Indan Journal of Medical Research Indan Journal of Medical Research Indan Journal of Medical Research Indan Journal of Medical Research
  Home About us Editorial board Search Ahead of print Current issue Archives Submit article Instructions Subscribe Contacts Login  
  Home Print this page Email this page Small font sizeDefault font sizeIncrease font size Users Online: 636       

   Table of Contents      
Year : 2020  |  Volume : 151  |  Issue : 1  |  Page : 65-70

Aetiological agents for pulmonary exacerbations in children with cystic fibrosis: An observational study from a tertiary care centre in northern India

1 Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
2 Translational Health Science & Technology Institute, Faridabad, Haryana, India
3 Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India

Date of Submission09-Jul-2018
Date of Web Publication24-Feb-2020

Correspondence Address:
Dr Sushil Kumar Kabra
Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110 029
Login to access the Email id

Source of Support: None, Conflict of Interest: None

DOI: 10.4103/ijmr.IJMR_1275_18

Rights and Permissions

Background & objectives: Pulmonary disease is the main cause of morbidity and mortality in cystic fibrosis (CF). The infection occurs with a unique spectrum of bacterial pathogens that are usually acquired in an age-dependent fashion. The objective of this study was to find out the aetiological agents in respiratory specimens from children with CF during pulmonary exacerbation and relate with demographic variables.
Methods: In this observational study, airway secretions from children (n=104) with CF presenting with pulmonary exacerbations were collected and tested for bacteria, fungi, mycobacteria and viral pathogens using appropriate laboratory techniques. The frequencies of isolation of various organisms were calculated and associated with various demographic profiles.
Results: Bacteria were isolated in 37 (35.5%) and viral RNA in 27 (29.3%) children. Pseudomonas was the most common bacteria grown in 31 (29.8%) followed by Burkholderia cepacia complex (Bcc) in three (2.8%) patients. Among viruses, Rhinovirus was the most common, identified in 16 (17.4%) samples followed by coronavirus in four (4.3%). Fungi and mycobacteria were isolated from 23 (22.1%) and four (3.8%) children, respectively. Aspergillus flavus was the most common fungus isolated in 13 (12.5%) children.
Interpretation & conclusions: Pseudomonas was the most common organism isolated during exacerbation. Non-tuberculous mycobacteria were not isolated, whereas infection with Bcc and Mycobacterium tuberculosis was observed, which could probably have a role in CF morbidity. Polymicrobial infections were associated with severe exacerbations.

Keywords: Acute exacerbation - children - cystic fibrosis - microbiology - Pseudomonas - polymicrobial infection

How to cite this article:
Arvind B, Medigeshi GR, Kapil A, Xess I, Singh U, Lodha R, Kabra SK. Aetiological agents for pulmonary exacerbations in children with cystic fibrosis: An observational study from a tertiary care centre in northern India. Indian J Med Res 2020;151:65-70

How to cite this URL:
Arvind B, Medigeshi GR, Kapil A, Xess I, Singh U, Lodha R, Kabra SK. Aetiological agents for pulmonary exacerbations in children with cystic fibrosis: An observational study from a tertiary care centre in northern India. Indian J Med Res [serial online] 2020 [cited 2020 Dec 5];151:65-70. Available from:

Cystic fibrosis (CF) is a common life-limiting inherited disease in the western population. In India, CF was first reported in 1968[1]. The exact prevalence of the disease among Indian population is not known, but the prevalence has been estimated to be 1/43,321 to 1/100,323 based on carrier frequency studies[2].

Pulmonary involvement is the predominant cause of morbidity in CF. The disease course is punctuated by periods of acute worsening of the pulmonary disease, termed exacerbations. The aetiological agents responsible for these pulmonary exacerbations are different from those causing pneumonia in normal children. Children with CF are also at risk of acquiring mycobacterial, viral and fungal infections[3].

