Rationale: Achromobacter species are increasingly identified in individuals with cystic fibrosis (CF), but the clinical outcomes in these patients remain poorly understood.
Objectives: We aimed to determine the association of Achromobacter infection on clinical outcomes in pediatric and adult patients with CF.
Methods: A cohort study of pediatric and adult patients with CF was conducted from 1997 to 2014 in Toronto, Ontario, Canada. Achromobacter spp. infection was categorized as no history of infection, intermittent infection, and chronic infection (two or more positive cultures in the preceding 12 months). Cox models were used to estimate risk of death or transplantation. Mixed-effects models were used to assess odds of pulmonary exacerbations and effect on lung function (FEV1%) by Achromobacter spp.
Results: A total of 1,103 patients were followed-up over the course of 18 years; 88 patients (7.3%) had one or more culture for Achromobacter species. Chronic Achromobacter infection was associated with a greater risk of death or transplantation compared with in patients with no history of infection (adjusted hazard ratio, 2.03; 95% confidence interval, 1.05–3.95; P = 0.036). Pulmonary exacerbations were more common in patients with chronic infection, but after adjusting for confounding factors, the effect was no longer significant. The chronic group had lower FEV1%, but it did not worsen after developing chronic infection.
Conclusions: Patients with CF and chronic Achromobacter infection are at increased risk of death or transplantation.
Progressive airways disease characterized by recurrent infective exacerbations remains the primary cause of premature death in cystic fibrosis (CF). Although Pseudomonas aeruginosa and Staphylococcus aureus remain the most common bacterial pathogens implicated in CF pulmonary infections, the epidemiology of these infections has become increasingly complex in recent decades (1). A number of additional pathogens have been identified in patients with CF, including Stenotrophomonas maltophilia, nontuberculous mycobacteria, and Achromobacter species (1–7).
Achromobacter species are gram-negative bacteria that are widely distributed in the environment and have increasingly been isolated in respiratory samples of patients with CF globally (8, 9). The prevalence of pulmonary colonization with Achromobacter in individuals with CF varies between studies, ranging from 3% to 30% (10–18). Sequencing studies have identified 14 genogroups, with Achromobacter xylosoxidans and Achromobacter ruhlandii as the most prevalent Achromobacter species in patients with CF, accounting for 42% and 23.5% of infections, respectively (8). The Achromobacter genus has undergone taxonomic reclassifications (19), and bacterial isolates have occasionally been misidentified as P. aeruginosa, leading to a possible underestimation of the prevalence in historic CF cohorts (20, 21). The factors contributing to the emergence of Achromobacter species have not been fully elucidated, but may relate to selective antimicrobial pressures, enhanced survival in CF, and improved detection methods (22).
Despite the increasing prevalence of Achromobacter species infection, its effect on CF lung disease has not been well described. One study demonstrated a greater decline in lung function in 15 patients with anti-Achromobacter antibodies (16). Another study demonstrated that eight CF patients with chronic Achromobacter infection had worse initial lung function and more pulmonary exacerbations treated with intravenous antibiotics, but did not find a difference in lung function decline when compared with patients without Achromobacter infection (17). As data are restricted to small case control studies and definitions of chronic infection vary, we have yet to understand the clinical effect of persistent Achromobacter spp. infection in patients with CF. Thus, we aimed to determine the association of Achromobacter species infection on clinical outcomes in a large cohort of adult and pediatric patients with CF.
