Deep Learning Technology: Sebastian Arnold, Betty van Aken, Paul Grundmann, Felix A. Gers and Alexander Löser. Learning Contextualized Document Representations for Healthcare Answer Retrieval. The Web Conference 2020 (WWW'20)
Funded by The Federal Ministry for Economic Affairs and Energy; Grant: 01MD19013D, Smart-MD Project, Digital Technologies
Viral pneumonia occurs in about 200 million people a year which includes about 100 million children and 100 million adults.
Common causes of viral pneumonia are:
- "Influenza virus" A and B
- "Respiratory syncytial virus" (RSV)
- "Human parainfluenza viruses" (in children)
Rarer viruses that commonly result in pneumonia include:
- "Adenoviruses" (in military recruits)
- "Severe acute respiratory syndrome virus" (SARS coronavirus)
- "Middle East respiratory syndrome virus" (MERS coronavirus)
Viruses that primarily cause other diseases, but sometimes cause pneumonia include:
- "Herpes simplex virus" (HSV), mainly in newborns or young children
- "Varicella-zoster virus" (VZV)
- "Measles virus"
- "Rubella virus"
- "Cytomegalovirus" (CMV), mainly in people with immune system problems
- "Smallpox virus"
- "dengue virus"
The most commonly identified agents in children are "respiratory syncytial virus", "rhinovirus", "human metapneumovirus", "human bocavirus", and "parainfluenza viruses".
Vaccination helps prevent bronchopneumonia, mostly against influenza viruses, adenoviruses, measles, rubella, streptococcus pneumoniae, haemophilus influenzae, diphtheria, bacillus anthracis, chickenpox, and bordetella pertussis.
Lower respiratory infectious disease is the fifth-leading cause of death and the combined leading infectious cause of death, being responsible for 2·74 million deaths worldwide. This is generally similar to estimates in the 2010 Global Burden of Disease study.
This total only accounts for "Streptococcus pneumoniae" and "Haemophilus Influenzae" infections and does not account for atypical or nosocomial causes of lower respiratory disease, therefore underestimating total disease burden.
When comparing the bacterial-caused atypical pneumonias with these caused by real viruses (excluding bacteria that were wrongly considered as viruses), the term "atypical pneumonia" almost always implies a bacterial cause and is contrasted with viral pneumonia.
Known viral causes of atypical pneumonia include respiratory syncytial virus (RSV), influenza A and B, parainfluenza, adenovirus, severe acute respiratory syndrome (SARS)
Bacteria are the most common cause of community-acquired pneumonia (CAP), with "Streptococcus pneumoniae" isolated in nearly 50% of cases. Other commonly isolated bacteria include "Haemophilus influenzae" in 20%, "Chlamydophila pneumoniae" in 13%, and "Mycoplasma pneumoniae" in 3% of cases; "Staphylococcus aureus"; "Moraxella catarrhalis"; "Legionella pneumophila" and Gram-negative bacilli. A number of drug-resistant versions of the above infections are becoming more common, including drug-resistant "Streptococcus pneumoniae" (DRSP) and methicillin-resistant Staphylococcus aureus (MRSA).
The spreading of organisms is facilitated when risk factors are present. Alcoholism is associated with "Streptococcus pneumoniae", anaerobic organisms, and "Mycobacterium tuberculosis"; smoking facilitates the effects of "Streptococcus pneumoniae", "Haemophilus influenzae", "Moraxella catarrhalis", and "Legionella pneumophila". Exposure to birds is associated with "Chlamydia psittaci"; farm animals with "Coxiella burnetti"; aspiration of stomach contents with anaerobic organisms; and cystic fibrosis with "Pseudomonas aeruginosa" and "Staphylococcus aureus". "Streptococcus pneumoniae" is more common in the winter, and should be suspected in persons aspirating a large amount of anaerobic organisms.
CAP is common worldwide, and a major cause of death in all age groups. In children, most deaths (over two million a year) occur in newborn period. According to a World Health Organization estimate, one in three newborn deaths are from pneumonia. Mortality decreases with age until late adulthood, with the elderly at risk for CAP and its associated mortality.
More CAP cases occur during the winter than at other times of the year. CAP is more common in males than females, and more common in black people than Caucasians. Patients with underlying illnesses (such as Alzheimer's disease, cystic fibrosis, COPD, tobacco smoking, alcoholism or immune-system problems) have an increased risk of developing pneumonia.
Community-acquired pneumonia (CAP) is acquired in the community, outside of health care facilities. Compared with health care–associated pneumonia, it is less likely to involve multidrug-resistant bacteria. Although the latter are no longer rare in CAP, they are still less likely.
