**9. Nontuberculous mycobacteria**

*Cystic Fibrosis - Heterogeneity and Personalized Treatment*

activity against *P. aeruginosa* [67].

mechanism at play [68, 69].

induced by ivacaftor.

ongoing anti-infective chemotherapy in CF.

microbiota. There is evidence to support a similar effect in the GI tract, where CFTR modulation with ivacaftor was associated with improved proximal small intestinal pH, likely secondary to improved bicarbonate secretion [63]. Thirdly, a direct bactericidal effect of ivacaftor itself has been postulated given that its chemical structure contains a quinolone ring and many quinolone derivatives have antimicrobial properties [64]. This theory is supported by evidence that ivacaftor exerted in vitro antibacterial effects on clinical respiratory isolates of *S. aureus* (MSSA and MRSA) and *Streptococcus pneumoniae* [65, 66]. However, these studies found very little activity against Gram-negative organisms, which is uncharacteristic of a quinolone-based antibiotic [65]. Interestingly, the authors of the same study noted synergism of ivacaftor with antibiotics commonly used in CF, and this was recently supported by Payne et al., who again found that ivacaftor had activity against *Streptococcus* spp*.* and *S. aureus* and that the effect was potentiated in the presence of tobramycin. Again there was no evidence of direct antibacterial

Interest has since focussed on clinical microbiological outcomes of patients commenced on ivacaftor therapy in an effort to investigate differences post-treatment initiation. Interestingly, despite ivacaftor appearing to have no innate activity against *P. aeruginosa,* a number of studies have reported reductions in counts and density post initiation, perhaps suggesting that quinolone activity is not the only

In contrast to the relative lack of focus on inhaled antibiotics, a number of studies have investigated the effects of ivacaftor on the respiratory microbiome. Peleg et al. [70] conducted the only placebo-controlled trial in this field when they performed a double-blind, placebo-controlled, cross-over study of 28-day ivacaftor treatment. Sputum was collected at the start and end of each 28-day treatment period, and 16S rRNA sequencing with qPCR correlation was subsequently performed. No significant differences were observed for either total bacterial load or *P. aeruginosa* load following ivacaftor therapy, and no significant difference in the microbiota composition (based on 16S rRNA microbiome analysis) was observed between the placebo and treatment samples. However, the authors noted that when they adjusted for consistent or changing antibiotic exposure in the 28-day study period, ivacaftor was associated with a significant reduction in *P. aeruginosa* load. That is to say, changes in the microbiota induced by acute changes in antibiotic administration during the 28-day treatment periods may have masked the effect

In longer-term observational studies, a number of changes have been observed.

Bernarde et al. [71] noted no significant changes in bacteria load and also no significant changes in overall community composition at 1 year following ivacaftor initiation. However, individual taxa were observed to change in that the relative abundance of *Streptococcus mitis* group was significantly diminished and a *Porphyromonas* OTU was significantly increased. Elsewhere, in perhaps the most comprehensive study of microbiological outcomes following ivacaftor initiation, Hisert et al. [72] found marked reductions in *P. aeruginosa* sputum densities using conventional culture and also reduced sputum inflammatory markers in regular follow-up throughout the first 2 years of ivacaftor use. These findings were mirrored in the 16S rRNA-based analysis, where decreases in mean *P. aeruginosa* relative abundance and subsequent increases in diversity measures were observed. However, no patient eradicated *P. aeruginosa*, and after 12 months of treatment, relative abundance, sputum counts and inflammatory markers began to increase again. The authors interpreted these findings to suggest that *P. aeruginosa* may adapt to a CFTR-restored environment and this clearly has implications for the need for

