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Respiratory infections are caused by different germs — bacteria, viruses and occasionally fungi — and knowing which one is involved guides the right treatment. Some bugs cause sudden illnesses like pneumonia or whooping cough; others settle into already-damaged airways and cause repeated flare-ups. Sputum (phlegm) tests help identify the organism and which antibiotics will work, while vaccines prevent many infections in the first place. Using antibiotics carefully keeps them effective for when they are truly needed. This page is a professional reference to the main organisms and why they matter.
Microbiology of Respiratory Infection
Why This Matters to Physiotherapy
Knowledge of the likely pathogens by clinical context informs cohorting and infection-control decisions, the choice and intensity of airway clearance, recognition of treatment failure or new colonisation, and timely escalation. It also underpins meaningful conversations with patients and referrers about sputum results, antibiotic choice, and prognosis.1
Bacteria in community-acquired pneumonia
These "typical" bacteria cause most community-acquired chest infections and usually produce an acute, productive illness.2
Streptococcus pneumoniae (pneumococcus)
The single most common identified cause of community-acquired pneumonia in Australia, producing a rapid-onset lobar pneumonia with fever, a productive cough and pleuritic chest pain.
Why it matters: It can progress quickly to severe pneumonia, sepsis, empyema and respiratory failure, and consolidated lung gives up its secretions poorly. It is largely vaccine-preventable.
How chest physiotherapy helps: As the acute illness settles, airway clearance (ACBT, huffing) shifts loosened secretions, while early mobilisation, deep breathing and positioning re-expand the affected lung and offset the deconditioning of a prolonged admission.
Haemophilus influenzae
A leading driver of exacerbations in COPD and bronchiectasis, and a common cause of pneumonia in older adults and smokers.
Why it matters: In chronic airway disease it persists between flares, and a change in sputum colour and volume often heralds an exacerbation.
How chest physiotherapy helps: Regular airway clearance lowers the secretion load it thrives in, and teaching patients to recognise a change in their sputum supports earlier treatment and self-management.
Moraxella catarrhalis
A frequent cause of COPD exacerbations and a cause of pneumonia in older and immunocompromised people.
Why it matters: Like H. influenzae, it feeds the cycle of recurrent infective exacerbations in chronic airway disease.
How chest physiotherapy helps: Airway clearance during an exacerbation eases sputum removal and breathlessness, and a maintenance routine between flares reduces stagnation.
Staphylococcus aureus (including MRSA)
A less common but more aggressive cause of pneumonia, classically following influenza, and able to cause cavitating or necrotising infection.
Why it matters: It can cause severe, rapidly deteriorating illness; MRSA additionally mandates contact precautions and alters antibiotic choice.
How chest physiotherapy helps: Airway clearance supports removal of purulent secretions, delivered with strict hand hygiene, PPE and decontamination of PEP devices and shared equipment to prevent spread.
Atypical bacterial pathogens
"Atypical" organisms tend to cause a drier cough and a more systemic, "flu-like" illness, and do not appear on a standard Gram stain.
Mycoplasma pneumoniae
A common cause of milder "walking pneumonia," often in younger adults and in periodic community epidemics.
Why it matters: The cough is usually dry with little sputum, so it is rarely a secretion-clearance problem, but fatigue and deconditioning can outlast the infection.
How chest physiotherapy helps: The role is less about clearance and more about breathing retraining for a lingering cough and graded exercise to rebuild fitness during recovery.
Legionella pneumophila
Causes Legionnaires' disease — a severe pneumonia linked to aerosols from cooling towers, warm-water systems, spa baths and potting mix. It is notifiable in Queensland.
Why it matters: It frequently causes severe illness needing hospital or intensive-care admission, with prominent systemic features.
How chest physiotherapy helps: In the acute severe phase the focus is positioning and lung re-expansion; recovery is usually dominated by rehabilitation and reconditioning after a prolonged, debilitating illness.
Chlamydia psittaci and Chlamydia pneumoniae
C. psittaci (psittacosis) follows exposure to birds; C. pneumoniae causes sporadic respiratory infection. Both produce an atypical, often dry pneumonia.
