumonia

It is a fungal pneumonia caused by Pneumocystis jirovecii. P. jirovecii inhabit lungs of healthy individuals and make them susceptible to other lung infections. They are seen in people with weak immune system (Aliouat-Denis et al. 2008).

3.4.3.8 Pythiosis

It is a difficult-to-treat and life-threatening infectious disease caused by a water mold Pythium insidiosum. This disease is found in temperate, tropical, and subtropical regions of the world. Depending on the site of infection, they can be classified as systemic or vascular, cutaneous, and ocular. Vascular pythiosis is the most common and lethal form of pythiosis in humans (Sudjaritruk and Sirisanthana 2011).

3.4.3.9 Tinea Capitis

Tinea capitis is a fungal infection of the scalp and is also known as scalp ringworm, ringworm of the scalp, ringworm of hair, herpes tonsurans, and tinea tonsurans. It is caused by Trichophyton and Microsporum sp. that colonize hair shaft. It is mainly seen in prepubertal children and occurs more in boys than girls (Bongomin et al. 2017).

3.5 Protozoa

Protozoa, also called as protists, are unicellular eukaryotic organisms. They have complex intracellular structures and perform complex metabolic activities. They have vesicular nucleus (except ciliates) in which the chromatin is scattered. They are aerobic organisms, that is, they require oxygen for their survival. Protozoan forms a link between plants, animals, and fungi. In terms of number, diversity, and biomass, they constitute the largest group of organisms. They consist of nucleus, complex cell organelles, and cellulosic cell wall. Their mode of nourishment is by absorption or ingestion of organic compounds through specialized structures.

3.5.1 Various Classes of Protozoa

Earlier the classification of protozoa was based on their mode of locomotion or the presence of different locomotory organs which are as follows:

• Class I: Mastigophora/Flagellata.

  They consist of a whip-like structure called flagella which helps the protozoan to propel forward. Their body is covered with chitin, silica, or cellulose. They are generally free-living or parasitic and reproduce sexually by longitudinal fission. Examples of this class are Euglena, Giardia, and Trypanosoma.

• Class II: Ciliata.

  They have tiny hair that beat to produce movement. Their body is covered by pellicle and their locomotion is by cilia. The asexual reproduction is by binary fission, whereas sexual reproduction is by conjugation. They consist of two types of nuclei, micronucleus and macronucleus. Examples of Ciliata are Balantidium, Paramecium, and Vorticella.

• Class III: Sarcodina/Amoeboids.

  Amoeboids have pseudopodia, false feet, which are used for feeding and locomotion. They are free-living and reproduce sexually by syngamy and asexually by binary fission. Some examples include Amoeba and Entamoeba.

• Class IV: Sporozoa.

  Sporozoans are non-motile. They are endoparasites, and their body is covered with pellicle. Their asexual reproduction is by fission and sexual reproduction is by spores. Examples of this class are Monocystis and Plasmodium.

In 1985, the Society of Protozoologists classified protozoa into six phyla: Sarcomastigophora, Apicomplexa, Entamoebidae, Trichomonadida, Naegleria, and Balantidium. Sarcomastigophora and Apicomplexa are the protozoan species which cause diseases in humans. Sarcomastigophora consists of a wide range of protozoa that either consists of flagella (Class Mastigophora) or pseudopods (Class Amoeboids). This phylum has both free-living and parasitic protozoans with reproduction by closed mitosis. Trichomonas, Giardia, Leishmania, and Trypanosoma are the disease-causing protozoa under this phylum.

Apicomplexa are parasitic protozoans comprising of ciliates and dinoflagellates. This phylum consists of cortical alveolae which are flattened vesicle-like structures found beneath the plasma membrane. Initially, this phylum was a part of Class Sporozoa. These cause serious illness in birds, animals, and humans, such as leucocytozoonosis in birds, babesiosis in cattle and dogs, and malaria in humans. The species under this phylum consist of a group of secretory organelles called apicoplast. This helps in invasion of host cells by parasitic cells.

Entamoebidae is a family of Archamoeba and comprise of Entamoeba, Endolimax, and Iodamoeba. They lack mitochondria and perform anaerobic respiration. They consist of vesicular nucleus with a central endosome. The microorganisms belonging to this phylum are responsible for causing diseases of digestive systems in animals and humans. Trichomonadida consists of four to six flagella and one or two nuclei. They reproduce asexually by binary fission. They are further subdivided into Monocercomonadidae and Trichomonadidae. They consist of both pathogenic and non-pathogenic strains. The non-pathogenic strains are found in alimentary canal and reproductive tract. The pathogenic Trichomonadida belong to the genus Giardia, Hexamita, Trichomonas, and Tritrichomonas.

Naegleria is a free-living protozoan which is found in soil and aquatic environments. The life cycle of Naegleria consists of three stages, amoeboid, cyst, and flagellated stages, and it can easily change from amoeboid to flagellated stage. Naegleria fowleri, also called as brain-eating amoeba, is a human pathogenic strain responsible for causing primary amoebic meningoencephalitis (PAM). Balantidium coli, belonging to the phylum Balantidium, is a large ciliated protozoan and causes infection in humans. It is responsible for causing balantidiasis in humans. It also infects domestic and wild mammals, such as pigs and monkeys.