The most common causative organisms are (often intracellular living) bacteria:
- "Chlamydophila pneumoniae": Mild form of pneumonia with relatively mild symptoms.
- "Chlamydophila psittaci": Causes psittacosis.
- "Coxiella burnetii": Causes Q fever.
- "Francisella tularensis": Causes tularemia.
- "Legionella pneumophila": Causes a severe form of pneumonia with a relatively high mortality rate, known as legionellosis or Legionnaires' disease.
- "Mycoplasma pneumoniae": Usually occurs in younger age groups and may be associated with neurological and systemic (e.g. rashes) symptoms.
Atypical pneumonia can also have a fungal, protozoan or viral cause.In the past, most organisms were difficult to culture. However, newer techniques aid in the definitive identification of the pathogen, which may lead to more individualized treatment plans.
Several studies found that healthcare-associated pneumonia is the second most common type of pneumonia, occurring less commonly than community-acquired pneumonia but more frequently than hospital-acquired pneumonia and ventilator-associated pneumonia. In a recent observational study, the rates for CAP, HCAP and HAP were 60%, 25% and 15% respectively. Patients with HCAP are older and more commonly have simultaneous health problems (such as previous stroke, heart failure and diabetes).
The number of residents in long term care facilities is expected to rise dramatically over the next 30 years. These older adults are known to develop pneumonia 10 times more than their community-dwelling peers, and hospital admittance rates are 30 times higher.
Bronchiolitis typically affects infants and children younger than two years, principally during the fall and winter . Bronchiolitis hospitalization has a peak incidence between two and six months of age and remains a significant cause of respiratory disease during the first two years of life. It is a leading cause of hospitalization in infants and young children.
Dogs will typically recover from kennel cough within a few weeks. However, secondary infections could lead to complications that could do more harm than the disease itself. Several opportunistic invaders have been recovered from the respiratory tracts of dogs with kennel cough, including Streptococcus, Pasteurella, Pseudomonas, and various coliforms. These bacteria have the potential to cause pneumonia or sepsis, which drastically increase the severity of the disease. These complications are evident in thoracic radiographic examinations. Findings will be mild in animals affected only by kennel cough, while those with complications may have evidence of segmental atelectasis and other severe side effects.
A full spectrum of microorganisms is responsible for CAP in adults, and patients with certain risk factors are more susceptible to infections of certain groups of microorganisms. Identifying people at risk for infection by these organisms aids in appropriate treatment.
Many less-common organisms can cause CAP in adults, and are identified from specific risk factors or treatment failure for common causes.
Numerous factors have been suggested and linked to a higher risk of acquiring the infection, inclusive of malnutrition, vitamin A deficiency, absence of breastfeeding during the early stages of life, environmental pollution and overcrowding.
Mortality caused by HPIVs in developed regions of the world remains rare. Where mortality has occurred, it is principally in the three core risk groups (very young, elderly and immuno-compromised). Long term changes can however be associated with airway remodelling and are believed to be a significant cause of morbidity. The exact associations between HPIVs and diseases such as chronic obstructive pulmonary disease (COPD) are still being investigated.
In developing regions of the world, the highest risk group in terms of mortality remains pre-school children. Mortality may be as a consequence of primary viral infection or secondary problems such as bacterial infection. Predispositions, such as malnutrition and other deficiencies may further elevate the chances of mortality associated with infection.
Overall, LRI's cause approximately 25–30% of total deaths in pre-school children in the developing world. HPIVs is believed to be associated with 10% of all LRI cases, thus remaining a significant cause of mortality.
Nursing home-acquired pneumonia is an important subgroup of HCAP. Residents of long term care facilities may become infected through their contacts with the healthcare system; as such, the microbes responsible for their pneumonias may be different from those traditionally seen in community-dwelling patients, requiring therapy with different antibiotics. Other groups include patients who are admitted as a day case for regular hemodialysis or intravenous infusion (for example, chemotherapy). Especially in the very old and in demented patients, HCAP is likely to present with atypical symptoms.
Viral croup or acute laryngotracheitis is most commonly caused by parainfluenza virus (a member of the paramyxovirus family), primarily types 1 and 2, in 75% of cases. Other viral causes include influenza A and B, measles, adenovirus and respiratory syncytial virus (RSV). Spasmodic croup is caused by the same group of viruses as acute laryngotracheitis, but lacks the usual signs of infection (such as fever, sore throat, and increased white blood cell count). Treatment, and response to treatment, are also similar.
