Introduction

Cystic fibrosis (CF) is a multisystem autosomal recessive genetic disease affecting more than 160 000 people worldwide [1–4]. It is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, which result in the abnormal production, function or transport of the CFTR protein [5]. As the CFTR protein is responsible for the regulation of the flow of chloride, natrium and bicarbonate ions across epithelial cell membranes, its dysfunction results in the production of a thick mucus [6–11]. CF-causing mutations are divided into different classes based on their impact on protein production, function and stability. The most common mutation is F508del, a class II mutation, leading to a misfolded protein that undergoes degradation before reaching the cell membrane. This mutation is associated with a severe course of the disease. The most common gating mutation (class III mutation) is G551D.

Mutations in the CFTR gene impact many organs, including the pancreas, gall bladder, intestine, reproductive system and bile ducts, but the respiratory system is the most affected [12]. The viscous mucus produced causes decreases mucociliary clearance, creating an environment conducive to chronic or recurrent bacterial infections, which leads to chronic inflammation and subsequent structural damage of the airways [5]. Respiratory system infections in people with CF (pwCF) are caused by various bacteria, with the most prevalent being Pseudomonas aeruginosa, Haemophilus influenzae and Staphylococcus aureus [13–15]. Other notable pathogens include Achromobacter species, Stenotrophomonas maltophilia and species of the Burkholderia cepacia complex (Bcc) [16]. Respiratory tract infections contribute to a gradual deterioration in lung function and, ultimately, respiratory failure, which stands as the primary cause of death in individuals with CF [2, 17].

Traditionally, the treatment of pwCF has focused on managing symptoms and complications by applying mucolytics, respiratory physiotherapy, antibiotics and pancreatic enzymes [12]. The invention of CFTR modulators that address the cause of the disease marked a significant milestone in treating pwCF. There are two categories of modulators, namely potentiators (ivacaftor (IVA)), which improve the function of the CFTR protein at the cell surface, and correctors (elexacaftor, tezacaftor and lumacaftor), which stabilise the conformation, trafficking and embedding of the CFTR protein to the cell surface [18].

The first modulator therapy was IVA, which is used in patients with a gating mutation and has been considered the benchmark for modulator therapy since its introduction. In recent years, triple therapy with elexacaftor–tezacaftor–IVA (ETI) has been approved for patients with at least one F508del allele. Reports are emerging on ETI use in certain non-F508del mutations with a similar clinical response [19, 20]. ETI shows a significantly higher efficacy than dual therapies, which currently and in the future will probably play a very subordinate role. Therefore, in this review we focus on effects of IVA and ETI.

Randomised controlled trials investigating ETI showed substantial improvements in sweat chloride concentrations, lung function, respiratory symptoms, weight gain and a reduction in the risk of acute pulmonary exacerbations (PEx) [18, 21–25].

Evidence exists that the reduced frequency of PEx under IVA/ETI is also related to a reduction in bacterial infections and a change in the lung microbiome towards greater microbiome diversity [26]. This review summarises the evidence on changes in lung infections and the microbiome, focusing on bacterial infections in pwCF following CFTR modulator treatment to provide evidence for the use of antibiotics in the era of ETI. Treatment with IVA in patients with gating mutations and ETI in patients with at least one F508del mutation is currently the most effective CFTR modulator therapy (CFTRmt), which is why we focus on data on these two CFTR modulator treatments in this review.

Infection of CF airways prior to CFTRmt

In this section we provide an overview of CF lung infections before CFTRmt. A complete review of host–pathogen interactions is beyond the scope of this article and has been done elsewhere [23, 27].

Bacterial infection of CF airways prior to CFTRmt

The bacterial microflora of the respiratory system comprise a type of ecosystem (microbiome) extending between the nasal and oral cavities and the alveoli. The composition of the microbiome varies according to location. Contrary to previous belief, bacteria are present in the bronchioles and alveoli of healthy people, mainly of the genera Prevotella, Veillonella and Streptococcus. The upper respiratory tract is dominated by species from the genera Streptococcus, Haemophilus, Moraxella, Corynebacterium and Staphylococcus [28]. In pwCF, chronic infection with pathogenic bacterial strains plays a key role in the onset and development of chronic lung disease [23].

