Infectious disease & Survey of bacteria
What are normal microbiota (resident flora) and their benefits?
Normal flora is found in all areas of the human body exposed to the environment (one exception is the lungs), but internal organs and body fluids are considered sterile in a healthy individual
They prevent colonization by pathogens by competing for attachment & nutrients
In other words… they are preventing the overgrowth of harmful microorganisms
Some synthesize vitamins that are absorbed as nutrients by the host
General understanding of the resident flora of various anatomical areas (not specific names of bacteria) and how they may function to protect or to be opportunistic pathogens
(https://bio.libretexts.org/Courses/Manchester_Community_College_(MCC)/Remix_of_Openstax%3AMicrobiology_by_Parker_Schneegurt_et_al/12%3A_Microbial_Interactions_Flora_Pathogenicity_and_Epidemiology/12.01%3A_Normal_Microbiota_of_the_Body)
Skin
derive nutrition from skin cells and secretions such as sweat and sebum
inhibit transient-microbe colonization by producing antimicrobial substances and outcompeting other microbes that land on the surface of the skin
This helps to protect the skin from pathogenic infection
GI tract
aid in digestion and contribute to the production of feces, the waste excreted from the digestive tract, and flatus, the gas produced from microbial fermentation of undigested food
can synthesize vitamins
Urogenital system
(vaginal microbiota) defend against vaginal infections and sexually transmitted infections by occupying cellular binding sites and competing for nutrients.
Infection
occurs when a pathogen or parasite enters and begins to grow on the host
Most infections do cause signs or symptoms and go unnoticed
Signs can be observed by examination (objective marker of disease)
Ex. Fluid-filled rash, Fever of 102°F
Symptoms are experienced by the person (subjective indicator of disease)
Ex. Pain, Fatigue
Disease occurs when the patient develops symptoms
pathogen (primary (frank pathogen) versus opportunistic) (COPs)
A pathogen is any bacterium, virus, fungus, protozoan, or worm (helminth) that causes disease in humans
Primary pathogens are likely to cause disease after infection in a healthy host
Rapidly reproduce/increase in number
Moderate to high virulence
Opportunistic pathogens are less likely to cause disease in a healthy host; they often affect immune-compromised hosts
Low virulence
Part of microbiota, transient microbes
Colonizing opportunistic pathogens (COPs) are microbes that asymptomatically colonize the human body and, when the conditions are right, can cause infections
Persist indefinitely and transmit w/o detection
Virulence
the degree of pathogenicity; describes the level of harm by a pathogen following infection
Pathogenicity is the ability of the organism to cause disease
Increased virulence, increased death*
Infectious dose (ID)
the amount of a pathogen that's required to establish an infection
ID50 refers to the dose or number of organisms that will infect 50% of an experimental group of hosts within a specified time.
Lethal dose (LD)
the amount of a pathogen following injection that's required for death
LD50 refers to the dose or number of organisms that will kill 50% of an experimental group of hosts within a specified time.
used as an indicator of a substance’s relative toxicity
Thus, a substance with a high LD50 would have a low toxicity (less virulence), while a substance with a low LD50 would have a high toxicity (high virulence)
Infectious Disease
a disease caused by a pathogen and may or may not be communicable or contagious to another
In other words, they are caused by an infectious agent, they cause an infection but don’t have to be transmissible
Communicable Disease
a disease caused by an infectious agent that is transmissible to another person
Characteristics of virulence (what about the cell itself, or molecules it produces, allow it to cause damage)
Aspects of the pathogen that contribute to virulence:
adhesion
invasion, the entry of a pathogen into a living cell, where it then lives
invasiveness, the ability of a bacterial pathogen to spread rapidly through tissues, can produce enzymes that degrade host tissue
toxigenicity, capacity to produce toxins at the site of multiplication
Reservoirs and Sources - human, animal, inanimate(fomite, food, water, soil)
Reservoir = an animal (including humans) or an environment (soil, water, etc.) that normally harbors the pathogen
Source - where you specifically acquired the pathogen
Sometimes source and reservoir are the same or different
Carriers - Asymptomatic - Passive, Incubatory, Convalescent, Chronic
Asymptomatic carrier harbors the potential disease agent but does not have the disease
May also be considered healthy carriers - no history of having the infection
Passive carriers are those who never experience symptoms despite being infected.