According to the means of nutrition, they are grouped as autotrophs or heterotrophs. Euglena contains chloroplasts and synthesizes their own food, and hence they are classified as autotrophs. Amoeba, on the other hand, cannot synthesize their food, and hence, they are heterotrophs. Protozoans can either be free-living or parasitic, unicellular, or colonial. Protozoa reproduce either asexually, as in amoeba and flagellates, or both asexually and sexually as in Apicomplexa. Binary fission is the most common type of asexual reproduction seen in protozoans. Protozoans help in controlling biomass as they consume bacteria. The diseases caused by protozoans can be mild or life-threatening depending upon the species and strain of the parasite.

3.5.2 Pathogenesis of Protozoa

Even though protozoa are eukaryotic pathogens, they also produce adhesins and toxins analogous to bacterial pathogens. They undergo antigenic variation and are able to survive inside phagocytic vesicles. Different strains of protozoa have different mechanism for invasion of host cells.

Giardia lamblia have a large adhesive disk of microtubules which helps in their attachment to intestinal mucosa of host cells. When the protozoa adhere to the host cells, the protozoan flagella move in a way that removes fluid from under the disk. This results in generation of an area of low pressure which helps in its adhesion to epithelial cells. Giardia causes inflammation through the release of cytopathic substances and shortens the intestinal villi. This inhibits the absorption of nutrients.

Plasmodium falciparum resides inside the red blood cells and produces PfEMP1, an adhesin membrane protein. This protein is present on the surface of infected red blood cells and causes the blood cells to stick to each other and to the walls of blood vessels. This leads to reduced blood flow and, in severe cases, anemia, jaundice, organ failure, and death. PfEMP1 is recognized by host immune system, but antigenic variation in its structure prevents the protein from getting easily recognized by host immune cell.

Trypanosoma brucei produces capsules made up of a dense glycoprotein (similar to bacterial capsule) to prevent phagocytosis by host immune system. The antibodies produced by host immune system can recognize the coat, but the pathogen alters the structure of capsules by antigenic variations and thereby evades its recognition by immune system.

3.5.3 Current Scenario of Pathogenic Protozoa

Infections caused by pathogenic protozoa cause around 58 million cases of diarrhea every year with 1.8 million deaths per year (Putignani and Menichella 2010; Thompson and Ash 2016). It has also been reported by WHO in 2004 that diarrhea affects more individuals worldwide than any other disease (Press and Geneva 2008). Most intestinal parasites result in malnutrition, iron deficiencies, and long-term adverse effects (Organization 2002), while many species of enteric protozoa are linked with diarrhea in humans. Some of the pathogenic protozoa that cause diarrhea are discussed below.

3.5.3.1 Cryptosporidium Species

These species are responsible for causing infections in AIDS patients (Sterling and Adam 2006). Cryptosporidium causes approximately 20% of diarrheal cases in children in developing countries and 9% in developed countries (Xiao 2010; Rimšelienė et al. 2011).

3.5.3.2 Giardia i ntestinalis

Giardia intestinalis is another common protozoan parasite that causes giardiasis. Giardiasis infects approximately 280 million people every year and results in 2.5 million deaths annually which consists of 2–7% in developed countries and 20–30% in developing countries (Franzen et al. 2009; Jerlström-Hultqvist et al. 2010). Hence, this becomes the second largest protozoan infection causing morbidity and mortality next to malaria (Menkir and Mengestie 2014).

3.5.3.3 Entamoeba Species

Six species of Entamoeba have been found in human: E. histolytica, E. coli, E. dispar, E. hartmanni, E. moshkovskii, and E. polecki. Only E. histolytica is pathogenic among these, and as per WHO reports, it infects approximately 500 million people annually with around 100,000 deaths worldwide every year (Jackson 1998; World Health Organization 2004; Lebbad 2010; Santos et al. 2010).

3.5.3.4 Balantidium c oli

Balantidium coli is the largest protozoan infecting humans (Farthing and Kelly 2005; Solaymani-Mohammadi and Petri Jr. 2006) and causes balantidiasis. This leads to perforation in the intestine. It has a mortality rate of 30% (Ferry et al. 2004; Schuster and Ramirez-Avila 2008). Balantidiasis has been reported in Finland, Sweden, northern Russia, rural South America, Southeast Asia, and Western Pacific Islands (Esteban et al. 1998; Ferry et al. 2004; Schuster and Visvesvara 2004; Solaymani-Mohammadi and Petri Jr. 2006; Schuster and Ramirez-Avila 2008).

Cyclospora cayetanensis also causes epidemic or endemic diarrhea in children and adults (Chacín-Bonilla 2010). Other protozoans causing diarrhea in humans are Dientamoeba fragilis, Blastocystis species, and Cystoisospora belli (Fletcher et al. 2012).

Some of the other common diseases caused by protozoa are:

• Malaria caused by Plasmodium falciparum, P. malariae, P. vivax, and P. ovales.

• Trypanosomiasis (African sleeping sickness) caused by Trypanosoma brucei gambiense (TbG) and Trypanosoma brucei rhodesiense (TbR).

• Chagas disease (American trypanosomiasis) caused by Trypanosoma cruzi.

• Lambliasis (beaver fever) caused by Giardia lamblia.

• Babesiosis caused by Babesia microti.

• Sappinia amoebic encephalitis (SAE) caused by Sappinia pedata.

• Blastocystosis caused by Blastocystis hominis.

• Trichomoniasis caused by Trichomonas vaginalis.

• Toxoplasmosis caused by Toxoplasma gondii.

• Schistosomiasis caused by Schistosoma species.

