Practical Guidance for Clinical Microbiology Laboratories: Updated guidance for processing respiratory tract samples from people with cystic fibrosis

Abstract

SUMMARYThis guidance presents recommendations for clinical microbiology laboratories for processing respiratory samples from people with cystic fibrosis (pwCF). Appropriate processing of respiratory samples is crucial to detect bacterial and fungal pathogens, guide treatment, monitor the epidemiology of cystic fibrosis (CF) pathogens, and assess therapeutic interventions. Thanks to CF transmembrane conductance regulator modulator therapy, the health of pwCF has improved, but as a result, fewer pwCF spontaneously expectorate sputum. Thus, the collection of sputum samples has decreased, while the collection of other types of respiratory samples such as oropharyngeal and bronchoalveolar lavage samples has increased. To optimize the detection of microorganisms, including Pseudomonas aeruginosa, Staphylococcus aureus, Haemophilus influenzae, and Burkholderia cepacia complex; other less common non-lactose fermenting Gram-negative bacilli, e.g., Stenotrophomonas maltophilia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species; and yeasts and filamentous fungi, non-selective and selective culture media are recommended for all types of respiratory samples, including samples obtained from pwCF after lung transplantation. There are no consensus recommendations for laboratory practices to detect, characterize, and report small colony variants (SCVs) of S. aureus, although studies are ongoing to address the potential clinical impact of SCVs. Accurate identification of less common Gram-negative bacilli, e.g., S. maltophilia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species, as well as yeasts and filamentous fungi, is recommended to understand their epidemiology and clinical importance in pwCF. However, conventional biochemical tests and automated platforms may not accurately identify CF pathogens. MALDI-TOF MS provides excellent genus-level identification, but databases may lack representation of CF pathogens to the species-level. Thus, DNA sequence analysis should be routinely available to laboratories for selected clinical circumstances. Antimicrobial susceptibility testing (AST) is not recommended for every routine surveillance culture obtained from pwCF, although selective AST may be helpful, e.g., for unusual pathogens or exacerbations unresponsive to initial therapy. While this guidance reflects current care paradigms for pwCF, recommendations will continue to evolve as CF research expands the evidence base for laboratory practices.

Keywords: MALDI-TOF MS; cystic fibrosis; pathogen identification; respiratory pathogens; small colony variants; susceptibility testing.

Fig 1

Prevalence of respiratory microorganisms by age cohort, 2021. The prevalence of specific microorganism by eight age strata is shown. Abbreviations used in figure: MSSA, methicillin-susceptible S. aureus; MRSA, methicillin-resistant S. aureus; MDR-PA, multidrug-resistant P. aeruginosa. Source of data: data are obtained from pwCF under care at CFF-accredited care centers in the United States, who consented to have their data or their child’s data entered. Cystic Fibrosis Foundation Patient Registry, 2021 Unpublished Data (personal communication), Cystic Fibrosis Foundation.

Fig 2

Prevalence of respiratory microorganisms in people with cystic fibrosis, 1991–2021. The prevalence of common microorganisms over time in shown in (A), and the prevalence of less common microorganisms over time is shown in (B). Source of data: data are obtained from pwCF under care at CFF-accredited care centers in the United States, who consented to have their data or their child’s data entered. Cystic Fibrosis Foundation Patient Registry, 2021 Unpublished Data (personal communication), Cystic Fibrosis Foundation.

Fig 3

Types of respiratory tract specimens from people with CF, 2016–2021. The types of respiratory tract specimens in adults (A) and children <17 years (B) with CF are shown. Source of data: data are obtained from pwCF under care at CFF-accredited care centers in the United States, who consented to have their data or their child’s data entered. Cystic Fibrosis Foundation Patient Registry, 2021 Unpublished Data (personal communication), Cystic Fibrosis Foundation.

Fig 4

Factors influencing discordance between AST results and clinical outcomes in pwCF. Drug factors: low pH and anaerobic milieu in CF airways can decrease the activity of antibiotics; these conditions are not accounted for in standard AST. Tissue concentrations of antibiotics can vary significantly throughout CF lung. Antibiotics may also have non-bactericidal effects, such as the anti-inflammatory effect of azithromycin. Bacterial factors: bacteria in CF airways exhibit phenotypic and genotypic diversity and a biofilm mode of growth, neither of which are represented in standard AST. Polymicrobial interactions: Airway infections in pwCF are polymicrobial and interactions between species, not represented in standard AST, can affect antimicrobial susceptibility. Causative pathogen: it is not clear which phenotype of which species should undergo AST. Non-infectious causes of respiratory decline also exist.