Bacteria, viruses and fungi that have been reported as colonisers in Cystic Fibrosis






Colonisation and effects on symptoms


Acinetobacter baumanii

Isolated from Russian children with CF 1


Burkholderia Cepacia

Associated with cystic fibrosis 2


Chlamydia pneumoniae

Associated with exacerbation of symptoms 3


Clostridium difficile

Increased in CF patients 4


Corynebacterium pseudodiphtheriticum

Isolated from CF children’s sputum 5


Haemophilus influenzae

Often recorded in CF sputum 6


Helicobacter pylori

Increased in patients with pancreatic sufficiency 7: Certain Mutations protect against H.Pylori infection in patients with pancreatic insufficiency 7


Multiple strains of Mycobacteria

UK case report 8


Pneumocystis jirovecii

Isolated from French children with CF 9


Prevotella species

Isolated from the airways of CF patients 10


Pseudomonas Aeruginosa

Infections decrease the life expectancy of CF patients 11


Staphylococcus Aureus

Infections decrease the life expectancy of CF patients 11


Stenotrophomonas maltophilia

Associated with worsened clinical status 12-14


Streptococcus Millerii

Isolated from CF airways 15


Pseudomonadaceae, Xanthomonadaceae, Moraxellaceae and Enterobacteriaceae

These species are prevalent in the airways of cystic fibrosis patients 16



Over 60 bacterial genera, not typically associated with cystic fibrosis  were isolated from the sputum of CF patients including species of :- Actinobacillus, Aggregatibacter, Chryseomonas, Flavimonas, Haemophilus, Pseudomonas, Strenotrophomonas,  Vibrio, Acidovorax, Azonexus, Comomonas, Delftia, Eikenella, Kingella, Neisseria, Brevundimonas, Spingobium, Sphingopyxis, Xanthobacter, Abiotrophia, Enterococcus, Gemella, Granulicatella, Lactobacillus, Lactococcus, Leuconostoc, Staphylococcus, Streptococcus, Butyrovibrio, Catonella, Dialister, Megasphaera, Moryella, Oribavterium, Peptoniphilus, Peptostyreptococcus, Selenomonas, Veillonella, Bulleida, Fusobacterium, Leptotrichia, Actinomyces, Arthrobacter, Atopobium, Corynebacterium, Micrococcus, Propionibacterium, Rhodococcus, Rothia, Scardovia, Tessaracoccus, Bacteroides, Porphyromonas, Prevotella, Bergeyella, Capnocytophage, Mycoplasma, treponema   17



Infection can exacerbate respiratory symptoms 18


Herpes simplex

Association has been observed but appears to be rare 19


Hepatitis B

Occasionally observed in CF patients 20


Hepatitis C

Increased in CF patients 21



Infection worsens symptoms 22


Respiratory syncytial virus

Increased in CF children 23



Rhinoviruses exacerbate CF symptoms 24


Candida and Aspergillus species ;  Scedosporium apiospermum Exophiala dermatitidis

Isolated from the respiratory tract of CF patients 25






















































1. Shaginian I.A., Kapranov N.I., Chernukha M.I., Alekseeva G.V., Semykin S.I., Avetisian L.R., Kashirskaia N.I., Pivkina N.V., Danilina G.A., Batov A.B., & Busuek T.P. (2010) Microbial population of lower respiratory tract in children from different age groups with cystic fibrosis. Zh.Mikrobiol.Epidemiol.Immunobiol. 15-20.

2.             Butler S.L., Doherty C.J., Hughes J.E., Nelson J.W., & Govan J.R. (1995) Burkholderia cepacia and cystic fibrosis: do natural environments present a potential hazard? J.Clin.Microbiol. 33, 1001-1004.

3.             Emre U., Bernius M., Roblin P.M., Gaerlan P.F., Summersgill J.T., Steiner P., Schachter J., & Hammerschlag M.R. (1996) Chlamydia pneumoniae infection in patients with cystic fibrosis. Clin.Infect.Dis. 22, 819-823.

4.             Welkon C.J., Long S.S., Thompson C.M., Jr., & Gilligan P.H. (1985) Clostridium difficile in patients with cystic fibrosis. Am.J.Dis.Child. 139, 805-808.

5.             Bittar F., Cassagne C., Bosdure E., Stremler N., Dubus J.C., Sarles J., Reynaud-Gaubert M., Raoult D., & Rolain J.M. (2010) Outbreak of Corynebacterium pseudodiphtheriticum infection in cystic fibrosis patients, France. Emerg.Infect.Dis. 16, 1231-1236.

6.             Millar F.A., Simmonds N.J., & Hodson M.E. (2009) Trends in pathogens colonising the respiratory tract of adult patients with cystic fibrosis, 1985-2005. J.Cyst.Fibros.  8, 386-391.