This was a retrospective cohort study of individuals with CF followed at the Hospital for Sick Children and St. Michael’s Hospital (Toronto, Ontario, Canada) from January 1, 1997, to December 31, 2014. Data for this study were extracted from the Toronto CF Database housed at the Hospital for Sick Children. This encounter-based database prospectively collects information from all pediatric and adult patients with CF from every visit, including sputum microbiology, medications, and pulmonary function testing. Patients are included in this database if they have a confirmed diagnosis of CF based on (1) the presence of clinical features consistent with CF; or (2) a positive family history for CF and either two documented sweat chloride values higher than 60 mEq/L, measured by quantitative pilocarpine iontophoresis test, or genetic testing showing two CF-causing mutations or a nasal potential difference consistent with CF (23). All patients followed at the pediatric and adult CF centers in Toronto, Canada, consented to have detailed records for every clinical encounter captured in the Toronto CF Database. During the study period, taxonomic classification was consistent, and there were no standard treatment protocols for Achromobacter species infection. The analyses conducted in this study were approved by the Research Ethics Boards at the Hospital for Sick Children (REB 100,052,199) and the University of Calgary (REB15-3266).
At each point when a respiratory tract culture was taken, we reviewed the previous 12 months of microbiological data for each patient. On the basis of that previous 12 months of microbiological data, we classified each patient as no history of Achromobacter infection, intermittent infection (one positive respiratory tract culture for Achromobacter in the preceding 12 months), or chronic infection (two or more positive respiratory tract cultures of Achromobacter spp. in the preceding 12 months). During the course of the observation period, patients could change microbiological categories, except once a patient had one positive culture, they were considered intermittent unless they became chronically infected. These infection categorizations were adapted from previous epidemiologic studies of other CF pathogens (4, 24, 25).
Time-independent characteristics included sex (male/female) and pancreatic status (sufficient/insufficient based on use of enzymes). Time-dependent characteristics included body mass index (BMI, absolute value converted to centiles calculated using Centers for Disease Control and Prevention growth charts; centiles were calculated for adults, assuming all adults are 19 years old) (26); cystic fibrosis-related diabetes (CFRD; presence/absence on the basis of an oral glucose tolerance test); FEV1 in percentage predicted, calculated using Global Lung Function Initiative equations (27); P. aeruginosa, Burkholderia cepacia complex, or methicillin-resistant S. aureus (MRSA) infection (based on minimum of one positive respiratory tract culture in the preceding 12 months); and pulmonary exacerbation (PEx) episodes treated with intravenous antibiotics.
Cox proportional hazard models were used to estimate the hazard ratios (HRs) of death from any cause or transplantation. The transplants were composed of 95% lung transplants; 5% were other/unknown. The multivariable Cox proportional hazard analysis adjusted for time-independent factors (sex, pancreatic status) as well as time-dependent factors (BMI, CFRD, FEV1% predicted, microbiology, PEx). As data were left truncated, patients who died or were lost to follow-up before 1997 were excluded; the analyses used age as the time variable conditioning on the age at entry: Subjects entered the survival analyses on January 1, 1997, or their age at diagnosis if they were diagnosed after 1997. Subjects exited the survival analysis at age of death or transplant or December 31, 2014. To determine whether Achromobacter infection simply occurred as an association with aggressive treatment in the last year of life/pretransplant, we also did a time-lagged analysis of mortality/transplantation, as has previously been performed with survival analyses of MRSA infection in patients with CF (28). In the time-lagged analysis, we took the value of Achromobacter at the time of death/transplant and substituted it with the status of Achromobacter from the previous year.
To assess PExs, a mixed-effects model allowing for repeated exacerbations per patient was used to estimate the odds of having an exacerbation by Achromobacter infection status. Lung function was assessed using a mixed-effects model, allowing for repeated lung function measurements in the same participant. Infection status was treated as a time-varying variable, such that the estimate reflects the FEV1% predicted at the time of infection.
The multivariable models were constructed using a forward stepwise approach incorporating variables that were significant at a P value of 0.15 in univariate analyses. All hypotheses were two-sided at α significance of 0.05, and analyses used Stata 14.2 (StataCorp, College Station, TX).
This work was presented in abstract form at the North American Cystic Fibrosis Conference in October 2016 in Orlando, Florida (29).
