cdc-rfa-ck12-120205cont16 final 08 01 15.docx

Centers for Disease Control and Prevention (CDC) Procurement and Grants Office Instructions for Preparing an Annual Performance Report (APR) Catalog of Federal Domestic Assistance (CFDA): 93.317 Funding Opportunity Announcement (FOA) Number: CDC-RFA-CK12-120205CONT16

Emerging Infections Program National Center for Emerging and Zoonotic Infectious Diseases

Eligibility:

This award will be a continuation of funds intended only for grantees previously awarded under CK12-1202: Emerging Infections Program

Application Submission:

CDC requires grantees to submit their Annual Performance Reports (APR), which serves as the continuation application, through www.Grants.gov NLT 120 days prior to the end of the budget period.

If you encounter any difficulties submitting your annual performance report through www.Grants.gov, please contact CDC’s Technical Information Management Section at 770-488-2700 prior to the submission deadline. If you need further information regarding the annual performance report process, please contact Sheila Edwards, Grants Management Officer, at 770-488-1644. For programmatic information, please contact Mark Frank, Project Officer, at 404-639-3743.

Reports must be submitted by September 18, 2015, by 11:59 P.M. EST on Grants.gov, for the Reporting Period of January 1, 2016 – December 31, 2016. Late or incomplete reports could result in an enforcement action such as a delay in the award or a reduction in funds. CDC will accept requests for a deadline extension on rare occasions and after adequate justification has been provided.

General Application Packet Tips:

· Properly label each item of the application packet

· Each section should use 1.5 spacing with one-inch margins

· Number all narrative pages only

· This report must not exceed 125 pages excluding administrative reporting

· Where the instructions on the forms conflict with these instructions, follow these instructions

1. CDC requires the use of PDF format for ALL attachments.

2. Use of file formats other than PDF may result in the file being unreadable by CDC staff.

3. Directions for creating PDF files can be found on www.Grants.gov

Checklist of required contents of application packet:

1. SF-424 Application for Federal Domestic Assistance-Short Organizational Form

2. SF-424A Budget Information-Non-Construction Programs

3. Budget Justification

4. Indirect Cost Rate Agreement

5. Project Narrative

Instructions for accessing and completing required contents of the application package:

a) Go to: www.Grants.gov

b) Select: “Apply for Grants”

c) Select: “Step 1: Download a Grant Application”

d) Insert the CDC-RFA-CK12-120205CONT16 only

e) Download application package and complete all sections.

1. SF-424 Application for Federal Domestic Assistance-Short Organizational Form:

Complete all sections:

A. In addition to inserting the legal name of your organization in Block #5a, insert the CDC Award Number provided in the CDC Notice of Award. Failure to provide your award number could cause delay in processing your application.

B. Please insert your organization’s Business Official information in Block #8.

SPECIAL NOTE: Items 2, 3, and 4 should be attached to the application through the “Mandatory Documents” section of the “Grant Application” page. Select “Other Attachments Form” and attach as a PDF file.

2. SF-424A Budget Information and Justification:

A. Download the form from www.grants.gov.

B. Complete all applicable sections.

C. A budget and budget justification is required for each Project/Program Area in which you are applying. In a separate narrative, provide a detailed, line-item budget justification of the funding amount requested to support the activities to be carried out with those funds. Attach in the “Mandatory Documents” box under “Budget Narrative Attachment Form.” Document needs to be in the PDF format.

D. The budget justification must be prepared in the general format and to the level of detail described in the CDC Budget Guidance. The sample budget guidance is provided on CDC’s internet at: http://www.cdc.gov/od/pgo/funding/grants/foamain.shtm.

E. For any new proposed subcontracts provide the information specified in the Budget Guidance.

F. Base the proposed budget on the federal funding level stated in the letter from CDC or anticipated level funding.

G. Estimated Un-obligated

1. Awardees may request up to 75% of anticipated unobligated funds from the current budget period. Carryover requests must include a list of the proposed activities, an itemized budget (broken out by project), and a narrative justification for the proposed activities. Please note that carryover request should be submitted as a separate document and should not be included as part of your continuation budget. The request can be submitted through Grants.gov along with your continuation application or emailed to PGO and the EIP Program Office separately. A signed and dated cover letter must be included even if the request is being submitted through Grants.gov as part of your continuation application.

2. If use of estimated un-obligated funds is requested, complete all columns in Section A of SF-424A and submit along with your carryover request and a signed and dated interim Federal Financial Report (FFR), Standard Form-425, available on the CDC internet at http://grants.nih.gov/grants/forms.htm#closeout.

3. The estimated un-obligated balance should be realistic in order to be consistent with the annual FFR to be submitted via eRA Commons following the end of the budget period. The interim FFR must reflect all funds awarded in the current budget period (since January 01, 2015) and report estimated total expenditures for the full 12-month period that will end December 31, 2015. Therefore, the resulting unobligated balance (if any) will be an estimate of what will remain unobligated as of December 31, 2015.

