OMNI/RÉUNIS Course on One Health Modelling for Emerging Infectious Diseases
Julien Arino - Course material (slides and code).
Environmental transmission of bacterial,
parasitic, viral and fungal pathogens
12-16 December 2022
Julien Arino (julien.arino@umanitoba.ca) 
Department of Mathematics & Data Science Nexus University of Manitoba*
Canadian Centre for Disease Modelling NSERC-PHAC EID Modelling Consortium (CANMOD, MfPH, OMNI/RÉUNIS)
Environmental transmission of bacterial,
parasitic, viral and fungal pathogens
A.k.a. Environmentally transmitted pathogens (ETP)
Theme 3 of the OMNI/RÉUNIS course
Bibliographic resources
- Charles Gerba. Chapter on Environmentally Transmitted Pathogens in Environmental Microbiology. Where applicable, I follow the same order
- CDC
- Wikipedia and linked resources
- Google Scholar
Images sources
- Wikipedia, Google Image Search, papers…
- Note that some diagrams have weird colours: I am inverting them to have a black background…
Outline
- Common features in ETP
- Bacteria
- Parasites
- Viruses
- Fungi
- In summary
Common features in ETP
A wide variety of diseases and pathogens
Characteristic is that the pathogens replicate or survive in an abiotic environment
- Enteric diseases
- Food-borne diseases
Important to define precisely what it is we mean by ETP, since the environment can be taken to mean anything outside the body, allowing most pathogens to fall into this class
See, e.g., the US CDC Division of Foodborne, Waterborne, and Environmental Diseases
Enteric diseases
Group of diseases associated with the ingestion of food or water contaminated by microorganisms and microbial toxins that attack the gastrointestinal tract
From chatGPT:
An enteric disease is an illness that affects the digestive system, specifically the intestines. Enteric diseases can be caused by a variety of factors, including viral, bacterial, or parasitic infections, as well as toxins or other harmful substances. These diseases can result in a range of symptoms, including stomach pain, nausea, vomiting, diarrhea, and fever
The “celebrated” fecal-oral route ;)
Cannot remember who I heard using the expression originally… Joke aside, a common dissemination route for ETP; I will write F-OR
Fomites
An inanimate object that can transfer a pathogen to a new host after being contaminated or exposed to the pathogen
- Extremely important in hospital settings
- Elevator buttons and door knobs of SARS-CoV-1
Climate change … changes things
Example of fungi
Another common theme - AMR
Antimicrobial resistance occurs when microorganisms (such as bacteria, fungi, viruses, and parasites) develop the ability to survive exposure to antimicrobial drugs (such as antibiotics, antifungals, antivirals, and antimalarials). This means that the drugs that were previously effective at killing the microorganisms or preventing their growth no longer work, and the infections they cause can become difficult or even impossible to treat. Antimicrobial resistance can lead to longer-lasting and more severe infections, and it can spread to other people. It is a major public health concern, and efforts are underway to address it.
Now we take a short tour
Warning : some images are not pretty!
Environmentally transmitted bacteria
- Salmonella
- Escherichia coli
- Campylobacter
- Vibrio
- Helicobacter pylori
- Legionella
- Listeria
Gram-negative and Gram-positive bacteria
- Gram-negative bacteria are not reactive to the Gram staining method, i.e., they do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation
- Gram-positive bacteria retain the violet stain
Salmonella
Genus of Gram-negative bacteria
Most infections due to ingestion of food contaminated by animal or human feces (e.g., bad handwashing practices at food vendor)
Typhoid fever
Caused by Salmonella Typhi
Symptoms vary from mild to severe; usually begin six to 30 days after exposure
Spread by eating or drinking food or water contaminated with the feces of an infected person
Escherichia coli
Gram-negative bacterium of genus Escherichia commonly found in intestines of warm-blooded organisms
Some serotypes cause serious food poisoning
Unwashed vegetables, poorly butchered and undercooked meat
Cause gastroenteritis, urinary tract infections and neonatal meningitis in humans
Campylobacter
Genus of Gram-negative bacteria
Causes campylobacteriosis (diarrhoeal disease) in humans
Self-limiting (no treatment required)
Mostly transmitted from poultry but also present in water
Vibrio
Genus of Gram-negative bacteria
Name comes from latin vibro, “to move rapidly to and fro, to shake, to agitate”
Several species cause foodborne infections:
- cholera
- vibriosis
- also involved in wound infections
Commonly found in salt water environments
Vibrio cholerae
Transmitted through the ingestion of fecally contaminated food and water
Cholera remains prevalent in many parts of Central America, South America, Asia, and Africa.