The unique spectrum of bacterial pathogens is usually acquired in a time-dependent fashion. Early in the course of the disease, the organisms commonly isolated include Staphylococcus aureus and non-typeable Haemophilus influenzae[4]. Pseudomonas aeruginosa is more commonly isolated later in the course of the disease and infects approximately 80 per cent of the patients with CF. Burkholderia cepacia complex (Bcc) is another organism unique to CF and patients harbouring these have a worse prognosis[5]. Early and aggressive treatment with appropriate antibiotics may eradicate infection, prevent colonization, reduce the degree of inflammation and help delay progression of pulmonary disease[6]. Non-tuberculous mycobacteria (NTM) infection in CF is a serious concern. Multiple factors such as malnutrition, CF related diabetes mellitus, steroid treatment and chronicity of illness predispose these children to mycobacterial infection[3],[7].

The incidence of viral infections in children with CF though is not elevated; the severity of infection is increased[8]. In vitro studies have suggested that viral infection increases bacterial adhesion to epithelial cells and impairs macrophage immune responses to bacterial products[9]. Various species of fungi have also been isolated from respiratory specimens of CF patients presenting with exacerbations[10]. There is a scarcity of data from India, therefore, this study was conducted to document aetiological agents of pulmonary exacerbation in Indian children with CF.

   Material & Methods Top

This was a single-centre observational study conducted in the Paediatrics department, All India Institute of Medical Sciences (AIIMS), New Delhi, India, over a period of 18 months, from October 2013 to March 2015. Sample size was calculated to be 94 (95% CI and 10% precision) based on a retrospective study of 120 patients conducted at our center[11], where Pseudomonas was detected in 42 per cent of CF patients. The study protocol was approved by the Institutional Ethics Committee of AIIMS and written informed consent was obtained from the parents of the children. Respiratory specimens were collected, either expectorated or induced sputum, nasopharyngeal aspirates or throat swabs, from 104 children who were diagnosed with CF, based on sweat chloride levels, aged up to 18 yr, who presented with pulmonary exacerbation either to the Pediatric outpatient department or admitted to the Pediatric ward. Children presenting within six months of the previous exacerbation were excluded. Pulmonary exacerbation was defined as per the criteria suggested by Fuchs et al[12].

Microbiological methods:The samples were sent for bacteria, fungi, mycobacteria culture and viral RNA detection in the microbiology laboratory. Samples for bacterial isolation were smeared for Gram stain and also inoculated on MacConkey, blood, chocolate and B. cepacia Selective Agar. If any colonies were grown, these were further processed for phenotypic identification and antimicrobial susceptibility testing by Kirby-Bauer disk diffusion method as per Clinical and Laboratory Standards Institute guidelines[13]. Samples were also mounted on 10 per cent potassium hydroxide and Sabouraud dextrose agar for fungus identification. In the mycobacteria laboratory, samples were examined for acid-fast bacilli and then inoculated to Löwenstein-Jensen medium and BD BACTEC™ Mycobacteria growth indicator tube (Becton, Dickinson and Company, NJ, USA), after decontamination with N-acetyl L-cysteine - 2% NaOH and 2.5 per cent oxalic acid solution, for mycobacterial identification[14]. These samples were subjected to real-time multiplex PCR using the commercial assay platform provided by Fast-track Diagnostics® (FTD) respiratory kit (FTD, Luxembourg) for detection of viral nucleic acid.

Statistical methods: The frequencies of detection (single as well as multiple) of each pathogen were calculated and related with various demographic profiles. Significance of difference between two related proportions was assessed using the McNemar's test.

   Results Top

A total of 104 patients (10.42±3.2 yr age; 71 male, 33 female) were enrolled in the study. The mean age at the onset of illness was 2.0±1.1 yr and at the time of diagnosis was 4.2±1.8 yr. Of the 104 patients, 41 (39.4%) were inpatients and 63 (60.5%) were outpatients.