H. When non-federal matching is required, provide a line-item list of non-federal contributions including source, amount, and/or value of third party contributions proposed to meet a matching requirement.

3. Indirect Cost Rate Agreement:

A. If indirect costs are requested, include a copy of the current negotiated federal indirect cost rate agreement or a cost allocation plan approval letter for those Grantees under such a plan.

B. Clearly describe the method used to calculate indirect costs. Make sure the method is consistent with the Indirect Cost Rate Agreement.

C. To be entitled to use indirect cost rates, a rate agreement must be in effect at the start of the budget period.

D. If an Indirect Cost Rate Agreement is not in effect, indirect costs may be charged as direct if (1) this practice is consist with the grantee’s/applicant’s approved accounting practices; and (2) if the costs are adequately supported and justified. Please see the Budget Guidelines (http://www.cdc.gov/od/pgo/funding/grants/foamain.shtm) for additional information.

E. If applicable, attach in the “Mandatory Documents” box under “Other Attachments Form”. Name document “Indirect Cost Rate.”

4. Project Narrative:

Section I. Current Budget Period Progress:

Provide a brief report addressing the following elements of each objective or activity.

The annual performance report must include the following:

A. Status (met, ongoing, or unmet). Awardees must report on the progress of completing activities outlined in the work plan, as well as performance measures.

B. Successes - Include a description of successes achieved in the past year along with specific success stories.

C. Challenges – If applicable, include a description of barriers encountered in the past year and how they were addressed, such as challenges that affected or might affect their ability to achieve annual and project period outcomes, conduct performance measures, or complete activities outlined in the work plan. Awardees should also describe how CDC could help them overcome the challenges.

D. Major findings, significance of those findings (a description of how the findings impact or contribute to the public health goal).

E. Attach in the “Mandatory Documents” box under “Project Narrative Attachment Form”. Document needs to be in the PDF format.

Section II. New Budget Period Proposed Objectives and Activities:

A. List proposed objectives for the upcoming budget period (January 1, 2016 – December 31, 2016). These objectives must support the intent of the original Funding Opportunity Announcement (FOA).

B. Each objective and activity must contain a performance or outcome measure that assesses the effectiveness of the project.

C. For each objective:

1. List activities that will be implemented;

2. Provide a timeline for accomplishment;

3. Identify and justify any redirection of activities; and

4. Explain the methods you will use to implement the new, redirected activities.

D. In addition to this information, include comments pertaining to budgetary issues that might hamper the success or completion of the project as originally proposed and approved. Please utilize the work plan format in the original work plan, if applicable.

5. Additional Program Requirements (If applicable)

Detailed guidance follows.

EIP FY 2016 DETAILED GUIDANCE

This document provides guidance for the 2016 Emerging Infections Programs (EIP) renewal applications. All applications should contain proposals for core ABCs, FoodNet, Influenza, and Healthcare Associated Infections – Community Interface (HAIC) surveillance, as well as flexible response activities. Sites may also submit proposals for optional projects within the core activities and/or other/site-specific activities described below.

Active Bacterial Core Surveillance (ABCs) NOTE: In order to extend available resources for new ABCs activities, existing ABCs sites may elect to scale back on routine surveillance for one or two pathogens. Sites may propose such changes in their applications. The actual pathogen and extent of change (not collecting isolates for certain pathogens, discontinuing completion of case report forms for a specific age group, etc., should be discussed with CDC prior to change in surveillance to ensure that critical data elements are captured by the overall ABCs system (important trends, geographic distribution of strains data, etc.).

ABCs Core Surveillance: REQUIRED

1. Conduct active, population-based, laboratory surveillance for invasive bacterial disease due to group A Streptococcus (GAS), group B Streptococcus (GBS), Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae. Active surveillance includes:

a. Complete standardized case report forms through review of medical records.

b. Collection of isolates for all pathogens under surveillance (GAS, GBS, H. influenzae, N. meningitidis and S. pneumoniae) and shipment to ABCs referral labs on a monthly or bi-monthly basis.

c. Conduct periodic (at least annual) audits of all clinical laboratories within ABCs surveillance area and of labs outside of the surveillance area (this includes annual assessment with point of contacts at large dialysis referral laboratories) that test a large proportion of isolates from residents of the ABCs surveillance area to verify completeness of case ascertainment.

2. Collect live births denominators (including stratification by birthweight and gestational age) from vital statistics annually.

3. Collect missing race and ethnicity data on all ABCs cases less than 5 years of age using birth certificates annually.

4. Submit data electronically to CDC (in our secure format) by the specified deadline and upon CDC request.

5. Provide timely responses to reports and requests for information to assist in preliminary & final analyses, reports, and data close-outs.

