An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches

Lamoureux, Claudie; Guilloux, Charles-Antoine; Gouriou, S.; Ramel, Sophie; Dirou, Anne; Bihan, Jean Le; Revert, K.; Ropars, Thomas; Lagrafeuille, Rosyne; Vallet, Sophie; Berre, Rozenn Le; Nowak, Emmanuel; Héry-Arnaud, Geneviève

doi:10.1038/s41598-021-85592-w

Cited by 15 publications

(13 citation statements)

References 45 publications

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“…Second, we cannot exclude that the limited detection of slow-growing or anaerobic bacteria may result from technical limitations inherent to the conventional culture-based approach. We did not want to change frameworks for sampling by the physicians, so we did not use any collecting device that could ensure the preservation of an anaerobic atmosphere for the sputa until processing in the laboratory ( Lamoureux et al, 2021 ). Moreover, we did not compare our results obtained by culture methods with sequencing-based data, as we only focused on culture methods applicable in most clinical microbiology laboratories.…”

Section: Discussionmentioning

confidence: 99%

Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease

et al. 2021

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Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease characterized by airflow limitation. This chronic respiratory disease represents the third leading cause of death worldwide. Alteration of the airway microbiota has been reported to be associated with exacerbation frequency in COPD, but its role on the symptoms in patients at stable state is still incompletely described. This study aimed to determine whether bacteria isolated in sputum can be associated with the clinical features of COPD patients within stable state. Our study highlights, for the first time, that altered microbiota with Enterobacterales is associated with pejorative clinical symptoms in stable COPD patients. The airway microbiota of 38 patients was analyzed using an extended culture approach and mass spectrometry identification. Cluster analysis by principal coordinate analysis of the bacterial communities showed that the patients could be classified into three distinct clusters in our cohort. The clusters showed no differences in proportions of the phylum, but one of them was associated with a high prevalence of Enterobacterales (71.4% in cluster 1 vs. 0% in cluster 3), loss of microbiota diversity, and higher bacterial load (107 vs. 105 CFU/ml, respectively) and characterized by predominant cough and impact on mental health. These novel findings, supported by further studies, could lead to modifying the processing of COPD sputum in the everyday practice of clinical microbiology laboratories.

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Section: Discussionmentioning

confidence: 99%

Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease

et al. 2021

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“…Employing cultureindependent approaches, anaerobes have now been shown to be key members of the CF airway microbiome. Up to 91.1% of CF sputa have been shown to be positive for at least one anaerobic bacterial species [179]. Anaerobes are increasingly dominant in patients with better lung function [95], and several studies have reported the negative impact of antibiotics on anaerobic populations in the CF airway [87,89,104,105].…”

Section: Anaerobes Impact P Aeruginosa Antibiotic Resistancementioning

confidence: 99%

Polymicrobial Interactions in the Cystic Fibrosis Airway Microbiome Impact the Antimicrobial Susceptibility of Pseudomonas aeruginosa

2021

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Pseudomonas aeruginosa is one of the most dominant pathogens in cystic fibrosis (CF) airway disease and contributes to significant inflammation, airway damage, and poorer disease outcomes. The CF airway is now known to be host to a complex community of microorganisms, and polymicrobial interactions have been shown to play an important role in shaping P. aeruginosa pathogenicity and resistance. P. aeruginosa can cause chronic infections that once established are almost impossible to eradicate with antibiotics. CF patients that develop chronic P. aeruginosa infection have poorer lung function, higher morbidity, and a reduced life expectancy. P. aeruginosa adapts to the CF airway and quickly develops resistance to several antibiotics. A perplexing phenomenon is the disparity between in vitro antimicrobial sensitivity testing and clinical response. Considering the CF airway is host to a diverse community of microorganisms or ‘microbiome’ and that these microorganisms are known to interact, the antimicrobial resistance and progression of P. aeruginosa infection is likely influenced by these microbial relationships. This review combines the literature to date on interactions between P. aeruginosa and other airway microorganisms and the influence of these interactions on P. aeruginosa tolerance to antimicrobials.

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“…Fifty isolates of Prevotella melaninogenica cultured from sputum of 50 PWCF collected at the Western Brittany CF center (Roscoff, France) have been included in this study. Cultural methods from sputum (three different media, 21 days of culture at 37 • C in anaerobic atmosphere) have been previously described [5]. These 50 isolates have been identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS Biotyper MBT) (Bruker, Billerica, MA, USA); a score of ≥ 2.0 was considered as accurate species-level identification; a score ≥ 1.7 but < 2.0 as a probable genus-level identification; a score < 1.7 as "unidentified".…”

Section: Clinical Isolates and Antibiotic Susceptibility Testingmentioning

confidence: 99%

“…The importance and abundance of strict anaerobic bacteria in the respiratory microbiota of people with cystic fibrosis (PWCF) is now established. These recent data are based on high-throughput sequencing [1,2] and cultural techniques [3][4][5]. Anaerobes colony count has been evaluated between 1.10 4 to 9.10 7 colony forming units per milliliter in sputum culture [3].…”

Section: Introductionmentioning

confidence: 99%

“…However, these bacteria remain the unknowns of the lung, both in terms of diversity, resistance or impact on the pathophysiology of CF disease [8]. One of the most prevalent and abundant anaerobic genera described in CF lung is Prevotella, and particularly the species Prevotella melaninogenica [4,5,9]. Contradictory hypotheses on the potential role of Prevotella genus have been previously developed [8].…”

Section: Introductionmentioning

confidence: 99%

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Prevotella melaninogenica, a Sentinel Species of Antibiotic Resistance in Cystic Fibrosis Respiratory Niche?

et al. 2021

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The importance and abundance of strict anaerobic bacteria in the respiratory microbiota of people with cystic fibrosis (PWCF) is now established through studies based on high-throughput sequencing or extended-culture methods. In CF respiratory niche, one of the most prevalent anaerobic genera is Prevotella, and particularly the species Prevotella melaninogenica. The objective of this study was to evaluate the antibiotic susceptibility of this anaerobic species. Fifty isolates of P. melaninogenica cultured from sputum of 50 PWCF have been included. Antibiotic susceptibility testing was performed using the agar diffusion method. All isolates were susceptible to the following antibiotics: amoxicillin/clavulanic acid, piperacillin/tazobactam, imipenem and metronidazole. A total of 96% of the isolates (48/50) were resistant to amoxicillin (indicating beta-lactamase production), 34% to clindamycin (17/50) and 24% to moxifloxacin (12/50). Moreover, 10% (5/50) were multidrug-resistant. A significant and positive correlation was found between clindamycin resistance and chronic azithromycin administration. This preliminary study on a predominant species of the lung “anaerobiome” shows high percentages of resistance, potentially exacerbated by the initiation of long-term antibiotic therapy in PWCF. The anaerobic resistome characterization, focusing on species rather than genera, is needed in the future to better prevent the emergence of resistance within lung microbiota.

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An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches

Cited by 15 publications

References 45 publications

Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease

Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease

Polymicrobial Interactions in the Cystic Fibrosis Airway Microbiome Impact the Antimicrobial Susceptibility of Pseudomonas aeruginosa

Prevotella melaninogenica, a Sentinel Species of Antibiotic Resistance in Cystic Fibrosis Respiratory Niche?

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