Among the criteria suggested by Fuch et al[12], increase in cough was the most common symptom [100 (96.1%)], followed by increased dyspnoea [86 (82.7%)] and change in sputum volume or colour [79 (75.9%)]. Of the enrolled children, 68 (65.3%) were positive for at least one of the organisms, bacteria, fungi, mycobacteria or viruses. [Table 1] summarizes all the groups of organisms isolated in these children.
Table 1: Summary of microbial pathogens demonstrated in respiratory tract secretions of children with cystic fibrosis and pulmonary exacerbations

Click here to view

Bacteria: Bacteria were isolated from 37 of the 104 samples; P. aeruginosa was the predominant species, isolated from 31 (29.8%) samples. Burkholderia was grownfrom three (2.8%), Staphylococcus aureus from two (1.9%) and Acinetobacter spp. from one (0.9%) sample.

Pseudomonas and clinical variables:Though insignificant, children who grew Pseudomonas in their respiratory specimens were relatively younger (9.66±1.86 yr) compared to children in whom Pseudomonas was not isolated (10.45±1.32 yr). They became symptomatic at a younger age (1.13±0.51 yr) and were diagnosed at an early age (3.65±1.26 yr) and required frequent outpatient department visits or hospital admissions for antibiotic administration (either oral or intravenous). A significant observation was that a higher proportion of children, who were admitted, requiring hospital care, grew Pseudomonas than those who received treatment as outpatient basis [Table 2].
Table 2: Comparison of baseline characteristics of children who grew Pseudomonas as compared to those who did not

Click here to view

Other microorganisms: Fungi were grown in 23 specimens, and filamentous fungus was the more common one (17%) (Aspergillus flavus - 12.5% and A. fumigatus - 4.5%). Candida sp. was grown in five (4.7%) specimens [Table 1]. Mycobacterium tuberculosis was cultured from four of the specimens, whereas NTM was not identified in any of the samples. All of the four children from who grew M. tuberculosis were boys (P=0.01) and were older than 10 yr (12.6±5.8 yr). Viral nucleic acid was found in 27 of the 92 specimens (29.3%) subjected to PCR; 29 viruses were detected in these 27 individuals as two children were tested positive for two viruses each. Rhinovirus was the most common virus, positive in 16 (17.4%) individuals, followed by coronavirus (4.3%) [Table 1].

Children who were tested positive for virus were younger (9.1±6.2 yr) than the children who were not (10.8 ±5.3 yr) and had only mild exacerbation, receiving ambulatory treatment rather than in-hospital care. [Table 3] describes the clinical variables in children who had grown various groups of microorganisms compared to those who had not.
Table 3: Comparison of clinical variables of children who had grown various microorganisms and children who had not

Click here to view

Polymicrobial infection: Multiple microbial agents were identified in airway specimens from 16 children (15.3%). The most common combination observed was that of virus + bacteria seen in nine children (8.6%), followed by viral and fungus infection in six (5.7%). Infection with more than two groups of organisms, i.e., bacteria, virus and mycobacteria was found in one patient. With regard to individual organism, co-infection with Rhinovirus and Pseudomonas was the most common, seen in three children (2.8%), all of whom required hospitalized care.

Association between the different age groups and the prevalence of various bacterial species showed that S. aureus was grown in relatively older age group than Pseudomonas sp. Hospitalized care was required in children who had co-infection with bacteria + virus or bacteria + fungus.

   Discussion Top

At least one of the microbial agents was identified in 68 children (65.3%). In studies from various parts of the world, Pseudomonas was the predominant bacteria[15],[16],[17],[18]. The percentage of children who grew Pseudomonas in our study was 29.8 per cent, which was lesser than the results of a study (36%) from Brazil[15] and (40%) Italy[16]. In a retrospective study Razvi et al[19] reported a significant decline in the annual prevalence of Pseudomonas from 60.4 per cent in 1995 to 56.1 per cent in 2005 (P <0.001). In an earlier study on 120 CF children between 1995 to 2002 at our centre, Pseudomonas was documented in 42 per cent[11], which has declined to 29.8 per cent in 2015 in the current study. Possible explanations include increased awareness about infection control methods, use of long-term immunosuppressive therapy with azithromycin and rational use of antimicrobials for early eradication of P. aeruginosa.

