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)

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

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!

• Salmonella
• Escherichia coli
• Campylobacter
• Vibrio
• Helicobacter pylori
• Legionella
• Listeria

• 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

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 ( contamination of vegetables) and can be carried by animal

• Giardia lamblia
• Cryptosporidium parvum
• Naegleria fowleri
• Toxoplasma gondii
• Ascaris lumbricoides
• Taenia saginata
• Schistosoma

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

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

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

• 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

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

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

• 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

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...

Fungus living in the environment worldwide

In immunocompromised or immunodeficient people, can cause cryptococcal meningitis

Est. 152K cases and 112K deaths worldwide / year

Coccidioides

Fungus living in the soil in SW USA, parts of Mexico and Central and South America, with expanding range

Causes Valley fever

• 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