A summary of the patient population is represented in Figure 1. Table 1 represents the clinical characteristics of the entire cohort at the time of entry into the study and patients with Achromobacter infection at the time of first infection. A total of 1,103 patients (54.4% male) were followed for a median of 8.5 years (interquartile range, 2.4–14.6 years). Of these, 88 patients (58.0% male) acquired infection with Achromobacter species, representing an overall prevalence of Achromobacter infection of 8%. During the study period, patients with Achromobacter infection were followed (a median of 10.7 years; interquartile range, 5.6–15.6 years) longer than the total cohort. At the time of first infection, patients with Achromobacter infection were older, had a lower BMI centile, and were more likely to have CFRD. Of the 88 patients with Achromobacter, 48 (55%) patients developed chronic infection. Among patients who developed chronic infection, the vast majority remained chronically infected for the remainder of the observation period (92% of subsequent follow-up visits). Those with chronic Achromobacter infection had the least coinfection with B. cepacia complex and MRSA, but were the oldest, with the lowest lung function, and a greater proportion had CFRD, representing a sicker patient population (Table 1).
|Parameters||Total Cohort (N = 1,103)||Achromobacter Cohort (N = 88)||Chronic Achromobacter (N = 48)|
|Follow-up time, yr, median (IQR)||8.5 (2.4–14.6)||10.7 (5.6–15.6)||7.7 (1.0–11.4)|
|Average number of cultures/yr/patient (IQR)||4 (3–5)||5 (3–7)||5 (4–7)|
|Male sex, n (%)||600 (54.4)||51 (58.0)||29 (60.4)|
|Age, yr, median (IQR)||15.0 (4.7–27.2)||18.2 (13.3–28.4)||18.6 (14.5–27.4)|
|Diagnosis < 2 yr, n (%)||725 (65.7)||63 (71.6)||33 (68.7)|
|Body mass index centile, median (IQR)||43.8 (20.2–70.0)||32.2 (12.0–58.4)||27.9 (8.8–59.7)|
|Pancreatic insufficiency, n (%)||916 (83.5)||77 (87.5)||41 (85.4)|
|FEV1 % predicted median (IQR)||65.7 (44.0–85.5)||60.3 (40.6–80.0)||55.8 (36.1–77.5)|
|Genotype, n (%)|
|Class I–III mutation||863 (78.2)||71 (80.7)||39 (81.2)|
|Class IV–V mutation||137 (12.4)||5 (5.7)||4 (8.3)|
|Unknown||103 (9.3)||12 (13.6)||5 (10.4)|
|Copathogens, n (%)|
|Pseudomonas aeruginosa||426 (38.6)||32 (36.4)||17 (35.4)|
|Burkholderia cepacia complex||115 (10.3)||2 (2.3)||0 (0)|
|Methicillin-resistant Staphylococcus aureus||9 (0.8)||0 (0)||0 (0)|
|Comorbidities, n (%)|
|Cystic fibrosis related diabetes||77 (7.0)||14 (15.9)||11 (22.9)|
A total of 348 patients (31.6%) died or underwent transplantation between 1997 and 2014 (183 deaths, 165 transplantations). The average age at death or transplantation was 21.5 years (95% confidence interval [CI], 18.4–24.6 years; n = 18) in the chronic Achromobacter group, 29.5 years (95% CI, 23.2–35.8 years; n = 16) in the intermittent Achromobacter group, and 30.3 years (95% CI, 29.0–31.6 years; n = 314) in the group with no history of Achromobacter infection (P < 0.02). Of note, the death-to-transplant ratio was higher in the no history of Achromobacter infection group (171 deaths; 143 transplants) compared with in the chronic (6 deaths, 12 transplants) and intermittent (6 deaths, 10 transplants; P = 0.1) Achromobacter infection groups. The overall probability of transplant-free survival during the study period according to Achromobacter infection status is depicted in Figure 2. Chronic Achromobacter infection was associated with a significantly greater risk of death or transplantation compared with patients with no history of Achromobacter infection (unadjusted HR, 3.44 [95% CI, 2.04–5.80; P < 0.001]; adjusted HR, 2.03 [95% CI, 1.05–3.95; P = 0.036]; Table 2).