Bcc was another important pathogen, isolated from three (2.8%) patients. Bcc is associated with a poor prognosis and a rapid deterioration of pulmonary function as evidenced by frequent exacerbations and worse lung capacities in children who had grown Bcc[5],[20]. The youngest children from whom Pseudomonas and Burkholderia were isolated were three and nine months old, respectively. This is a matter of concern since younger age of acquisition has been associated with accelerated deterioration of lung function and frequent exacerbations leading to a poor quality of life. The multicentric Standardized Treatment of Pulmonary Exacerbations (STOP) study conducted in 11 US centres has identified P. aeruginosa in 71 per cent of the 220 participants of all age groups and Bccwere cultured in three per cent[21].

The yield of Staphylococcus our study was only 1.9 per cent whereas other studies reported as high as 78 per cent[15],[22],[23],[24]. In the STOP study, methicillin-resistant S. aureus was detected in 39 per cent whereas methicillin-susceptible S. aureus was detected in 36 per cent of study population[21]. The Staphylococcus isolated in our study was methicillin resistant.

Paugam et al[25] conducted a study in 201 adult patients with CF, and showed Aspergillus fumigatus in 56.7 per cent and other Aspergillus (non-fumigatus) species in 10.4 per cent patients. In another study conducted by Güngör et al[10] in Istanbul, 48 CF patients were followed up. Contrary to the present observation they reported Candida albicans asthe most common isolate (62.5%), followed by A. fumigatus (10.4%). Paugam et al[25] also reported increased percentage recovery of Pseudomonas, NTM and Stenotrophomonas maltophilia in patients colonized with A. fumigatus, however no such association was observed in the present study.

Growth of NTM was not seen in any of the patients, whereas M. tuberculosis was grown in four patients. Seddon et al[26] in their multicentre questionnaire based study reported a NTM prevalence of 3.3 per cent among 3,317 children. M. tuberculosis has been rarely associated with CF and there are only a few case reports available in literature[27],[28]. In the STOP study, the positivity for NTM was seven per cent[21]. In our study, samples at multiple occasions could be obtained only for those patients who received in-hospital treatment which may explain the nil yield of NTM.

Hoek et al[29] reported presence of viruses in 33 per cent of their adult population of CF patients, and Asner et al[30] showed in 60.5 per cent, whereas in our study, 29.3 per cent of patients were tested positive for at least one of the respiratory viruses. Hospitalized care was required in all the children who had co-infection suggesting increased severeity of exacerbations in these patients. Our study has reiterated the role of non-bacterial microorganisms causing pulmonary exacerbations in children with CF.

In conclusion, Pseudomonas was the most common organism isolated during exacerbation. Infection with Bcc and M. tuberculosis was observed in our study whereas NTM were not isolated. Aspergillus was the commonest fungus isolated. Viruses resulted in exacerbations in a significant number of CF children. Polymicrobial infections were associated with severe exacerbations.

Financial support & sponsorship: None.

Conflicts of Interest: None.