Active carriers = actively sick with the infection
Convalescent carriers = recovering from the illness
Incubatory carriers = still in the incubation stage of the infection
Chronic carriers = those who continue to harbor a pathogen for months or even years after their initial infection
Animals: zoonosis and vectors
Zoonotic diseases are infections of animals that can be transmitted to humans
Pathogens may or may not cause the animal reservoir to have a disease
Transmission may be direct or indirect “spillover” to humans
The majority of emerging diseases are zoonotic in origin
A vector is a living organism that transmits an infectious agent from an infected animal to a human or another animal.
Cycle - Incubation, Prodromal, Invasion (Illness), Convalescence, and comparison between no. of organisms and symptoms
Incubation = This refers to the time elapsed between exposure to a pathogenic organism, and from when symptoms and signs are first apparent
Prodromal = In this phase, the numbers of infectious agents start increasing and the immune system starts reacting to them
It is characterized by early symptoms that might indicate the start of a disease before specific symptoms occur
Invasion = is characterized by active replication or multiplication of the pathogen and its numbers peak exponentially, quite often in a very short period of time.
includes the time when a person shows apparent symptoms of an infectious disease
Symptoms are very pronounced, both specific to the organ affected as well as in general due to the strong reaction of the immune system
Convalescence = the patient recovers gradually and returns to normal
may continue to be a source of infection even if feeling better
Depending on the severity of the infection, some people may have permanent damage even after the infection resolves.
Types of Infections - Local, systemic, mixed, primary and secondary, acute and chronic, asymptomatic
Local infection = an infection that affects only one body part or organ
Systemic infection = affects the entire body
Mixed infection = infected with more than one strain of the same species of bacteria
Primary infection = when you are initially exposed to a pathogen?
Secondary infection = one that occurs when a different infection, known as a primary infection, has made a person more susceptible to disease
occurs either after or because of another infection
Acute infection = symptoms develop and resolve rapidly (i.e. the common cold)
Chronic infection = involves symptoms that develop gradually and resolve slowly
Asymptomatic infection = where a disease or infection does not lead to any (noticeable) symptoms
Sequelae
Pathological consequences that may develop after a disease resolves
Types of Direct and Indirect Transmission, paying particular attention to respiratory droplets, aerosols, droplet nuclei
Direct contact transmission = organisms may spread directly from person to person
Touching, kissing, sex, droplets from direct sneezing or coughing (this occurs when someone is sneezing or coughing in your personal space; IF they cough or sneeze and it lingers in the air until someone enters the space OR the secretions dry up and then become airborne later - that is INDIRECT transmission)
Indirect transmission = pathogens may spread indirectly through an intermediary, which may be living or nonliving
Airborne transmission (droplet nuclei, aerosols)
Fomites (inanimate objects)
Vehicles (food, water, or air)
Vectors (ticks, mosquitoes, flies)
Adherence and colonization (list a few characteristics that influence)(also associated with virulence)
Adhesins enable the microbiota to attach to host cells
Like cell surface layers or appendages that aid in attachment (virulence factor)
Colonization refers to the ability of the microbe to say attached to the surface and replicate, despite the host defenses
Toxin production - Endotoxins and Exotoxins and comparisons between the 2
Endotoxin = toxin that is not secreted but released after the cell is damaged
Composed of LPS
Target organs are damaged; the heart, muscles, blood cells, and intestinal tract show dysfunctions
General physiological effects (fever, malaise, diarrhea, aches, shock)
Weakly immunogenic/antigenic
Usually heat stable
