Comparison of respiratory pathogen colonization and antimicrobial susceptibility in people with cystic �brosis versus non cystic �brosis bronchiectasis: A systematic review

Abstract


Background
Cystic brosis (CF) is an autosomal recessive disorder caused by mutations in cystic brosis transmembrane conductance regulator (CFTR) gene, which regulates the activity of sodium and chloride channels across the epithelial cells, thereby facilitating appropriate hydration of mucins and effective mucociliary clearance in various organs of the body (1).Impaired secretion of chloride and bicarbonate ions due to CFTR mutation leads to the formation of mucus, which is too thick to be cleared (2).This predisposes CF patients to pulmonary bacterial infections caused by Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus in uenzae or Burkholderia cepacia complex (Bcc) (3).The in ammatory response of the body to these recurrent infections eventually leads to bronchiectasis, characterized by permanent bronchial dilation, leading to impaired mucociliary clearance allowing bacterial adherence, increased bacterial load and the development of chronic infection.The bacteria gradually adapt to these conditions by forming bio lms, which ensures protection from phagocytic attack as well as antibiotics (4).
There are many similarities between CF and non-CF bronchiectasis.Both are associated with exacerbations and severe in ammation, progress to complications, are associated with impaired mucociliary function leading to mucus obstruction and reduced lung function, predispose to microbial infections, and can cause permanent damage (6, 7).However, there are also many differences between the two.These include the differences in the etiology, age, and lung predominance.Bronchiectasis in CF patients is associated with mutations in the CFTR gene while non-CF bronchiectasis is associated with various underlying conditions like immunode ciency disorders, ciliary dyskinesis or demonstrates post-infectious etiology.Non-CF bronchiectasis affects mainly older population (age > 60 years) unlike CF patients, which is a genetic disorder thereby manifesting in both children and adults.Furthermore, non-CF bronchiectasis is associated with lower lung lobe predominance as compared to upper lung lobe predominance in CF (7).
Although the core airway microbiota is similar in both CF and non-CF bronchiectasis, particular satellite microbes are associated with speci c conditions.Sputum is the preferred specimen for culturing the bacterial organisms, and is also tested for acid-fast bacilli in case of non-CF bronchiectasis (5).However, bronchioalveolar lavage (BAL) is reserved for patients who are unable to produce sputum or whose CT (computed tomography) scan indicates microbial infection but sputum culture is negative.In case of CF bronchiectasis, culture of sputum or BAL or epithelial lining uid (ELF) guides the antimicrobial therapy.Staphylococcus aureus, Pseudomonas aeruginosa, Burkholderia cepacia complex, Haemophilus in uenzae, Stenotrophomonas maltophilia and Achromobacter xylosoxidans are commonly associated with CF bronchiectasis (8) while Haemophilus in uenzae, Pseudomonas aeruginosa, Moraxella catarrhalis, or non-tuburculous mycobacteria (NTM) are the predominant bacterial species associated with non-CF bronchiectasis (5,9).Gram-positive bacteria including Streptococcus pneumoniae and Staphylococcus aureus are rarely associated with non-CF bronchiectasis unlike CF bronchiectasis (10).Interestingly, the core microbiota in both the conditions is similar in childhood and eventually diverges by adulthood (6,11).
Antibiotics are the mainstay of treatment of bronchiectasis in both CF and non-CF patients, the choice of which is based on the understanding of the predominant respiratory tract colonizers as well as the results of local antimicrobial susceptibility testing (AST).The use of antibiotics is associated with substantially less devastating pulmonary disease in these patients, thereby improving their survival (12).
AST is used to predict the success or failure of an antibiotic by sorting out the resistant bacteria from the susceptible ones on the basis of Minimal Inhibitory Concentration (MIC) breakpoints, which are determined by breakpoint committees like European Committee on Antimicrobial Susceptibility Testing (EUCAST) or Clinical & Laboratory Standards Institute (CLSI).However, the epidemiological cut-off is determined using the susceptibility data from the wild-type population and does not take into consideration any mutant strains (13), which are commonly encountered for the bacteria to survive in the mucus obstructed airways of the CF patients and to combat the antibiotic treatment, which is often given for longer duration in CF patients and at doses higher than those in non-CF patients (14).So clinicians cannot rely only on such data for prescribing empirical therapy to the CF patients.Besides this there are several other factors, which may be responsible for the disparity in antibiotic susceptibility pro le between the CF and non-CF populations.For instance, in response to the oxygen or nutrient de cit conditions in CF lungs, the bacteria adapt by slowing down their growth rate or by altering their metabolism (4), which fosters resistance to several antibiotics among these microorganisms (e.g. the cell-wall acting antibiotics might not be effective in eradicating such bacteria, which are not actively dividing or are growing slowly) or the bacteria form bio lms, which likewise is responsible for antibiotic resistance (15).In addition to this, different colonial types of bacteria such as small colony variants (SCVs) are observed in the respiratory samples of the CF patients (16) (17), which are often missed in the routine laboratory testing.A single sample from CF patients may contain a mixed population of the same organism with varied antibiotic susceptibility pro le thereby requiring utmost caution while culturing the microorganisms and testing for antibiotic susceptibility (18).Therefore, a detailed insight into the comparison of respiratory pathogen colonization in both the conditions would pave way for improved management strategies of bronchiectasis in both the CF and non-CF populations.