   References Top

Mehta S, Wadhwa UN, Mehta SK, Chhuttani PN. Fibrocystic disease of pancreas in India. Indian Pediatr 1968; 5 : 185-91.  Back to cited text no. 1
Kapoor V, Shastri SS, Kabra M, Kabra SK, Ramachandran V, Arora S, et al. Carrier frequency of F508del mutation of cystic fibrosis in Indian population. J Cyst Fibros 2006; 5 : 43-6.  Back to cited text no. 2
Filkins LM, O'Toole GA. Cystic fibrosis lung infections: Polymicrobial, complex, and hard to treat. PLoS Pathog 2015 31; 11 : e1005258.  Back to cited text no. 3
Coburn B, Wang PW, Diaz Caballero J, Clark ST, Brahma V, Donaldson S, et al. Lung microbiota across age and disease stage in cystic fibrosis. Sci Rep 2015; 5 : 10241.  Back to cited text no. 4
Folescu TW, da Costa CH, Cohen RWF, Neto OC da C, Albano RM, Marques EA. Burkholderia cepacia complex: Clinical course in cystic fibrosis patients. BMC Pulm Med 2015; 15 : 158.  Back to cited text no. 5
Ranganathan SC, Hall GL, Sly PD, Stick SM, Douglas TA. Early lung disease in infants and preschool children with cystic fibrosis. What have we learned and what should we do about it? Am J Respir Crit Care Med 2017; 195 : 1567-75.  Back to cited text no. 6
Olivier KN, Weber DJ, Wallace RJ Jr, Faiz AR, Lee JH, Zhang Y, et al. Nontuberculous mycobacteria. I: Multicenter prevalence study in cystic fibrosis. Am J Respir Crit Care Med 2003; 167 : 828-34.  Back to cited text no. 7
Gulla KM, Balaji A, Mukherjee A, Jat KR, Sankar J, Lodha R, et al. Course of illness after viral infection in Indian children with cystic fibrosis. J Trop Pediatrics 2019; 65 : 176-82.  Back to cited text no. 8
Wang JH, Kwon HJ, Jang YJ. Rhinovirus enhances various bacterial adhesions to nasal epithelial cells simultaneously. Laryngoscope 2009; 119 : 1406-11.  Back to cited text no. 9
Güngör O, Tamay Z, Güler N, Erturan Z. Frequency of fungi in respiratory samples from Turkish cystic fibrosis patients. Mycoses 2013; 56 : 123-9.  Back to cited text no. 10
Kabra SK, Kabra M, Lodha R, Shastri S. Cystic fibrosis in India. Pediatr Pulmonol 2007; 42 : 1087-94.  Back to cited text no. 11
Fuchs HJ, Borowitz DS, Christiansen DH, Morris EM, Nash ML, Ramsey BW, et al. Effect of aerosolized recombinant human DNase on exacerbations of respiratory symptoms and on pulmonary function in patients with cystic fibrosis. The pulmozyme study group. N Engl J Med 1994; 331 : 637-42.  Back to cited text no. 12
Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing; 24th informational supplement. CLSI Document M100-S24. Wayne, PA: CLSI; 2014. p. 230.  Back to cited text no. 13
De Bel A, De Geyter D, De Schutter I, Mouton C, Wellemans I, Hanssens L, et al. Sampling and decontamination method for culture of nontuberculous mycobacteria in respiratory samples of cystic fibrosis patients. J Clin Microbiol 2013; 51 : 4204-6.  Back to cited text no. 14
Santana MA, Matos E, do Socorro Fontoura M, Franco R, Barreto D, Lemos AC. Prevalence of pathogens in cystic fibrosis patients in Bahia, Brazil. Braz J Infect Dis 2003; 7 : 69-72.  Back to cited text no. 15
Lambiase A, Raia V, Del Pezzo M, Sepe A, Carnovale V, Rossano F. Microbiology of airway disease in a cohort of patients with cystic fibrosis. BMC Infect Dis 2006; 6 : 4.  Back to cited text no. 16
Quintas S, Pereira L, Lito L, Barreto C. Epidemiological survey of bacteria isolated from the respiratory tract of cystic fibrosis patients. Rev Port Pneumol 2003; 9 : 337-52.  Back to cited text no. 17