In the first years of life, the pathogen most often isolated from the respiratory tract is Staphylococcus aureus. It is believed that this infection affects more than 60% of children with CF. The increasing occurrence of MRSA (methicillin-resistant S. aureus) strains is of concern. It was shown that chronic MRSA infection is associated with deterioration of lung function, body weight and growth parameters in children, in addition to an increase in the frequency of antibiotic therapy and hospitalisation [29, 30].

The incidence of infections caused by Gram-negative, nonfermenting bacilli increases with the age of the patients (figure 1). These infections significantly worsen the course of the disease and the increasing antibiotic resistance of these pathogens limits treatment options [23]. Pseudomonas aeruginosa infection is by far the most common. Chronic P. aeruginosa infection significantly increases the frequency of PEx, accelerates disease progression and increases mortality [31]. The airway microenvironment of pwCF predisposes their respiratory tract to the development of chronic P. aeruginosa infection [32]. In the initial phase of P. aeruginosa infection, bacterial cells exist in a planktonic form and their adhesion to the substrate is reversible. In this phase of infection, the phenomenon of resistance to antibiotics is rare and eradication of the pathogen from the respiratory tract can be achieved with aggressive antibacterial treatment [33].

FIGURE 1

Frequency of respiratory tract infections in cystic fibrosis patients by age. Reproduced from [152]. MRSA: methicillin-resistant Staphylococcus aureus.

If a P. aeruginosa eradication treatment fails, the infection may become chronic. P. aeruginosa develops multiple adaption strategies, such as biofilm formation, which creates organised bacterial colonies with cells exhibiting variable gene expression and metabolic profiles (aerobic and anaerobic) and an ability to communicate with one another. Although these changes are associated with chronic infection, it has been shown in children that they are already present in a significant proportion of newly acquired PA infections [34]. A predominance of the mucoid phenotype (capable of producing a biofilm) is associated with a more severe course of lung disease and higher mortality [35, 36].

In addition to P. aeruginosa, other Gram-negative bacteria associated with an unfavourable effect on the course of the CF lung disease include Bcc, Achromobacter spp. and Stenotrophomonas maltophilia. The Bcc consists of over 20 species, of which the most frequently isolated are Burkholderia cenocepacia and Burkholderia multivorans [37]. Although in some pwCF the course of infection may be asymptomatic, these infections are most often associated with a decline in lung function [38]. The Bcc is characterised by significant natural resistance to antibiotics, which causes great therapeutic difficulties and a high potential for causing cross-infections [37, 39]. Achromobacter spp. (mainly Achromobacter xylosoxidans) are detected in 10–20% of patients and usually occur in the second decade of life and older [40]. Reports on their clinical significance are controversial and derive from single centres. However, there is a growing body of evidence describing a decline in lung function, as well as more frequent exacerbations and hospitalisations in pwCF from whom these pathogens were isolated [41, 42]. There have also been isolated reports of cross-infections [40]. Achromobacter strains are characterised by high antibiotic resistance. Stenotrophomonas maltophilia infection is an independent risk factor for severe PEx and is associated with increased risk of death or lung transplantation [43, 44]. It is a species characterised by natural resistance to most groups of antibiotics commonly used in CF patients, which significantly limits treatment options [44].

Over the past three decades, there has been a worldwide increase in the prevalence of nontuberculous mycobacteria (NTM) pulmonary infections. These pathogens are widely found in the natural environment and exhibit high levels of antimicrobial drug resistance. The most frequently cultured species in pwCF are Mycobacterium abscessus (MABS) and Mycobacterium avium complex (MAC) [45, 46]. NTM infection occurs in about 10% of pwCF, but only a subset of these individuals will develop NTM disease [47]. NTM therapy requires a combination of multiple drugs with a treatment duration of months or even years [48]. MABS lung disease is associated with a more severe course compared to MAC disease.

