Cause
The most common causative organisms are (often intracellular living) bacteria:
Chlamydia pneumoniae
Mild form of pneumonia with relatively mild symptoms. Chlamydia 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. Viral
Known viral causes of atypical pneumonia include respiratory syncytial virus (RSV), influenza A and B, parainfluenza, adenovirus, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), COVID-19
and measles. Diagnosis
Chest radiographs (X-ray photographs) often show a pulmonary infection before physical signs of atypical pneumonia are observable at all. This is occult pneumonia. In general, occult pneumonia is rather often present in patients with pneumonia and can also be caused by Streptococcus pneumoniae, as the decrease of occult pneumonia after vaccination of children with a pneumococcal vaccine suggests.Infiltration commonly begins in the perihilar region (where the bronchus begins) and spreads in a wedge- or fan-shaped fashion toward the periphery of the lung field. The process most often involves the lower lobe, but may affect any lobe or combination of lobes. Epidemiology
Mycoplasma is found more often in younger than in older people. Older people are more often infected by Legionella.
As the levels of cystine in the urine increase, it forms cystine crystals, resulting in kidney stones. Cystine crystals form hexagonal-shaped crystals that can be viewed upon microscopic analysis of the urine. The other amino acids that are not reabsorbed do not create crystals in urine.The overall prevalence of cystinuria is approximately 1 in 7,000 neonates (from 1 in 2,500 neonates in Libyan Jews to 1 in 100,000 among Swedes). Pathophysiology
Cystinuria is characterized by the inadequate reabsorption of cystine in the proximal convoluted tubules after the filtering of the amino acids by the kidneys glomeruli, thus resulting in an excessive concentration of this amino acid in the urine. Cystine may precipitate out of the urine, if the urine is neutral or acidic, and form crystals or stones in the kidneys, ureters, or bladder. It is one of several inborn errors of metabolism included in the Garrods tetrad. The disease is attributed to deficiency in transport and metabolism of amino acids. Diagnosis
Blood: Routine hemogram along with blood sugar, urea, and creatinine. Urine: For cystine crystals, and casts. The most specific test is the cyanide–nitroprusside test
Ultrasound/CT scan to reveal if a stone is present. Genetic analysis to determine which mutation associated with the disease may be present. Currently genotyping is not available in the United States but might be available in Spain, Italy, UK, Germany and Russia (by private companies in Germany and Russia).Regular X-rays often fail to show the cystine stones, however they can be visualized in the diagnostic procedure  that is called intravenous pyelogram (IVP).