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An opportunistic infection is an infection caused by pathogens (bacteria, fungi, parasites or viruses) that take advantage of an opportunity not normally available. These opportunities can stem from a variety of sources, such as a weakened immune system (as can occur in acquired immunodeficiency syndrome or when being treated with immunosuppressive drugs, as in cancer treatment), an altered microbiome (such as a disruption in gut microbiota), or breached integumentary barriers (as in penetrating trauma). Many of these pathogens do not necessarily cause disease in a healthy host that has a non-compromised immune system, and can, in some cases, act as commensals until the balance of the immune system is disrupted. Opportunistic infections can also be attributed to pathogens which cause mild illness in healthy individuals but lead to more serious illness when given the opportunity to take advantage of an immunocompromised host. A wide variety of pathogens are involved in opportunistic infection and can cause a similarly wide range in pathologies. A partial list of opportunistic pathogens and their associated presentations includes: Clostridioides difficile (formerly known as Clostridium difficile) is a species of bacteria that is known to cause gastrointestinal infection and is typically associated with the hospital setting. Legionella pneumophila is a bacterium that causes Legionnaire’s disease, a respiratory infection. Mycobacterium avium complex (MAC) is a group of two bacteria, M. avium and M. intracellulare, that typically co-infect, leading to a lung infection called mycobacterium avium-intracellulare infection. Mycobacterium tuberculosis is a species of bacteria that causes tuberculosis, a respiratory infection. Pseudomonas aeruginosa is a bacterium that can cause respiratory infections. It is frequently associated with cystic fibrosis and hospital-acquired infections. Salmonella is a genus of bacteria, known to cause gastrointestinal infections. Staphylococcus aureus is a bacterium known to cause skin infections and sepsis, among other pathologies.
[2]Paolo Prandoni, [3]LCAV, EPFL
In [1]:
import matplotlib.pyplot as plt
import numpy as np
import scipy.signal as sp
import seaborn as sns
sns.set()
In [2]:
plt.rcParams["figure.figsize"] = (14,4)
The basic reproduction number[4]¶
The propagation mechanism of an epidemic such as the one caused by
SARS-CoV-2 virus can be roughly modeled, at least in its inital phase,
as a process in which each infected individ