Longitudinal bacterial prevalence in cystic fibrosis airways: Fact and artifact.

BACKGROUND: Opportunistic bacterial infection is a hallmark of cystic fibrosis (CF) lung disease and early mortality. Poorly characterized prevalence changes have accompanied two decades of health improvements, with CFTR modulators likely to further affect infection epidemiology. METHODS: Bacterial prevalence change trends across birth cohorts were assessed with linear regression using 2001-2019 US CF Foundation Patient Registry data. Informative missingness was assessed, as was age-to-age infection status. RESULTS: Bacterial prevalence constantly changed from 2001 to 2019, with changes differing across birth cohorts. Informative censoring affected prevalence change for some organisms. Age-to-age infection status changes were greater than net changes in bacterial prevalence and varied by age. CONCLUSIONS: CF infection epidemiology changed over two decades and will continue to do so. Understanding how modulators affect infection epidemiology will require creative designs for longitudinal prevalence change studies emphasizing prevalence changes independent of effects on lung biology.

Cystic Fibrosis Mice Develop Spontaneous Chronic Bordetella Airway Infections.

Chronic pulmonary disease and infection is the primary cause of morbidity and mortality in people with cystic fibrosis (CF). Though Pseudomonas aeruginosa, is most commonly found in the airways of individuals with CF, there is increasing appreciation for the diversity of the CF microbiome, including other taxa such as Bordetella. Here we describe the identification and impact of Bordetella pseudohinzii infection in CF mice, which previously have not been thought to develop spontaneous airway infections. We determined that CF mice are more susceptible to the B. pseudohinzii infections, and less able to resolve the infection than non-CF mice. Moreover, in both CF and non-CF mice, B. pseudohinzii infections lead to markedly reduced respiratory rates and a CF-specific immune response. These results establish the CF mouse model as an important tool for the study of CF-relevant infection and highlight the potential contribution of Bordetella to CF clinical pathology.

Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain.

Pandoraea species, in particular Pandoraea apista, are opportunistic, multidrug-resistant pathogens in persons with cystic fibrosis (CF). To aid in understanding the role of P. apista in CF lung disease, we used Illumina MiSeq and nanopore MinION technology to sequence the whole genome of the P. apista LMG 16407(T).

Rhizobium radiobacter bacteremia in a neonate.

Rhizobium radiobacter bacteremia is an infrequent cause of human infection. We report a rare manifestation of R. radiobacter infection in which bacteremia occurred in a newborn infant without other risk factors.

Induction of immune response to the 17 kDa OMPA Burkholderia cenocepacia polypeptide and protection against pulmonary infection in mice after nasal vaccination with an OMP nanoemulsion-based vaccine.

Burkholderia cepacia complex (Bcc) are opportunistic bacteria associated with life-threatening illness in persons with cystic fibrosis. Once Bcc colonization is established, these antimicrobial-resistant and biofilm-forming bacteria are difficult to eradicate and are associated with increased rates of morbidity and mortality. At present, no vaccines are available to prevent the Bcc infection. There is currently a paucity of published information regarding the development of vaccines designed to prevent Burkholderia colonization. This work expands on the recent studies published by Bertot et al. [Infect Immun 75(6):2740-2752, 2007], where successful protective immune responses were generated in mice using a B. multivorans OMP-based vaccine. Here, we evaluate an experimental mucosal vaccine against Bcc using a novel mucosal adjuvant (nanoemulsion) and a novel B. cenocepacia-based OMP antigen. The OMP antigen derived from B. cenocepacia was mixed with either nanoemulsion or with PBS and delivered intranasally to CD-1 mice. Serum analysis showed robust IgG and mucosal secretory IgA immune responses in vaccinated versus control mice. The antibodies had cross-neutralizing activity against both B. cenocepacia and B. multivorans species. We found that immunized mice were protected against pulmonary colonization with B. cenocepacia. We have also identified that a 17 kDa OmpA-like protein highly conserved between Burkholderia and Ralstonia species as a new immunodominant epitope in mucosal immunization.