Study Aim and Objectives
This systematic review aims to compare the microbiota and antimicrobial susceptibility pro le in CF and non-CF bronchiectasis.We propose to undertake a systematic review of literature to address the following research questions: 1. What are the bacteria colonizing the respiratory tract in patients with cystic brosis bronchiectasis compared to non cystic brosis bronchiectasis?2. How does the antibiotic susceptibility pro le of speci c bacteria, differ between CF bronchiectasis and non-CF bronchiectasis patients?

Types of studies
The data required for this review could be available in Observational studies including cohort studies or case-control studies (case arm), one or other arm of controlled clinical trials (randomized or non-randomized) or case series.

Types of participants
Adults and children diagnosed with bronchiectasis in either CF subjects or non-CF subjects.

Inclusion criteria
Studies reporting bacterial colonization of the respiratory tract (upper or lower) determined by examination of any respiratory tract specimen, by conventional bacterial culture or specialized techniques; and/or antimicrobial susceptibility testing by any method.

Exclusion criteria
We will exclude the below mentioned studies: 1.Those in which include patients with CF or non-CF, but patients do not have bronchiectasis.
2. Those in which data of patients with and without bronchiectasis cannot be distinguished.
3. Those in which the underlying cause(s) of bronchiectasis cannot be distinguished as CF or non-CF 4. Those in which non-standard culture methods were used to identify organisms.5.Those wherein multiple clinical conditions have been studied, and it is not possible to separately analyze the data for CF and non-CF or retrospective microbiology studies wherein the underlying clinical condition(s) are not speci ed. .Case series with less than 10 participants.
7. Studies conducted in animals or animal models or studies wherein already identi ed organisms were evaluated further for genotypic or phenotypic characteristics will be excluded.
Comparisons considered in this review 1. Clinical or microbiological studies of any design (observational, controlled clinical trials or case series), reporting bacterial colonization of the respiratory tract (from any type of biological specimen), and/or antimicrobial susceptibility in both types of patients i.e.CF and non-CF.Such studies will be considered direct comparisons.
2. Clinical or microbiological studies of any design (observational, controlled clinical trials or case series), reporting bacterial colonization of the respiratory tract, and/or antimicrobial susceptibility in either CF or non-CF patients, if they are within a three-year period.Such studies will be considered indirect comparisons.
3. Clinical or microbiological studies of any design (observational, controlled clinical trials or case series), reporting bacterial colonization of the respiratory tract, and/or antimicrobial susceptibility in either CF or non-CF patients, within any time period, if they are from the same institution.Such studies will also be considered indirect comparisons.
Types of outcome measures 1. List of bacteria identi ed in the respiratory tract in patients with CF versus non-CF bronchiectasis.
2. Relative proportion of various bacterial species identi ed in the respiratory tract in patients with CF versus non-CF bronchiectasis.

