REGISTRY ANNUAL DATA REPORT

Transcription

1 216 PAT I E N T REGISTRY ANNUAL DATA REPORT

2 MISSION OF THE CYSTIC FIBROSIS FOUNDATION The mission of the Cystic Fibrosis Foundation is to cure cystic fibrosis and to provide all people with the disease the opportunity to lead full, productive lives by funding research and drug development, promoting individualized treatment and ensuring access to high-quality, specialized care. SOURCE OF DATA Cystic fibrosis patients under care at CF Foundation-accredited care centers in the United States, who consented to have their data entered. SUGGESTED CITATION Cystic Fibrosis Foundation Patient Registry 216 Annual Data Report Bethesda, Maryland 217 Cystic Fibrosis Foundation PHOTOGRAPHY BY Michael Barley and Joe McNally SPECIAL ACKNOWLEDGMENTS Those who contributed to the maintenance of PortCF, analysis of data, and creation of this report: Bruce Marshall Al Faro Alexander Elbert Aliza Fink Ase Sewall Deena Loeffler Kristofer Petren Thomas O Neil Samar Rizvi

3 August 217 Dear Friends and Colleagues: It is a pleasure to share the 216 Patient Registry Annual Data Report with you. The Cystic Fibrosis Foundation Patient Registry remains a very important resource to the CF community, contributing to clinical trial design, real world observational research including safety and effectiveness studies of newly approved therapies, and quality improvement. Many thanks to each and every one of you who contribute to the success of the Registry. It would not be possible without the vital contributions of many, most notably the people with CF and their families who generously agree to share their data and the Registry coordinators and care team members who collect and enter the data. We hope that you feel a sense of pride as you read through this report. I call your attention to a few highlights in the 216 data. First the good news is that median predicted survival as well as pulmonary function and measures of nutritional status continue to show trends upwards. Also of note, over 7,5 individuals were prescribed a CFTR modulator drug. The data also show us that much work remains. Nearly one third of people with CF require one or more courses of intravenous antibiotics for treatment of a pulmonary exacerbation. The treatment burden remains high, with approximately 35 percent of people with CF prescribed three or more inhaled medications as well as other standard therapies. Complications such as anxiety and depression are highly prevalent. On a positive note, the screening rates for anxiety and depression show marked improvement in 216, an important first step in identifying people who might benefit from support and therapeutic interventions. This is a truly exciting time in CF, with advances in health care delivery and new therapeutics that have transformative potential. Together, we will continue to track these and other important developments in the Registry. Thank you all for your hard work throughout the year and your commitment to the CF Foundation s mission. Bruce C. Marshall, M.D. Senior Vice President of Clinical Affairs Cystic Fibrosis Foundation Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 1

4 TABLE OF CONTENTS SUMMARY TABLE 4 DEMOGRAPHICS 6 Characteristics of Adults with CF 8 Health Insurance Information 1 DIAGNOSIS 11 Diagnostic Characteristics of Individuals with CF 11 Diagnostic Tests 14 Sweat Chloride Testing 14 Genotyping 15 CFTR GENE MUTATIONS 16 GUIDELINES: CARE, SCREENING AND PREVENTION 21 Patient Care Guidelines 21 Infant Care Guidelines 26 MICROBIOLOGY 29 Pseudomonas aeruginosa 31 Staphylococcus aureus 32 Nontuberculous Mycobacteria 33 NUTRITION 35 Infant Feeding 4 PULMONARY FUNCTION 41 Variation in Pulmonary Function by Mutation Class 43 PULMONARY AND NUTRITIONAL OUTCOMES 44 PULMONARY EXACERBATIONS 46 THERAPIES 48 Gastrointestinal (GI) Therapies 48 Pulmonary Therapies 5 Pulmonary Medication Prescriptions by Age 51 Medications Recommended for Chronic Use 53 Medications with Insufficient Evidence to Recommend for or Against Chronic Use 54 Medications Not Recommended for Chronic Use 54 Medication Use in Young Children 55 Airway Clearance Techniques 56 CFTR Modulator Therapies 57 Ivacaftor 57 Ivacaftor / Lumacaftor 58 2 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

5 COMPLICATIONS 6 CF Complications by Age 62 CF Complications by Mutation Class 64 Cystic Fibrosis-Related Diabetes (CFRD) 66 Depression and Anxiety 69 TRANSPLANTATION 71 Lung Transplantation 71 SURVIVAL 73 Median Predicted Survival 73 Median Conditional Predicted Survival 74 Mortality Rate 74 Median Age at Death 75 Causes of Death 75 APPENDIX 76 Survival 76 Survival Metrics 77 Mutation Class 78 CF FOUNDATION PATIENT REGISTRY QUESTIONNAIRE 79 REFERENCES 89 Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 3