7.             Yahav J., Samra Z., Blau H., Dinari G., Chodick G., & Shmuely H. (2006) Helicobacter pylori and Clostridium difficile in cystic fibrosis patients. Dig.Dis.Sci. 51, 2274-2279.

8.             Brown S.M. (2010) Multiple strains of non-tuberculous mycobacteria in a patient with cystic fibrosis. J.R.Soc.Med. 103 Suppl 1, S34-S43.

9.             Gal S.L., Hery-Arnaud G., Ramel S., Virmaux M., Damiani C., Totet A., & Nevez G. (2010) Pneumocystis jirovecii and cystic fibrosis in France. Scand.J.Infect.Dis. 42, 225-227.

10.          Field T.R., Sibley C.D., Parkins M.D., Rabin H.R., & Surette M.G. (2010) The genus Prevotella in cystic fibrosis airways. Anaerobe. 16, 337-344.

11.          Doring G., Albus A., & Hoiby N. (1988) Immunologic aspects of cystic fibrosis. Chest. 94, 109S-115S.

12.          Schultz H., Schinke S., Mosler K., Herlyn K., Schuster A., & Gross W.L. (2004) BPI-ANCA of pediatric cystic fibrosis patients can impair BPI-mediated killing of E. coli DH5alpha in vitro. Pediatr.Pulmonol. 37, 158-164.

13.          Talmaciu I., Varlotta L., Mortensen J., & Schidlow D.V. (2000) Risk factors for emergence of Stenotrophomonas maltophilia in cystic fibrosis. Pediatr.Pulmonol. 30, 10-15.

14.          Waters V., Yau Y., Prasad S., Lu A., Atenafu E., Crandall I., Tom S., Tullis E., & Ratjen F. (2010) Stenotrophomonas Maltophilia in Cystic Fibrosis: Serologic Response and Effect on Lung Disease. Am.J.Respir.Crit Care Med.

15.          Sibley C.D., Sibley K.A., Leong T.A., Grinwis M.E., Parkins M.D., Rabin H.R., & Surette M.G. (2010) The Streptococcus milleri population of a cystic fibrosis clinic reveals patient specificity and intraspecies diversity. J.Clin.Microbiol. 48, 2592-2594.

16.          Cox M.J., Allgaier M., Taylor B., Baek M.S., Huang Y.J., Daly R.A., Karaoz U., Andersen G.L., Brown R., Fujimura K.E., Wu B., Tran D., Koff J., Kleinhenz M.E., Nielson D., Brodie E.L., & Lynch S.V. (2010) Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS.One. 5, e11044.

17.          Guss A.M., Roeselers G., Newton I.L., Young C.R., Klepac-Ceraj V., Lory S., & Cavanaugh C.M. (2010) Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. ISME.J.

18.          Winnie G.B. & Cowan R.G. (1992) Association of Epstein-Barr virus infection and pulmonary exacerbations in patients with cystic fibrosis. Pediatr.Infect.Dis.J. 11, 722-726.

19.          Goyal R., Nada R., Das A., & Marwaha R.K. (2006) Disseminated herpes simplex infection with cystic fibrosis: a case report. Indian J.Pathol.Microbiol. 49, 607-609.

20.          Santini B., Boscarato S., Gay V., & Barbera C. (1990) Il rischio di infezione da virus epatite B nei pazienti con fibrosi cistica. Minerva Pediatr. 42, 367-370.

21.          Desenclos J.C., Bourdiol-Razes M., Rolin B., Garandeau P., Ducos J., Brechot C., & Thiers V. (2001) Hepatitis C in a ward for cystic fibrosis and diabetic patients: possible transmission by spring-loaded finger-stick devices for self-monitoring of capillary blood glucose. Infect.Control Hosp.Epidemiol. 22, 701-707.

22.          Dharmaraj P. & Smyth R.L. (2009) Vaccines for preventing influenza in people with cystic fibrosis. Cochrane.Database.Syst.Rev. CD001753.

23.          Armstrong D., Grimwood K., Carlin J.B., Carzino R., Hull J., Olinsky A., & Phelan P.D. (1998) Severe viral respiratory infections in infants with cystic fibrosis. Pediatr.Pulmonol. 26, 371-379.

24.          Brownlee J.W. & Turner R.B. (2008) New developments in the epidemiology and clinical spectrum of rhinovirus infections. Curr.Opin.Pediatr. 20, 67-71.

25.          Muller F.M. & Seidler M. (2010) Characteristics of pathogenic fungi and antifungal therapy in cystic fibrosis. Expert.Rev.Anti.Infect.Ther. 8, 957-964.

Last update: July 27, 2015

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