Data collection and analysis
Studies will be screened by study titles and abstracts.Those identi ed as potentially relevant will be retrieved and full text examined.The studies will be evaluated for eligibility to be included in the review.Manual search of the reference lists of the retrieved studies will also be performed.In case of disagreements/ discrepancies, the senior author will do arbitration.

Data extraction and management
A special data extraction form will be prepared, for the following data.Data will be independently extracted by two reviewers, and analyzed by the joint team.
From each included study, information regarding the following will be extracted: Identi cation data (Author, year), study design, institution, country or countries, time-period of study, whether clinical or microbiological analysis, inclusion criteria of patients (CF and non-CF), age of patients, clinical state of patients (stable, acute exacerbation, surveillance culture etc.), underlying clinical condition, duration of illness if known, presence of co-morbidity, specimen tested, specimen collection method, whether already on antibiotics, microorganisms identi ed, bacteriological method used for identi cation (culture, biochemical tests, MALDI-TOF, PCR, other), quanti cation if any, bio lm formation, antibiotic therapy, antimicrobial susceptibility pro le, method of testing antimicrobial susceptibility, de nition of sensitivity, and clinical/bacteriological outcome (Tables 1 and 2).

Remarks
Assessment of risk of bias included studies authors will independently assess the risk of bias for each included trial using the Newcastle Ottawa Scale (NOS) (19).NOS is used to assess the quality of non-randomised studies including case-control and cohort studies to be used in a systematic review.The NOS contains eight items, categorized into three broad perspectives: the selection of the study groups; the comparability of the groups; and the ascertainment of either the exposure or outcome of interest for case-control or cohort studies, respectively.For each item a series of response options is provided.A star system is used to allow a semi-quantitative assessment of study quality.A study can be awarded a maximum of one star for each numbered item within the selection and exposure categories.A maximum of two stars can be given for comparability.High-quality studies will be de ned as a score 6 or more of 9 total points (20).

Statistical analysis
We will present the data with descriptive statistics and provide pooled estimates of outcome parameters, wherever it is feasible to perform meta-analysis using a random effects model.Pooled estimates will be presented with a 95% con dence interval.

Dealing with missing data
We will the corresponding authors of studies where data is/are missing and try to obtain the missing data.If this fails, we will try and impute data where possible.If that is not feasible, we will state as such.

3 .
Number of bacterial species identi ed per patient with CF versus non-CF bronchiectasis.4. Proportion of speci c bacterial species susceptible to speci c antimicrobial agents.5. Proportion of speci c bacterial species resistant to speci c antimicrobial agents. .Proportion of speci c bacterial species with intermediate susceptibility to speci c antimicrobial agents.7. Time-trend of antimicrobial sensitivity patterns in 10-year epochs.Search methods for identi cation of studies Two authors will independently search the electronic database PubMed and EMBASE using search MeSH terms for the below mentioned keywords: 1. Bronchiectasis AND Cystic brosis AND non-cystic brosis AND (antibiotic OR antimicrobial) AND (susceptibility OR sensitivity OR resistance) 2. Cystic brosis AND bronchiectasis AND (antibiotic OR antimicrobial) AND (susceptibility OR sensitivity OR resistance) 3. Non-cystic brosis AND bronchiectasis AND (antibiotic OR antimicrobial) AND (susceptibility OR sensitivity OR resistance) 4. Pulmonary exacerbation AND (antibiotic OR antimicrobial) AND (susceptibility OR sensitivity OR resistance) 5. Bronchiectasis AND Cystic brosis AND non-cystic brosis AND (microbiota OR pathogens OR colonizers OR bacteria OR microbiology) .Cystic brosis AND bronchiectasis AND (microbiota OR pathogens OR colonizers OR bacteria OR microbiology) 7. Non-cystic brosis AND bronchiectasis AND (microbiota OR pathogens OR colonizers OR bacteria OR microbiology)

Table 1
Respiratory pathogen colonization in people with cystic brosis versus non cystic brosis bronchiectasis le in people with cystic brosis versus non cystic brosis bronchiectasis