Bacterial Pneumonia: Etiology, Risk Factors, and Diagnosis

MICROBIOLOGY / By /

Introduction:

Lower respiratory tract infections are the most common human infections, estimated to cause 2.74 million deaths annually. LRTIs are diverse and can present as tracheitis, bronchitis, bronchiolitis and pneumonia. Community Acquired Pneumonia (CAP) is the one that is contracted outside hospital settings. Hospital-Acquired Pneumonia (HAP) is the infection of the lungs whose evidence was not present when the patient was admitted to the hospital and occurs after 2 or more days of hospital admission. Ventilator-Associated Pneumonia (VAP) occurs more than or equal to 48-72 hours after endotracheal intubation. But it can also occur after developing severe HAP in some people.

Etiology of Pneumonia:

Pneumonia can be of viral (>20%) or bacterial (>10%) origin (Cilloniz et al., 2016). Fungal etiologies, especially Candida species, Aspergillus species, and Mucor species, cause pneumonia in immunocompromised individuals, while fungi like Histoplasma capsulatum, Cryptococcus neoformans, etc, cause pneumonia in both healthy and immunocompromised individuals. Infections with viruses like Influenza virus, Parainfluenza virus, Respiratory Syncitial Virus (RSV), Metapneumovirus, Adenovirus, etc, can also lead to pneumonia.

Escherichia coli, Klebsiella species, Enterobacter species, Citrobacter species, Acinetobacter species, Pseudomonas species, Haemophilus influenzae, Staphylococcus aureus, Enterococcus species, Streptococcus pneumoniae, Mycobacteria, etc, are responsible for CAP. S. pneumoniae causes lobar pneumonia and bronchopneumonia in young children, in those co-infected with HIV, the elderly, the bedridden, and other debilitated persons. While a few patients infected with S. pneumoniae or K. pneumonia will have classical pneumonia, the most frequent form of the disease is bronchopneumonia. S. aureus can produce a severe pneumonia (forming abscesses), especially in children, and following influenza, M. pneumoniae causes primary atypical pneumonia. Legionella pneumophila causes Legionnaire’s disease, a severe and often fatal form of pneumonia.

Risk factors:

 Pneumonia is found to be responsible for more than 90% of hospitalizations due to LRTI in children below 5 years. Surgery of the thorax or abdomen, COPD, old age, and chemotherapy are the risk factors of Pneumonia. Smoking and alcohol consumption have also been found to increase the risk of bacterial pneumonia. HAP is the most fatal having fatality rate of 30% to 70% as per a Multistate survey. The risk of HAP is much higher in patients who have undergone intubation and mechanical ventilation. Treatment of patients in the supine position is known to facilitate aspiration, leading to the high incidence of HAP. VAP may result from the microaspiration of oropharyngeal secretions tainted by normal flora surrounding the endotracheal tube cuff due to microbial invasion of the lower respiratory tract. One cohort study implicated the duration of mechanical ventilation in increasing the risk of VAP.

Diagnosis:

Specimens for pneumonia of bacterial origin and culture specifications:

Sputum

    A properly obtained sputum should contain fewer than 10 squamous epithelium cells and greater than 25 polymorphonuclear cells per low-power field. The first early morning sputum is optimal for the recovery of pathogens. Patients must be instructed to cough deeply. Sputum samples of less than 2 ml in volume should not be processed unless the material is purulent.

    There are infections in which little or no sputum is produced: Legionnaire’s disease (caused by L. pneumophila), pneumonia due to M. pneumoniae, and Chlamydia pneumonia. If sputum is produced, the specimen should be subjected to Gram staining using the purulent part of the sputum and culture.

    Blood

    Bacteremia usually occurs when pathogens enter the bloodstream from abscesses, areas of localized disease as pneumococcal pneumonia. Blood (10 ml for adults, 2–5 ml for children, 1-2 ml for infants and neonates) is withdrawn and incubated both aerobically and anaerobically.

    Bronchoalveolar lavage (BAL)

    BAL is used to wash cells out of small airways that bronchoscopy cannot reach. Then it can be subjected to blood culture or quantitative culture. In quantitative culture, a colony number of more than 104 CFU/ml is considered significant for a pathogen.

    Tracheal Aspirate

    Tracheal aspirate is collected through a tracheostomy or endotracheal tube. The specimen should be transported to the laboratory quickly and not refrigerated. The specimen should be subjected to Gram staining and culture.