**10**

Nontuberculous mycobacteria (NTM) are identified in approximately 10% of CF patients, but only a small proportion will go on to develop NTM pulmonary disease (NTM-PD) warranting treatment. First and foremost, the management of CF pulmonary disease should be optimised, including antibiotic therapy targeted to the individual's usual airway bacteria, prior to considering treatment for NTM-PD. Those who fulfil criteria for NTM lung disease may not necessarily require treatment and could be monitored expectantly if symptoms and radiographic findings are minimal or stable over a period of surveillance. However, the presence of *Mycobacterium abscessus* complex (MABSC), deteriorating lung function, worsening radiology and/or anticipated lung transplant should prompt NTM therapy initiation (**Table 2**). For CF patients with *Mycobacterium avium* complex (MAC), recommended treatment includes triple antibiotic therapy with a macrolide, rifampin and ethambutol. Azithromycin is generally the preferred macrolide of choice in CF as it is better tolerated and has fewer drug–drug interactions. An initial course of injectable amikacin or streptomycin should be considered in the presence of (i) acid-fast bacillus smear-positive respiratory tract samples, (ii) radiological evidence of lung cavitation or severe infection and (iii) systemic signs of illness. MABSC treatment is more complicated and requires an induction phase (oral macrolide and two IV agents including amikacin with one or more additional intravenous antibiotics including tigecycline, imipenem, cefoxitin) for 3 to 12 weeks as well as a maintenance phase (nebulised amikacin and a macrolide with two to three oral antibiotics including minocycline, clofazimine, moxifloxacin, linezolid). Baseline and interval testing for drug toxicity is essential. The treatment duration for both MAC and MABSC is extended 1-year post-culture conversion. However, in patients who do not achieve culture negative status but tolerate therapy, ongoing treatment for mycobacterial suppression and prevention of disease progression can be considered. There are no randomised controlled trials of MABSC therapy in the general population or in CF; however, there is MABSC treatment outcome data in non-CF populations from several clinical studies [74]. In a study of 57 non-CF

Clinical (both required)

1.Pulmonary symptoms with nodular or cavitary opacities on chest radiograph or a high-resolution CT scan that shows multifocal bronchiectasis with multiple small nodules

2.Appropriate exclusion of other diagnoses.

Microbiologic (one of the following required)


**Table 2.**

*ATS/IDSA clinical and microbiologic criteria for diagnosing nontuberculous mycobacterial pulmonary disease (NTM-PD) [73].*

**Figure 2.**

*Typical treatment schedules for individuals with CF with* Mycobacterium abscessus *or MAC pulmonary disease [74].*

subjects that compared *M. abscessus* ssp. *massiliense* and ssp. *abscessus* infections and treatment outcomes, all individuals were treated with clarithromycin-containing regimen in combination with an initial 4-week course of cefoxitin and amikacin, was given to 57 patients (24 with *M. abscessus* and 33 with *M. massiliense*) for more than 12 months. The proportion of patients with sputum conversion and maintenance of negative sputum cultures was higher in patients with *M. massiliense* infection (88%) than in those with *M. abscessus* infection (25%; *p* < 0.001). Inducible resistance to clarithromycin (minimal inhibitory concentrations ≥ 32 μg/ml) was found in all tested *M. abscessus* isolates (n = 19), but in none of the *M. massiliense* isolates (n = 28) [75].

Inhaled liposomal amikacin for maintenance treatment has also drawn interest. In a randomised placebo-controlled trial, CF subjects with NTM lung disease refractory to standard therapy were assigned to 590 mg OD inhaled liposomal amikacin or placebo, in addition to their standard CF treatments and ongoing NTM therapy [76]. The group of 90 patients was stratified based on MAC (64%) and MABSC (36%) [77]. At the end of the 6-month treatment period, there was a statistically significant increase in culture negativity overall and for the MAC group.