Exotoxin = toxin molecule (protein) secreted by a living bacterial cell into the infected tissue
Usually G+ bacteria
Strong specificity for a target cell
Very specific in their action (entero-, neuro-, cyto- toxin)
Strongly antigenic
Can produce toxoids or antitoxins
Very toxic in small amounts
Usually heat labile
(From one host to the next:) Portals of entry/exit
Fecal-oral: portal is the mucosa of the GI tract
Skin: portal is the skin epithelium
Respiratory: portal is the mucosa of the respiratory tract
Urogenital: portal is the mucosa of the genital and urinary tract
Parenteral: portal is through breaks in the skin
Entry via the eye: portal is conjunctiva (mucous membranes on the eyeball and inner eyelid)
Communicable verses Non-communicable
Communicable = infectious disease
Non-communicable = chronic disease; not passed from person to person
Prevalence
Refers to the total number of cases and reflects the length of the illness, recovery, and deaths
Incidence
The rate of new cases that occur during a specified time period (usually expressed in relation to a population number such as 1000, 10000, or 100000)
morbidity and mortality rates
Morbidity is the rate of illness due to a disease
Mortality is the rate of death due to a disease
Endemic
Endemic disease is one that is always present in a community at a low rate, often in an animal reservoir
Ex. plague, Lyme disease
Epidemic
Epidemic disease is one in which the number of cases increases in a community in a short time
Ex. outbreaks
Pandemic
Pandemic disease is an endemic that spreads worldwide
Ex. influenza, HIV, covid-19
Enterococcus faecalis and VREs
E. faecalis is the most abundant GPC in the human intestinal tract and is frequently used as an indicator organism in colder environments (i.e. water, frozen foods, brackish, and saltwater)
VRE, or Vancomycin Resistant Enterococci, are responsible for many serious HAIs
Identified as a Serious Threat by CDC
Staphylococcus aureus
Troublesome hospital pathogen and common foodborne illness
Possess enzymes that coat the bacteria and protect it from the immune system and antibiotics (virulence factor)
Exotoxins damage the host tissue and weaken host defenses (i.e. Toxis shock syndrome toxin (TSST), exfoliative toxin, enterotoxin)
Skin infections
Folliculitis (superficial)
Boil or furuncle (deep)
Carbuncles are boils joined together
Impetigo (collection of multiple infective lesions)
Nonbullous
Bullous
Food poisoning
Methicillin-resistant S. aureus (MRSA)
Was an HAI but is now no longer confined to a hospital
Streptococcus pyogenes
Necrotizing fasciitis = “flesh-eating,” extremely rapid spread, life-threatening infection that frequently arises from superficial wounds and in healthy individuals with no medical history, can also be associated with compromised individuals
bacteria produce enzymes that cause necrosis of fat and fascia that surrounds muscles and organs, making treatment extremely difficult
Natural reservoirs = human nasopharynx and parts of the skin
Streptococcal pyogenic exotoxins (SPEs)
Can produce high levels of inflammation and lead to shock
Hemolysin
Lyses RBCs
Erysipelas
Acute infection (swollen lymph nodes, fever, systemic symptoms)
Rash (may be on the face)(“butterfly” appearance)
Cellulitis
Uncomplicated, non-necrotizing inflammation of the dermis related to acute infection
Symptoms: localized pain, swelling, tenderness, erythema, and warmth
Streptococcal pharyngitis
Also known as strep throat
Contagious; spreads through person-to-person contact and indirect contact with items contaminated by secretions
Symptoms: high fever, sore throat, and tender, enlarged lymph nodes
Some strains of S. pyogenes produce exotoxins
Streptococcal pyogenic exotoxins (SPEs) can cause fever and scarlet fever (red rash)
“strawberry tongue”
Post-streptococcal sequelae:
Acute rheumatic fever (ARF)
Glomerulonephritis (kidney disease)
Bacillus cereus
Common airborne and dust borne
Resistant to usual methods of disinfection and antisepsis (b/c of endospores)
Spores survive cooking and reheating
Clostridium botulinum
Rare but severe intoxication usually from home-canned food
Botulism = intoxication associated with inadequate food preservation
Foodborne pathogen
Spore-forming
Associated with vegetables and honey
