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Saiman L, Waters V, LiPuma JJ, Hoffman LR, Alby K, Zhang SX, Yau YC, Downey DG, Sermet-Gaudelus I, Bouchara JP, Kidd TJ, Bell SC, Brown AW. Practical Guidance for Clinical Microbiology Laboratories: Updated guidance for processing respiratory tract samples from people with cystic fibrosis. Clin Microbiol Rev 2024; 37:e0021521. [PMID: 39158301 PMCID: PMC11391703 DOI: 10.1128/cmr.00215-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024] Open
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.
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Affiliation(s)
- Lisa Saiman
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
- Department of Infection Prevention and Control, NewYork-Presbyterian Hospital, New York, New York, USA
| | - Valerie Waters
- Division of Infectious Diseases, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lucas R Hoffman
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Kevin Alby
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Sean X Zhang
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yvonne C Yau
- Division of Microbiology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Damian G Downey
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, Ireland
| | | | - Jean-Philippe Bouchara
- University of Angers-University of Brest, Infections Respiratoires Fongiques, Angers, France
| | - Timothy J Kidd
- Microbiology Division, Pathology Queensland Central Laboratory, The University of Queensland, Brisbane, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Scott C Bell
- The Prince Charles Hospital, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- The Translational Research Institute, Brisbane, Australia
| | - A Whitney Brown
- Cystic Fibrosis Foundation, Bethesda, Maryland, USA
- Inova Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Falls Church, Virginia, USA
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Naqvi S, Varadhan H, Givney R. Is prolonged incubation required for optimal recovery of Burkholderia cepacia complex in sputum from cystic fibrosis patients? Data versus dogma. Pathology 2020; 52:366-369. [PMID: 32113671 DOI: 10.1016/j.pathol.2019.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 10/19/2019] [Accepted: 11/27/2019] [Indexed: 11/27/2022]
Abstract
Cystic fibrosis (CF) expert groups globally recommend using selective medium for isolation of Burkholderia cepacia complex (BCC) from respiratory specimens of CF patients. However, there is no consensus available for optimal duration of incubation and recommendations are variable. The purpose of our study was to compare the difference in recovery of BCC in CF samples at 48 hours versus 7 days when inoculated on Burkholderia cepacia selective agar. A total of 307 consecutive clinical respiratory specimens from our local CF unit were studied prospectively (August 2017 to December 2017). All specimens were inoculated on Burkholderia cepacia medium, containing polymyxin B, gentamicin and ticarcillin. In our laboratory, these plates are routinely incubated for 48 hours as per the manufacturer's recommendation. However, for this study all plates with no growth at 48 hours were further incubated for total of 7 days at 35°C in O2. Plates were read daily to look for any growth. Microbial identification was performed using MALDI-TOF Vitek MS (database V3.0). Of the 307 CF respiratory specimens cultured, 177 (58%) were from paediatric and 130 (42%) were from adult patients; 155 (50%) specimens were sputum, 148 (48%) were cough swabs and four (1%) were bronchoalveolar lavage (BAL). All specimens from adults were sputum except one BAL. Thirteen (4%) cultures from eight adult and five paediatric specimens grew BCC. The majority (294, 96%) of specimens had no growth when incubated for 7 days. All 13 positive isolates recovered within 48 hours and there were no additional positive isolates found beyond 48 hours of incubation. We conclude from our analysis that prolonged incubation is not warranted for recovery of BCC in CF specimens if selective medium containing gentamicin and polymyxin is used. By adopting this approach of non-extended incubation, the burden of work on laboratory personnel can be significantly reduced and much faster turnaround time for CF cultures achieved. Our study confirms the results of recently published data on this point and challenges the prevailing dogma of utility of extended incubation for BCC isolation. For devising consensus statements for microbiology laboratories on this issue, CF societies and expert groups should consider reviewing data from the recent studies.
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Affiliation(s)
- Syeda Naqvi
- NSW Health Pathology, John Hunter Laboratory, Newcastle, NSW, Australia.
| | | | - Rodney Givney
- NSW Health Pathology, John Hunter Laboratory, Newcastle, NSW, Australia
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Kidd TJ, Canton R, Ekkelenkamp M, Johansen HK, Gilligan P, LiPuma JJ, Bell SC, Elborn JS, Flume PA, VanDevanter DR, Waters VJ. Defining antimicrobial resistance in cystic fibrosis. J Cyst Fibros 2018; 17:696-704. [PMID: 30266518 DOI: 10.1016/j.jcf.2018.08.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/21/2018] [Accepted: 08/31/2018] [Indexed: 12/31/2022]
Abstract
Antimicrobial resistance (AMR) can present significant challenges in the treatment of cystic fibrosis (CF) lung infections. In CF and other chronic diseases, AMR has a different profile and clinical consequences compared to acute infections and this requires different diagnostic and treatment approaches. This review defines AMR, explains how it occurs, describes the methods used to measure AMR as well as their limitations, and concludes with future directions for research and development in the area of AMR in CF.