CF lung microbiome prior to CFTRmt

Many studies focus on the airway microbial community structure (microbiome) in CF patients due to the importance of infections in CF pathology [49–53]. Such studies have been facilitated by the development of culture-independent methods of identifying pathogens, including next-generation sequencing (NGS) [54]. Studies have shown that the diversity of bacterial species is higher in healthy individuals than in those suffering from CF [52, 55]. In patients with CF, a reduction of bacterial diversity in the airways correlated with older age, increased levels of inflammatory parameters, higher antibiotic use, deterioration in lung function and disease progression. It was also associated with the dominance of one of the typical CF pathogens, such as S. aureus, P. aeruginosa and Burkholderia spp. [49, 50, 56–60]. Moreover, while healthy subjects exhibited a continuum in the upper (nasal, nasopharyngeal and oral) and lower (bronchial and lung) airway microbiome [61], sample analysis of the CF respiratory tract showed important differences between the upper and lower airways. These differences were more pronounced in patients with more advanced lung disease [50, 62, 63]. More than 1000 bacterial species have been identified in the airways of pwCF using NGS [62, 64]. Bacteroidetes, Proteobacteria, Actinobacteria, Fusobacteria and Firmicutes constitute the vast majority of this airway community, primarily represented by the genera Streptococcus, Prevotella, Rothia, Veillonella, Actinomyces, Gemella, Porphyromonas, Fusobacterium, Neisseria and Atopobium [58, 65–67]. During PEx, changes in the microbiome profile were observed. Apart from P. aeruginosa and other typical pathogens [68], anaerobes may play a role in developing PEx [51]. Antibiotics used during PEx modulate the microbiome by decreasing diversity and reducing the population of commensal bacteria [49, 57, 69]. On the other hand, lower microbiome richness at baseline may be predictive of a PEx [70].

Changes of CF airway infection in pwCF receiving CFTRmt

Increasing research attention has been focused on the effects of CFTR modulators on respiratory tract infections and exacerbations over prolonged periods (see figure 2).

FIGURE 2

Effects of cystic fibrosis transmembrane conductance regulator modulator therapy (CFTRmt) on the lung and open questions regarding the effects of therapy. PEx: pulmonary exacerbation; pwCF: people with cystic fibrosis. Created with BioRender.com.

Changes in airways bacterial infection in pwCF receiving modulator therapy

IVA became the first CFTR modulator approved for clinical use in 2012 for patients with gating variants. IVA therapy leads to a swift and substantial reduction in P. aeruginosa burden within 48 h [71]. Durfey et al. [72] found that there was a tenfold reduction in the amount of P. aeruginosa and S. aureus bacteria [71, 72]. This immediate effect of IVA therapy on sputum pathogens may possibly involve direct antimicrobial activity [73–76]. IVA contains a quinolone ring in its chemical structure, which has been demonstrated to have the ability to inhibit the growth of S. aureus and P. aeruginosa by weakly affecting bacterial DNA gyrase and topoisomerase IV [73, 77]. Cigana et al. [78] demonstrated that IVA and ETI possess direct antibacterial properties against S. aureus, but not against P. aeruginosa. They also observed additional or synergistic effects when combining CFTR modulators with antibiotics against both bacterial species [78]. Several studies have shown that the reduction of P. aeruginosa in sputum is sustained during the first year of IVA treatment [14, 79–83]. Nevertheless, eradication of P. aeruginosa infection occurred only in a minority of patients, even when IVA treatment was combined with an intense antibiotic therapy [71, 84]. Worryingly, there is evidence that following the initial decrease, P. aeruginosa density in sputum increases again to initial levels [71]. Patients displaying intermittent positive cultures and higher forced expiratory volume in 1 s (FEV1) are more prone to transitioning to a culture-negative status [14, 71].

Other CF pathogens, such as S. aureus, Bcc or Stenotrophomonas maltophilia, also show a decline under IVA, although the difference is much less pronounced than for Pseudomonas [14, 80, 85]. However, the likelihood of acquiring new infections with both S. aureus and P. aeruginosa is reduced [86].

The approval of ETI in 2019/2020 marked a significant milestone in the management of CF. Several studies observed a notable decrease in the presence of P. aeruginosa after starting ETI treatment [25, 87–91]. A shift from positive to negative culture of P. aeruginosa within 1 year of therapy occurs in 36–45% of patients [90, 92]. Age, prior colonisation status and extent of lung disease play pivotal roles in shaping the microbiological changes of S. aureus and P. aeruginosa following the introduction of ETI [93]. PwCF who are chronically infected experience notable decreases in the detection of S. aureus or P. aeruginosa. However, they are less prone to clear these pathogens compared to pwCF with intermittent infections [89, 93]. In addition, the detection rate of P. aeruginosa in patients with severely impaired lung function (percent predicted FEV1<40) did not fall to the level of patients with better preserved lung function after the start of ETI treatment [93].