6 Summary of the Cystic Fibrosis Foundation Patient Registry, Demographics People with CF (n) 22,619 23,898 27, 29,57 29,497 Newly diagnosed individuals (n) A 1,7 1, Detected by newborn screening (%) Mean age at diagnosis for all people with CF (years) Median age at diagnosis for all people with CF (months) Mean age (years) Median age (years) Adults 18 years (%) Race (not mutually exclusive) White (%) African American (%) Other race (%) Hispanic (any race) (%) Males (%) Mortality Total deaths (n) Annual mortality rate (per 1) (%) Predicted median survival (years) % confidence interval (years) Median age at death (years) GI/Nutrition BMI percentile in individuals 2 to 19 years (median) Weight < 1th CDC percentile (%) Height < 5th CDC percentile (%) BMI in individuals 2 to 4 years (median) Pancreatic enzyme replacement therapy (%) Supplemental feeding - tube (%) Supplemental feeding - oral only (%) Pulmonary FVC % predicted (mean) B FEV 1 % predicted (mean) B FEV 1 /FVC ratio (mean) B Respiratory Microbiology P. aeruginosa (PA) (%) C Multidrug-resistant PA (%) D B. cepacia complex (%) S. aureus (SA) (%) E Methicillin-sensitive S. aureus (MSSA) (%) Methicillin-resistant S. aureus (MRSA) (%) S. maltophilia (%) Mycobacterial species (%) F Table continues on the next page 4 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

7 Summary of the Cystic Fibrosis Foundation Patient Registry, continued Health Care Utilization and Pulmonary Exacerbations (PEX) G Outpatient visits to CF centers reported per year (mean) Treated with IV antibiotics for a pulmonary exacerbation (%) Number of pulmonary exacerbations per year (mean) Number of days of treatment for all PEX per year (mean) H Number of days of home IV treatment for all PEX per year (mean) H Number of days of hospitalization for all PEX per year (mean) H Pulmonary Therapies I Dornase alfa ( 6 years) (%) Inhaled tobramycin (PA+ and 6 years) (%) J Inhaled aztreonam (PA+ and 6 years) (%) Azithromycin (PA+ and 6 years) (%) K Hypertonic saline ( 6 years) (%) Ivacaftor ( 6 years with G551D mutation) (%) Ivacaftor/Lumacaftor ( 12 years and F58del Homozygous) (%) Oxygen (%) L Non-invasive ventilation (%) Transplants Lung (all procedures) (n) Liver (n) Kidney (n) Lost to Follow Up M Lost to follow up (per 1 patients) (%) A We anticipate that additional 216 diagnoses will be entered into the Registry in 217. B Pulmonary function data throughout this report reflect the use of Global Lung Initiative (GLI) equations 1 for both children and adults. C Includes PA and multidrug-resistant PA, found in any culture during the year. D Defined as resistant to all antibiotics tested in two or more classes. E Includes MSSA and MRSA and reflects the prevalence of S. aureus among individuals who had a bacterial culture during the year. The percentages for MSSA and MRSA individually are greater than the total S. aureus percentage because MSSA and MRSA are not mutually exclusive. F Percentage of people with CF with one or more mycobacterial species isolated out of those who had a mycobacterial culture during the year. This includes M. tuberculosis as well as nontuberculous mycobacteria (NTM) species. G Defined as a period of treatment with IV antibiotics in the hospital and/or at home. H Among those with one or more pulmonary exacerbations in the year. I Percent of people with CF on therapy at any clinical visit in the year. All individuals noted as intolerant or having an allergy to a specific therapy were excluded. J Includes TOBI, TOBI Podhaler and Bethkis in 215 and 216. In prior years, only TOBI was available. K Individuals were considered eligible if they met the selection criteria used in the U.S. azithromycin trial. 2 L Includes continuous, nocturnal or with exertion. M Defined as individuals seen in the previous reporting year (215) but not the current reporting year (216). Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 5

8 DEMOGRAPHICS The Registry contains data on people with CF from 1986 to 216. During that time, substantial changes in specialized CF care have led to improved survival. This section shows the current and longitudinal distribution of demographic characteristics of individuals with CF in the Registry. In 216, there were 29,497 individuals with CF in the Registry. The number of adults with CF continues to increase, while the number of children remains relatively stable. In 216, adults were 52.7 percent of the CF population, compared with 29.2 percent in Number of Children and Adults with CF, , 25, Adults Years and Older Children Under 18 Years % Number of Individuals 2, , % 1, 7.8% 5, 47.3% Year The decrease in the number of individuals in 23 is due to a delay in obtaining informed consent forms before the close of the calendar year at some CF care centers. Currently, 8.5 percent of the individuals in the Registry have identified themselves as Hispanic. There has been a steady increase over the past 15 years, reflecting national population trends. 3 Hispanics with CF tend to be younger than the overall CF population, with a median age of 12.9 years. 6 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

9 The median age of people with CF currently in the Registry is 19. years. The range is from birth to 86.7 years. Despite gains in survival, the age distribution remains markedly skewed toward younger ages. Age Distribution of the CF Population in 216 1, 1 Number of Individuals Number of Individuals Cumulative Percentage Cumulative Percentage Age (Years) Throughout this report, a number of age distribution charts are used to display particular characteristics of individuals in the Registry. Each of these charts includes the gray bars seen in the chart above to display the total number of individuals in the Registry in 216. Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 7

10 Characteristics of Adults with CF As a growing number of individuals with CF enter adulthood, it is encouraging to note that many are pursuing higher education and employment, are in committed relationships, and having children of their own. About two-thirds of adults with CF are either studying or working. tw Socioeconomic Characteristics of Adults 18 Years and Older with CF, 216 Education Less than High School 6.9% Master s or Doctoral Degree 6.8% High School Diploma 24.1% College Graduate 29.8% Some College 31.5% Marital Status Married/ Living Together 42.5% Single 52.3% Separated/Divorced 4.8% Widowed.3% Employment Homemaker 3.7% Unemployed 7.7% Disabled 17.3% Retired 2.% Student 18.8% Full-time 38.3% Parttime 12.3% 8 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