3.6 Algae

Algae are unicellular or multicellular eukaryotes. They are also called cyanobacteria or blue-green algae. These organisms obtain nourishment by photosynthesis and produce carbohydrates and oxygen. Their habitats include damp soil, water, and rocks. Cyanobacteria are aquatic organisms that are unicellular or colonial.

Cyanobacteria are thought to be the precursors of green land plants. Millions of years ago, chloroplast, the organelle of the plant which produces chlorophyll, was believed to be free-living cyanobacteria. In the late Proterozoic era, cyanobacteria began to reside within eukaryotic cells, and these cyanobacteria generate energy for host cells through a process called endosymbiosis. This theory of endosymbiosis is supported by the structural and genetic similarities between cyanobacteria and chloroplasts.

Some of the algae reproduce by spores which are motile reproductive cells. Algae reproduce both sexually and asexually. The sexual reproduction of algae is by the formation of genetically diverse gametes by meiosis. Two gametes from different individuals join to form a new individual. Some types of algae undergo simple sexual reproduction where the algae themselves act as gametes. In other types of algae, the process involves egg- and sperm-like cells and sex-attractant pheromones. Algae are believed to be one of the first organisms to undergo sexual reproduction seen in plants and animals today.

Based on the estimates by Guiry (2012), around 37,000 species of algae and 4000 species of cyanobacteria have been identified, and 30,000 species are yet to be discovered. Algae have existed for more than two billion years now. Algae, being autotrophs, are the key producers of the food in the aquatic ecosystem. They are the major source of food for fishes which are indirectly the food for many animals. Hence, they are an energy source which powers the entire ecosystem. Apart from being a food source, they supply oxygen to marine animals. The kelps (kombu) and red algae Porphyra (nori) have been cultivated and harvested in the Pacific Basin to be used as a source of food in Asia for hundreds of years. Kelp is also used as fertilizer. Kelp ash has been industrially used for its potassium and sodium salts. Agar and carrageen are some of the other algal products which are used as stabilizer in foods, cosmetics, and paints.

3.6.1 Algal Classification

Fritsch, in 1938, provided the classification of algae in his book The Structure and Reproduction of Algae. He classified algae into 11 classes based on types of pigments present, types of flagella, mode of reproduction, structure of thallus, and assimilatory products.

Class I: Chlorophyceae.

These are green algae and contain chlorophyll a and b, carotenoids, and xanthophylls as pigments. The cell wall is made up of cellulose and chloroplast has pyrenoids. The flagella are of equal lengths. Reproduction in Chlorophyceae is by vegetative, sexual, and asexual means. Chlorophyceae is subdivided into nine orders:

Order 1: Volvovales, for example, Volvox.

Order 2: Chlorococcales, for example, Chlorella.

Order 3: Ulotrichales, for example, Ulothrix.

Order 4: Cladophorales, for example, Cladophora.

Order 5: Chaetophorales, for example, Fritschiella.

Order 6: Oedogoniales, for example, Oedogonium.

Order 7: Conjugales, for example, Zygnema.

Order 8: Siphonales, for example, Vaucheria.

Order 9: Charales, for example, Chara.

Class II: Xanthophyceae.

These are yellow-green algae and have chlorophyll a and e, β-carotene, and xanthophylls. They have plastids without pyrenoids. Their cell wall is made up of pectic substance and cellulose. They store reserve food material in the form of oil. They have two unequal flagella inserted anteriorly with short whiplash and longer tinsel type. Reproduction is by vegetative, sexual, and asexual means. Xanthophyceae is divided into four orders:

Order 1: Heterochloridales, for example, Heterochloris and Chloramoeba.

Order 2: Heterococcales, for example, Myxochloris and Halosphaera.

Order 3: Heterotrichales, for example, Tribonema and Microspora.

Order 4: Heterosiphonales, for example, Botrydium.

Class III: Chrysophyceae.

The dominant pigment present in this class is phycochrysin which gives it brown or orange color. Chromatophores have naked pyrenoid-like bodies. Their cell wall consists of silica or calcium. They store reserve food in the form of chrysolaminarin and leucosin. They are motile cells with two equal or unequal flagella inserted anteriorly. Sexual reproduction is rare in this class but, if occurs, is isogamous. This class is further classified into three orders:

Order 1: Chrysomonadales, for example, Chrysococcus, Chrysodendron, and Chromulina.

Order 2: Chrysosphaerales, for example, Chrysosphaera and Echinochrysis.

Order 3: Chrysotrichales, for example, Nematochrysis and Chrysoclonium.

Class IV: Bacillariophyceae.

They are diatoms and yellow or golden-brown algae. The dominating pigments in this class are golden-brown pigments, fucoxanthin, diatoxanthin, and diadinoxanthin. The chromatophores have pyrenoids, and their cell wall is made up of pectin and silica. They produce fats and volutin as a result of photosynthesis. The mitotic cells are flagellated with a single flagellum. The reproduction is sexual by fusion of gametes. This class is subdivided into two orders:

Order 1: Centrales, for example, Cyclotella and Chaetoceras.

Order 2: Pennales, for example, Grammatophora, Navicula, and Pinnularia.

Class V: Cryptophyceae.

The main pigment in this class is xanthophylls which gives the algae red or brown color. They have pyrenoid-like bodies which are independent of chromatophores. The cells are motile with anteriorly inserted unequal flagella. Sexual reproduction in this class is rare. Cryptophyceae is further subdivided into two orders:

Order 1: Cryptomonadales, for example, Cryptomonas, Rhodomonas, and Cyanomonas.