The effect of ETI on the detection rates of methicillin-sensitive S. aureus and MRSA are incongruent [87, 93, 94]. As in the period before ETI, in which S. aureus was mainly found in children with well-preserved lung function (see figure 1), it has also been shown under ETI therapy that S. aureus remains the predominant pathogen in people with good lung function [93]. The studies mentioned above involved participants aged 6 years and older, many of whom had already developed infections by the time modulator therapy commenced. Respiratory infections contribute significantly to the inevitable decline in lung function and therefore are the main factor influencing length and quality of life in CF. Based on the observed effects of CFTR modulators. it can be assumed that initiating modulator therapy before the establishment of chronic infections may prevent the emergence of typical CF pathogens such as P. aeruginosa. Therefore, infants with CF are likely to derive the greatest benefit from CFTRmt.

Evidence of the effect of CFTRmt on NTM infections is also emerging. Registry data from the US Cystic Fibrosis Foundation Patient Registry from 2011 to 2018 found an association between IVA therapy and a decreased risk of NTM positivity [95]. In concordance with this previous data, a reduction in NTM infection after initiating ETI treatment was found in a multicentre study from Israel. Eradication of NTM was associated with improved lung function tests [96]. In a case report on a patient who was not responding to anti-mycobacterial therapy, M. abscessus was eradicated after initiation of ETI [97]. The evidence for the effect of CFTRmt on NTM infections remains limited and the impact of reduced sputum availability on detection is not yet known. Table 1 summarises the studies on changes under CFTRmt in pwCF.

TABLE 1

Summary of studies on effect of ivacaftor (IVA) cystic fibrosis transmembrane conductance regulator (CFTR)-modulator monotherapy or triple therapy with elexacaftor, tezacaftor and ivacaftor (ETI) on lung infection in people with cystic fibrosis (pwCF)

Study, yearCFTR modulatorNumber of participantsCFTR mutationsppFEV1SampleEffect on lung infectionRowe et al. [79], 2014IVA151At least one G551DMean: 82.4SputumReduction of PA concentration in sputumHeltshe et al. [149], 2015IVA151At least one G551DMean
PA persistent: 72.6
PA intermittent: 93.6
PA free: 88.4Sputum (spontaneously or induced) or oropharyngeal swabReduction of PA prevalence
No change in SA prevalenceHisert et al. [71], 2017IVA12At least one G551DMean: 64.2Sputum (spontaneously expectorated)Reduction of PA concentration in sputumBessonova et al. [80], 2018IVA1667 (1256 US +411 UK)At least one G551DFrom <40 to ≥70SputumReduction of PA prevalence
No change in SA prevalenceSingh et al. [86], 2019IVA147 pre-CFTRmt
46 with CFTRmtF/F, heterozygous F otherPre-modulator: ≥79.8
Post-modulator: ≥82.7Sputum, oropharyngeal swab, bronchoalveolar lavageLower likelihood of developing new infections caused by SA and PAFrost et al. [85], 2019IVA276At least one G551D81.1Sputum, oropharyngeal swabReduction of PA prevalenceVolkova et al. [81], 2020IVA635 (US)
247 (UK)At least one G551DFrom <40 to ≥70SputumReduction of PA prevalenceGuimbellot et al. [83], 2021IVA82At least one G551D82.0Sputum (spontaneous or induced)Reduction of PA prevalenceKawala et al. [82], 2021IVA114At least one G551D68.4SputumReduction of PA prevalenceDurfey et al. [72], 2021IVA13F/R117H
R117H/M156R
R117H/2622+1G>A
R117H/3849+4A>G65Sputum (spontaneous or induced), oropharyngeal swabsReduction of PA and SA concentration in sputumPallenberg et al. [91], 2022ETI31F/F, F/MF
Heterozygous F85Induced sputum and deep cough swabsReduction of PA prevalenceMigliorisi et al. [92], 2022ETI13F/F, F/MF<40SputumReduction of PA prevalenceNichols et al. [89], 2023ETI236F/F, F/MF
F/G551D
Other heterozygous FMean: 80.4Sputum (spontaneous or induced)Reduction of PA prevalenceSchnell et al. [90], 2023ETI69F/F
Heterozygous FMean: 69.3Sputum or throat swabsReduction of PA prevalenceBeck et al. [87], 2023ETI124F/F
Heterozygous F
OtherNASputum and throat cultureReduction of PA prevalenceBower et al. [88], 2023ETI16116F/F, F/MF, F/RF, F/G, F/other, otherMean: 72.1Sputum (spontaneous or induced), throat/nasal, bronchoscopyReduction of PA prevalenceDittrich et al. [93], 2024ETI1092F/F
Heterozygous FMedian: 63Throat swabs, sputumReduction of PA and SA concentration in sputum
Reduction of PA prevalence in pwCF with intermittent infectionChanges of CF lung microbiome in pwCF receiving CFTRmt