11 Over the last ten years, there has been almost a doubling of the number of people who are married or living together and the number with a college degree. Characteristics of Adults with CF, ,263 Number of Adults ,696 4, ,81 1,857 2, Married/Living Together Bachelor's/Advanced Degree The number of pregnancies among women with CF has increased steadily since the 199s. Registry data show that 27 women with CF were pregnant in 216. The overall pregnancy rate among women with CF has remained relatively constant, in contrast to the pregnancy rate in the general U.S. population, which has declined during this time. 4 Number of Pregnancies in Women 14 to 45 Years with CF, Number of Pregnancies Year Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 9

12 Health Insurance Information Access to insurance coverage for specialized care and treatments is a challenge for some individuals with CF. Across all age groups, about half of the individuals in the Registry receive at least some component of their health insurance through federal or state-funded programs. Registry data show that in 216, a majority of people with CF who were age 18 to 25 were covered under their parents health insurance plan. Insurance Coverage in 216 Under 18 Years 18 to 25 Years 26 Years and Older All Number of individuals (n) 13,741 5,742 9,412 28,895 Health insurance policy (e.g. private insurance) (%) Medicare/Indian Health Services (%) Medicaid/state programs (%) TriCare or other military health plan (%) Other (%) No health insurance (%) Insurance coverage reflects coverage at any point during the year, thus, these categories are not mutually exclusive (except for the no health insurance option). Additional Insurance Information in 216 Individuals who participated in a patient assistance program (%) 37.8 Individuals 18 to 25 years covered under parents insurance (%) 55.1 Patient assistance program refers to any program that provides free medication or copay assistance. A large proportion of children with CF use Medicaid or state programs, including 56. percent of children under age 1. Though the overall prevalence of Medicare use is low, among adults age 3, 2. percent report Medicare coverage. This increases to 4. percent among adults in their early 6 s. Individuals under age 65 who receive Medicare have met the federal criteria for disability. Medicare/Indian Health Service and Medicaid/State Programs by Age in Years, 216 Number of Individuals n All Individuals n Medicaid or State Program n Medicare or Indian Health Service < Age (Years) Percentage of Individuals 1% 9% 8% 7% 6% 5% 4% 3% 2% 1% % < Age (Years) 1 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

13 DIAGNOSIS Diagnostic Characteristics of Individuals with CF This section examines characteristics of individuals diagnosed with CF, as well as trends over time for two key diagnostic tests: genotyping and sweat test. In 216, 62.4 percent of total new diagnoses and 86. percent of diagnoses among those less than 6 months old were detected by newborn screening (NBS). There is evidence that individuals diagnosed prior to the onset of symptoms have better lung function and nutritional outcomes later in life. 5 Diagnosis in the newborn period also represents an important opportunity for CF care centers to partner with community physicians and families to ensure the best possible care and outcomes for infants with CF. Number of New CF Diagnoses, ,2 New Diagnoses Percentage Detected by NBS 1 Number of New Diagnoses Percentage Detected by NBS Year The implementation of a screening program is typically associated with an increase in the number of newly diagnosed individuals. This is known as lead time bias since individuals who would have presented with symptoms later in life are detected earlier by a screening program. Thus, lead time bias is potentially the explanation for the increase in new cases during In recent years, we see a decrease in the number of individuals newly diagnosed with CF. Some of the decrease observed in 216 is the result of a yearly issue that infants born late in the year (i.e. late 215) were not seen at a CF care center before the close of the reporting year; therefore, their data are not yet included in the Registry. Future reports will be adjusted to include these individuals for the 216 diagnosis year. With the widespread use of newborn screening for CF, it was necessary to develop terminology for individuals with a positive NBS who have inconclusive sweat test results and/or less than two CF-causing genetic mutations. In the United States, this is referred to as CFTR-related metabolic syndrome 6 (CRMS); other countries use the term CF screen positive, inconclusive diagnosis (CFSPID). Recently released diagnosis guidelines harmonized the criteria for CRMS/CFSPID. 7 CRMS was added to the Registry as a diagnostic option in 21. In 216, data were entered for 688 individuals diagnosed with CRMS, 86 of whom were given this diagnosis during 216. Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 11