|Achromobacter Infection Status||Model 1: Hazard Ratio (95% CI)||Model 2: Hazard Ratio (95% CI)|
|No history of infection||Ref||Ref|
|Intermittent infection||1.18 (0.74–1.89)||1.02 (0.60–1.74)|
|Chronic infection||3.44 (2.04–5.80)||2.03 (1.05–3.95)|
|No history of infection||Ref||Ref|
|Intermittent infection||1.20 (0.73–2.00)||1.17 (0.63–2.17)|
|Chronic infection||2.60 (1.51–4.46)||1.06 (0.56–2.03)|
To assess whether Achromobacter infection was simply an end event in the year before death/transplant, we performed a time-lagged analysis. Chronic Achromobacter infection was still associated with a greater risk of death or transplantation compared with patients with no history of Achromobacter infection (unadjusted HR, 2.60; 95% CI, 1.51–4.46), but when we adjusted for confounding, time-dependent factors (BMI, FEV1%, CFRD, and coinfection), this association was no longer significant (Table 2).
Pulmonary exacerbations were more frequent in the group with chronic infection (10.9%) compared with the intermittent (8.6%) and never-infected groups (6.3%; P < 0.01). The odds of a pulmonary exacerbation were increased in both the intermittent and chronic Achromobacter infection status (odds ratio, 1.46 [95% CI, 1.03–2.07] and 1.84 [95% CI, 1.23–2.72], respectively), but the effect was attenuated and no longer significant after adjustment for confounding factors (Table 3).
|Achromobacter Infection Status||Model 1: Odds Ratio (95% CI)||Model 2: Odds Ratio (95% CI)|
|No history of infection||Ref||Ref|
|Intermittent infection||1.46 (1.03–2.07)||1.02 (0.74–1.42)|
|Chronic infection||1.84 (1.23–2.72)||1.10 (0.76–1.61)|
As a group overall, at the time of development of chronic Achromobacter infection, patients had lower lung function compared with others (Table 1). Without adjusting for other factors affecting lung function, the chronically infected group had a −1.51% predicted/year (95% CI, −1.73% to −1.28%) decline in FEV1 compared with −1.28% predicted/year (95% CI, −1.31% to −1.25%) decline in those who had no history of Achromobacter infection (Figure 3). The greatest FEV1 decline was observed in the intermittent group (slope, −1.62; 95% CI, −1.76 to −1.47).
However, within an individual patient, there was no marked change in the rate of FEV1 decline before and after chronic infection developed (data not shown). Furthermore, when comparing Achromobacter infection status at the time of a lung function measure, neither intermittent (0.82%; 95% CI, −0.28% to 1.91%) nor chronic (0.37%; 95% CI, −0.97% to 1.71%) infection status was associated with lower FEV1% predicted values compared with no history of Achromobacter infection (Table 4).
|Achromobacter Infection Status||FEV1% Predicted (95% CI)|
|No history of infection||Ref|
|Intermittent infection||0.82 (−0.28 to 1.91)|
|Chronic infection||0.37 (−0.97 to 1.71)|
Our study demonstrated that more than half of patients with CF who acquired Achromobacter infection developed persistent infection, and that chronic Achromobacter infection was independently associated with more than a twofold increased risk of death or transplantation. However, we did not find an independent association between chronic infection and either lung function or pulmonary exacerbation, or in the time-lag analyses for mortality/transplantation, suggesting other factors may also play a role.