Botulinum toxin can cause paralysis; considered the most potent acute toxin known
Infant botulism & wound botulism
Clostridium perfringens
Clostridial myonecrosis: muscle tissue is affected
Extremely serious, life-threatening disease
True saprophyte, growing only on dead tissue
Produces toxins
C. perfringens enterotoxin (CPE) produced by some strains can lead to gastrointestinal disease
Gastroenteritis
Spores contaminate food that has not been cooked thoroughly
Mild, intestinal illness; 2nd most common form of food poisoning worldwide
Associated with “thick” foods - meats w/gravy, casseroles, stews
Clostridioides difficile
Antibiotic-associated colitis/Pseudomembranous colitis (PMC)
Urgent threat
Caused by chronic antibiotic use
Nosocomial infection
Toxin production
G+, endospore forming
Listeria monocytogenes
G+ non-spore-forming coccobacilli
Associated with animals and animal products
Causes mild gastroenteritis to more severe cases of meningitis, fetal demise
3rd leading cause of fatalities of food born illness
Foodborne pathogen → causes diarrhea and fever
Streptomyces
Phylum actinobacteria
Actinomycetes
Form mycelia with branching filaments
Streptomyces - source of most currently used antibiotics
Abundant in soil
Bifidobacterium bifidus
Pioneer colonizer of the human intestinal tract
Associated with vaginal births and breastfeeding
Responsible for many of the significant benefits of breastmilk
Probiotic agent
Mycobacterium tuberculosis (tuberculosis)
Acid-fast
Cases are on the rise in developed nations due to HIV and a growing indigent population
Multidrug resistant (MDR) tuberculosis
highly infectious
produces rapid onset and fatal disease among patients with HIV
Spread from person to person (no animal reservoir)
Mycobacterium leprae (leprosy)
Hansen’s bacillus/Disease
Strict parasite
Causes leprosy, a chronic disease that begins in the skin and mucous membranes and progresses into nerves
Endemic regions throughout the world
Not highly virulent
Bartonella henselae
Cat-scratch disease
A lymphatic infection associated with a clawing injury by cats
Rickettsia rickettsia
Rocky Mountain spotted fever
Zoonosis carried by dog and wood ticks (and lice)
First symptoms are fever, chills, headache, and a distinct spotted rash
May damage the heart and CNS
fatality rates are 20% if not treated
Burkholderia cepacia
active in biodegradation of a variety of substances; opportunistic agent in the respiratory tract, urinary tract, and occasionally skin infections; drug-resistant, numerous outbreaks in consumer products
Neisseria gonorrhoeae
Gonorrhea (“the clap”)
Pelvic inflammatory disease
infection spreads to uterus and fallopian tubes
Opthalmia neonatorum
eye infection
Most women do not exhibit symptoms but most men do
Escherichia coli and Escherichia coli 0157:H7 - STECs
Escherichia coli - commensal
live in intestines
Escherichia coli 0157:H7 - pathogen
causes a severe intestinal infection
most common strain to cause illness in people
Shiga Toxin-Producing E. coli (STECs)
causes bloody diarrhea (similar to that caused by Shigella)
CREs - Carbapenem Resistant Enterobacteraceae
Untreatable and hard-to-treat infections from CRE bacteria are on the rise in patients in medical facilities
Have become resistant to nearly all antibiotics we have today
Almost half of the hospital patients who get bloodstream infections from CRE bacteria die from the infection
Legionella pneumophila
Legionnaire’s disease
Intracellular pathogen
Contaminates various water sources, ranging from lakes to the hot water and air-conditioning distribution systems of large buildings
Transmission via inhalation of contaminated water droplets
Causes atypical pneumonia
Fatality rate 3-30%
Pseudomonas aeruginosa
Commonly grows in the soil as a decomposer, but in humans, it can infect surgical wounds or form biofilms in the lungs of cystic fibrosis patients
MDR
Very common HAI
Most common cause of hospital-acquired pneumonia
Cause of endocarditis, meningitis, UTIs, abscesses, corneal disease
Opportunistic pathogen
Salmonella enterica
Salmonellosis
Typhoid fever
No animal reservoir
Associated with food preparation
Fecal-oral route
Intermittent fevers and diarrhea
Enterocolitis
Associated with animal contact
Shigella spp.