Reported NTM prevalence in CF ranges from 3 [78] to 23% [79]. The majority (95%) of NTM isolated from CF patients are *Mycobacterium avium* complex (MAC) (*M. avium-intracellulare* and four *M. avium* subspecies) and *M. abscessus* complex (MABSC) (subspecies abscessus, massiliense, and bolletii) [80, 81]. Bryant et al. [82] reported the largest outbreak occurred in Cambridge, England, where 11 of 31 patients with MABSC had a shared strain of *M. abscessus* subsp. *massiliense* with similar antibiotic resistance patterns by whole genome sequencing despite a lack of exposure to the same antibiotics, raising the possibility of cross infection amongst the CF cohort albeit conventional cross infection measures (**Figure 2**).

MABSC has been demonstrated to accelerate lung function decline in CF patients compared to uninfected CF controls [83, 84]. In CF, a common measure

**13**

*The Pulmonary Microbiome in Cystic Fibrosis DOI: http://dx.doi.org/10.5772/intechopen.91765*

absence of contraindications [85].

**10. Fungal lung disease in CF**

lung transplantation.

post-lung transplantation.

beyond the scope of discussion in this chapter.

ATS guidelines, with exclusion of other aetiologies [73].

of lung disease severity is percent-predicted forced expiratory volume in 1 second (FEV1), with lower values indicating more severe lung disease. Qvist et al. showed that MABSC had a greater rate of FEV1% predicted decline than other organisms, including *Pseudomonas aeruginosa* and *Burkholderia cepacia* [84]. However, no lung function decline was noted in patients growing MAC [83]. Likewise, a large study found no significant effect of NTM infection on lung function decline, although analyses were not based on different NTM subtypes [80]. A diagnosis of NTM pulmonary disease must meet both clinical and microbiologic criteria as outlined by

Individuals who are NTM culture positive but who do not meet ATS criteria for disease should be monitored closely [74]. Patients with CF meeting criteria for NTM-PD should be considered for therapy; however, treatment decisions should be individualised [74, 85]. It may be reasonable to monitor individuals with mild CF lung disease, MAC lung disease with mild symptoms and radiographic changes or a high possibility of drug intolerance or drug interactions [85]. However, CF patients with MABSC and/or severe CF lung disease should generally be treated in the

Clinical manifestations of respiratory fungal diseases in adult CF patients are very heterogeneous, ranging from asymptomatic colonisation to chronic infections, allergic disorders or invasive diseases in immunosuppressed CF patients following

*Aspergillus* spp. are amongst the most widespread filamentous fungi in the environment, especially in areas with high humidity [86]. In CF patients, the most frequently isolated species is *Aspergillus fumigatus*, accounting for 67–73% of *Aspergillus*-positive sputum cultures [87]. Isolation of other species such as *A. flavus*, *A. niger* and *A. terreus* is less frequent but not rare (4, 4 and 2% of *Aspergillus*-positive sputum cultures, respectively) [87]. Notably, the prevalence of isolation of *Aspergillus* spp. from sputum cultures in CF patients increases with age, possibly reaching 46–78% in adult CF patients, although with important interregion and inter-centre variability [88–90]. However, knowledge of the prevalence of *Aspergillus* spp. isolation from sputum does not automatically allow to infer the prevalence of the various *Aspergillus*-related manifestations in CF patients, which range from asymptomatic colonisation to invasive diseases, especially in patients

Allergic bronchopulmonary aspergillosis (ABPA) refers to a complex hypersensitivity reaction which often occurs in patients affected by CF or asthma. ABPA is

In CF patients, the disease-related progressive damage of the lungs may favour the development of chronic *Aspergillus* infection, commonly defined as '*Aspergillus* bronchitis', although aspergilloma(s) might also develop in some cases, especially in pre-existing cavities or bronchiectasis [91–93]. *Aspergillus* bronchitis has an estimated prevalence of ~2–8% in CF patients and may be suspected in the case of pulmonary exacerbation unresponsive to antibacterial treatment [94, 95]. As per Baxter et al.'s [96] classification, diagnosis of *Aspergillus* bronchitis can be made in the presence of a positive sputum galactomannan, high levels of *Aspergillus*-specific IgG and negative total and *Aspergillus*-specific IgE. Since *Aspergillus* bronchitis does reflect infection and not an immune-mediated response as in ABPA, corticosteroids are not the cornerstone of treatment. Treatment with azole derivatives is the current standard of care, although the overall duration of treatment is still not clearly