See CDC, WHO or WHO cholera dashboards
London cholera epidemic of 1854
Near Broad Street, London (UK)
Studied by John Snow
I found that nearly all the deaths had taken place within a short distance of the [Broad Street] pump
Vibrio vulnificus
Severe form stemming from consumption of raw or undercooked seafood (mainly oysters)
Can lead to necrotising fasciitis (flesh eating disease)
Patient on the left had to be amputated
Helicobacter pylori
Small, Gram-negative, rod-shaped bacterium
F-OR
Major cause of peptic ulcer disease and gastritis
Legionella
Genus of Gram-negative bacteria
L. pneumophila is causative agent of legionellosis and Pontiac fever
Most commonly spread by cooling towers (well known outbreak of 1976 in Philadelphia infecting 221 and killing 34)
Listeria
Genus of Gram-positive bacteria with 21 species
L. monocytogenes causes most human cases
CFR ~ 20%
Can be found in soil ($\Rightarrow$ contamination of vegetables) and can be carried by animal
Environmentally transmitted parasites
- Giardia lamblia
- Cryptosporidium parvum
- Naegleria fowleri
- Toxoplasma gondii
- Ascaris lumbricoides
- Taenia saginata
- Schistosoma
Giardia lamblia
Flagellated microorganism of genus Giardia
Colonises small intestine
Causes diarrhea (giardiasis)
Found on surfaces, in soil, food or water contaminated with feces of infected people or animals
Cryptosporidium parvum
Protozoan
Infects wide variety of vertebrate hosts
Wide range of signs and symptoms; immunocompetent patients may present self-limiting diarrheal illness, typically resolving within 2–3 weeks; immunocompromised patients may have more severe complications
Naegleria fowleri
A.k.a. “brain-eating amoeba”…
Shapeshifting amoeboflagellate excavate
Lives in soil and warm fresh water
3 infections/year in the US, typically fatal
Toxoplasma gondii
Protozoan parasite infecting most species of warm-blooded animals and causes toxoplasmosis
Toxoplasmosis: only definitive hosts are domestic cats and their relatives
Ascaris lumbricoides
Very large (adult females: 20 to 35 cm; adult males: 15 to 30 cm) nematodes (roundworms) that parasitise the human intestine
A. lumbricoides primary species involved in human infections globally, but Ascaris derived from pigs (A. suum) may also infect humans
Taenia saginata
Cestodes Taenia saginata (beef tapeworm), T. solium (pork tapeworm) and T. asiatica (Asian tapeworm). Taenia solium can also cause cysticercosis
Sometimes called Charlie ;)
Schistosoma
Genus of trematodes, parasitic flatworms responsible for schistosomiasis
Released from infected freshwater snails
Burden estimate vary, but ~ 240M affected and 4K-200K deaths per year
F-OR with a twist
Environmentally transmitted viruses
- Adenoviruses
- Enteroviruses
- Hepatitis A virus (HAV)
- Hepatitis E virus (HEV)
- Rotaviruses
Adenoviruses
Medium-sized (90-100 nm) double-stranded DNA viruses
More than 50 types cause infections in humans, mostly respiratory illnesses
Resistant to many common disinfectants and can remain infectious for long periods on environmental surfaces and medical instruments
Enteroviruses
Positive-sense single-stranded RNA virus
Named because of enteric transmission (through the intestine)
Enteroviruses can be found in an infected person’s
- feces
- secretions
- blister fluid
So, of course, F-OR; plus fomites
Poliovirus
Enterovirus C with 3 serotypes
Single-stranded positive-sense RNA genome with protein capsid
F-OR
Vaccine preventable
Rhinoviruses
Used to be a genus, now part of enteroviruses
H2H but also through fomites
Hepatitis A virus (HAV)
Found in stool and blood of infected individuals
Transmission through close personal contact with an infected person or through eating contaminated food or drink (F-OR)
Vaccine preventable
Hepatitis E virus (HEV)
Found in the stool of an infected person
In developing countries, people most often get HEV via F-OR. In developed countries, people have gotten sick with hepatitis E after eating raw or undercooked pork, venison, wild boar meat, or shellfish
Rotaviruses
Genus of double-stranded RNA viruses, with Rotavirus A causing >90% of human infections (mostly in kids due to acquired immunity)
Estimated +150K deaths in 2019
Also pathogen of livestock
F-OR and through contaminated surfaces
Vaccine preventable
Environmentally transmitted fungi
- Aspergillus
- Cryptococcus
- Coccidioides
Aspergillus
Genus with 837 species
Named after aspergillium (holy water sprinkler), first observation in 1729 by Pier Antonio Micheli, biologist and … priest
On the left: aspergillus niger
Aspergillus fumigatus causes >90% infections, in particular in individuals with an immunodeficiency
Aspergillus fumigatus infections
Invasive pulmonary aspergillosis (IPA): fungi enter the lung, invade and damage lung tissue and enter blood vessels. CFR 50%-95% depending on speed of diagnosis, condition…
Cryptococcus neoformans
Fungus living in the environment worldwide
In immunocompromised or immunodeficient people, can cause cryptococcal meningitis
Est. 152K cases and 112K deaths worldwide / year
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Coccidioides
Fungus living in the soil in SW USA, parts of Mexico and Central and South America, with expanding range
Causes Valley fever
In summary
- Wide variety of pathogens
- Some infections are vaccine preventable
- Many infections go through the F-OR and highlight the need for improved sanitation
- Problem of resistance to antimicrobials (AMR) is wide-spread and should be considered