6. Geocode all ABCs cases to the census tract level as a means of capturing area-level socioeconomic factors, such as poverty, educational level, household crowding, and access to healthcare. CDC and site regulations will determine what data may be transmitted to CDC.

Other ABCs Core Activities: REQUIRED

1. Participate in Steering Committee, Surveillance Officer, and Pathogen committee conference calls.

2. Participate in annual ABCs Steering Committee and Surveillance Officer meetings.

3. Collect additional information on infant and maternal cases of all early- and late-onset GBS disease.

4. For participating sites: Evaluate the effectiveness of the 13-valent pneumococcal conjugate vaccine for prevention of S. pneumoniae infections among adults using a case-control methodology. Collaborate with CDC to develop methods for case and control enrollment, which could include collaboration with the Center for Medicare and Medicaid Services as well as geocoding of cases and controls.

5. Evaluate trends in hospitalizations for community-acquired pneumonia using state-based hospital discharge data.

6. Perform surveillance for non-invasive pneumococcal pneumonia among adults by identifying cases with a positive urinary antigen test or sputum culture and clinically or radiographically-confirmed pneumonia within the designated surveillance area. Surveillance activities include collection of case report form data. Using ICD9/10-coded discharge data from hospitals that perform urine antigen testing, assess the frequency of such testing among pneumonia hospitalizations. Within the entire catchment area, assess the proportions of pneumonia hospitalizations admitted to hospitals that perform urine antigen testing vs. those that do not.

7. Collect additional demographic, medical and vaccination history information on all invasive pneumococcal infections in children aged 3 months through 59 months with an isolate available for serotyping. This includes contacting parents to identify healthcare providers who provide immunizations to their children, contacting all identified providers to ascertain PCV13 vaccination status, and review of state vaccine registries to obtain complete vaccine information for cases of invasive pneumococcal disease.

8. Contact healthcare providers or state vaccine registries to obtain complete vaccine information for cases of Hib disease age <5 years to monitor impact of new vaccines.

9. For ABCs cases for which disease outcome is unknown, compare ABCs case outcomes to state vital statistics deaths registry within the surveillance area to maximize completeness and accuracy of information on potential deaths due to ABCs infections.

10. Work to integrate ABCs data needs with sites’ changing landscape of access to electronic medical records and public health records. Maintain flexibility to rapidly respond to changes in core surveillance. Sites must have the ability to quickly (within three months) modify data collection methods and site databases to respond to changes in ABCs surveillance. Changes may include addition or deletion of variables submitted to CDC.

11. Legionellosis Surveillance: Perform at least annual audits of laboratories conducting Legionella testing within the ABCs legionellosis surveillance catchment area to ensure that all laboratory-confirmed cases of legionellosis are being identified by the state-based reporting systems.

Additional ABCs Activities: OPTIONAL These activities may be restricted to sites that have successfully participated in core activities for at least two years, except as noted.

1. Expand surveillance for invasive bacterial infections for ABCs pathogens to include patients who test positive by nucleic acid tests obtained from sterile site specimens. This would include gathering data on the type of test used and how it was validated.

2. Non-invasive pneumococcal pneumonia surveillance: In addition to routine surveillance listed in the required section, sites can choose to collect urine specimens from patients with positive urine antigen tests. The specimens would be used to evaluate a serotype-specific pneumococcal assay that is being developed. Collection of specimens would not have to be population-based, but could occur at select facilities. Sites may also choose to collect isolates from sputum cultures which would be used to determine the pneumococcal-specific serotype.

3. Participate in activities investigating population host factors that are potential risks for ABCs infections. This may include but is not limited to underlying conditions such as diabetes and obesity, and co-infections.

4. Conduct evaluation of Legionella urine assays under development that 1) Detect non-Legionella pneumophila serogroup 1 (Lp1) infections and 2) Detect Lp1 strain types. This would involve collecting paired urine and respiratory specimens from patients at select laboratories (i.e. does not need to be population-based) and would not require additional collection of patient information.

5. Conduct a study to understand differences in legionellosis testing practices across facilities and regions. This would entail measuring the proportion of patients tested for Legionnaires’ Disease (by urine antigen or respiratory culture) with admitting or discharge diagnoses related to pneumonia at select facilities. Facilities would be selected based on incidence rates in the region (high, medium and low incidence areas would be selected) and hospital characteristics (level of acuity, size, etc.).

6. Conduct surveillance for neonatal sepsis in children less than three days old (first 72 hours of life). This would include the optional collection of isolates.