For pwCF with 508del mutations, it has also been shown that the lung microbiome changes significantly under ETI therapy; specifically, diversity increases, the distribution of the individual bacteria becomes more even and the load of classic CF pathogens decreases. A shift was reported from a wide range of varied microbial compositions, including both monocultures and diverse communities of commensals, towards microbial communities predominantly comprising Rothia, Streptococcus, Veillonella and Prevotella species, typical flora of healthy airways [98, 99]. The reduction of CF pathogens could also be due to improved mucociliary clearance through improved airway fluid dynamics under ETI therapy [100]. In addition, restoration of CFTR function in immune cells such as phagocytes leading to improved phagocytosis and changes in T-helper cell differentiation may support pathogen reduction [101, 102].

However, these changes in microbiome diversity and improvements in lung inflammation and sputum viscosity did not reach the levels observed in healthy controls [103].

To summarise, most studies show an improvement in microbiome composition after the initiation of CFTRmt. Favourable changes result in an increase of the diversity and richness of bacterial species and a decrease in the relative abundance of P. aeruginosa. Variations in the airway microbiome are possibly caused by decreased sputum viscosity, improved mucociliary clearance or the antimicrobial and anti-inflammatory effects of CFTR modulators [77].

Changes in the clinical impact of infection of CF pathogens in pwCF receiving CFTRmtChanges of PEx in pwCF receiving CFTRmt

Multiple studies involving large patient cohorts have demonstrated that IVA therapy leads to fewer PEx and associated hospitalisations [80, 81, 104–106]. Moreover, the use of antibiotics and their duration have been reduced [104, 105, 107]. Simmonds et al. [105] observed a 79% decrease in the likelihood of PEx and a 77% decrease in the use of antibiotics for PEx. In contrast, Kawala et al. [82] demonstrated an insignificant reduction in PEx. The reason for this could be the inclusion of individuals with gating mutations other than G551D variants in the study group. There is evidence suggesting that patients with non-G551D mutations show a smaller improvement in FEV1 values compared to those with the G551D mutation [108], as well as a smaller reduction in the number of respiratory exacerbations.

In addition to pivotal studies, real-world data from studies and patient registries have also demonstrated a significant impact of ETI on reducing PEx by a maximum of 76% [88, 109–112]. Miller et al. [113] and O'Shea et al. [114] observed a significant decrease in the frequency of outpatient visits due to infection, antibiotic prescriptions and hospitalisations in individuals treated with ETI even within the first week of treatment. Martin et al. [115] discovered not only a reduced need for intravenous antibiotic therapy and hospitalisations (by 86%), but also a decreased need for oxygen therapy (by 59%) and noninvasive ventilation (by 62%). In addition, a sharp decline in the number of lung transplantations has been noted since the arrival of ETI [116]. On the other hand, a secondary analysis of data from the STOP2 trial showed that, in PEx, changes in FEV1, symptoms and C-reactive protein during antibiotic therapy do not differ in pwCF treated with modulators compared to modulator-naïve patients [117].

In the pre-ETI era, the identification of P. aeruginosa prompted eradication treatment, as it detrimentally affects pulmonary function and correlates with pulmonary deterioration. As part of the European Cystic Fibrosis Society-Clinical Trials Network, principal investigators were asked about their decision-making process when prescribing inhaled antimicrobials for P. aeruginosa infections [118]. It was shown that the decision-making process for prescribing inhaled antimicrobials is multifactorial and that CFTRmt has little influence on it. Similarly, once the diagnosis of a PEx is made, physicians stated that its management remains unchanged despite use of CFTR modulators [119].