Order 2: Cryptococcales, for example, Tetragonidium.

Class VI: Dinophyceae (Peridineae).

The main pigment is xanthophylls which gives the algae red or brown color. Many species of this class are colorless saprophytes. The cell wall is made up of cellulose. The cells are motile with two flagella. Food is stored in the form of starch or fats. Sexual reproduction is rare in this class but, if present, is of isogamous type. This class can be classified into six orders:

Order 1: Desmonadales, for example, Desmocapsa, Pleromonas, and Desmomastix.

Order 2: Thecatales, for example, Exuviaella and Prorocentrum.

Order 3: Dinophyceales, for example, Dinophysis, Ornithocercus, and Phalacroma.

Order 4: Dinoflagellata, for example, Amphidinium, Blastidinium, Ceratium, and Heterocapsa.

Order 5: Dinococcales, for example, Dinastridium, Cystodinium, and Dissodinium.

Order 6: Dinotrichales, for example, Dinothria and Dinoclonium.

Class VII: Chloromonadineae.

They have bright green tint due to the presence of excess of xanthophylls. They do not have pyrenoids but have numerous disk-shaped chromatophores. They are motile cells with equal flagella. Their reserve food material as fats and oil. Chloromonadineae is subdivided into only one order:

Order 1: Chloromonadales, for example, Trentonia and Vacuolaria.

Class VIII: Euglenineae.

They are unicellular green algae with many chromatophores in all cells and pyrenoid-like bodies in some. They have one or two flagella that arise from an invagination at the anterior end of the cell. The reserve food material is a polysaccharide, paramylon. This class is subdivided into three orders:

Order 1: Euglenaceae, for example, Euglena.

Order 2: Astasiaceae, for example, Astasia.

Order 3: Peranemacea, for example, Anisonema.

Class IX: Phaeophyceae.

They are brown algae and contain the pigment, fucoxanthin, in the chromatophores. The lower forms of Phaeophyceae have naked pyrenoid-like bodies. The cell wall is made up of cellulose with alginic acid and fucinic acid. The cells have two lateral or subapical flagella. They reserve food material as laminarian (polysaccharide) and mannitol (alcohol). The reproduction is sexual from isogamous to oogamous type. They are divided into nine orders:

Order 1: Ectocarpales, for example, Ectocarpus, Punctaria, and Holothrix.

Order 2: Tilopteridales, for example, Tilopteris.

Order 3: Cutleriales, for example, Cutleria.

Order 4: Sporochnales, for example, Sporochnus.

Order 5: Desmarestiales, for example, Desmarestia.

Order 6: Laminariales, for example, Laminaria, Chorda, and Alaria.

Order 7: Sphacelariales, for example, Sphacelaria and Halopteria.

Order 8: Dictyotales, for example, Dictyota, Hormosira, and Ascoseira.

Order 9: Fucales, for example, Fucus and Sargassum.

Class X: Rhodophyceae.

These are mostly marine algae with uniaxial or multiaxial thalli. The chromatophores contain pigments such as r-phycoerythrin and r-phycocyanin which impart red color. The outer cell wall is made up of pectin, whereas the inner cell wall is made of cellulose. The reserve food is floridean starch. They are non-motile and sexual reproduction is oogamous type. This class consists of seven orders:

Order 1: Bangiales, for example, Bangia and Porphyra.

Order 2: Nemationales, for example, Batrachospermum.

Order 3: Gelidiales, for example, Gelidium.

Order 4: Cryptonemiales, for example, Corallina and Gloiopeltis.

Order 5: Gigartinales, for example, Chondrus, Gigartina and Gracilaria.

Order 6: Rhodomeniales, for example, Rhodymenia.

Order 7: Ceramiales, for example, Polysiphonia, Ceramium, and Lophosiphonia.

Class XI: Myxophyceae.

The pigments present in Myxophyceae are chlorophyll a, β-carotene, and c-phycocyanin. They have rudimentary nucleus with no chromatophores. Their cell wall is made up of mucopolymers. Sexual reproduction is absent in this class. The reserve food is in the form of cyanophycean starch. They are subdivided into five orders:

Order 1: Chlorococcales, for example, Chlorococcus, Gloeocapsa, and Microcystis.

Order 2: Chaemaesiphonales, for example, Chamesiphon and Dermocarpa.

Order 3: Pleurocapsales, for example, Pleurocapsa.

Order 4: Nostocales, for example, Nostoc, Oscillatoria, and Spirulina.

Order 5: Stigonematales, for example, Stigonema

3.6.2 Microscopic Algae as Pathogens: Mechanism of Pathogenicity

Although algae are non-pathogenic, some might produce toxins. For example, algal blooms produce high concentrations of toxins that hampers with functions of the nervous system and liver in humans and animals. Neurotoxins produced by some dinoflagellates cause paralysis in fish and human. The neurotoxins can be taken up by feeding on the organisms that have consumed dinoflagellates or by coming in contact with water contaminated with toxins of dinoflagellates.

