{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T00:18:44Z","timestamp":1790381924213,"version":"4.1.0"},"reference-count":226,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2024,9,12]],"date-time":"2024-09-12T00:00:00Z","timestamp":1726099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/doi.org\/10.1128\/ASMCopyrightv2"},{"start":{"date-parts":[[2024,9,12]],"date-time":"2024-09-12T00:00:00Z","timestamp":1726099200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Clin Microbiol Rev"],"published-print":{"date-parts":[[2024,9,12]]},"abstract":"<jats:title>SUMMARY<\/jats:title>\n          <jats:p>\n            This 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\n            <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n            ,\n            <jats:italic>Staphylococcus aureus<\/jats:italic>\n            ,\n            <jats:italic>Haemophilus influenzae<\/jats:italic>\n            , and\n            <jats:italic>Burkholderia cepacia<\/jats:italic>\n            complex; other less common non-lactose fermenting Gram-negative bacilli, e.g.,\n            <jats:italic>Stenotrophomonas maltophilia<\/jats:italic>\n            ,\n            <jats:italic>Inquilinus<\/jats:italic>\n            ,\n            <jats:italic>Achromobacter<\/jats:italic>\n            ,\n            <jats:italic>Ralstonia<\/jats:italic>\n            , and\n            <jats:italic>Pandoraea<\/jats:italic>\n            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\n            <jats:italic>S. aureus<\/jats:italic>\n            , although studies are ongoing to address the potential clinical impact of SCVs. Accurate identification of less common Gram-negative bacilli, e.g.,\n            <jats:italic>S. maltophilia<\/jats:italic>\n            ,\n            <jats:italic>Inquilinus<\/jats:italic>\n            ,\n            <jats:italic>Achromobacter<\/jats:italic>\n            ,\n            <jats:italic>Ralstonia<\/jats:italic>\n            , and\n            <jats:italic>Pandoraea<\/jats:italic>\n            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.\n          <\/jats:p>","DOI":"10.1128\/cmr.00215-21","type":"journal-article","created":{"date-parts":[[2024,8,19]],"date-time":"2024-08-19T13:00:53Z","timestamp":1724072453000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":25,"title":["Practical Guidance for Clinical Microbiology Laboratories: Updated guidance for processing respiratory tract samples from people with cystic fibrosis"],"prefix":"10.1128","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7231-8451","authenticated-orcid":true,"given":"Lisa","family":"Saiman","sequence":"first","affiliation":[{"name":"Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA"},{"name":"Department of Infection Prevention and Control, NewYork-Presbyterian Hospital, New York, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1566-6510","authenticated-orcid":true,"given":"Valerie","family":"Waters","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4033-7794","authenticated-orcid":true,"given":"John J.","family":"LiPuma","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas R.","family":"Hoffman","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Washington, Seattle, Washington, USA"},{"name":"Department of Microbiology, University of Washington, Seattle, Washington, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Alby","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1166-2563","authenticated-orcid":true,"given":"Sean X.","family":"Zhang","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yvonne C.","family":"Yau","sequence":"additional","affiliation":[{"name":"Division of Microbiology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damian G.","family":"Downey","sequence":"additional","affiliation":[{"name":"Wellcome-Wolfson Institute for Experimental Medicine, Queen\u2019s University, Belfast, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabelle","family":"Sermet-Gaudelus","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris Cit\u00e9, H\u00f4pital Necker-Enfants Malades, Assistance Publique, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Philippe","family":"Bouchara","sequence":"additional","affiliation":[{"name":"University of Angers-University of Brest, Infections Respiratoires Fongiques, Angers, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Kidd","sequence":"additional","affiliation":[{"name":"Microbiology Division, Pathology Queensland Central Laboratory, The University of Queensland, Brisbane, Australia"},{"name":"School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8651-7139","authenticated-orcid":true,"given":"Scott C.","family":"Bell","sequence":"additional","affiliation":[{"name":"The Prince Charles Hospital, Faculty of Medicine, The University of Queensland, Brisbane, Australia"},{"name":"The Translational Research Institute, Brisbane, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. 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