Survival after lung transplantation of cystic fibrosis patients infected with Burkholderia cepacia complex.

Within the Burkholderia cepacia complex (Bcc), B. cenocepacia portends increased mortality compared with other species. We investigated the impact of Bcc infection on mortality and re-infection following lung transplant (LT). Species designation for isolates from Bcc-infected patients was determined using 16S rDNA and recA gene analyses. Of 75 cystic fibrosis patients undergoing LT from September 1992 to August 2002, 59 had no Bcc and 16 had Bcc (including 7 B. cenocepacia) isolated in the year before LT. Of the latter, 87.5% had Bcc recovered after transplantation, and all retained their pretransplant strains. Survival was 97%, 92%, 76% and 63% for noninfected patients; 89%, 89%, 67% and 56% for patients infected with Bcc species other than B. cenocepacia; and 71%, 29%, 29% and 29% for patients with B. cenocepacia (p = 0.014) at 1 month, 1 year, 3 years and 5 years, respectively. Patients infected with B. cenocepacia before transplant were six times more likely to die within 1 year of transplant than those infected with other Bcc species (p = 0.04) and eight times than noninfected patients (p < 0.00005). Following LT, infection with Bcc species other than B. cenocepacia does not significantly impact 5-year survival whereas infection with B. cenocepacia pretransplant is associated with decreased survival.

Identification of Bordetella spp. in respiratory specimens from individuals with cystic fibrosis.

Bordetella spp. are not normally included when considering the opportunistic bacterial species that are typically involved in respiratory tract infections in individuals with cystic fibrosis (CF). By using a combination of bacterial genotyping and 16S rDNA sequencing, Bordetella spp. were identified in cultures obtained from 43 individuals with CF. Most (n = 23) patients were infected with Bordetella bronchiseptica/parapertussis; five were infected with Bordetella hinzii, four with Bordetella petrii, three with Bordetella avium, and eight with unidentified Bordetella spp. Consideration should be given to the presence of these organisms in the evaluation of CF sputum cultures.

Chronic colonization with Pandoraea apista in cystic fibrosis patients determined by repetitive-element-sequence PCR.

Pandoraea apista is recovered with increasing frequency from the lungs of patients with cystic fibrosis (CF) and may represent an emerging pathogen (I. M. Jorgensen et al., Pediatr. Pulmonol. 36:439-446, 2003). We identified two CF patients from our hospital whose sputum specimens were culture positive for P. apista over the course of several years. Repetitive-element-sequence PCR was employed to determine whether sequential isolates that were recovered from these patients represented a single clone and whether each patient had been chronically colonized with the same strain. Banding patterns generated with ERIC primers, REP primers, and BOX primers showed that individual patient isolates had a high degree of similarity (>97%) and were considered identical. However, only the banding patterns from the ERIC primers and BOX primers were able to show that the strains from patients I and II were unique (similarity indices of 79.8% and 70.0%, respectively). We concluded that all strains of P. apista from patient I were identical, as were all strains from patient II, establishing chronic colonization. Only two of the three methods employed indicate that the strains from the two patients are distinct. This implied that the organism was not transferred from one patient to the other, suggesting that the choice of methodology could generate misleading results when examining person-to-person transmission regarding this organism.

Recovery of Burkholderia cenocepacia strain PHDC from cystic fibrosis patients in Europe.