#### *The Pulmonary Microbiome in Cystic Fibrosis DOI: http://dx.doi.org/10.5772/intechopen.91765*

*Cystic Fibrosis - Heterogeneity and Personalized Treatment*

subjects that compared *M. abscessus* ssp. *massiliense* and ssp. *abscessus* infections and treatment outcomes, all individuals were treated with clarithromycin-containing regimen in combination with an initial 4-week course of cefoxitin and amikacin, was given to 57 patients (24 with *M. abscessus* and 33 with *M. massiliense*) for more than 12 months. The proportion of patients with sputum conversion and maintenance of negative sputum cultures was higher in patients with *M. massiliense* infection (88%) than in those with *M. abscessus* infection (25%; *p* < 0.001). Inducible resistance to clarithromycin (minimal inhibitory concentrations ≥ 32 μg/ml) was found in all tested *M. abscessus* isolates (n = 19), but in none of the *M. massiliense* isolates (n = 28) [75]. Inhaled liposomal amikacin for maintenance treatment has also drawn interest. In a randomised placebo-controlled trial, CF subjects with NTM lung disease refractory to standard therapy were assigned to 590 mg OD inhaled liposomal amikacin or placebo, in addition to their standard CF treatments and ongoing NTM therapy [76]. The group of 90 patients was stratified based on MAC (64%) and MABSC (36%) [77]. At the end of the 6-month treatment period, there was a statistically significant increase in culture negativity overall and for the MAC group. Reported NTM prevalence in CF ranges from 3 [78] to 23% [79]. The majority (95%) of NTM isolated from CF patients are *Mycobacterium avium* complex (MAC) (*M. avium-intracellulare* and four *M. avium* subspecies) and *M. abscessus* complex (MABSC) (subspecies abscessus, massiliense, and bolletii) [80, 81]. Bryant et al. [82] reported the largest outbreak occurred in Cambridge, England, where 11 of 31 patients with MABSC had a shared strain of *M. abscessus* subsp. *massiliense* with similar antibiotic resistance patterns by whole genome sequencing despite a lack of exposure to the same antibiotics, raising the possibility of cross infection amongst

*Typical treatment schedules for individuals with CF with* Mycobacterium abscessus *or MAC pulmonary* 

the CF cohort albeit conventional cross infection measures (**Figure 2**).

MABSC has been demonstrated to accelerate lung function decline in CF patients compared to uninfected CF controls [83, 84]. In CF, a common measure

**12**

**Figure 2.**

*disease [74].*

of lung disease severity is percent-predicted forced expiratory volume in 1 second (FEV1), with lower values indicating more severe lung disease. Qvist et al. showed that MABSC had a greater rate of FEV1% predicted decline than other organisms, including *Pseudomonas aeruginosa* and *Burkholderia cepacia* [84]. However, no lung function decline was noted in patients growing MAC [83]. Likewise, a large study found no significant effect of NTM infection on lung function decline, although analyses were not based on different NTM subtypes [80]. A diagnosis of NTM pulmonary disease must meet both clinical and microbiologic criteria as outlined by ATS guidelines, with exclusion of other aetiologies [73].

Individuals who are NTM culture positive but who do not meet ATS criteria for disease should be monitored closely [74]. Patients with CF meeting criteria for NTM-PD should be considered for therapy; however, treatment decisions should be individualised [74, 85]. It may be reasonable to monitor individuals with mild CF lung disease, MAC lung disease with mild symptoms and radiographic changes or a high possibility of drug intolerance or drug interactions [85]. However, CF patients with MABSC and/or severe CF lung disease should generally be treated in the absence of contraindications [85].