7. Conduct expanded surveillance for H. influenzae neonatal sepsis and H. influenzae in pregnant and post-partum women.

8. Conduct supplemental surveillance for severe GAS infections. Participating sites will either a) conduct enhanced surveillance for streptococcal toxic shock syndrome (STSS) and necrotizing (NF) using a single page supplemental form; b) conduct enhanced surveillance for NF including collection of special reports (imaging, pathology, or surgical); c) conduct enhanced surveillance for NF using ICD9/10 codes; or, d) combination of options above.

9. Conduct a study to identify potential human genetic factors associated with severe presentations of GAS such as NF and STSS. After appropriate IRB approvals, participating sites will retrospectively and prospectively contact persons (cases) who have had NF or STSS to obtain consent, to enroll them and to mail potential participants saliva collection kits. Genomics work will be completed by external partners.

10. Complete studies of nasopharyngeal colonization with S. pneumoniae among children targeted for vaccination with 13-valent pneumococcal conjugate vaccine. Sites with baseline data are encouraged to evaluate the effects of the new pneumococcal conjugate vaccine after it is introduced into the routine infant immunization program.

11. Launch studies of nasopharyngeal colonization with S. pneumoniae among adults. These studies will assist in evaluating the indirect effects of vaccinating children with PCV13 and the direct effects of vaccinating adults.

12. Conduct surveillance and special studies related to antimicrobial resistant infections:

a. Establish and implement methods for monitoring potential complications from antibiotic stewardship efforts aimed at reducing unnecessary antibiotic use (e.g. complications from reduced treatment of otitis media)

b. Develop and evaluate programs related to appropriate antibiotic prescribing for community-associated invasive and noninvasive infections.

c. Participate in developing and conducting risk factor studies related to community-associated antimicrobial-resistant infections.

d. Conduct pharyngitis surveillance with associated isolate collection in 1-2 ABCs sites in order to compare GAS emmtype and resistance profiles between pharyngitis and invasive GAS infections. Where possible, correlation between microbiologic profiles and local antibiotic use patterns will be evaluated.

13. Perform enhanced surveillance for Bordetella pertussis:

a. Utilize state-based pertussis reporting systems to conduct enhanced surveillance for Bordetella pertussis that is characterized by enhanced case ascertainment and augmented data collection.

b. Follow-up on all serology-positive pertussis laboratory results in addition to persons PCR and culture positive for B. pertussis.

c. Collect complete information on clinical course of infection, vaccination history (DTP/DTaP and Tdap), laboratory testing, and other epidemiologic information of interest (e.g., source of infection) as outlined in the case report form instruction sheet. Incorporate new variables as agreed on by CDC, participating sites, and/or the pertussis pathogen committee.

d. Collect isolates of Bordetella pertussis, when available, and periodically ship to CDC for further laboratory characterization.

e. Collect clinical specimens/DNA extracts that are PCR positive for Bordetella pertussis (based on specifications provided by CDC) and periodically ship to CDC for further laboratory characterization.

f. Utilize state immunization registries and other methods outlined in the case report form instruction sheet to obtain/verify pertussis vaccination history.

g. Conduct annual audits of laboratories (commercial, public health and/or hospital laboratories) conducting testing for B. pertussis to ensure the identification of all laboratory-confirmed cases of B. pertussis.

h. Build and strengthen pertussis case finding infrastructure in order to conduct special studies including evaluations of pertussis prevention and control strategies.

i. When available, collect epidemiologic information and specimens on other Bordetella species (specifically, B. parapertussis, B. bronchiseptica, and B. holmesii).

j. Participate in routine conference calls with CDC and other participating sites to standardized surveillance methodology and address issues.

14. Complete expanded medical record review of hospitalized pertussis cases (all ages) identified through Enhanced Pertussis Surveillance to better understand reasons for hospitalization, severity of illness, underlying medical conditions, factors associated with treatment, and outcomes.

15. Evaluate secondary transmission of B. pertussis among household contacts following a 5-day course of Azithromycin post-exposure prophylaxis.

a. Enroll household contacts (all ages) of pertussis cases identified through EPS; household contacts will be recommended PEP based on existing local public health guidelines and as part of routine follow-up and case investigation.

b. Conduct study visits at two time points (enrollment and 2-3 weeks post-enrollment) to interview and collect nasopharyngeal and blood samples from consenting, eligible household contacts; conduct an additional telephone interview 2-3 weeks post second visit on a subset of eligible participants.

c. Utilize CDC-developed data management systems and routinely transmit study data to CDC.

d. Participate in routine conference calls with CDC and other participating sites to discuss progress, monitor enrollment and address methodology-related questions.

e. For a subset of eligible household contacts, conduct additional specimen collection (nasopharyngeal and blood samples) at time points up to 1 year post enrollment.

16. Assess the effectiveness of pertussis vaccines (DTaP and Tdap) against circulating B. pertussis strains.

a. Develop protocol and identify appropriate methodology and sample size in collaboration with CDC and the pertussis pathogen committee.

b. Initiate/conduct evaluation as funding permits.