14 Entry of a diagnosis of CF versus CRMS into the Registry is a clinical decision; there is no requirement that individuals meet published diagnostic criteria for CF or CRMS. A comparison of clinical diagnoses of CF and CRMS in 21 and 211 showed that 41. percent of infants (n=126) who met the published diagnostic criteria for CRMS were entered into the Registry with a diagnosis of CF. 8 Analyses involving this cohort of patients must account for this apparent misclassification. Individuals can be diagnosed with CFTR-related disorder. This option has also been available in the Registry since 21. Individuals with this diagnosis do not meet diagnostic criteria for CF or CRMS, are affected by CF-related conditions such as congenital bilateral absence of the vas deferens (CBAVD), and often have mutations in the CFTR gene. 9 Collection and analysis of data from individuals with CRMS and CFTR-related disorder will provide new and important information for these distinct populations. CF, CRMS/CFSPID and CFTR-related Disorder Diagnoses, 216 CRMS/CFSPID 8.3% (n = 86) Cystic Fibrosis 85.6% (n=892) CFTR-related Disorder 6.1% (n = 64) In 216, 619 newborn infants were diagnosed with CF. Of those with a known gestational age at birth, 88.7 percent were born full-term, comparable with the figure for the general U.S. population. 1 The mean birthweight for full-term infants with CF is also about the same as for the U.S. population, 11 suggesting that babies born with CF do not initially show nutritional deficiencies. The graph does not include the 122 infants who were born and diagnosed with CF in 216, who did not have a gestational age recorded in the Registry (19.7 percent). Gestational Age of Infants Born and Diagnosed with CF in 216 Full-term 88.7% Preterm 11.3% Mean Birth Weight kg Mean Birth Length cm Preterm refers to infants born at a gestational age less than 37 weeks. Full-term refers to infants born at a gestational age greater than or equal to 37 weeks. 12 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

15 The majority of those diagnosed in their first year are asymptomatic or minimally symptomatic at time of diagnosis. Among the 11.3 percent of infants diagnosed in 216 under age one with meconium ileus (or other intestinal obstruction), 24. percent had bowel perforation. Those diagnosed after age one often present with acute or persistent respiratory abnormalities. Symptoms Reported at CF Diagnosis All Patients (%) Diagnosed in 216 (%) Diagnosed in 216 Age < 1 (%) Diagnosed in 216 Age 1 (%) Number of Individuals (n) 29, Asymptomatic DNA Analysis Family history Newborn (neonatal) screening Prenatal Screening (CVS A, Amniocentesis) N/A Symptomatic Meconium ileus/other intestinal obstruction Acute or persistent respiratory abnormalities CBAVD B or Infertility/GU C abnormalities Digital clubbing Edema.6... Electrolyte imbalance Failure to thrive/malnutrition Liver problems Nasal polyps/sinus disease Rectal prolapse Steatorrhea/abnormal stools/malabsorption Other Data are not mutually exclusive. We anticipate that additional 216 diagnoses will be entered into the Registry in 217. A Chorionic villus sampling B Congenital bilateral absence of the vas deferens C Genitourinary abnormalities Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 13

16 Previous figures in this section refer to infants born or diagnosed in 216; the following figure includes all individuals followed in the Registry in 216. Age at Diagnosis of All Individuals with CF Seen in 216 Number of Individuals 1, 9, 8, 7, 6, 5, 4, 3, 2, 1, Number of Individuals Cumulative Percentage Pre over natal Months _ Years Age Cumulative Percentage Among all individuals in the Registry in 216, 66.9 percent were diagnosed in the first year of life. Diagnostic Tests Sweat Chloride Testing Sweat chloride testing is an important diagnostic test recommended for all individuals regardless of genotype. 7 In 216, 88.5 percent of individuals in the Registry had a sweat chloride test result recorded. Individuals who are homozygous for F58del, the most common CF-causing genetic mutation, are less likely to have sweat chloride values in the Registry than those with other mutations. Baseline sweat chloride tests are becoming more important, as changes in sweat chloride are now viewed as indicators of the physiological effects of CFTR modulators. Percentage of Individuals with a Sweat Chloride Test Reported by Year of Diagnosis, Percentage of Individuals F58del Homozygotes Other Year Some individuals diagnosed in 216 may not have had a sweat chloride test result entered in the Registry before the close of the reporting year. 14 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

17 Median sweat chloride test results have remained consistent over time for individuals who are F58del homozygous. In contrast, there has been a steady decline in median sweat chloride values among individuals who are not homozygous for F58del, suggesting that more individuals with less severe mutations are being entered into the Registry. Sweat Chloride Value of F58del Homozygous Individuals by Year of Diagnosis, Sweat Chloride Value of Individuals Not Homozygous for F58del by Year of Diagnosis, Sweat Chloride Value (mmol/l) Year 25th Percentile Median 75th Percentile Sweat Chloride Value (mmol/l) Year 25th Percentile Median 75th Percentile Genotyping The cystic fibrosis transmembrane conductance regulator (CFTR) gene and the most prevalent CF-causing mutation (F58del) were discovered in Since then, genotyping has become a key component of the diagnostic work-up. In addition, with the introduction of CFTR modulators, genotyping all people with CF is becoming more important for research and clinical care. In 216, 97.7 percent of individuals (n=28,84) in the Registry had been genotyped. Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 15

18 CFTR GENE MUTATIONS To date, more than 1,8 mutations have been found in the CFTR gene. 12 Some mutations result in virtually no CFTR function and others are associated with some residual function. To help categorize CF disease-causing mutations on the basis of their resulting functional impact, researchers have created five classes This classification schema is an oversimplification, as some mutations lead to more than one defect in CFTR function. For example, the R117H mutation results in both gating and conductance defects in CFTR. In addition, functional status has not been determined for all mutations. One Way of Classifying CFTR Mutations Cl - Cl - Cl - Cl - Cl - Cl - Cl - Cl - Cl - Cl - X X X X X Normal Class I Class II Class III Class IV Class V EXAMPLES DESCRIPTION CFTR is created, reaches cell surface and functions properly, allowing transfer of chloride and water. No functional CFTR created. G542X W1282X R553X CFTR protein is created, but misfolded, keeping it from reaching the cell surface. F58del N133K I57del CFTR protein is created and reaches cell surface, but the gate does not function properly. G551D S549N V52F R117H The opening in the CFTR protein ion channel is faulty. R117H D1152H R347P CFTR is created in insufficient quantities kbC->T G->A A455E Adapted from: 16 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