BACKGROUND: Burkholderia cenocepacia can cause life threatening respiratory tract infections in patients with cystic fibrosis (CF) and has a significant impact on survival. There is extensive evidence for patient to patient spread and nosocomial transmission of this organism, and several widespread B cenocepacia strains have been described including the transatlantic ET12 clone. A study was performed to compare B cenocepacia isolates recovered from CF patients receiving care in several European countries and strains isolated from other clinical samples and the environment, with reference isolates from the epidemic B cenocepacia strain PHDC which has so far only been recovered from CF patients and soil in the USA. METHODS: A large collection of B cenocepacia isolates, including a large number recovered from CF patients receiving care in several European countries, Canada and the USA, were genotyped by means of randomly amplified polymorphic DNA typing (RAPD) and rep-PCR using the BOX-A1R primer (BOX-PCR). RESULTS: Nineteen Burkholderia cenocepacia isolates cultured from clinical samples in Europe (18 recently recovered from CF patients in France and Italy and one recovered in 1964 from urine in the UK) showed RAPD fingerprinting patterns that were similar to patterns obtained from isolates of B cenocepacia strain PHDC. Subsequent analysis of these isolates using BOX-PCR confirmed that the European isolates and strain PHDC represent the same clone. CONCLUSION: Strain PHDC represents a second transatlantic B cenocepacia clone capable of colonising patients with CF.

Lung transplantation for cystic fibrosis patients with Burkholderia cepacia complex. Survival linked to genomovar type.

The number of cystic fibrosis (CF) patients undergoing lung transplant has risen over the past decade, because of a clear-cut survival benefit. However, patients with Burkholderia cepacia complex are often excluded from transplantation because of increased mortality. To determine the influence of B. cepacia complex genomovar type on transplant outcome, we undertook a retrospective study in 121 CF patients transplanted at UNC. Twenty-one and three patients, respectively, were infected pre- or postoperatively with B. cepacia complex. All posttransplant acquisitions were successfully treated. However, excess mortality occurred over the first 6 postoperative months in those infected preoperatively with B. cepacia complex compared with those not infected (33% versus 12%, p = 0.01). The 1-, 3-, and 5-yr survival were significantly lower in the B. cepacia complex cohort. Of the patients infected preoperatively, genomovar III patients were at the highest risk of B. cepacia complex-related mortality (5 of 12 versus 0 of 8, one isolate not typed; p = 0.035). Each of the B. cepacia complex-related deaths was caused by a unique genotype as determined by pulsed-field gel electrophoresis. All isolates were negative for the cable pilin gene. These results warrant a multicenter analysis of B. cepacia complex-infected patients with genomovar-typing to confirm that genomovar III patients are at highest risk for post-transplant complications.

Identification of Pandoraea species by 16S ribosomal DNA-based PCR assays.

The recently described genus Pandoraea contains five named species (Pandoraea apista, Pandoraea pulmonicola, Pandoraea pnomenusa, Pandoraea sputorum, and Pandoraea norimbergensis) and four unnamed genomospecies. Pandoraea spp. have mainly been recovered from the respiratory tracts of cystic fibrosis (CF) patients. Accurate genus- and species-level identification by routine clinical microbiology methods is difficult, and differentiation from Burkholderia cepacia complex organisms may be especially problematic. This can have important consequences for the management of CF patients. On the basis of 16S ribosomal DNA sequences, PCR assays for the identification of Pandoraea spp. were developed. A first PCR assay was developed for the identification of Pandoraea isolates to the genus level. PCR assays for the identification of P. apista and P. pulmonicola as a group, P. pnomenusa, P. sputorum, and P. norimbergensis were also developed. All five assays were evaluated with a panel of 123 bacterial isolates that included 69 Pandoraea sp. strains, 24 B. cepacia complex strains, 6 Burkholderia gladioli strains, 9 Ralstonia sp. strains, 5 Alcaligenes xylosoxidans strains, 5 Stenotrophomonas maltophilia strains, and 5 Pseudomonas aeruginosa strains. The use of these PCR assays facilitates the identification of Pandoraea spp. and avoids the misidentification of a Pandoraea sp. as a B. cepacia complex isolate.

Endemicity and inter-city spread of Burkholderia cepacia genomovar III in cystic fibrosis.