Participate in other activities as determined appropriate and important for the ABCs sites by the ABCs Steering Committee.

ABCs Performance Measures Routine ABCs activities:

1. Participation in conference calls related to ABCs, i.e., >1 site participant per call: 90%.

2. Identification of all labs located within and adjacent to the ABCs surveillance area that test a significant proportion of isolates from surveillance area residents, performed prior to initiating ABCs surveillance and periodically (e.g., every 2-3 years): 100%

3. Completion of audits of all clinical laboratories within the ABCs surveillance area and of labs outside of the surveillance area that test a significant proportion of isolates from residents of the ABCs surveillance area to verify completeness of case ascertainment, performed at least annually: 100%

4. On time reporting of complete case counts according to pre-established timelines: 100%

5. Entry of data abstractions, into a CDC approved database, and the transfer of that data to CDC, through established mechanisms, according to established timelines: 90%

6. Proportion of enrolled cases from which isolates are forwarded for serotyping and other laboratory characterization: >85%

7. Shipment of isolates to CDC, according to established isolate shipping schedules.

Special or optional ABCs studies:

1. Proportion of eligible cases enrolled in special studies, to be determined for each study by ABCs sites and CDC.

2. Proportion of cases and controls enrolled in special studies (e.g., vaccine effectiveness) with provider verified vaccination status reported: >95%

Foodborne Diseases Active Surveillance Network (FoodNet)

FoodNet Core Activities: REQUIRED NOTE: In addition to core EIP FoodNet activities listed below, FoodNet sites are expected to participate in PulseNet, National Outbreak Reporting System (NORS), and National Antimicrobial Resistance Monitoring System (NARMS) human isolate surveillance activities. However, funding for those other activities is provided through non-EIP mechanisms. Sites should request funding for PulseNet, NORS, and NARMS human surveillance activities through the Epidemiology and Laboratory Capacity for Infectious Diseases ELC process.

1. Conduct active, population-based surveillance for Salmonella, Shigella, Campylobacter, Listeria, Yersinia, Shiga toxin-producing E. coli (STEC), Vibrio, Cryptosporidium, and Cyclospora infections. Active surveillance includes:

a. Obtain complete information on all FoodNet variables for all cases diagnosed by culture or by culture-independent methods.

b. For cases diagnosed by culture this includes, but is not limited to, information on foreign travel and outbreak association for STEC, Salmonella, and Campylobacter cases.

c. For cases diagnosed by culture-independent methods this includes, but is not limited to, collection of information on laboratory tests used, test results, clinical data, and patient information.

d. For cases for which whole genome sequence (WGS) information is obtained, the WGS information will be submitted to National Institute of Health’s National Center for Biotechnology Information (NCBI) with appropriate metadata so CDC can link isolate information to epidemiologic information. Isolates will also be subtyped by PFGE and patterns uploaded to PulseNet.

e. Interview all persons with Listeria, Vibrio, and Salmonella serotype Typhi and Paratyphi infections using national case report forms.

f. Conduct audits at least annually of every clinical laboratory within the FoodNet surveillance area and of laboratories outside the surveillance area that test a large proportion of isolates from residents of the surveillance area to verify completeness of case ascertainment.

g. Conduct routine standardized surveillance of clinical laboratories in the FoodNet surveillance area and of laboratories outside the surveillance area that test a large proportion of isolates from residents of the surveillance area to ascertain changes in testing practices for FoodNet pathogens. Inform CDC of changes monthly. Submit data for all labs to CDC once a year or upon request.

h. Submit all available isolates to a state public health laboratory for confirmation, including speciation or serotyping, when appropriate.

i. Write a plan for obtaining at least a portion of isolates from specimens with a positive CIDT test, with guidance from the Steering Committee.

ii. Conduct reflex culturing at state public health laboratory (or make arrangements with other institutions to conduct reflex culturing) of enteric pathogens diagnosed by culture-independent methods, as resources allow.

i. Provide appropriate identification variables to allow linking of FoodNet data with data from other data systems (e.g., PulseNet, NORS, NARMS).

j. Submit data electronically to CDC in an ASCII file format via Public Health Information Network (PHIN) messaging monthly by the specified deadline and on CDC request.

i. Incorporate a data cleaning process before monthly data transmission to CDC.

ii. Provide responses to data exception reports and requests for information from CDC within 2 week of receipt of request.

iii. Adhere to CDC timelines for preliminary and final data closeout.