Pfiesteria piscicida produces toxins in its life cycle that kill fish. The exposure to water containing P. piscicida can cause memory loss and confusion in humans. Desmodesmus armatus is a green alga which has found to cause swelling and redness of injured knee and foot along with fever and leukocytosis in patients who suffered injuries in freshwater. Prototheca species of algae grow in soil and sewage water. They do not contain chlorophyll and hence do not undergo photosynthesis and cause infections in immunocompromised humans and animals by entering through wounds. They cause skin infections such as discharging ulcers and protothecosis in cats, dogs, cattle, and humans. P. cutis causes human chronic skin ulcers, whereas P. wickerhamii causes septicemia or meningitis. Prototheca sp. also causes infections in cattle, such as bovine mastitis, an inflammatory disease of the udder (Satoh et al. 2010).

The mechanism by which algae negatively affect humans and animals is unknown. The biofilms formed by Prototheca sp. consist of surface-attached cells which are linked together by matrix containing DNA and polysaccharides. These biofilms decrease the release of IL-6 by mononuclear immune cells, which renders them less susceptible to antimicrobial agents (Kwiecinski 2015).

3.6.3 Disease-Causing Algae

Infections caused by algae in humans are very uncommon. Protothecosis is an infection caused by achlorophyllous algae, Prototheca wickerhamii and P. zopfii, in humans and animals with majority being caused by P. wickerhamii (Krcmery Jr. 2000, Consuelo Quinet Leimann et al. 2004). Prototheca sp. colonizes the fingernails, skin, digestive system, and respiratory tracts in humans (Huerre et al. 1993; Wirth et al. 1999). The introduction of Prototheca inside humans is via traumatic inoculation. Protothecosis is reported in all continents except Antarctica (Nelson et al. 1987).

Protothecosis are of three forms: cutaneous, disseminated, and olecranon bursitis (Krcmery Jr. 2000; Torres et al. 2003; Consuelo Quinet Leimann et al. 2004). Simple cutaneous infections account for almost half of protothecosis cases (Krcmery Jr. 2000; Consuelo Quinet Leimann et al. 2004). These occur in immunocompromised individuals undergoing treatment for AIDS, cancer, renal or hepatic diseases, or autoimmune disorders (Woolrich et al. 1994; Carey et al. 1997; Wirth et al. 1999; Torres et al. 2003; Consuelo Quinet Leimann et al. 2004). Lesions occur at the site of algal inoculation. Disseminated protothecosis is rare and also occurs in immunocompromised patients with cancer, AIDS, and organ transplant (Heney et al. 1991; Kunova et al. 1996; Wirth et al. 1999; Torres et al. 2003). The infected organs are subcutaneous tissue (Torres et al. 2003). In some cases, this might also result in central venous catheter-related algaemia along with fever and sepsis syndrome (Kunova et al. 1996; Torres et al. 2003). On the other hand, individuals with olecranon bursitis are not immunocompromised but have penetrating/non-penetrating trauma to the affected elbow (Nosanchuk and Greenberg 1973; de Montclos et al. 1995; Pfaller and Diekema 2005).

3.7 Virus

Viruses are non-cellular entities, that is, even though they are considered as microorganisms, they are non-living organisms. This is because they cannot reproduce outside a host and cannot perform metabolism on their own. Viruses are pathogens causing diseases in prokaryotes and eukaryotes. They are smaller than most of the microbes. They are made up of a nucleic acid core (DNA or RNA) surrounded with a protein coat called capsid.

Viruses are classified based on symmetry of capsid, dimensions of virion and capsid, presence or absence of envelope, and nature of nucleic acid. On the basis of morphology and symmetry of capsid, they can have helical or icosahedral symmetry. A virus is considered to have helical symmetry if the capsid is shaped into a filamentous or rod-shaped structure. The viruses with helical symmetry exhibit flexibility which is dependent upon the arrangement of capsomeres, subunits of capsid, in the capsid. Viruses with icosahedral symmetry have identical subunits making equilateral triangles and arranged symmetrically. Icosahedral symmetry is found in many animal viruses. This shape provides the virus a very stable shape and a lot of space inside to store nucleic acid.

3.7.1 Classification of Virus

Depending upon the nature of nucleic acid, David Baltimore classified viruses into seven groups in the early 1970s:

• Group I: Double-stranded DNA.

  These viruses have double-stranded DNA (dsDNA) as their genetic material. They replicate either in the nucleus using cellular proteins (adenoviruses) or in the cytoplasm by making their own enzymes for replication of nucleic acid (poxviruses). The transcription for the production of viral mRNA is similar to its cellular DNA. Adenoviruses, herpes viruses, papovaviruses, and poxviruses fall into this category.

• Group II: Single-stranded sense (+) DNA.

  Their genetic material is single-stranded DNA (ssDNA) which gets converted to double-stranded DNA intermediate before transcription. Replication takes place in nucleus. This involves the formation of a (−) sense strand, which serves as a template for (+) strand DNA and RNA synthesis. This group includes parvoviruses, circoviruses, anelloviruses, nanoviruses, and geminiviruses.

• Group III: Double-stranded RNA.

  This group has double-stranded RNA as the genetic material. The genomes of these viruses are segmented, and each genomic segment is separately transcribed to produce monocistronic mRNAs using RNA-dependent RNA polymerase encoded by virus. Examples of this group of viruses include reoviruses and birnaviruses.

• Group IV: Single-stranded sense (+) RNA.

  In this group, the genetic material is single-stranded RNA with positive polarity. The RNA can be directly accessed by host ribosomes to form proteins. They can be polycistronic mRNA where the genomic RNA is directly used as mRNA for protein translation which results in mature protein after cleavage or have a complex transcription process. They form replicative intermediates or intermediates of dsRNA while replicating genomic RNA. These intermediates result in the formation of RNA strands with negative polarity which acts as a template for the production of single-stranded RNA with positive polarity. This group includes picornaviruses, hepatitis A, togaviruses, astroviruses, coronaviruses, flaviviruses, calciviruses, and arteriviruses.