OBJECTIVES: We sought to determine whether the same Burkholderia cepacia complex strain has persisted as the dominant clonal lineage among patients in a large cystic fibrosis (CF) treatment center during the past 2 decades. STUDY DESIGN: The inter-city spread of B cepacia through transfer of a colonized patient and the impact of infection control measures in containing inter-patient transmission were investigated. We analyzed all available B cepacia complex isolates recovered from 1981 to 1987 and from 1996 to 2000 at one large CF treatment center (Center A) and from 1997 to 2000 at another center (Center B). Incidence of B cepacia complex infection and infection control measures in both centers were assessed. RESULTS: Seventeen (81%) of 21 Center A patients from whom B cepacia complex bacteria were recovered between 1981 and 1987 and 40 (97%) of 41 patients culture-positive between 1996 and 2000 were infected with the same genomovar III strain. Transfer of a colonized patient from Center A to Center B was associated with an increase in B cepacia complex infection in Center B, all of which was with the Center A dominant strain. This strain, designated PHDC, lacks both B cepacia epidemic strain and cblA markers. CONCLUSIONS: B cepacia complex strains may remain endemic in CF treatment centers for many years. Responsible bacterial and host factors and optimal infection control measures to prevent inter-patient spread remain to be identified.

An episodic outbreak of genetically related Burkholderia cepacia among non-cystic fibrosis patients at a university hospital.

OBJECTIVE: To investigate an outbreak of Burkholderia cepacia. DESIGN: Observational study and chart review. PATIENTS: Adult non-cystic fibrosis (CF) patients. SETTING: Intensive care units (ICUs) at a university-affiliated teaching hospital. METHODS: As part of the epidemiological investigation, we conducted a chart review and collected environmental samples. A review of work schedules of healthcare workers also was performed. We used B. cepacia selective agar for preliminary screening for all isolates, which subsequently were confirmed as members of the B. cepacia complex by polyphasic analysis employing conventional biochemical reactions and genus- and species-specific polymerase chain reaction assays. Pulsed-field gel electrophoresis, randomly amplified polymorphic DNA typing, and automated ribotyping were used to genotype the isolates. As part of the intervention, contact isolation precautions were initiated for all patients identified as having had a culture positive for B. cepacia. RESULTS: Between September 1997 and September 1999, B. cepacia was isolated from 31 adult patients without CF in ICUs at a university-affiliated teaching hospital. Based on geographic clustering and genotypic analysis, three distinct clusters were observed involving 20 patients. Isolates from 17 of these patients were available for testing and were found to be of the same strain (outbreak strain). Further taxonomic analysis indicated that the outbreak strain was B. cepacia complex genomovar III. Twelve (71%) of the 17 patients were judged to be infected, and 5 (29%) were colonized with this strain. Six of 200 environmental cultures from multiple sources in the hospital's ICUs yielded B. cepacia. Two of these isolates, both recovered from rooms of colonized patients, were the same genotype as the outbreak strain recovered from patients. CONCLUSION: Despite an extensive investigation, the source of the B. cepacia clone involved in this outbreak remains unknown. The spatial and temporal pattern of cases suggests that cross-transmission of a genetically related strain contributed to clustering among patients. The initiation of contact isolation may have limited the extent of this transmission. Additional studies are needed to elucidate better the epidemiology of nosocomial B. cepacia infection among non-CF adult patients.

Microbiological and immunologic considerations with aerosolized drug delivery.