However, Pust et al. [120] have demonstrated that P. aeruginosa can be detected in the lungs of healthy individuals without necessitating treatment. Prospective data is essential to determine whether children and young adults with CF, benefiting from preserved lung function due to early initiation of CFTRmt and improved mucociliary clearance, will still require aggressive eradication treatment for P. aeruginosa or if P. aeruginosa may manifest as a transient pathogen in this population.

As mentioned above, a marked decline of PEx under CFTR modulators was noted. However, even before the introduction of CFTR modulators, PEx were not uniformly defined. Commonly used definitions included symptoms such as difficulties in breathing, fever, increased or changed sputum, haemoptysis, decline of oxygen saturation measured by pulse oximetry and decrease in FEV1 [121]. Under CFTRmt, the PEx symptom profile might change or be less obvious and the diagnosis as well as the decision to start antibiotic treatment might be less clear [3]. To determine the factors that contribute to a PEx, early studies on new biomarkers aimed at recognising airway inflammation as surrogate markers for lung disease in pwCF might provide more insights (TERRIFIC-MILE, NCT05752019). Additionally, the use of remote monitoring and the definition of new digital end-points will help our understanding of the “new feature” of PEx [122] (Project Breathe NCT06222905).

According to current international guidelines, treatment of PEx usually consists of initiation of inhaled or systemic antibiotics irrespective of the use of CFTRmt [3, 123, 124]. The STOP2 trial provided substantial evidence that treatment of a PEx can be shortened in patients responding within the first days of antibiotic treatment. If intensive dual antibiotic therapy with a β-lactam antibiotic plus an aminoglycoside is needed or if a single antibiotic therapy with a β-lactam antibiotic might be sufficient is currently under investigation in the large international STOP360° study aiming to include more than 700 pwCF (NCT05548283).

Changes in airway sampling in pwCF receiving CFTRmt

In the pre-ETI era, pwCF exhibited increased mucus production, facilitating the detection of lower respiratory tract pathogens. Under ETI, a significant reduction in sputum production occurs and alternative sampling methods need to be considered in order to ensure microbial surveillance of the lower respiratory tract [125].

In paediatric CF care, deep-throat or cough swabs are commonly taken despite only inadequately representing the lung microbiome and lower respiratory tract pathogens [126, 127]. In patients who do not spontaneously expectorate sputum, the induction of sputum by inhalation of hypertonic saline offers a possible alternative method for obtaining samples from the lower respiratory tract. The CF-Sputum Induction Trial (CF-SpIT) [128] demonstrated that induced sputum (IS) surpasses cough swabs in pathogen yield and provides valuable insights into the lung microbiome. Additionally, Weiser et al. [129] demonstrated the comparability of IS with bronchoalveolar lavage samples in children. Nevertheless, IS and bronchoscopy are time- and resource-consuming procedures, possibly hindering their implementation in routine care. The follow-up study of the CF-SpIT trial, the CF-Home Sputum Induction Trial (CF-HomeSpIT) compares early morning saliva and IS collected at home versus same-day samples from clinical IS, saliva and cough swab samples [130]. Preliminary results suggest a comparable pathogen yield in home sampling compared to supervised clinic sampling.

Remote sputum sampling, e.g. in the morning or after physiotherapy, may yield a higher number of sputum samples. It is reassuring that posted sputum samples seem to reliably reproduce the culture-based and molecular microbiology of freshly collected samples [131].

Future studies on remote sputum sampling or alternative specimen collection will not only provide further information on long-term changes, but also on the extent of the influence of the sampling method on the significantly reduced detection of CF pathogens under ETI.

Implication of culture-negative but molecular-positive status in pwCF receiving CFTRmt

For routine clinical practice and the assessment of the patient's disease prognosis, it is not only considered imperative to diagnose a new infection with P. aeruginosa at early stages but also to ascertain whether “intermittent” or “chronic” P. aeruginosa is completely eradicated from the patient's airways.

Detailed investigations, encompassing not only culture-based but also DNA-based detection methods, demonstrate a decrease in bacterial density following the initiation of ETI [89]. However, PCR-based detection methods still reveal the presence of bacterial DNA, primarily due to the heightened sensitivity of PCR approaches, as well as potential identification of nonviable bacteria [132] and contamination with saliva in sputum- and swab-based studies [89]. Furthermore, Blanchard et al. [133] previously demonstrated, albeit in a relatively small and underpowered study, that PCR-based diagnosis of new P. aeruginosa colonisation did not supersede P. aeruginosa detection by culture. Notably, there were no discernible trends in PCR results concerning the prognosis for the success or failure of P. aeruginosa eradication therapy. On the other hand, molecular detection of P. aeruginosa in throat swabs was linked to a positive sputum culture and detected the infection earlier than culture [134, 135].