19 The most common CFTR mutation is F58del: 86.4 percent of individuals in the Registry have at least one copy of this mutation. There is a substantial drop in prevalence from F58del to the next most common mutations. No other mutation is currently found in more than 5 percent of the U.S. CF population. Prevalence of the 25 Most Common CFTR Mutations in People with CF Seen in 216 CFTR Mutation Legacy Name cdna Name Protein Name Mutation Class Number of Individuals Percent of All People with CF F58del c.1521_1523delctt p.phe58del 2 24, G542X c.1624g>t p.gly542x 1 1, G551D c.1652g>a p.gly551asp 3 1, R117H c.35g>a p.arg117his N133K c.399c>g p.asn133lys W1282X c.3846g>a p.trp1282x R553X c.1657c>t p.arg553x G->A c g>a kbC->T c c>t G->T c.489+1g>t G->A c g>a G->A c g>a D1152H c.3454g>c p.asp1152his I57del c.1519_1521delatc p.ile57del T c [5] R1162X c.3484c>t p.arg1162x delC c.3528delc p.lys1177serfsx G85E c.254g>a p.gly85glu G->A c g>a insA c.252_253insa p.gln685thrfsx R347P c.14g>c p.arg347pro A455E c.1364c>a p.ala455glu R56T c.1679g>c p.arg56thr R334W c.1c>t p.arg334trp L26W c.617t>g p.leu26trp The number and percentage of individuals with a given mutation include those with one or two copies of the mutation. F58del Mutation Prevalence F58del Mutation Percent of All People with CF Homozygous F58del 45.8 Heterozygous F58del 4.7 Neither F58del or Unknown 13.5 Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 17

20 Among less common mutations, the number of individuals with an R117H mutation has increased over the years. Among those genotyped in 1993, less than 1 percent had an R117H mutation, compared with almost 5 percent of those genotyped in 216. This may be due to the inclusion of R117H in newborn screening algorithms. Of note, 12 (11.8 percent) of the 865 patients with an R117H mutation had a sweat chloride value less than 3 mmol/l. The clinical significance of the R117H mutation depends in part on the poly-t tract variant on the chromosome. Research indicates that a shorter poly-t tract is associated with a higher likelihood of having CF. 16,17 Unfortunately, the Registry has incomplete information on the poly-t tract status for the majority of individuals (66. percent) who are reported as having a diagnosis of CF and an R117H mutation. Of the 285 individuals with poly-t tract status recorded in the Registry, 18 (38. percent) are classified as having 5T. Poly-T Tract Status of Individuals with an R117H Mutation, 216 5T 18 Unknown 58 Known 285 Not 5T 177 Throughout this report, we use mutation class categories. Individuals with two mutations in classes I, II, or III are grouped together because these mutations typically lead to little or no CFTR function. Individuals with one or two mutations in classes IV or V are grouped together because these mutations are typically associated with residual CFTR function. Research has shown that this grouping of classes is associated with meaningful clinical differences between the groups. 14,15 The majority of patients in the Registry are in the mutation class I-III grouping. More information about how alleles are grouped into classes is provided in the Appendix (page 78). Mutation Class Group of Genotyped Individuals Number Percent Mutation Class I-III 2, Mutation Class IV-V 3, Mutation Class Unknown 4, Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

21 The majority of children and young adults with CF have genetic mutations in classes I-III. The number and proportion of individuals in this group decreases in older ages. Conversely, we see a greater number of individuals with genotypes in classes IV-V who are under age 1, and older ages. This is likely due to the implementation of NBS and survivor bias, respectively. Mutation Class Status by Age in Years, 216 (Stacked Bar Chart) Number Number of of Individuals Individuals n Mutation Class Not Identified n Mutation Class IV-V n Mutation Class I-III Percentage of Individuals of Individuals 1% 9% 8% 7% 6% 5% 4% 3% 2% 1% < Age Age (Years) (Years) % < Age Age (Years) (Years) Individuals in the class I-III group are younger and more likely to be prescribed pancreatic enzyme replacement therapy (PERT) than individuals in the class IV-V group (97. percent of individuals in the class I-III group and 35.6 percent in the class IV-V group are taking PERT). Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 19

22 In relation to disease severity, higher sweat test values are observed among individuals in classes I-III than in classes IV-V. Sweat Chloride Value (mmol/l), by Mutation Class Group Median 5th Percentile 95th Percentile Mutation Class I-III N=17, Mutation Class IV-V N=2, Genotyped But Not Identified in Mutation Classes I-III or IV-V N=4, All Individuals N=25, These charts use the most recent sweat test value reported to the Registry. For some individuals, this value may reflect sweat chloride values after initiation of CFTR modulator therapy. 2 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