• Group V: Single-stranded (−) sense RNA.

  These viruses have single-stranded RNA with negative polarity. Here, the RNA and genes cannot be directly accessed by host ribosomes to form proteins and so must be transcribed by viral polymerases. Hence, in this group also, double-stranded RNA intermediates are formed to produce mRNA. The positive RNA strands act as template for the synthesis of negative RNA strands. The site of replication of viruses containing non-segmented genomes is cytoplasm, whereas replication occurs in nucleus for viruses with segmented genomes. In both of the cases, viral RNA-dependent RNA polymerases produce monocistronic mRNAs. Examples of this group are orthomyxoviruses, rhabdoviruses, filoviruses, bunyaviruses, arenaviruses, and paramyxoviruses.

• Group VI: Single-stranded (+) sense RNA with DNA intermediate in life cycle.

  The viruses that belong to this group have two copies of single-stranded RNA genomes. This group uses the enzyme reverse transcriptase to convert RNA to DNA which is then transported to the nucleus of host cell. Instead of using RNA as templates for protein synthesis, they use DNA. The DNA is spliced in the host genome using integrase. Replication occurs with the help of host cell’s polymerases. The viral DNA, integrated into the host genome, is transcribed into mRNA which is later translated into proteins. The viruses belonging to this group are retroviruses.

• Group VII: Double-stranded DNA with RNA intermediate.

  They consist of partial double-stranded DNA genome which makes single-stranded RNA intermediates acting as mRNA. They can also be converted to double-stranded DNA by undergoing reverse transcription, but this process occurs inside the virus particle upon maturation. The double-stranded genome is gapped which is filled to form covalently closed circular DNA to be used as template for mRNA production. This group includes hepadnaviruses.

Viruses are further classified based on many factors, such as the morphology of the virus, the presence of envelope, the type of nucleic acid present, the type of host, the mode of replication, etc. Their hosts range from single-celled bacteria, fungi, and protozoa to multicellular fungi, plants, and animals.

On the basis of the type of genetic material present, viruses can be classified into three types:

• 1. DNA viruses.

  These viruses use DNA as the genetic material and affect animals and humans. Their effects range from benign symptoms to serious health issues. Example: herpesvirus, papillomavirus, and parvovirus

• 2. RNA viruses.

  They have RNA as genetic material. Example: dengue virus, Ebola virus, hepatitis C virus, influenza virus, measles virus, poliovirus, rabies virus, rotavirus, and yellow fever virus

• 3. DNA-RNA viruses.

  This type contains both DNA and RNA as genetic material. Example: leukovirus and Rous’s virus.

On the basis of the number of strands of genetic material present, viruses are classified into four types:

• 1. Double-stranded DNA.

  Example: adenovirus; bacteriophages T2, T3, T4, T6, T7, and lambda; herpesvirus, and pox virus

• 2. Single-stranded DNA.

  Example: bacteriophages X, 74, and Ф

• 3. Double-stranded RNA.

  Example: reovirus of animals, rice dwarf virus of plants, and wound tumor virus

• 4. Single-stranded RNA.

  Example: avian leukemia virus, bacteriophage MS-2, influenza virus, poliomyelitis, and tobacco mosaic virus.

Viral envelope is the lipid-containing membrane which surrounds some virus particles. They are obtained during the process of viral maturation by budding through a cellular membrane. Glycoproteins encoded by virus are present on the surfaces of viral envelope as projections called as peplomers. On the basis of the presence of envelope, viruses are classified as:

• 1. Enveloped virus.

  Example:

• DNA viruses: hepadnavirus, herpesvirus, and poxvirus.

• RNA viruses: bunyavirus, coronavirus, filovirus, flavivirus, hepatitis D, orthomyxovirus, paramyxovirus, rhabdovirus, and togavirus.

• Retroviruses.

• 2. Non-enveloped virus.

  Example:

• DNA viruses: adenovirus, papovavirus, and parvovirus.

• RNA viruses: hepatitis A virus, hepatitis E virus, and picornavirus.

Mostly animal viruses are roughly spherical in shape except for few viruses. On the basis of the shape of viruses, they are classified as:

• 1. Bullet shaped.

  Example: rabies virus

• 2. Filamentous shaped.

  Example: Ebola virus

• 3. Brick shaped.

  Example: poxvirus

• 4. Space vehicle shaped.

  Example: adenovirus.

On the basis of structure, viruses are classified into the following four types:

• 1. Cubical virus.

  They are also termed as icosahedral symmetry virus. Example: picornavirus and reovirus

• 2. Spiral virus.

  They are also known as helical symmetry virus. Example: orthomyxovirus and paramyxovirus

• 3. Radial symmetry virus.

  Example: bacteriophage

• 4. Complex virus.

  Example: poxvirus.

On the basis of capsid structure, viruses are classified as:

• 1. Naked icosahedral.

  Example: hepatitis A virus and poliovirus

• 2. Enveloped icosahedral.

  Example: Epstein-Barr virus, herpes simplex virus, HIV-1, rubella virus, and yellow fever virus

• 3. Enveloped helical.

  Example: influenza virus, measles virus, mumps virus, and rabies virus

• 4. Naked helical.