The development of drug resistance is a major theoretical concern with the long-term delivery of aerosolized antibiotics via inhalation. A randomized, placebo-controlled, double-blind study, which compared inhaled tobramycin plus standard cystic fibrosis (CF) care to placebo plus standard CF care, examined the following microbiological parameters: percentage of patients with at least one Pseudomonas aeruginosa (PA) strain with a minimal inhibitory concentration (MIC) > 16 microg/mL (ie, the breakpoint for tobramycin resistance delivered by the parenteral route); changes in the levels of the lowest concentration required to inhibit the growth of 50% of strains tested (MIC(50)) and 90% of strains tested (MIC(90)); the percentage of patients with an increase, decrease, or change in the MIC of the most resistant and most prevalent PA strains; and the percentage of patients in whom the PA strain with the highest MIC also was the most prevalent. During the first 6 months, which included three on-drug and off-drug cycles of 4 weeks' duration each, the percentage of tobramycin-treated patients with at least one PA isolate and with an MIC > 16 microg/mL was 13% at baseline, 26% at 20 weeks, and 23% at 24 weeks vs 10%, 17%, and 8%, respectively, for placebo-treated patients. No significant change was observed in MIC(50) at 20 and 24 weeks. The increase in MIC(90) was not statistically significant. At 24 weeks, there was no increase in the percentage of patients in either group in whom the PA strain with the highest MIC became most the prevalent strain. After the third on-drug cycle, 33% of the tobramycin group showed an increase in the MIC of the strain with the highest MIC. This decreased to 26% after 1 month off drug therapy. A preliminary analysis of the 12-month and 18-month data showed a decrease in the proportion of resistant PA isolates after each off-drug cycle. This return to susceptibility following an off-drug cycle was not observed at 24 months. The mechanism of resistance in this setting is believed to be increased impermeability to drug. At all time points, pulmonary function improved even in patients with MICs of > or = 128 microg/mL. At 6 months, no increase was seen in the rates of superinfection with tobramycin-resistant, Gram-negative pathogens. Increases in Stenotrophomonas maltophilia were detected in patients after 18 and 24 months of tobramycin therapy and were similar to those rates in patients receiving placebo. These rates may be independent of inhalation therapy.

Burkholderia cepacia complex: a contraindication to lung transplantation in cystic fibrosis?

Previous studies have indicated that pulmonary infection with Burkholderia cepacia is associated with poor clinical outcome after lung transplantation in cystic fibrosis (CF). Many treatment centers consider B. cepacia infection an absolute contraindication to lung transplantation. However, the B. cepacia complex actually consists of several closely related bacterial species. Although each of these has been isolated from CF sputum culture, certain species are much more frequently recovered than others, and it is not yet clear whether all species have the same potential for virulence in CF. Additional study is needed to better define the relative risks associated with each species of the B. cepacia complex.

Burkholderia ambifaria sp. nov., a novel member of the Burkholderia cepacia complex including biocontrol and cystic fibrosis-related isolates.

A polyphasic taxonomic study, including amplified fragment length polymorphism (AFLP) fingerprinting, DNA-DNA hybridizations, DNA base-ratio determinations, phylogenetic analysis, whole-cell fatty acid analyses and an extensive biochemical characterization, was performed on 19 Burkholderia cepacia-like isolates from the environment and cystic fibrosis (CF) patients. Several of the environmental isolates have attracted considerable interest due to their biocontrol properties. The polyphasic taxonomic data showed that the strains represent a new member of the B. cepacia complex, for which the name Burkholderia ambifaria sp. nov. is proposed. The type strain is strain LMG 19182T. B. ambifaria can be differentiated from the other members of the B. cepacia complex by means of AFLP fingerprinting, whole-cell fatty acid analysis, biochemical tests (including ornithine and lysine decarboxylase activity, acidification of sucrose and beta-haemolysis) and a newly developed recA gene-based PCR assay. 16S rDNA-based RFLP analysis and PCR tests allowed differentiation of B. ambifaria from Burkholderia multivorans, Burkholderia vietnamiensis and B. cepacia genomovar VI, but not from B. cepacia genomovars I and III and Burkholderia stabilis. The finding that this new taxon includes both strains isolated from CF patients and potentially useful biocontrol strains supports the general consensus that the large-scale use of biocontrol strains belonging to the B. cepacia complex would be ill-advised until more is known about their potential pathogenic mechanisms.

Disproportionate distribution of Burkholderia cepacia complex species and transmissibility markers in cystic fibrosis.