    Pleural fluid

    An aspirate of pleural fluid is achieved by needle aspiration. Direct Gram stains may be very helpful in deriving a presumptive diagnosis and may also help select the proper culture media. Pleural fluids should be inoculated into enriched media.

     It may be necessary to use an anticoagulant because Pleural fluid often contains proteins and clotting factors, and Bacteria may be trapped in the clots. Thus, it is better to centrifuge the pleural fluid to concentrate any bacteria present.

    Routine culture media and cultural characteristics of the bacterial etiology of pneumonia:

    • Routinely, Blood Agar, MacConkey Agar, and chocolate Agar are employed for the isolation of bacteria causing pneumonia.
    • Blood agar is employed to isolate streptococci, MacConkey agar to isolate Gram-negative rods, and
    • Cooked meat medium or thioglycollate medium for anaerobes like Peptostreptococci.
    • The blood agar and chocolate agar plates are incubated at 35–36 â—¦C in a candle jar, and the MacConkey plate is incubated aerobically.
    • On blood agar, flat, S. pneumoniae shows clear zones of green alpha hemolysis. An optochin disc is added to the blood agar plate within the area of the 2nd spread to identify S. pneumoniae.
    • On MacConkey agar, gram-negative isolates are inoculated.
    • H. influenzae shows mucoid colonies on Chocolate agar after overnight incubation at 35–37 ºC in a moist carbon dioxide atmosphere. H. influenzae grows well on chocolate agar because it contains
    • factors X and V. On blood agar, a streak of S. aureus is used to facilitate satellite growth of H. influenzae, and with an optochin disc.
    • S. aureus on Mannitol Salt Agar shows medium-sized, golden-buff colonies.
    • Buffered charcoal-yeast extract (BCYE) agar media and selective BCYE media are used to culture L. pneumophila.
    • M. pneumoniae is not routinely cultured from respiratory specimens because it is fastidious.

    References:

    • American Thoracic Society; Infectious Diseases Society of America. (2005). Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcare-associated pneumonia. American journal of respiratory and critical care medicine, 171(4), 388-416. https://doi.org/10.1164/rccm.200405-644ST
    • Cheesbrough, M. (2006). District laboratory Practice in Tropical Countries (2nd edition). New York: Cambridge University Press
    • Craven, D.E., & Steger, K.A. (1996). Nosocomial pneumonia in mechanically ventilated adult patients: epidemiology and prevention in 1996. Seminars in respiratory infections, 11(1), 32-53
    • Dessie, T., Jemal, M., Maru, M., & Tiruneh, M. (2021). Multiresistant Bacterial Pathogens Causing Bacterial Pneumonia and Analyses of Potential Risk Factors from Northeast Ethiopia. International Journal of Microbiology.10.1155/2021/6680343
    • Drakulovic, M.B., Torres, A., Bauer, T.T., Nicolas, J.M., Nogué, S., & Ferrer, M. (1999). Supine body position as a risk factor for nosocomial pneumonia in mechanically ventilated patients: a randomised trial. Lancet (London, England),354(9193), 1851-1858. https://doi.org/10.1016/S0140-6736 (98)12251-1
    • Emori, T.G., & Gaynes, R.P. (1993). An overview of nosocomial infections, including the role of the microbiology laboratory. Clinical microbiology reviews, 6(4), 428-442. https://doi.org/10.1128/CMR.6.4.428
    • GBD LRI Collaborators. (2015). Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory tract infections in 195 countries: a systematic analysis for the Global Burden of Disease Study 2015. The Lancet. Infectious diseases, 17(11), 1133-1161. https://doi.org/10.1016/S1473-3099 (17)30396-1
    • Gebre, A.B., Begashaw, T.A., & Ormago, M.D. (2021). Bacterial profile and drug susceptibility among adult patients with community acquired lower respiratory tract infection at tertiary hospital, Southern Ethiopia. BMC infectious diseases, 21(1), 440. https://doi.org/10.1186/s12879-021-06151-2
    • Holter, J.C., Müller, F., Bjørang, O., Samdal, H.H., Marthinsen, J.B., Jenum, P, A,, Ueland, T., Frøland, S.S., Aukrust, P., Husebye, E., & Heggelund, L. (2015). Etiology of community-acquired pneumonia and diagnostic yields of microbiological methods: a 3-year prospective study in Norway. BMC infectious diseases, 15, 64. https://doi.org/10.1186/s12879-015-0803-5
    • Horie, H., Ito, I., Konishi, S., Yamamoto, Y., Yamamoto, Y., Uchida, T., Ohtani, H., & Yoshida, Y. (2018). Isolation of ESBL-producing Bacteria from Sputum in Community-acquired Pneumonia or Healthcare-associated Pneumonia Does Not Indicate the Need for Antibiotics with Activity against This Class.  Internal medicine (Tokyo, Japan), 57(4), 487-495.  https://doi.org/10.2169/internalmedicine.8867-17
    • Hyun, H., Song, J.Y., Yoon, J.G., Seong, H., Noh, J.Y., Cheong, H.J., & Kim, W.J. (2022). Risk factor-based analysis of community-acquired pneumonia, healthcare- associated pneumonia and hospital-acquired pneumonia: Microbiological distribution, antibiotic resistance, and clinical outcomes. PLoS One, 17(6), e0270261. https://doi.org/10.1371/journal.pone.0270261
    • Lacherade, J.C., De Jonghe, B., Guezennec, P., Debbat, K., Hayon, J., Monsel, A., Fangio, P., Appere de Vecchi, C., Ramaut, C., Outin, H., & Bastuji-Garin, S. (2010). Intermittent subglottic secretion drainage and ventilator-associated pneumonia: a multicenter trial. American journal of respiratory and critical care medicine, 182(7), 910-917. https://doi.org/10.1164/rccm.200906-0838OC
    • Magill, S.S., Edwards, J.R., Bamberg, W., Beldavs, Z.G., Dumyati, G., Kainer, M.A., Lynfield, R., Maloney, M., McAllister-Hollod, L., Nadle, J., Ray, S.M., Thompson, D.L., Wilson, L.E., & Fridkin, S.K. (2014). Emerging Infections Program Healthcare-Associated Infections and Antimicrobial Use Prevalence Survey Team. Multistate point-prevalence survey of health care-associated infections. The New England journal of medicine, 370(13), 1198-1208. https://doi.org/10.1056/NEJMoa1306801
    • Mandanas, R.A. (2021). Fungal Pneumonia. https://emedicine.medscape.com/article/300341-overview?form=fpf Accessed 25 May 2025
    • Muthumbi, E., Lowe, B.S., Muyodi, C., Getambu, E., Gleeson, F., & Scott, J.A.G. (2017). Risk factors for community-acquired pneumonia among adults in Kenya: a case-control study. Pneumonia (Nathan), 9, 17. https://doi.org/10.1186/s41479-
    • Santella, B., Serretiello, E., De Filippis, A., Veronica, F., Iervolino, D., Dell’Annunziata, F., Manente, R., Valitutti, F., Santoro, E., Pagliano, P., Galdiero,M., Boccia, G., & Franci, G. (2021). Lower Respiratory Tract Pathogens and Their Antimicrobial Susceptibility Pattern: A 5-Year Study. Antibiotics (Basel, Switzerland), 10(7), 851. https://doi.org/10.3390/antibiotics10070851
    • Sethi, S. (2024). Community-Acquired Pneumonia. MSD Manual. https://www.msdmanuals.com/professional/pulmonarydisorders/pneumonia/com munity-acquired-pneumonia Accessed 11 May 2025
    • Simou, E., Britton, J., & Leonardi-Bee, J. (2018). Alcohol and the risk of pneumonia: a systematic review and meta-analysis. BMJ Open, 8(8), e022344. https://doi.org/10.1136/bmjopen-2018-022344
    • Singleton, R.J., Holman, R.C., Folkema, A.M., Wenger, J.D., Steiner, C.A., & Redd, J.T. (2012). Trends in lower respiratory tract infection hospitalizations among American Indian/Alaska Native children and the general US child population. The Journal of pediatrics, 161(2), 296-302. https://doi.org/10.1016/j.jpeds.2012.02.004
    • Torres, A., Gatell, J.M., Aznar, E., el-Ebiary, M., Puig de la Bellacasa, J., González, J., Ferrer, M., & Rodriguez-Roisin, R. (1995). Re-intubation increases the risk of nosocomial pneumonia in patients needing mechanical ventilation. American journal of respiratory and critical care medicine, 152(1), 137-141. https://doi.org/10.1164/ajrccm.152.1.7599812
    • Torres, A., Peetermans, W.E., Viegi, G., & Blasi, F. (2013). Risk factors for community-acquired pneumonia in adults in Europe: a literature review. Thorax, 68(11), 1057-1065. https://doi.org/10.1136/thoraxjnl-2013-204282

    Leave a Comment

    Your email address will not be published. Required fields are marked *