  Example: tobacco mosaic virus

• 5. Complex with many proteins.

They have a combination of icosahedral and helical capsid structures. Example: hepatitis B virus, herpesvirus, smallpox virus, and T4 bacteriophage.

On the basis of the type of host, viruses are classified into three types:

• 1. Animal viruses.

  These viruses infect and live inside animal cells. Their genetic material is either RNA or DNA. Example: influenza virus, mumps virus, poliovirus, and rabies virus

• 2. Plant viruses.

  These viruses infect plants and their genetic material is RNA enclosed in a protein coat. Example: beet yellows virus, potato virus, tobacco mosaic virus, and turnip yellows virus

• 3. Bacteriophages.

They infect bacterial cells. Their genetic material is DNA, and each bacteriophage will infect only a particular strain or species of bacteria. Example: lambda and T4.

On the basis of mode of transmission, viruses are classified as:

• 1. Virus transmitted through respiratory route.

  Example: rhinovirus and swine flu virus

• 2. Virus transmitted through fecal-oral route.

  Example: hepatitis A virus, poliovirus, and rotavirus

• 3. Virus transmitted through sexual contacts.

  Example: retrovirus

• 4. Viruses transmitted through blood transfusion.

  Example: hepatitis B virus and HIV

• 5. Zoonotic viruses transmitting through the bite of infected animals.

  Example: alphavirus, flavivirus, and rabies virus.

On the basis of site of replication and replication properties, viruses are classified into the following five types:

• 1. Replication and assembly in cytoplasm of host.

  All RNA viruses replicate and assemble in cytoplasm of host cell except influenza virus.

• 2. Replication in nucleus and assembly in cytoplasm of host.

  Example: influenza virus and poxvirus.

• 3. Replication and assembly in nucleus of host.

  All DNA viruses replicate and assemble in nucleus of host cell except poxvirus.

• 4. Replication through double-stranded DNA intermediate.

  Example: all DNA viruses, retroviruses, and some tumor-causing RNA virus.

• 5. Replication through single-stranded RNA intermediate.

  Example: all RNA viruses except reovirus and tumor-causing RNA viruses.

3.7.2 Mechanism of Pathogenesis of Viruses

Similar to bacteria, viruses also use adhesins to bind to host cells. Antigenic variation is a mechanism used by some enveloped viruses to evade host immune system. Adhesins are present on viral capsid or membrane envelope. The viral adhesin interacts with specific cell receptors of certain cells, tissues, and organs of hosts, for example, hemagglutinin on influenza virus. Hemagglutinin is a spike protein and helps in attachment of virus to sialic acid present on the membrane of intestinal and respiratory cells of host. Glycoprotein gp120 is also an adhesin which is found on HIV. Infection of HIV requires its interaction with two receptors present on host cells. In the first interaction, gp120 is bound to CD4 marker present on T helper cells. The second interaction of HIV with the host occurs before entry of virus into the cell. This interaction is between gp120 and either CCR5 and CXCR4 (chemokine receptors). The glycoproteins gB, gC, and gD are the adhesin molecules of herpes simplex virus I or II. These adhesins attach to heparan sulfate present on mucosal surface of the mouth and genitals.

Antigenic variation occurs in enveloped viruses with the most common being in influenza virus. Antigenic variation occurs by antigenic drift or antigenic shift. Antigenic drift results from mutations in genes involved for the synthesis of spike proteins, hemagglutinin, and/or neuraminidase. These variations are a result of antigenic changes occurring over time. Antigenic shift occurs by a process of gene reassortment of spike proteins between two influenza viruses which infect the same host. In this process, infection of a host cell with two different influenza viruses simultaneously leads to mixing of genes. As a result, the new virus consists of a mixture of proteins from both of the unmutated viruses. The antigenic variation in influenza virus occurs at a high rate, and hence the immune system cannot recognize the different strains of influenza virus leading to frequent outbreaks of flu.

3.7.3 Deadliest Diseases Caused by Various Strains of Virus in Humans

Viruses are responsible for causing many diseases in humans, animals, and plants. Some of them also infect bacteria called as bacteriophages. The most deadly diseases caused by viruses are mentioned below.

• 1. Marburg virus.

  Marburg virus was identified in 1967. Small outbreaks of this virus were seen in lab workers in Germany when they came in contact with infected monkeys from Uganda. It causes hemorrhagic fever that leads to high fever and bleeding throughout the body. This results in shock, organ failure, and death. According to the reports of the World Health Organization, the mortality rate during the outbreak was 25% which increased to 80% in the Democratic Republic of the Congo during 1998–2000 and in Angola during 2005 outbreak (Harding 2020).

• 2. Rabies.

  Due to the development of rabies vaccines in the 1920s, the disease has become rare in the developed world. But still the disease is present on all continents except Antarctica and is a serious problem in India and parts of Africa with over 95% of deaths in Asia and Africa. It generally affects populations living in remote areas. It causes inflammation of the brain and leads to death once symptoms appear (World Health Organization 2020a).

• 3. Ebola virus.

  Ebola virus causes Ebola virus disease (EVD) which was formerly known as Ebola hemorrhagic fever. The outbreak of Ebola was first struck simultaneously in 1976 in the Democratic Republic of the Congo and the Republic of Sudan. Ebola virus spreads through blood or other body fluids. The virus is transmitted from wild animals to humans and then spreads through contact with blood or other body fluids. The outbreak of Ebola in West Africa during 2014–2016 was largest since the discovery of the virus. The average fatality rate of EVD is around 50%. EVD also leads to external bleeding, diarrhea, and multiple organ failure along with fever, sore throat, muscle pain, and headache (World Health Organization 2020b).