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Affiliation(s)
- Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.
| | - Miquel Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Peter Gilligan
- Clinical Microbiology-Immunology Laboratories, UNC HealthCare, Chapel Hill, NC, USA.
| | - John J LiPuma
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital and QIMR Berghofer Medical Researhc Institute, Brisbane, Australia.
| | - J Stuart Elborn
- Imperial College and Royal Brompton Hospital, London, Queen's University Belfast, United Kingdom.
| | - Patrick A Flume
- Departments of Medicine and Pediatrics, Medical University of South Carolina, Charleston, SC, USA.
| | - Donald R VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, USA.
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Hector A, Kirn T, Ralhan A, Graepler-Mainka U, Berenbrinker S, Riethmueller J, Hogardt M, Wagner M, Pfleger A, Autenrieth I, Kappler M, Griese M, Eber E, Martus P, Hartl D. Microbial colonization and lung function in adolescents with cystic fibrosis. J Cyst Fibros 2016; 15:340-9. [PMID: 26856310 DOI: 10.1016/j.jcf.2016.01.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/24/2016] [Accepted: 01/24/2016] [Indexed: 11/18/2022]
Abstract
With intensified antibiotic therapy and longer survival, patients with cystic fibrosis (CF) are colonized with a more complex pattern of bacteria and fungi. However, the clinical relevance of these emerging pathogens for lung function remains poorly defined. The aim of this study was to assess the association of bacterial and fungal colonization patterns with lung function in adolescent patients with CF. Microbial colonization patterns and lung function parameters were assessed in 770 adolescent European (German/Austrian) CF patients in a retrospective study (median follow-up time: 10years). Colonization with Pseudomonas aeruginosa and MRSA were most strongly associated with loss of lung function, while mainly colonization with Haemophilus influenzae was associated with preserved lung function. Aspergillus fumigatus was the only species that was associated with an increased risk for infection with P. aeruginosa. Microbial interaction analysis revealed three distinct microbial clusters within the longitudinal course of CF lung disease. Collectively, this study identified potentially protective and harmful microbial colonization patterns in adolescent CF patients. Further studies in different patient cohorts are required to evaluate these microbial patterns and to assess their clinical relevance.
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Affiliation(s)
- Andreas Hector
- Children's Hospital of the University of Tübingen, Tübingen, Germany
| | - Tobias Kirn
- Children's Hospital of the University of Tübingen, Tübingen, Germany
| | - Anjali Ralhan
- Children's Hospital of the University of Tübingen, Tübingen, Germany
| | | | - Sina Berenbrinker
- Children's Hospital of the University of Tübingen, Tübingen, Germany
| | | | - Michael Hogardt
- Institute of Medical Microbiology and Hygiene, University of Frankfurt, Frankfurt, Germany
| | - Marlies Wagner
- Department of Pediatrics and Adolescence Medicine, Medical University of Graz, Graz, Austria
| | - Andreas Pfleger
- Department of Pediatrics and Adolescence Medicine, Medical University of Graz, Graz, Austria
| | - Ingo Autenrieth
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany; German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Matthias Kappler
- Department of Pediatric Pneumology, Hauner Children's Hospital, Ludwig-Maximilians University, Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research (DZL), Munich, Germany
| | - Matthias Griese
- Department of Pediatric Pneumology, Hauner Children's Hospital, Ludwig-Maximilians University, Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research (DZL), Munich, Germany
| | - Ernst Eber
- Department of Pediatrics and Adolescence Medicine, Medical University of Graz, Graz, Austria
| | - Peter Martus
- Institute of Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany
| | - Dominik Hartl
- Children's Hospital of the University of Tübingen, Tübingen, Germany.