23 GUIDELINES: CARE, SCREENING AND PREVENTION The CF Foundation has sponsored the development of clinical practice guidelines to promote high quality physical and mental health care for individuals with CF during infancy, childhood, and adulthood In accordance with guidelines for people with CF over age six, 2 many CF care centers report four office visits, two pulmonary function tests, and at least one microbiology culture annually for the majority of their CF patients. Similarly, among children age 2 to 5, the majority have at least four visits and at least one culture. However, adherence to the recommendation that CF care centers perform quarterly respiratory cultures continues to be lower and more variable across the CF care center network. 21 CF care centers report that respiratory therapists/physical therapists, dietitians/ nutritionists, and social workers evaluate most of their patients at least once per year, as recommended. 22 There is significant variation by CF care center in several key screening measures, including dual-energy X-ray absorptiometry (DXA) scans for osteopenia/ osteoporosis. The influenza vaccination rate for people with CF age 6 months and older remains high across the CF care center network. Smoking and secondhand smoke exposure remain challenges, particularly for infants and young adults. Patient Care Guidelines The percentage of individuals receiving care that meets CF Foundation care guidelines has increased in recent years. Because individuals should be able to perform reliable pulmonary function tests (PFTs) at age 6 and older, we use guidelines criteria for those age 7 and older to ensure that individuals were eligible to perform a reliable PFT for the entire year. Over the past decade, the number of children and adults receiving, at a minimum, the annual recommended four office visits, four respiratory cultures and two PFTs 2,21 has doubled. The percentage of adults who receive care that meets guidelines criteria remains lower than that observed in children. However, the percent of those meeting guidelines continues to rise. Currently, over half of adults are being seen at least four times, complete two or more PFTs, and are cultured at least once during the year. While we strive for all patients to meet guideline recommendations, we acknowledge that many factors outside of the control of CF care centers may impact metrics. Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 21

24 Percentage of Individuals Meeting Guidelines for Visits, Cultures and PFTs, Percentage of Individuals Year 7-17 Years (4 visits, 4 cultures, 2 PFTs) 18 Years (4 visits, 4 cultures, 2 PFTs) 7-17 Years (4 visits,1 culture, 2 PFTs) 18 Years (4 visits, 1 culture, 2 PFTs) The guidelines on infection prevention and control recommend that individuals with CF have quarterly respiratory cultures Nearly 98 percent of individuals received at least one culture in 216, and 55.3 percent of individuals had four or more respiratory cultures. Those under age 18 were more likely to meet the recommendation for four cultures. The multidisciplinary care team plays an important role in CF care. 2 Over time, there has been an increase in the number of individuals with CF who receive at least an annual evaluation from a respiratory/physical therapist, dietitian/nutritionist, and social worker. In 216, 72.1 percent of individuals were evaluated by all three specialists. Percentage of Individuals Evaluated by Multidisciplinary Care Team Members, Percentage of Individuals Evaluated by a Respiratory/Physical Therapist Evaluated by a Dietitian/Nutritionist Evaluated by a Social Worker Year 22 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

25 The CF Foundation recently supported the inclusion of mental health professionals as part of the CF care team. Information on screening for anxiety and depression is included in the Complications section (page 69). The Centers for Disease Control and Prevention s Advisory Committee on Immunization Practices recommends influenza vaccination for all individuals with CF age six months and older. 24 The influenza vaccination rate of people with CF who are six months and older is 74.6 percent of the total population and 89.5 percent of those with a known vaccination status (excluding 16.6 percent with unknown status). Flu Vaccine Status by Age in Years, 216 (Stacked Bar Chart) Number of Individuals n Flu Vaccine Status Unknown n No Flu Vaccine Received (including those allergic or refused) n Received Flu Vaccine Percentage of Individuals 1% 9% 8% 7% 6% 5% 4% 3% 2% 1% < Age (Years) % < Age (Years) Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 23

26 The CF Foundation consensus statement on bone health and disease recommends screening all adults with CF with a DXA scan and subsequent follow-up based on the findings of the baseline scan. 25 Annual screenings are recommended only for individuals with DXA z-scores that are lower than two standard deviations below the mean, with less frequent screening recommended for those with higher values. Therefore, in the figure below, we group five years of data. Percentage of Individuals with a DXA Scan in the Past Five Years, by Center 5 1 Median Min Max Individuals 18 Years and Older Includes any DXA scans performed during Previously, we reported the percentage that had a DXA scan within the Registry reporting year. CF Foundation guidelines recommend annual measurement of fat-soluble vitamins to screen for vitamin deficiency. 22,26 The CF Foundation Hepatobiliary Disease Consensus Group recommends a yearly panel of liver blood tests for all people with CF to screen for possible liver disease. 27 Registry data suggest that these tests are being done on the majority of individuals. Percentage of Individuals Screened by or Monitored with Annual Labs, by Center 5 1 Median Min Max Individuals with Fat-Soluble Vitamins Measured Individuals with Liver Enzymes Measured Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

27 Tobacco Smoke Exposure by Age in 216 Percentage of Individuals Monthly Monthly Secondhand Secondhand Smoke Smoke Exposure Exposure Weekly Weekly Secondhand Secondhand Smoke Smoke Exposure Exposure Daily Daily Secondhand Smoke Smoke Exposure Exposure Smoker <2 2 to 5 6 to 1 11 to to to to Overall Age (Years) Tobacco smoke and secondhand smoke exposure remain significant concerns, especially for infants and young adults. 28 In 216, 2. percent of individuals with CF reported monthly or more frequent exposure to tobacco smoke, either secondhand or as a smoker. Cigarette smoking prevalence is lower in the CF population than in the general U.S. population; only 2.1 percent of adults with CF are smokers, compared with 17.5 percent in the general population in Smoke exposure was unknown for 35.2 percent of individuals with CF, who were excluded from the analyses. Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 25