Muñoz C, Juncosa T, Gené A, Fortea J, Séculi JL, Latorre C. Microbiological study of the respiratory tract in children with cystic fibrosis. Enferm Infecc Microbiol Clin 1996; 14 : 142-4.  Back to cited text no. 18
Razvi S, Quittell L, Sewall A, Quinton H, Marshall B, Saiman L. Respiratory microbiology of patients with cystic fibrosis in the United States, 1995 to 2005. Chest 2009; 136 : 1554-60.  Back to cited text no. 19
Whiteford ML, Wilkinson JD, McColl JH, Conlon FM, Michie JR, Evans TJ, et al. Outcome of Burkholderia (Pseudomonas) cepacia colonisation in children with cystic fibrosis following a hospital outbreak. Thorax 1995; 50 : 1194-8.  Back to cited text no. 20
Sanders DB, Solomon GM, Beckett VV, West NE, Daines CL, Heltshe SL, et al. Standardized Treatment of Pulmonary Exacerbations (STOP) study: Observations at the initiation of intravenous antibiotics for cystic fibrosis pulmonary exacerbations. J Cyst Fibros 2017; 16 : 592-9.  Back to cited text no. 21
Montagna MT, Barbuti G, Paglionico F, Lovero G, Iatta R, De Giglio O, et al. Retrospective analysis of microorganisms isolated from cystic fibrosis patients in Southern Italy, 2002-2010. J Prev Med Hyg 2011; 52 : 209-14.  Back to cited text no. 22
Paixão VA, Barros TF, Mota CM, Moreira TF, Santana MA, Reis JN. Prevalence and antimicrobial susceptibility of respiratory pathogens in patients with cystic fibrosis. Braz J Infect Dis 2010; 14 : 406-9.  Back to cited text no. 23
Valenza G, Tappe D, Turnwald D, Frosch M, König C, Hebestreit H, et al. Prevalence and antimicrobial susceptibility of microorganisms isolated from sputa of patients with cystic fibrosis. J Cyst Fibros 2008; 7 : 123-7.  Back to cited text no. 24
Paugam A, Baixench MT, Demazes-Dufeu N, Burgel PR, Sauter E, Kanaan R, et al. Characteristics and consequences of airway colonization by filamentous fungi in 201 adult patients with cystic fibrosis in France. Med Mycol 2010; 48 (Suppl 1) : S32-6.  Back to cited text no. 25
Seddon P, Fidler K, Raman S, Wyatt H, Ruiz G, Elston C, et al. Prevalence of nontuberculous mycobacteria in cystic fibrosis clinics, United Kingdom, 2009. Emerg Infect Dis 2013; 19 : 1128-30.  Back to cited text no. 26
Wood RE, Boat TF, Doershuk CF. Cystic fibrosis. Am Rev Respir Dis 1976; 113 : 833-78.  Back to cited text no. 27
Patil N, Marco A, Montales M, Bhaskar N, Mittadodla P, Mukasa L. Pulmonary tuberculosis in a patient with cystic fibrosis. North Am J Med Sci 2015; 7 : 233-5.  Back to cited text no. 28
Hoek RA, Paats MS, Pas SD, Bakker M, Hoogsteden HC, Boucher CA, et al. Incidence of viral respiratory pathogens causing exacerbations in adult cystic fibrosis patients. Scand J Infect Dis 2013; 45 : 65-9.  Back to cited text no. 29
Asner S, Waters V, Solomon M, Yau Y, Richardson SE, Grasemann H, et al. Role of respiratory viruses in pulmonary exacerbations in children with cystic fibrosis. J Cyst Fibros 2012; 11 : 433-9.  Back to cited text no. 30


  [Table 1], [Table 2], [Table 3]

This article has been cited by
1 Cystic Fibrosis: Fighting Together Against Coronavirus Infection
Sara Manti,Giuseppe Fabio Parisi,Maria Papale,Enza Mulè,Donatella Aloisio,Novella Rotolo,Salvatore Leonardi
Frontiers in Medicine. 2020; 7
[Pubmed] | [DOI]


    Similar in PUBMED
   Search Pubmed for
   Search in Google Scholar for
 Related articles
    Access Statistics
    Email Alert *
    Add to My List *
* Registration required (free)  

  In this article
    Material & M...
    Article Tables

 Article Access Statistics
    PDF Downloaded358    
    Comments [Add]    
    Cited by others 1    

Recommend this journal