Why it matters: A bird-exposure history is the key clue for psittacosis, which can be severe; both are usually non-productive infections.
How chest physiotherapy helps: As with other atypicals, the emphasis is breathlessness management, breathing control and reconditioning rather than sputum clearance.
Bacteria in chronic & complex airway disease
In bronchiectasis and cystic fibrosis the airways become chronically colonised. Here the goal shifts from curing a single infection to controlling bacterial load over years — and daily airway clearance is central to that.3,4,5
Pseudomonas aeruginosa
The dominant pathogen of concern in bronchiectasis and cystic fibrosis. Over time it adopts a mucoid, biofilm-forming phenotype that resists antibiotics and host defences, and chronic infection is associated with more frequent exacerbations and accelerated lung-function decline.6 A new isolate is a trigger for eradication; established infection is managed with long-term inhaled antibiotics and daily airway clearance.
Full guide: Pseudomonas aeruginosa →
Staphylococcus aureus and MRSA
Usually the first organism cultured from the cystic fibrosis airway, often in infancy, and a less common but under-studied pathogen in bronchiectasis. MRSA is the same organism with a narrower antibiotic choice rather than greater aggression, and it carries contact-precaution requirements.
Full guide: MRSA & Staphylococcus aureus →
Burkholderia cepacia complex
A group of more than twenty closely related species, highly transmissible between people with cystic fibrosis and rare outside it. It can cause a rapid, unpredictable decline ("cepacia syndrome"), and B. cenocepacia specifically may preclude lung transplantation — which is why strict segregation applies and species-level identification matters.
Full guide: Burkholderia cepacia complex →
Stenotrophomonas maltophilia and Achromobacter species
Increasingly identified, often multi-drug-resistant organisms in chronic airway disease.
Why it matters: Their impact ranges from harmless colonisation to a driver of decline, and their resistance narrows antibiotic options.
How chest physiotherapy helps: Optimising airway clearance keeps bacterial load and secretion stasis down while the team monitors whether the organism is contributing to symptoms.
Aspergillus species and ABPA
A mould (not a bacterium) that can colonise damaged airways or trigger an allergic reaction — allergic bronchopulmonary aspergillosis (ABPA) — particularly in asthma and CF.
Why it matters: ABPA causes mucus plugging, wheeze and fleeting lung infiltrates and can accelerate bronchiectasis; it is treated with corticosteroids ± antifungals rather than standard antibiotics.
How chest physiotherapy helps: Airway clearance helps shift the thick, tenacious mucus plugs that characterise ABPA, complementing medical treatment.
Mycobacteria
Non-tuberculous mycobacteria (M. avium complex, M. abscessus)
Environmental mycobacteria that cause indolent, slowly progressive lung disease in bronchiectasis, CF and structurally abnormal lungs, needing prolonged multi-drug treatment.7
Why it matters: NTM (especially M. abscessus) can drive ongoing decline, complicate CF transplant assessment, and demand months of difficult therapy; segregation principles similar to Pseudomonas apply.
How chest physiotherapy helps: Daily airway clearance reduces the mucus stasis that favours NTM, and maintaining clearance and exercise through long treatment supports tolerance and lung health.
Full guide: Non-Tuberculous Mycobacteria →
Mycobacterium tuberculosis
Uncommon but persistent in Australia, concentrated in overseas-born, Aboriginal and Torres Strait Islander, and immunosuppressed populations. It is notifiable.
Why it matters: Active pulmonary TB is airborne-transmissible, requiring airborne precautions (fit-tested P2/N95, negative-pressure room) and deferral of non-essential close-contact procedures until treatment renders the patient non-infectious.
How chest physiotherapy helps: Routine clearance is deferred while the patient is infectious; later, pulmonary rehabilitation and breathing strategies address the breathlessness and reduced capacity of post-TB lung disease and bronchiectasis.
Bordetella pertussis (whooping cough)
Endemic in Australia with periodic epidemics; non-immune adults and adolescents are the main reservoir for infecting vulnerable infants.