2. Conduct active, population-based surveillance for pediatric cases of hemolytic uremic syndrome (HUS). Conduct passive surveillance for adult cases of HUS or thrombotic thrombocytopenic purpura (TTP) that have a history of diarrhea in the three weeks before diagnosis. Surveillance includes the following:

a. Complete HUS case report forms A, B, and C.

b. Submit data electronically to CDC via PHIN messaging monthly by the specified deadline and on CDC request.

i. Incorporate a data cleaning process before monthly data transmission to CDC.

ii. Provide responses to data exception reports and requests for information from CDC within 2 week of receipt of request.

iii. Adhere to CDC timelines for preliminary and final data closeout.

c. Validate pediatric HUS case ascertainment through 1) annual review of hospital discharge data and 2) comparison of HUS cases to STEC cases from FoodNet active surveillance.

d. Submit serum from HUS patients to CDC, when available.

3. Obtain exposure information on all or a subset of Campylobacter cases (sample size to be determined by CDC). If resources allow, obtain exposure information on all or a subset of Salmonella cases. Sites must collect required variables on the case exposure ascertainment (CEA) variable list determined by the Steering Committee. Sites may use existing state-based questions if they can be mapped with a high degree of concordance to CEA questions. However, if states have not been using another questionnaire for several years, they must use the questions as written by the committee.

a. Place emphasis on interviewing cases for which isolates are available at the state public health laboratory or CDC.

b. Store all isolates with CEA information for future characterization

c. Extract and merge data into the routine surveillance data transmitted to CDC through PHIN MS. All available data should be sent monthly.

4. Submit outbreak-associated bacterial isolates and specimens to CDC as specified in the FoodNet surveillance protocol.

5. Maintain flexibility to rapidly respond to changes in core surveillance.

a. Be able to quickly (within three months) modify data collection methods and site databases to respond to changes in FoodNet surveillance. Changes may include addition or deletion of variables submitted to CDC.

b. Transmit data on all variables to CDC via PHIN MS.

6. Participate on all Steering Committee and Coordinator conference calls.

7. Participate in Working Groups, as appropriate.

8. Attend annual FoodNet Vision Meeting and Coordinator Meeting.

FoodNet Additional Activities: OPTIONAL

1. Participate in project to identify and develop information technology (IT) resources at state and CDC levels to enable transmission of relational data from states to CDC and enable the CDC FoodNet database to capture case-based data.

2. Participate in geospatial analysis projects by geocoding FoodNet cases to census tract and transmitting census tract information to CDC upon request.

3. Participate in projects that examine the relationship between antimicrobial resistance, exposure and clinical features to better characterize infections

4. Participate in pilot project to assess feasibility of expanding surveillance activities to other pathogens or co-infections

5. Arrange for whole genome sequencing (WGS) of all human STEC isolated in 2016 in the state public health lab, another public health lab, or CDC. Obtain clinical and epidemiologic data on all patients whose isolates are tested by WGS. This includes obtaining the exposure data approved by CSTE position statement 13-ID-01 in 2013 and the required FoodNet data. Work with CDC to build capacity to link sequence information with clinical and epidemiologic (including exposure) data.

a. Submit all sequence data to NCBI with appropriate metadata using identifiers that link the isolate information to PulseNet entries.

b. Interview STEC patients rapidly about exposures that occurred during the 7 days before symptoms began.

c. Extract exposure data from site-created databases and transmit to CDC. (CDC will develop timeframes and a mechanism for transmission.)

d. Ask clinical labs in the catchment area to follow procedures outlined by the site so that specimens positive by a culture independent test are cultured and then sequenced.

6. Submit specimens to the Minnesota State Public Health Laboratory from outbreaks with a thorough epidemiological and laboratory investigation in which etiology was not identified.

7. If state laws allow, explore agreements to allow CDC and other sites to assist with workload for surveillance or special studies when existing resources are insufficient to maintain best practices (e.g., during a major outbreak investigation). For example, one site may assist another with interviews while that site is busy with outbreak response, state laboratories may assist others with reflex culturing of positive CIDT reports or performing WGS on selected isolates.

8. Assume a leadership role by conducting activities such as leading the development of a study protocol, analyzing data for conference abstracts or manuscripts, or chairing a Working Group.

9. Participate in other activities as determined to be appropriate for FoodNet sites by the Steering Committee.

10. Participate in norovirus working group activities including estimation of norovirus community incidence through surveillance in select outpatient clinics with known population catchments, and norovirus testing of callers to foodborne illness complaint hotlines.

FoodNet Performance Measures

Sites are expected to meet performance standards for surveillance, submission of laboratory and patient information, study enrollment, and leadership. Performance standards will be calculated two times a year and results will be discussed at the mid-year coordinator meeting, Vision Meeting, Principal Investigator quarterly calls, or visits with individual sites. Below are the performance standards for 2016.

Expected minimum level

Surveillance

Laboratory Information

Special Studies

Leadership

*diarrhea, bloody diarrhea, and fever; greatest effort should be placed on obtaining this information on cases for which isolates are submitted to NARMS or are retained at state public health laboratory

**CEA_Beef; CEA_Chicken; CEA_Eggs; CEA_Seafd; CEA_Live_poultry; CEA_Tomatoes; CEA_Berries; CEA_Herbs; CEA_Well_water; CEA_Reptile_amphib.