Shigellosis
Bloody diarrhea
Produces Shiga toxin
Low infective dose
Also called bacillary dysentery
Similar pathogenesis to STEC
No animal reservoir; fecal-oral route via food or water
Yersinia pestis
Causes a deadly disease (plague) that can be transmitted from animals to humans by an infected flea
bubonic plague
organisms moves from site to lymph nodes
not transmissible
septicemic plague
pathogen enters bloodstream
not transmissable
pneumonic plague
pathogen infects lungs
transmissable, easily spread
Campylobacter jejuni
(I did not see anything on C. jejuni specifically*)
Vibrio cholerae
Fecal-oral route (contaminated water)
“Rice water stools”
Noninvasive → does not cause fever or bloody stools
Cholera toxin
Secretory diarrhea
Vibrio parahaemolyticus
gastroenteritis from raw seafood; symptoms similar to cholera
Vibrio vulnificus
gastroenteritis from raw oysters; serious complications in persons with diabetes or liver disease. Associated with necrotizing fasciitis from swimming in ocean water with an open wound
Bdellovibrio
Predatory bacteria
Has the ability to parasitize and kill other G- bacteria
Treponema pallidum
spirochete
“Great imitator”
primary syphilis
chancre: painless inflammatory reaction
latency
Leptospira interrogans
causes leptospirosis, a zoonosis
bacteria shed in urine; infection occurs by contact with contaminated urine; targets kidneys, liver, brain, eyes
sudden high fever, chills, headache, muscle aches, conjunctivitis, and vomiting
long term infections may affect the kidneys and liver
50-60 cases a year in the U.S.
increasing world wide
Borrelia burgdorferi
Lyme disease
the most common vector-borne illness
B. burgdorferi
spirochete
transmitted by tick bite
linear chromosome
complex life cycle
Bordetella pertussis
(I did not see anything on B. pertussis specifically*)
Chlamydia trachomatis
persistent infection with C. trachomatis can lead to pelvic inflammatory disease
most frequently reported sexually transmitted infectious disease
75% of infected women have no symptoms; most men are also asymptomatic
Chlamydia is the major cause of nongonococcal urethritis in the United States
Trachoma
caused by C. trachomatis serotypes A-C
transmitted by hand-to-hand contact, contact with infected soaps and towels, and flies
the greatest single cause of preventable blindness throughout the world
neglected disease
Rhizobium
Intracellular Symbionts and Predators
endosymbionts of plants that fix nitrogen
Bacteroides fragilis
Bacteriodes spp.
major inhabitants of the human colon
break down compounds that could be toxins
produce polysaccharide A and other communication molecules to communicate with and direct the immune system
removes side chains from bile acids
can be opportunistic
leading anaerobic HAI
(I did not see anything on B. fragilis specifically*)
Cyanobacteria (Oxygenic Phototrophic Bacteria)
oxygenic photoautotrophs = produce oxygen through photosynthesis
the only bacteria that produce oxygen
responsible for Earth’s atmosphere
endosymbiosis leading to eukaryotic plants
Anoxygenic Phototrophic Bacteria
Photosynthetic - utilize different wavelengths of light than the cyanobacteria; live in different depths
Contain photosynthetic pigment bacteriochlorophyll
Do not give off oxygen as a product of photosynthesis
Caulobacter
Budding Appendaged Bacteria
rods or cocci with an appendage
lives in very low-nutrient environments
Strongest biological adhesive known
Myxobacteria
Gliding and Fruiting bacteria
glide over moist surfaces and leave a slime trail
produces myxospores that are resistant to desiccation, heat, and UV and can survive for several years (still not as resistant as endospores)
Deinococcus radiodurans
extraordinarily resistant to desiccation and radiation
isolated from ground meat, feces, air, freshwater, and other sources, but natural habitat unknown
Archaea groups - Know Methanogens or any of the others from the table that lists the 5 groups - know 1 and give 3 characteristics
Methanogenic archaea
strict anaerobes
capable of methanogenesis, an anaerobic respiration that generates methane as the final product of metabolism
cells possess coenzyme M, factors 420 and 430, and methanopterin