Why it matters: It causes severe, paroxysmal coughing fits lasting weeks to months and is dangerous to unimmunised infants — booster vaccination is recommended for adults, pregnant women and healthcare workers.
How chest physiotherapy helps: There is little role for clearance in the acute paroxysmal phase; physiotherapy contributes cough-control and breathing techniques for the lingering cough, alongside PPE and staff vaccination.
Common viral pathogens
Viruses cause the majority of acute respiratory infections and are the dominant trigger for exacerbations of asthma and COPD. Most are self-limiting, but in people with heart or lung disease they can precipitate severe illness.
Influenza (A and B)
Seasonal influenza causes abrupt fever, muscle aches, headache and a dry cough, with a sharp rise in hospitalisations each winter. Antiviral therapy (oseltamivir or baloxavir) reduces severity if started within 48 hours of symptoms.
Why it matters: It causes excess deaths each year and frequently triggers exacerbations of COPD, asthma and heart failure; secondary bacterial pneumonia (often S. aureus or pneumococcus) is a feared complication.
How chest physiotherapy helps: Acute care is supportive; physiotherapy contributes once a secondary pneumonia or exacerbation develops, with airway clearance, mobilisation and reconditioning during recovery. Annual vaccination is the key preventive measure.
SARS-CoV-2 (COVID-19)
Now endemic and circulating year-round, it ranges from a mild upper-respiratory illness to viral pneumonia and, in some, prolonged symptoms (long COVID). Antivirals (nirmatrelvir–ritonavir, molnupiravir, remdesivir) are PBS-listed for higher-risk groups within defined symptom windows.
Why it matters: It can cause severe hypoxaemic pneumonia and thrombosis in vulnerable groups, and a minority develop persistent breathlessness and fatigue.
How chest physiotherapy helps: In recovery, paced, symptom-titrated activity and breathing retraining help — with caution around post-exertional symptoms in long COVID (see our Long COVID guide).
Respiratory syncytial virus (RSV)
Long known as a cause of infant bronchiolitis, RSV is now recognised as a major cause of lower-respiratory infection in older adults, where it can be as serious as influenza.
Why it matters: In older adults and those with COPD, asthma or heart failure it commonly precipitates exacerbations and hospitalisation. Australia has recently introduced a free RSV vaccination for adults aged 75 and over, alongside maternal vaccination in pregnancy and infant immunisation to protect babies.
How chest physiotherapy helps: As with other viral lower-respiratory infections, the role is airway clearance where secretions are retained, plus mobilisation and reconditioning during recovery from an exacerbation.
Rhinovirus (the common cold)
The most frequent respiratory virus and the single biggest trigger of asthma and COPD exacerbations.
Why it matters: What is "just a cold" in a healthy person can tip someone with airway disease into a significant exacerbation with wheeze, breathlessness and increased sputum.
How chest physiotherapy helps: During an exacerbation, airway clearance and breathing strategies ease symptoms, and a personalised action plan helps patients respond early.
Other respiratory viruses
Human metapneumovirus and parainfluenza cause influenza-like and lower-respiratory illness (parainfluenza classically causes croup in children), and adenovirus causes a range of respiratory infections.
Why it matters: In people with chronic lung disease or immunosuppression these "minor" viruses can still drive exacerbations and pneumonia.
How chest physiotherapy helps: Management mirrors the other viruses — supportive care, airway clearance where indicated, and reconditioning after the acute illness.
Sputum sampling & antimicrobial stewardship
A good-quality expectorated sputum specimen is essential for microbiological assessment. Induced sputum and bronchoscopic sampling are used when expectoration is unproductive. Multiplex PCR panels for respiratory viruses and atypical bacteria shorten diagnostic delay.
Antimicrobial stewardship — empirical therapy guided by Therapeutic Guidelines: Antibiotic, de-escalation based on culture results, and limiting duration of therapy — is core to reducing resistance.
Essential vaccinations in respiratory disease
For people with chronic heart or lung disease, vaccination is one of the most effective ways to prevent the infections that cause exacerbations and hospital admissions. The list below summarises the core vaccines — your GP or pharmacist confirms exactly what applies to you under the National Immunisation Program (NIP).