***assessed for each study

£based on species from SPHL or CDC

Influenza Activities:

Influenza-associated hospitalizations surveillance: REQUIRED

1. Conduct active, population-based surveillance for laboratory-confirmed influenza-associated hospitalizations among children and adults during the influenza season (typically beginning on October 1, and ending on April 30 of the following year).

a. Clearly identify hospital catchment areas in which surveillance is conducted so that population estimates can be obtained for rate calculations.

b. Utilize hospital laboratory, admissions information, infection control practitioner databases/logs, and review of reportable conditions databases to identify cases.

c. Complete a standardized case report form for all identified cases using data obtained from laboratory records and medical chart review. Influenza vaccination status should be obtained through medical chart review, verification of state vaccination registries, inquiries to primary care providers or long term care facilities where a case resided prior to hospitalization, or telephone interviews with the case or proxy (note: sites are not expected to routinely contact surveillance cases, and telephone interviews should not be the primary source of information but rather a means to fill in any gaps of information that could not be completed via other sources).

2. Enter case data into a standardized data collection database provided by CDC or send de-identified data extracts that match the format of the standardized database.

a. Submit data electronically to CDC (in an agreed upon secure format) by the specified deadline and upon CDC request.

b. Provide timely responses to reports and requests for information to assist in preliminary & final analyses, reports, and data close-outs.

3. Encourage influenza screening of patients hospitalized with acute respiratory illness at participating hospitals

a. Promote use of accepted diagnostic tests for influenza (e.g., direct or indirect fluorescent antibody testing, reverse transcriptase- polymerase chain reaction (RT-PCR) testing, rapid influenza diagnostic testing, or viral culture).

b. Collaborate with local Public Health Laboratories to offer RT-PCR testing, including subtyping, for patients hospitalized in the surveillance catchment area as a mean to improve influenza surveillance.

c. Diagnostic testing that can distinguish both influenza type and subtype (e.g., RT-PCR) can be conducted in the entire surveillance area, in a specific geographic region of the usual surveillance area, or in a subset of surveillance hospitals. Although determination of influenza subtype is not required for all cases, it is highly desirable and recommended.

d. Sites should ensure that subtype information is linked to patient clinical records for all cases, when available.

e. If sites are unable to determine subtype for all cases, an estimate of the proportion of cases for which subtype can be determined should be provided.

4. Describe a plan to engage participating hospitals and their staff (e.g., clinicians, ED staff, infection preventionists) to increase RT-PCR testing coverage among hospitalized persons with respiratory illness during influenza epidemics.

5. Collect information to distinguish between community-associated and healthcare facility-associated influenza infections to estimate the burden of hospital-acquired influenza infections.

6. Perform geocoding and linkage to US Census data using standardized methods for all cases identified as part of surveillance activity. Geocoding of all influenza hospitalization cases is a means of capturing socioeconomic factors, such as poverty, educational level, household crowding, and access to healthcare.

a. Site will send census track data to CDC and CDC will work on data abstraction from census data files or other sources (e.g., American Community Survey).

b. Sites are encouraged to join in working group discussions to define objectives and methodology to be used in future influenza-specific geospatial analytical proposals.

7. Ascertain influenza-associated deaths that may have been missed during hospitalization and /or occurred within the first 30 days of hospital discharge. Strategies for ascertaining death after hospital discharge should include:

a. Matching the dataset of hospitalized patients captured through regular surveillance with that from the U.S. Social Security Death Index (SSDI) online database to identify death-cases missed by surveillance and/or deaths occurring after hospital discharge.

b. Based on the local Vital Statistics/Death certificates available, obtain information about place of death and cause-of-death among those identified through SSDI data match.

Other core activities related to Influenza-associated hospitalization surveillance:

REQUIRED

1. Participate in scheduled Principal Investigator, Surveillance Officer, and working group conference calls.

2. Participate in annual EIP Steering Committee and Principal Investigator and Surveillance Officer meetings.

3. Contact healthcare providers or state vaccine registries to obtain complete influenza vaccine information for all hospitalized cases (per approved protocol) and conduct telephone interviews with the case or proxy (note: surveillance cases are not intended to be routinely contacted, and telephone interviews are not expected to be a primary source of information).

4. Maintain flexibility to rapidly respond to changes in core surveillance in response to a novel influenza A virus epidemic of pandemic potential.

a. Sites must have the ability to quickly modify data collection tools and site databases to respond to changes in surveillance.

b. Changes may include extensive clinical data collection to assess severity of the new epidemic/pandemic; identification of sentinel hospitals where prospective, systematic testing for influenza can be performed at the emergency department or elsewhere in the hospital unit to identify patients hospitalized with severe novel influenza; monitoring influenza vaccine adverse events; and timely report a set of demographic and clinical data to CDC in order to inform stake holders’ decision making and public health interventions early in the epidemic/pandemic.