In our cohort, the overall prevalence of Achromobacter infection was 8%, which is consistent with the most recent U.S. CF Foundation registry data (30) and slightly greater than the overall Canadian CF registry data (31). Previous studies that have assessed the clinical effect of Achromobacter infection in CF have been case control studies, with a largest sample size of 15 cases. Similar to our current study, the study by De Baets and colleagues demonstrated that individuals with CF with chronic Achromobacter infection had lower baseline lung function and more pulmonary exacerbations treated with intravenous antibiotics compared with age-, sex-, and P. aeruginosa–infected matched controls, thus representing a sicker patient population (17). Lambiase and colleagues and Tan and colleagues found that FEV1 decline did not change after acquisition of chronic Achromobacter infection (2, 6), which is consistent with our findings. Only one case control study, by Rønne Hansen and colleagues, showed that development of chronic Achromobacter infection was associated with worsening lung function (16). In that study, chronic infection was defined as six or more positive cultures (whereas most studies use two or more positive cultures) or an increase in precipitating antibodies, likely selecting out a heavily infected, more severely affected group, from whom more frequent microbiology cultures were obtained. None of these prior epidemiologic investigations, however, have examined the effect of chronic Achromobacter infection on mortality or the need for transplantation.
Subjects with CF with chronic Achromobacter infection in this study were considerably younger at death or transplant (approximately 9 years younger) than those with intermittent or no history of Achromobacter infection, and this was reflected in a more than twofold increased risk of death or transplantation in this patient population. We used a composite outcome of death or transplant, as has been done previously (25, 32), given the relatively few deaths in this cohort. Indeed, chronic infection status had a significantly greater hazard ratio for death or transplant, but there were relatively fewer deaths than transplants compared with the uninfected group. The exact mechanism through which chronic Achromobacter infection had this effect on mortality and transplantation is not entirely clear, as chronic infection itself was not an independent risk factor for pulmonary exacerbation or lower FEV1, both known risk factors for earlier death in individuals with CF.
It is possible that our study was underpowered to assess these outcomes in adjusted models, as we did observe an increased odds of pulmonary exacerbation, and a greater rate of FEV1 decline in unadjusted analyses, and it is possible that Achromobacter is merely a marker of poorer outcome and not causally related to it. We did a time-lagged analysis of mortality/transplantation, as has previously been performed with survival analyses of MRSA infection in patients with CF (28), to determine whether Achromobacter infection simply occurred as an association with aggressive treatment in the last year of life/pretransplant. In the time-lag analysis, chronic Achromobacter infection continued to be associated with earlier death/transplant; however, after adjusting for other factors, such as FEV1, which may be on the causal pathway, the association was no longer significant.
The question as to whether persistent pulmonary infection with gram-negative bacteria simply occurs in sicker patients or plays a causal role in the development of more severe lung disease has been raised before (33). It is clear there is a relationship between a pulmonary microbial community dominated by nonfermenting non-Pseudomonas gram-negative pathogens, such as Achromobacter species, and lower FEV1 in individuals with CF (34). However, to establish whether this relationship is causal, prospective interventional studies are needed to determine whether effective antimicrobial treatment of these infections changes outcomes.
The primary strength of our study was the relatively large sample size and nearly 20 years of follow-up data. Use of a prospective encounter-based registry with high levels of patient retention and minimal missing data permits longitudinal epidemiologic evaluations of this nature. However, our study assessed prevalent cases and was retrospective, which only permits us to conclude associations, rather than draw causal inferences related to Achromobacter infection in the CF population. In addition, our classification of chronic infection was based on previous epidemiologic studies in CF, but this definition is dependent on the number of cultures taken, which may be more frequent in sicker patients. However, in our study, the average number of cultures per year per patient was four (Table 1). Other limitations included left truncated data and possible unknown confounders not addressed in the statistical analysis.
In conclusion, chronic Achromobacter infection was associated with a twofold risk of death or transplantation in patients with CF. Given the potential deleterious effect of Achromobacter infection in individuals with CF, further epidemiologic analyses as well as in vitro studies assessing the pathogenicity of this organism are warranted.
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Author Contributions: All authors meet criteria for authorship based on AnnalsATS submission guidelines. S.S., V.W., and R.S. were responsible for data analysis and interpretation; R.S. and V.W. were responsible for the creation of the manuscript; V.W., S.S., and F.R. were responsible for the project’s inception and supervision; all authors contributed to development of the final manuscript; and R.S. serves as guarantor of the work.