Viral croup is usually a self-limiting disease, with half of cases resolving in a day and 80% of cases in two days. It can very rarely result in death from respiratory failure and/or cardiac arrest. Symptoms usually improve within two days, but may last for up to seven days. Other uncommon complications include bacterial tracheitis, pneumonia, and pulmonary edema.
As of March 2020, it was unknown if past infection provides effective and long-term immunity in people who recover from the disease. Immunity is seen as likely, based on the behaviour of other coronaviruses, but cases in which recovery from COVID-19 have been followed by positive tests for coronavirus at a later date have been reported. These cases are believed to be worsening of a lingering infection rather than re-infection.
The impact of the pandemic and its mortality rate are different for men and women. Mortality is higher in men in studies conducted in China and Italy. The highest risk for men is in their 50s, with the gap between men and women closing only at 90. In China, the death rate was 2.8 percent for men and 1.7 percent for women. The exact reasons for this sex-difference is not known, but genetic and behavioural factors could be a reason. Sex-based immunological differences, lesser prevalence of smoking in women and men developing co-morbid conditions such as hypertension at a younger age than women could have contributed to the higher mortality in men. In Europe, 57% of the infected individuals were men and 72% of those died with COVID-19 were men. As of April 2020, the US government is not tracking sex-related data of COVID-19 infections. Research has shown that viral illnesses like Ebola, HIV, influenza and SARS affect men and women differently. A higher percentage of health workers, particularly nurses, are women, and they have a higher chance of being exposed to the virus. School closures, lockdowns and reduced access to healthcare following the 2019–20 coronavirus pandemic may deferentially affect the genders and possibly exaggerate existing gender disparity.
Viral infections such as canine parainfluenza or canine coronavirus are only shed for roughly 1 week following recovery; however, respiratory infections involving "Bordetella bronchiseptica" can be transmissible for several weeks longer. While there was early evidence to suggest that "B. bronchiseptica" could be shed for many months post-infection, a more recent report places detectable nasal and pharyngeal levels of "B. bronchiseptica" in 45.6% of all clinically healthy dogs. This has potentially expanded the vector from currently or recently infected dogs to half the dog population as carriers. To put the relative levels of shedding bacteria into perspective, a study analyzing the shedding kinetics of "B. bronchiseptica" presents the highest levels of bacterial shedding one week post-exposure, with an order of magnitude decrease in shedding observed every week. This projection places negligible levels of shedding to be expected 6 weeks post-exposure (or ~5 weeks post-onset of symptoms). Dogs which had been administered intranasal vaccine 4 weeks prior to virulent "B. bronchiseptica" challenge displayed little to no bacterial shedding within 3 weeks of exposure to the virulent strain.
Acute bronchitis is one of the most common diseases. About 5% of adults are affected and about 6% of children have at least one episode a year. It occurs more often in the winter. More than 10 million people in the United States visit a doctor each year for this condition with about 70% receiving antibiotics which are mostly not needed. There are efforts to decrease the use of antibiotics in acute bronchitis.
The term usually refers to acute viral bronchiolitis, a common disease in infancy. This is most commonly caused by respiratory syncytial virus (RSV, also known as human pneumovirus). Other viruses which may cause this illness include metapneumovirus, influenza, parainfluenza, coronavirus, adenovirus, and rhinovirus.
Children born prematurely (less than 35 weeks), with a low birth weight or who have from congenital heart disease may have higher rates of bronchiolitis and are more likely to require hospital admission. There is evidence that breastfeeding provides some protection against bronchiolitis.
Gram-negative bacteria are seen less frequently: "Haemophilus influenzae" (), "Klebsiella pneumoniae" (), "Escherichia coli" (), "Pseudomonas aeruginosa" (), "Bordetella pertussis", and "Moraxella catarrhalis" are the most common.
These bacteria often live in the gut and enter the lungs when contents of the gut (such as vomit or faeces) are inhaled.
Since the start of the AIDS epidemic, PCP has been closely associated with AIDS. Because it only occurs in an immunocompromised host, it may be the first clue to a new AIDS diagnosis if the patient has no other reason to be immunocompromised (e.g. taking immunosuppressive drugs for organ transplant). An unusual rise in the number of PCP cases in North America, noticed when physicians began requesting large quantities of the rarely used antibiotic pentamidine, was the first clue to the existence of AIDS in the early 1980s.
Prior to the development of more effective treatments, PCP was a common and rapid cause of death in persons living with AIDS. Much of the incidence of PCP has been reduced by instituting a standard practice of using oral co-trimoxazole (Bactrim / Septra) to prevent the disease in people with CD4 counts less than 200/μL. In populations that do not have access to preventive treatment, PCP continues to be a major cause of death in AIDS.