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Pseudomonas aeruginosa Acquisition in Cystic Fibrosis Patients in Context of Otorhinolaryngological Surgery or Dentist Attendance: Case Series and Discussion of Preventive Concepts. Case Rep Infect Dis 2015; 2015:438517. [PMID: 25866686 PMCID: PMC4381717 DOI: 10.1155/2015/438517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/25/2015] [Accepted: 03/02/2015] [Indexed: 01/23/2023] Open
Abstract
Introduction. P. aeruginosa is the primary cause for pulmonary destruction and premature death in cystic fibrosis (CF). Therefore, prevention of airway colonization with the pathogen, ubiquitously present in water, is essential. Infection of CF patients with P. aeruginosa after dentist treatment was proven and dental unit waterlines were identified as source, suggesting prophylactic measures. For their almost regular sinonasal involvement, CF patients often require otorhinolaryngological (ORL) attendance. Despite some fields around ORL-procedures with comparable risk for acquisition of P. aeruginosa, such CF cases have not yet been reported. We present four CF patients, who primarily acquired P. aeruginosa around ORL surgery, and one around dentist treatment. Additionally, we discuss risks and preventive strategies for CF patients undergoing ORL-treatment. Perils include contact to pathogen-carriers in waiting rooms, instrumentation, suction, drilling, and flushing fluid, when droplets containing pathogens can be nebulized. Postsurgery mucosal damage and debridement impair sinonasal mucociliary clearance, facilitating pathogen proliferation and infestation. Therefore, sinonasal surgery and dentist treatment of CF patients without chronic P. aeruginosa colonization must be linked to repeated microbiological assessment. Further studies must elaborate whether all CF patients undergoing ORL-surgery require antipseudomonal prophylaxis, including nasal lavages containing antibiotics. Altogether, this underestimated risk requires structured prevention protocols.
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Caballero JDD, del Campo R, Tato M, Gómez G de la Pedrosa E, Cobo M, López-Causapé C, Gómez-Mampaso E, Oliver A, Cantón R. Microbiological diagnostic procedures for respiratory cystic fibrosis samples in Spain: towards standard of care practices. BMC Microbiol 2014; 14:335. [PMID: 25927861 PMCID: PMC4302700 DOI: 10.1186/s12866-014-0335-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 12/18/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The microbiological procedures for cystic fibrosis (CF) samples of 17 participating Spanish centers were examined to verify their compliance with current international and national guidelines and to implement the best standards of care for microbiology practices. A 47-item questionnaire covering different CF microbiology aspects was sent to participant laboratories. Telephone interviews were performed when necessary. Data about samples processing for bacteria, mycobacteria and fungi were collected. RESULTS Gene sequencing (71%), MALDI-TOF (59%) or both (94%) were available for most laboratories. Susceptibility testing was performed by automated microdilution systems (94%) and manual diffusion methods (59%). However, a low use of selective media for Staphylococcus aureus (59%) and Burkholderia cepacia complex (71%), and of epidemiological typing methods (41%) was reported. CONCLUSIONS Most Spanish laboratories are in agreement with consensus guidelines for the processing of CF respiratory samples, but need to improve in the use of specific selective media and typing methods for epidemiologic studies.
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Affiliation(s)
- Juan de Dios Caballero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, 28034, Spain.
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.
| | - Rosa del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, 28034, Spain.
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.
| | - Marta Tato
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, 28034, Spain.
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.
| | - Elia Gómez G de la Pedrosa
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, 28034, Spain.
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.
| | - Marta Cobo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, 28034, Spain.
| | - Carla López-Causapé
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain.
| | - Enrique Gómez-Mampaso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, 28034, Spain.
| | - Antonio Oliver
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain.
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, 28034, Spain.
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.
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Assessment of microbiological diagnostic procedures for respiratory specimens from cystic fibrosis patients in German laboratories by use of a questionnaire. J Clin Microbiol 2014; 52:977-9. [PMID: 24391197 DOI: 10.1128/jcm.02866-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Respiratory specimens from cystic fibrosis (CF) patients challenge microbiological laboratories with their complexity of pathogens and atypical variants. We evaluated the diagnostic procedures in German laboratories by use of a questionnaire. Although most laboratories followed guidelines, some of them served only a small number of patients, while others did not use the recommended selective agars to culture the particular CF-relevant species.
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Bjarnsholt T, Nielsen XC, Johansen U, Nørgaard L, Høiby N. Methods to classify bacterial pathogens in cystic fibrosis. Methods Mol Biol 2011; 742:143-171. [PMID: 21547731 DOI: 10.1007/978-1-61779-120-8_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Many bacteria can be detected in CF sputum, pathogenic and commensal. Modified Koch's criteria for identification of established and emerging CF pathogens are therefore described. Methods are described to isolate bacteria and to detect bacterial biofilms in sputum or lung tissue from CF patients by means of conventional culturing and staining techniques and by the PNA FISH technique. Additionally, the confocal scanning laser microscopy technique is described for studying biofilms in vitro in a flow cell system. The recA-gene PCR and the RFLP-based identification methods are described for identification of isolates from the Burkholderia complex to the species level. DNA typing by PFGE, which can be used for any bacterial pathogen, is described as it is employed for Pseudomonas aeruginosa. A commercially available ELISA method is described for measuring IgG antibodies against P. aeruginosa in CF patients.
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Affiliation(s)
- Thomas Bjarnsholt
- Department of Clinical Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark.
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