• 4. Hantavirus.

  Hantavirus causes hantavirus pulmonary syndrome (HPS) in humans. The first case of HPS was reported in the USA in 1993 with the death of two people. The virus is transmitted by the exposure to droppings of those infected with HPS in the USA with a mortality rate of 36% (Centers for Disease Control and Prevention 2017).

• 5. Influenza.

  Approximately 500,000 people die of influenza worldwide during a flu season. The pandemic spreads even faster when a new flu strain emerges with a high mortality rate. Spanish flu pandemic, the deadliest flu pandemic, began in 1918 and killed around 50 million people (Harding 2020).

• 6. HIV.

  HIV is the deadliest virus of all viruses. According to WHO reports, HIV has claimed almost 33 million lives so far. By the end of 2019, a total of approximately 38 million people were living with the virus. In 2019 alone, 1.7 million people were newly infected, whereas 690,000 died of the virus. The disease mainly affects middle- to low-income countries from where 95% of new cases are reported. It affects 1 in 25 adults in Africa which accounts for two-thirds of the infected patients (World Health Organization 2020c).

• 7. Dengue.

  The cases of dengue virus were first reported in the 1950s in the Philippines and Thailand, and since then, it has grown dramatically across the globe. It is estimated that almost 390 million people are infected with dengue virus every year (Bhatt et al. 2013). The infections of dengue virus occurred in 129 countries (Brady et al. 2012) with 70% of the cases in Asia itself (Tjaden et al. 2013). The total number of dengue cases, as reported by WHO, was 505,430 in 2000 which increased to 2.4 million in 2010 and 4.2 million in 2019 indicating an eightfold increase. The deaths increased from 960 in 2000 to 4032 in 2015.

  Year 2019 experienced the largest number of dengue cases globally with 3.1 million cases in the American region, 131,000 in Malaysia, 101,000 in Bangladesh, 320,000 in Vietnam, and 420,000 in the Philippines. Although the mortality rate of dengue fever is low, it can still cause dengue hemorrhagic fever and can increase the mortality to 20% if not treated. Even though the vaccine for dengue was approved by FDA in 2019, it can only be administered to patients who have previously contracted the disease; otherwise, there is a serious risk of developing severe dengue in unaffected people (World Health Organization 2020d).

• 8. Rotavirus.

  Rotavirus causes severe diarrheal disease in children. According to WHO in 2013, approximately 215,000 children under the age of 5 years die every year from rotavirus infections. Children in developing and low-income group countries are most severely affected by rotavirus. Due to the availability of vaccines against rotavirus, the total cases and mortality rates have declined sharply (World Health Organization 2018).

• 9. SARS-CoV.

  SARS-associated coronavirus (SARS-CoV) is a causative agent of viral respiratory disease, severe acute respiratory syndrome (SARS). It was first identified during an outbreak in China on February 2003 from where it spread to four other countries. Over the course of 2 years, the virus spread to 26 countries, infected more than 8000 people, and killed 770 people. The virus has a zoonotic origin which emerged in bats and was transmitted to nocturnal animals before infecting humans. During the progression of disease, the lungs of infected individuals become inflamed and filled with pus. The mortality rate associated with SARS was 3%. No new cases of SARS have been reported by WHO since May 2004 (World Health Organization 2004; Harding 2020).

• 10. MERS-CoV.

  MERS-CoV causes Middle East Respiratory Syndrome (MERS). The outbreak of MERS was seen in Saudi Arabia in 2012 and in South Korea in 2015. This virus belongs to a family of coronaviruses, similar to SARS, and also has a zoonotic origin. The virus was transmitted from bats to camels before reaching humans. It causes fever, cough, and shortness of breath and might even progress to severe pneumonia in certain cases. It is the most lethal coronavirus with a mortality rate between 30 and 40%. Till 31 January 2020, the total number of MERS-CoV cases globally was 2519 with 866 deaths. From December 2019 to January 2020 alone, 19 additional cases of MERS-CoV were reported including 8 deaths (Harding 2020, World Health Organization 2020e).

• 11. Zika virus.

  Zika virus disease is caused by mosquito-borne transmission of Zika virus. The outbreak of Zika virus was reported in Brazil in 2015 from where it spread to the Americas, Asia, and Africa (Lan et al. 2017). As of 2019, a total of 87 countries have reported cases of Zika. In 2018, the American region had 3473 of the laboratory-confirmed cases of Zika virus. In Brazil, the total cases were 19,020, and the highest cases were reported in Panama and Bolivia (World Health Organization 2019).

• 12. SARS-CoV-2.

  Since its outbreak in late December 2019 in China, SARS-CoV-2 has created havoc throughout the world. Similar to SARS-CoV and MERS-CoV, this virus is also a zoonotic virus and has thought to be originated in bats from where it was transmitted to pangolins before humans. The disease caused by SARS-CoV-2, termed as COVID-19, also results in pneumonia and in extreme cases leads to multiple organ failure in infected individuals. As per the reports of WHO on 24 July 2020, a total of 15,296,926 individuals have been infected with the virus globally, and 628,903 individuals have succumbed to death making its mortality rate as 4% which is still increasing day by day. The highest cases and deaths have been reported in the American region (World Health Organization 2020f).