28 Infant Care Guidelines The CF Foundation recommends that evaluation and treatment of infants detected by newborn screening should be done at an CF Foundation-accredited care center. Infants with CF should have an initial visit at an accredited care center within hours. It is important to make a definitive diagnosis as quickly as possible so families can be educated about the disease and treatment can be started. 5 Encouragingly, 88.6 percent of infants diagnosed have their first clinic encounter, genotyping, or sweat test within 3 days of birth. Time from Birth to First Recorded Sweat Test for Infants with CF Born in 215 and Detected by Newborn Screening (n=52) Number of Infants Cumulative Percentage < Weeks The chart shows data for children born in 215 because a full year of data is available for these individuals. Median time to first sweat test for these individuals is 27 days. Of individuals with CF born in 215, 63 infants (12.5 percent) who were detected by NBS did not have a sweat chloride test reported to the Registry by the end of 216 and thus are not included in this analysis. The CF Foundation infant care guidelines recommend monthly CF care center visits during the first 6 months of life and every 1 to 2 months in the second 6 months. 5 Therefore, we expect infants with CF detected by NBS to have 9 to 12 visits in the first year of life. There is marked variation in the number of encounters for individuals in the first year of life across the CF care center network. 26 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

29 Number of Encounters in the First Year of Life for Infants with CF Born in 215 and Detected by Newborn Screening (n=56) Number of Infants Cumulative Percentage Number of Encounters The chart shows data for children born in 215 because a full year of data is available for these individuals. The median number of visits in the first year of life is nine. Respiratory cultures are being collected at the majority of clinic visits for infants with CF. Infant care guidelines recommend that cultures be performed at least quarterly during the first two years of life. 5 Number of Respiratory Cultures in the First Year of Life for Infants with CF Born in 215 and Detected by Newborn Screening (n=56) Number of Infants Cumulative Percentage Number of Respiratory Cultures The chart shows data for children born in 215 because a full year of data is available for these individuals. The median number of cultures in the first year of life is six. Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 27

30 Fecal elastase testing, which provides an objective measure of pancreatic function, is recommended in the infant care guidelines. 5 There is marked variation in the use of this test across the CF care center network. The guidelines also recommend that infants begin salt supplementation after diagnosis, and this is widely followed across the CF care center network. We observe substantial variation in the utilization of palivizumab (respiratory syncytial virus, or RSV, prophylaxis) across the CF care center network, with a downward trend since 28. The current American Academy of Pediatrics recommendation is that palivizumab should not be routinely used in individuals with CF. 3 The CF Foundation infant care guidelines recommend that its use be considered for infants with CF. 5 Infant Care Guidelines, by Center 5 1 Median Min Max Fecal Elastase Value Reported for Individuals Less Than 24 Months Salt Supplements in Individuals Less Than 36 Months RSV Prophylaxis in Individuals Less Than 36 Months Testing and Therapies for Individuals Under 24 Months of Age, Percentage of Individuals Salt Supplementation Reported Fecal Elastase Value Reported RSV Prophylaxis Reported Year 28 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

31 MICROBIOLOGY Bronchiectasis with chronic pulmonary infections represents a serious problem for most individuals with CF. This section provides information on trends in CF airway pathogens over time and by age group. Updated infection prevention and control guidelines provide current best practices for reducing exposure to CF pathogens in the health care setting and in everyday life. 31 The prevalence of Pseudomonas aeruginosa (P. aeruginosa or PA) continues to decrease. This may relate in part to widespread implementation of therapy to eradicate initial acquisition. 23,31 Despite this, the prevalence of infection with multidrug-resistant P. aeruginosa (MDR-PA) has remained constant. Some of the increase in Staphylococcus aureus (S. aureus) may be due to improved microbiologic practices for detection and reporting of Gram-positive organisms. From 2 to 21, there was a significant increase in the numbers of individuals with CF with a positive culture for methicillin-resistant S. aureus (MRSA). Since 21, prevalence appears to have plateaued. The stabilization of prevalence is potentially due to increased awareness and infection prevention and control strategies. Prevalence of Respiratory Microorganisms, S. S. aureus Percentage of Individuals P. aeruginosa MRSA H. influenzae S. S. maltophilia MDR-PA Achromobacter B. B. cepacia complex Year The graph shows the proportion of individuals in various age groups who cultured positive for the bacterial species indicated during 216. Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 29