From the available data, a definitive answer remains elusive regarding whether a patient exhibiting no P. aeruginosa detection via culture and only minimal traces of bacterial DNA in PCR-based analysis has effectively cleared this pathogen.

Durability of impact of CFTRmt on airway infection

In longitudinal studies spanning over a year, individuals receiving monotherapy with IVA experienced a rebound in bacterial loads [71, 72, 85, 136, 137]. The mechanism underlying this is currently unclear. Accordingly, after the initial improvement, lung function returned to the initial level after 5 years of IVA therapy despite relatively good treatment compliance to IVA over the entire period [138].

From the data available so far, the effect of ETI appears to be more robust. The initial results from the open-label extension study for ETI in CF patients aged 12 and above with F508del/minimal function and F508del homozygous genotypes are promising, showing a sustained increase in FEV1 [121] and body mass index, and a reduction in exacerbations over a period of 144 weeks [139]. Consistent with clinical trials, real-world registry data from Germany and the US demonstrate a positive and stable treatment response over 12 and 24 months, respectively [88, 111].

However, it is crucial to note that the initiation of ETI treatment coincided with the onset of the coronavirus disease 2019 pandemic, which may have influenced outcome measures, including exacerbations, in these studies.

Role of other airway pathogens in pwCF receiving CFTRmt

In the pre-CFTR modulator era, high detection rates of viral infections, exceeding 70%, have been reported in adults and children with CF [140–142]. Given that a decline in FEV1, respiratory symptoms and PEx frequently correlate with viral infections, it is imperative to systematically gather additional data on the impact of these infections on pwCF, especially those undergoing ETI treatment. In a sub-study of the abovementioned STOP2 trial, the prevalence and clinical impact of respiratory viral infections during PEx were investigated using 1254 sputum samples from 621 participants. In this study, virus-positive participants were more likely to be receiving CFTRmt than virus-negative patients (45% versus 34%). Virus-positive participants were more symptomatic at initial presentation but had more favourable long-term outcomes [143]. A recent review on viral infections in pwCF has been published by Brackenborough et al. [144] and is beyond the scope of this study

One of the most common moulds found in the airways of CF patients is Aspergillus fumigatus, with a prevalence of up to around 40% of lower airway samples [145, 146]. Evidence exists that chronic Aspergillus infection is associated with an increased decline of lung function [145, 147]. Aspergillus sp. can also cause a hypersensitivity reaction called allergic bronchopulmonary aspergillosis (ABPA). In a meta-analysis, a prevalence of ABPA of 8.9% was found [148]. In patients with G551D variants receiving IVA, a reduction of Aspergillus cultures were seen [85, 149]. Preliminary data on the effect of ETI treatment on Aspergillus-related diseases gave encouraging results, demonstrating a decline in Aspergillus culture and total IgE antibodies, but not specific anti-Aspergillus IgE [150]. However, data is scarce and the impact of CFTRmt on fungal infections and their effects on lung function remain to be elucidated.

Conclusions on the use of antibiotics in the era of CFTRmt

As demonstrated in the previous sections of this review, CFTRmt reduces the burden of classic CF pathogens and shifts the microbiome toward a healthier profile, although it does not achieve a full health. This goes along with improved mucociliary clearance, reduced mucus plugs and improvements in the immune mechanisms of the host. All of this could contribute to inhaled antibiotics, mainly used to treat chronic P. aeruginosa infection, being able to reach the smallest airways better and to achieve higher levels at the site of action than previously. The reduced bacterial load could also have a positive impact on the effectiveness of inhaled antibiotics through the inoculum effect [3, 151].

In the majority of patients, however, neither complete eradication of the pathogens nor a lung microbiome similar to that of healthy individuals is achieved [103]. In addition, there is still limited data available on the effects of reduced sputum availability and alternative sampling methods on pathogen detection and long-term effects. In addition, the impact of CFTRmt on lung infections depends on factors such as the patient's age, the extent of the underlying lung disease and the infection status at the start of modulator therapy.

Systemic antibiotic the