Several distinct species (genomovars) comprise bacteria previously identified merely as Burkholderia cepacia. Understanding how these species, collectively referred to as the B. cepacia complex, differ in their epidemiology and pathogenic potential in cystic fibrosis (CF) is important in efforts to refine management strategies. B. cepacia isolates recovered from 606 CF patients receiving care at 132 treatment centers in 105 cities in the United States were assessed to determine species within the B. cepacia complex and examined for the presence of putative transmissibility markers (B. cepacia epidemic strain marker [BCESM] and cable pilin subunit gene [cblA]). Fifty percent of patients were infected with B. cepacia complex genomovar III, 38% with B. multivorans (formerly genomovar II), and 5% with B. vietnamiensis (formerly genomovar V); fewer than 5% of patients were infected with either genomovar I, B. stabilis (formerly genomovar IV), genomovar VI, or genomovar VII. BCESM was found in 46% of genomovar III isolates and not in any other species. Only one isolate, from a patient infected with the ET12 epidemic lineage, contained the complete cblA pilin subunit gene. Our data indicate a differential capacity for human infection among the phylogenetically closely related species of the B. cepacia complex. The low frequency of BCESM and cblA suggests that they are not sufficient markers of B. cepacia virulence or transmissibility.

Burkholderia cepacia genomovar VI, a new member of the Burkholderia cepacia complex isolated from cystic fibrosis patients.

A polyphasic taxonomic study was performed on 23 strains isolated from cystic fibrosis (CF) patients in the USA. These strains were tentatively identified as Burkholderia cepacia, Burkholderia vietnamiensis and Burkholderia or Ralstonia sp. using biochemical tests and 16S rDNA-based PCR assays. Visual comparison of protein profiles indicated that they belonged to a single new group ('group 13'). The polyphasic taxonomic data showed that 18 of these strains represent a new member of the B. cepacia complex, referred to in this report as B. cepacia genomovar VI, whereas the other five strains belonged to Burkholderia multivorans. By means of biochemical tests, B. cepacia genomovar VI strains can be separated from B. cepacia genomovars I and III, Burkholderia stabilis, B. vietnamiensis and Burkholderia gladioli, but not from B. multivorans. Separation of B. cepacia genomovar VI and B. multivorans is possible using AFLP (amplified fragment length polymorphism) fingerprinting and DNA-DNA hybridizations. Retrospective analysis of epidemiological and genotypic data suggests that strains of B. cepacia genomovar VI have been involved in chronic colonization of CF patients and have been spread from person to person.

Identification and detection of Stenotrophomonas maltophilia by rRNA-directed PCR.

Stenotrophomonas maltophilia has recently emerged as an important nosocomial pathogen in immunocompromised patients, in transplant recipients, and in persons with cystic fibrosis (CF). While this organism is nonpathogenic in healthy individuals, it is increasingly associated with morbidity and mortality in susceptible populations. Recent studies have indicated that for approximately 10% of CF patients with moderate lung disease, S. maltophilia can be cultured from respiratory tract secretions. Identification of S. maltophilia can be problematic, and analysis of isolates from the Burkholderia cepacia Research Laboratory and Repository showed that several isolates presumptively identified as B. cepacia by clinical microbiology laboratories were in fact S. maltophilia. To overcome the problems associated with definitive identification, we developed species-specific PCR (SS-PCR) primers, designated SM1 and SM4, directed to the 23S rRNA gene, and tested their utility to accurately identify S. maltophilia directly from sputum. The SS-PCR was developed and tested against a panel of 112 S. maltophilia isolates collected from diverse geographic locations. To test for specificity, 43 isolates from 17 different species were analyzed. PCR with the SM1-SM4 primer pair and isolated genomic DNA as a template resulted in amplification of a band from all S. maltophilia isolates and was uniformly negative for all other species tested, yielding a sensitivity and a specificity of 100% for the SS-PCR. The utility of the SS-PCR to directly identify S. maltophilia in sputum was examined. Thirteen expectorated sputum samples from CF patients were analyzed by SS-PCR. Three samples were PCR positive, in complete concordance with the conventional laboratory culture. Thus, we have developed an SS-PCR protocol that can rapidly and accurately identify S. maltophilia isolates and which can be used for the direct detection of this organism in CF patient sputum.