Influenza (annual)
A yearly flu vaccine is recommended for everyone and is funded under the NIP for people aged 65 and over, anyone with chronic respiratory or cardiac disease, Aboriginal and Torres Strait Islander people, pregnant women and young children. It is the single most important annual vaccine in lung disease.
COVID-19 (regular boosters)
Ongoing booster doses are recommended according to age and risk, following current ATAGI advice. People with chronic respiratory or cardiac disease and those who are immunocompromised are prioritised for more frequent boosters.
Pneumococcal
Protects against Streptococcus pneumoniae, the leading cause of bacterial pneumonia. The programme uses conjugate vaccines (PCV13/15/20) and the 23-valent polysaccharide vaccine (23vPPV), with the schedule and number of doses depending on age and risk — chronic lung disease, smoking and immunosuppression all bring it forward.
RSV
Australia has recently introduced a free RSV vaccine for adults aged 75 and over. Maternal RSV vaccination in pregnancy and infant immunisation protect newborns through their first RSV season. Discuss eligibility with your clinician, as the programme is expanding.
Pertussis (whooping cough)
A dTpa booster is recommended for adults in contact with infants, in every pregnancy, and as part of routine adult boosters — protecting both the individual and vulnerable babies.
Other vaccines to consider
Depending on age and risk, herpes zoster (shingles) for older adults, Haemophilus influenzae type b (in asplenia and some immunocompromised people), and routine MMR, varicella and hepatitis B may all be relevant. Healthcare workers — including physiotherapists — are expected to maintain influenza, COVID-19, pertussis, MMR, varicella and hepatitis B protection to safeguard vulnerable patients.
Implications for physiotherapy practice
- Hand hygiene per the WHO 5 Moments before and after every patient contact
- Source control and respiratory PPE matched to the suspected pathogen
- Cohorting in CF and bronchiectasis services to prevent cross-infection
- Airborne precautions for suspected or confirmed pulmonary tuberculosis, measles, and varicella
- Decontamination of nebulisers, PEP devices, and exercise equipment between patients
- Vaccination of physiotherapists to the same standard as other healthcare workers
- Deferral of patient contact when the physiotherapist is unwell with a respiratory illness
References & evidence base
- Saiman L, Siegel JD, LiPuma JJ, et al. Infection prevention and control guideline for cystic fibrosis: 2013 update. Infect Control Hosp Epidemiol 2014;35(S1):S1–S67.
- Metlay JP, Waterer GW, Long AC, et al. Diagnosis and treatment of adults with community-acquired pneumonia: an official ATS/IDSA clinical practice guideline. Am J Respir Crit Care Med 2019;200(7):e45–e67.
- Dickson RP, Erb-Downward JR, Martinez FJ, Huffnagle GB. The microbiome and the respiratory tract. Annu Rev Physiol 2016;78:481–504.
- Huffnagle GB, Dickson RP, Lukacs NW. The respiratory tract microbiome and lung inflammation: a two-way street. Mucosal Immunol 2017;10(2):299–306.
- Mac Aogáin M, Chotirmall SH. Bronchiectasis and cough: an old relationship in need of renewed attention. Pulm Pharmacol Ther 2019;57:101812.
- Hill AT, Sullivan AL, Chalmers JD, et al. British Thoracic Society guideline for bronchiectasis in adults. Thorax 2019;74(Suppl 1):1–69.
- Floto RA, Olivier KN, Saiman L, et al. US Cystic Fibrosis Foundation and European Cystic Fibrosis Society consensus recommendations for the management of non-tuberculous mycobacteria in individuals with cystic fibrosis. Thorax 2016;71(Suppl 1):i1–i22.
References are numbered in citation order (Vancouver/BMJ style) and were current at the time of writing. Guidelines are living documents — verify against the latest version before clinical use.
More than one of our services applies here, and which combination suits you depends on what your assessment shows.
Corrections: If something on this page is wrong, out of date or unclear, we want to know. Email reception@inspireclinic.au with the page name and what you believe is incorrect. Substantive corrections are made promptly, and the guide’s version and last-updated date are changed to reflect it.