32 Prevalence of Respiratory Microorganisms by Age Cohort, Percentage of Individuals <2 2 to 5 6 to 1 11 to to to to Age (Years) P. aeruginosa H. influenzae B. cepacia complex S. aureus MRSA Achromobacter S. maltophilia MDR-PA A note about the reporting of Burkholderia species: in 216, 721 people with CF were reported in the Registry as having had a culture positive for Burkholderia cepacia (B. cepacia) complex. A preliminary comparison of the Burkholderia species entered in the Registry as compared to those reported by the CF Foundation B. cepacia Research Laboratory and Repository at the University of Michigan shows discordant results. Further investigation is needed on the reporting practices for these variables before figures on B. cepacia complex sub-species can be included in the report. The table below displays prevalence of the key respiratory microorganisms in 216 along with median age at first positive culture for the species. Culture Data for Individuals Seen in 216 Bacteria Percent with Infection Median Age in Years at First Infection P. aeruginosa B. cepacia complex MRSA S. maltophilia Achromobacter xylosoxidans Non-tuberculous mycobacteria Distinctive Features In CF A leading cause of airway infection Associated with a decline in lung function 17.7% of strains are multi-drug resistant Small proportion of people with CF infected Can lead to rapid deterioration Multi-drug resistant Prevalent among people with and without CF Multi-drug resistant Healthcare and community-associated strains Found in water, soil, plants, animals and hospital environments Often multi-drug resistant Inhabits natural environment, including soil and water Often multi-drug resistant Found in water and soil Sporadic reports of person-to-person spread Treatment is rigorous and often poorly tolerated 3 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

33 Pseudomonas aeruginosa The percentage of individuals with a positive culture for P. aeruginosa has continued to decline over time, with the largest decrease observed among individuals younger than 18 years (49.8 percent had a positive culture in 1996 compared with 29.1 percent in 216). Many individuals with CF now transition to adult care without P. aeruginosa in their respiratory tract. Rates of MDR-PA infection are greatest in older adolescents and adults with CF. These findings likely reflect cumulative exposure to antibiotics. The clinical significance of this drug resistance is unclear. Among the individuals with CF who had at least one bacterial culture in 216, 8. were reported to have MDR-PA percent of individuals with a P. aeruginosa infection were reported to have MDR-PA. P. aeruginosa and Multidrug-Resistant P. aeruginosa by Age in Years, 216 Number of Individuals n All Individuals n P. aeruginosa n Multidrug-Resistant P. aeruginosa Percentage of Individuals 1% 9% 8% 7% 6% 5% 4% 3% 2% 1% < Age (Years) % < Age (Years) Multidrug resistance is defined as resistance to all antibiotics tested in two or more classes in a single culture. A classification system known as the Leeds criteria is used to categorize individuals on the basis of P. aeruginosa infection status. 32 The Leeds criteria categories are never having a positive P. aeruginosa culture, free of a positive P. aeruginosa culture in the past 12 months, intermittent infection (less than 5 percent of their cultures in the past year were positive for P. aeruginosa), and chronic infection (more than 5 percent of their cultures in the past year were positive for P. aeruginosa). In 216, 19.7 percent of individuals in the Registry had never had a positive culture for P. aeruginosa. Another 3. percent of individuals had cultures that were negative for P. aeruginosa during the entire calendar year, but had a positive culture in a previous year. Some 46.9 percent of individuals had at least one positive culture, of which 29.1 percent were categorized as having chronic infection, and 17.8 percent as having intermittent infection. Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 31

34 P. aeruginosa Status Using Leeds Criteria, % 17.8% Intermittent PA 46.9% 3.% 29.1% Chronic PA 3.4% Not Cultured Never Cultured Positive Cultured Negative (previously positive) Cultured Positive Staphylococcus aureus S. aureus is currently the most common microorganism reported among individuals with CF. Overall, more than half of individuals had at least one culture positive for methicillin-sensitive S. aureus (MSSA) in 216. This chart shows that the highest prevalence of MRSA occurs in individuals between the ages of 1 and 3, while MSSA peaks among those younger than 1. MSSA and MRSA by Age in Years, 216 Number of Individuals n All Individuals n MSSA n MRSA Percentage of Individuals 1% 9% 8% 7% 6% 5% 4% 3% 2% 1% < Age (Years) % < Age (Years) 32 Cystic Fibrosis Foundation Patient Registry Annual Data Report 216

35 Nontuberculous Mycobacteria Prevalence of nontuberculous mycobacteria (NTM) infections is increasing in the general population. 33 Since 21, the Registry has collected more robust information on mycobacterial cultures and NTM infections. The CF Foundation/European Cystic Fibrosis Society Guidelines Committee recommends that individuals with CF who are able to expectorate be cultured for NTM infections annually. 34 Individuals should also be screened before and six months after beginning azithromycin and annually thereafter. 2 The data show improvement in screening rates over time, but wide variation by CF care center persists in these measures. Percentage of Individuals with a Mycobacterial Culture, by Center 5 1 Median Min Max Individuals Who Produced a Sputum Sample During the Year Individuals Taking a Chronic Macrolide Who Produced a Sputum Sample During the Year A throat swab is insufficient for a mycobacterial culture, so a patient must be able to produce sputum in order for this culture to be performed. As shown in the chart below, a majority (78.1 percent) of the individuals who produced a sputum culture for a bacterial culture also had a mycobacterial culture performed during the year. Sputum Produced and Mycobacterial Cultures by Age in Years, 216 Number of Individuals n All Individuals n Sputum Produced n Mycobacterial Culture Percentage of Individuals 1% 9% 8% 7% 6% 5% 4% 3% 2% 1% < Age (Years) % < Age (Years) Annual Data Report 216 Cystic Fibrosis Foundation Patient Registry 33