Interested sites may propose one or more of these enhancements to influenza surveillance activities: OPTIONAL

Respiratory syncytial virus (RSV) pilot study: RSV is a major cause of respiratory infection and hospital visits in the United States especially in young children and increasingly recognized as a significant source of morbidity in older adults. Some predict a vaccine for RSV may be on the market in the next five to ten years; over 50 RSV candidate vaccines are currently in development with some in Phase II clinical trials. In the meantime, it is essential to establish population-based estimates of disease burden so that vaccine impact can be evaluated. We aim to conduct a pilot surveillance study to investigate the burden and characteristics of RSV in hospitalized children aged <2 years hospitalized (i.e., inpatient admissions). The objective of the pilot is to assess whether the FluSurv-NET platform can be used to collect population level data to describe the epidemiology and estimate the disease burden of RSV infection in the pre-vaccine era so that the vaccine impact can be measured as an RSV vaccine becomes available. This will be an expansion from the pilot activity funded among four sites, to better evaluate geographic and temporal variability of RSV circulation.

Interested applicant sites should describe the following elements in the applications:

A plan to prospectively identify laboratory-confirmed RSV cases, and a description of surveillance hospitals and testing practices. Some sites may have information to provide on whether RSV testing is done on all or some percentage of children in a relevant age group who are seen at the ER or admitted to hospital for respiratory illness, number of RSV tests performed during October-April among children < 2 years of age and percentage positive, and description of the catchment area (with estimated denominator population if different from that used for the influenza associated hospitalization surveillance). Applicants will be expected to collect data on risk factors for RSV such as gestational age at birth as well as other demographic and risk factor data.

Approximately 5-7 sites will be selected to participate depending on funding and strength of the applications. CDC anticipates that sites participating in this activity will use the infrastructure built for influenza associated hospitalization surveillance, but additional resources may be required such as a designated surveillance officer, and local travel expenses for case investigation. Protocols (including approach for disease burden estimates), data collection instruments and data entry software will be developed in collaboration with CDC and participating sites so that they may be standardized.

Evaluation of empiric antiviral therapy among patients hospitalized with acute respiratory illness: Neuraminidase inhibitors (NAIs) use in clinical practice has increased during recent years, and was widely recommended and used to treat hospitalized patients during the 2009 H1N1 pandemic. CDC guidelines for the use of antivirals recommends treatment with NAIs “as soon as possible for patients with confirmed or suspected influenza who have severe, complicated, or progressive illness, or who are hospitalized”. The deliberate language that clinicians need not wait for confirmatory testing for influenza before initiating treatment acknowledged the value of these medications to prevent severe outcomes if given early in the course of illness and the lack of sensitive rapid diagnostic assays. Currently we have limited data evaluating medical providers’ adherence to the recommendation of early empiric antiviral treatment for persons hospitalized with suspected influenza and physicians’ practice regarding influenza testing among patients with acute respiratory illness. The idea with this activity is to evaluate patterns of presentation and management of patients hospitalized with acute respiratory illness, describe patients tested for influenza (as compared to those not tested), and characterize the use of influenza antiviral drugs among patients suspected to have influenza vs. those tested positive for influenza to determine providers’ adherence to CDC guidance for empiric use of influenza antiviral drugs.

Interested applicant sites should describe the following elements in the applications:

A plan to utilize existing data to retrospective access a patients hospitalized with acute respiratory illness, using electronic medical records (accessing clinical, administrative and pharmacy level data). From hospital database, the participating institution should be able to obtain patient’s age, date of birth, race, ethnicity, date of hospital admission, date of hospital discharge, presence of CDC defined high risk conditions for influenza-complications (specific ICD9 codes), clinical outcomes during hospitalization, and data on influenza antiviral drug used, route of administration and duration of treatment. If antibiotic treatment was prescribed within first 24 hours of hospitalization (yes/no), we will also collect data on antibiotic name.

Approximately 5-7 sites will be selected to participate depending on funding and strength of the applications. CDC anticipates that sites participating in this activity will use their connection with participating hospitals to identify those with the appropriate infrastructure to produce such dataset. Costs associated with this activity are likely related to contractual costs with the selected health care facility and/or payment for coding and management of dataset. Protocol, data collection instruments, data dictionary, and data entry software will be developed in collaboration with CDC and participating sites so that they may be standardized.

Influenza Performance Measures:

Sites should propose to use the following performance measures which will be used to monitor and evaluate progress of activities:

1. Principle Investigator (PI) and Surveillance Officer (SO)…