April 5, 2017 Dear ELC Grantee Public Health Laboratory Directors:

APHL is pleased to provide a guidance tool to assist you in responding to the Epidemiology and Laboratory Capacity for Infectious Diseases (ELC) funding opportunity announcement (FOA), which was released on March 20, 2016 The FOA solicits applications for fiscal year 2017 funding for current ELC grantees under FOA Number CK14-1401PPHF17. The continuation application and progress reports on FY2016 activities must be submitted by May 16, 2017.

Your responses should include requests for continuation from projects that are cross-cutting (non-categorical) ELC projects (Section 1) as well as those that are Disease-Specific (Section 2). APHL encourages our members to be highly involved in the ELC grant writing process. Laboratory Directors and appropriate technical staff should contribute to the relevant sections of the grant proposal. Laboratory Directors are asked to share this guidance with appropriate technical staff. Once the application process is complete, summary comments and the budget markups will be sent to the ELC Governance Team members in each state/jurisdiction. If you are not the laboratory representative on the ELC Governance Team, please ensure that your laboratory representative shares this information with you. If you need assistance, please feel free to contact the APHL staff below. Sincerely,

Scott Becker, MS Executive Director APHL Staff Contacts

Subject Area Staff Contact Email Telephone

Infectious Diseases Kelly Wroblewski kelly.wroblewski@aphl.org 240-485-2728

Food Safety/ Pulse Net

Shari Shea sharon.shea@aphl.org 240-485-2777

Lab Systems and Standards

Karen Breckenridge karen.breckenridge@aphl.org 303-617-8827

Health Information Systems

Michelle Meigs michelle.meigs@aphl.org 240-485-2771

Biosafety Chris Mangal chris.mangal@aphl.org 240-485-2769

mailto:kelly.wroblewski@aphl.orgmailto:sharon.shea@aphl.orgmailto:karen.breckenridge@aphl.orgmailto:michelle.meigs@aphl.orgmailto:chris.mangal@aphl.org

Page 2 of 19

Section 1: Cross-cutting (non-categorical) ELC Activities (Guidance includes only sections relevant to the laboratory) Attachment B: Cross-Cutting Laboratory Capacity (p. 23-26)

64 Awards; average of $137,500 per award APHL suggests that you include activities that will improve integration with your health department partners, will broadly improve your laboratory practice, and will benefit testing activities across ELC-funded programs. 1. Sustain and Enhance laboratory diagnostic capacity APHL Suggested Activities

It is highly recommended that laboratories include travel to the 2018 ELC Annual Meeting in their request. Consider your needs to travel to other meetings or conferences. Travel that is approved and funded by CDC will be considered a required activity. Following is APHLs recommended list of key meetings for laboratory grantees:

Association of Public Health Laboratories Annual Meeting: Laboratory directors and

staff should plan to attend the 2018 meeting in Pasadena, CA. Other meetings as appropriate: Attendance at other professional meetings is

encouraged to build a broad knowledge base of current and new practices in the infectious disease arena. Examples include:

o Microbe/American Society for Microbiology (ASM) General Meeting/The Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC)

o Clinical Virology Symposium o Laboratory Director attendance at InFORM 2017 (Integrated Foodborne

Outbreak and Response and Management Conference) o International Association for Food Protection (IAFP) o American Public Health Association (APHA)

Travel to other PHLs to participate in training on new methods or knowledge sharing on specific program implementation (peer-to-peer travel). If you need suggestions on topics for trainings or PHLs that may be able to provide training or information on a specific topic, please contact APHL. Focus on disease areas traditionally funded through ELC.

Consider your need for training in disease areas traditionally funded through ELC or biosafety. A list of upcoming training opportunities offered by APHLs Department of Continuing Education and Training can be found here.

Consider implementation or expansion of MALDI-TOF for the identification of bacterial pathogens. This technology has demonstrated significant cost savings. However, ELCs ability to provide support for large instrument purchases in this section will be limited.

http://www.aphl.org/training/pages/default.aspx

Page 3 of 19

Build general capabilities for reverse transcription polymerase chain reaction (RT-PCR) to provide either qualitative or quantitative molecular analysis. Areas to consider maintaining or expanding capacity include arboviruses, respiratory pathogens, rabies, detection of antimicrobial resistance markers, etc.

When implementing new laboratory developed tests, consider putting them on the ABI 7500 Fast, QuantStudio Dx Real Time Instrument or other CDC recommended instrumentation and requesting funding for service contracts using the versatility of the instrument as justification.

Consider strategic implementation of multiplex PCR assays for outbreak detection and/or reflex testing in your jurisdiction, including GI or respiratory panels. Consider your need for equipment that has broad use in the laboratory, such as refrigerators, incubators, freezers, centrifuges, plate washers, water baths, microcentrifuges, microscopes (fluorescent, light/inverted), biosafety cabinets, extraction platforms and PCR workstations.

Consider your need for miscellaneous laboratory supplies such as packaging and shipping containers (plus shipping costs), viral transport media, culture media, PPE (including N-95s), commercial PCR reagents, nucleic acid extraction chemistries, pipettes/pipet tips. Especially consider including ancillary reagents required for the Trioplex rRT-PCR, which will no longer be provided through the International Reagent Resource (IRR) beginning in June 2017.

2. Improve Laboratory Coordination and Outreach

APHL Suggested Activities

Consider the costs involved with implementing some or all of the recommendations found in the second edition of the CIFOR Guidelines. If your laboratory has participated in a CIFOR Toolkit workshop or received a CSTE grant to utilize the CIFOR Toolkit (second edition), you may have a list of recommendations that are a priority to implement in your jurisdiction.

- Consider the costs of educating clinical labs about the importance of submitting foodborne isolates/clinical material to PHLs, particularly as Culture Independent Diagnostic Tests are implemented. See Interim Guidelines created with ASM as a reference.

- Consider the costs associated with setting up or supporting an existing courier system for the transport of ELC-funded organisms

Consider using ELC funds to establish partnerships with clinical and commercial laboratories to establish or enhance cross-cutting specimen and data sharing networks to enhance and create efficiencies amongst existing surveillance activities. Especially consider the benefit for influenza and other respiratory pathogens, antimicrobial resistant isolates, C. difficille, and foodborne specimens/ isolates. Consider using ELC funds to partner with other public health or university laboratories to deliver testing services for low volume tests. Tests to consider include but are not limited to: Dengue PCR; Mycology; Parasitology; Norovirus testing (i.e. CaliciNet). If ELC grantees wish

http://www.cifor.us/documents/CIFOR%20Industry%20Guidelines/CIFOR-Industry-Guideline.pdfhttp://www.cifor.us/toolkit.cfmhttp:/www.cifor.us/toolkit.cfmhttp://www.aphl.org/AboutAPHL/publications/Documents/FS-Enteric_Pathogens_Guidelines_0216.pdf

Page 4 of 19

to participate in test service sharing it should be noted in each grantees budget (both submitting and testing laboratory). Consider the costs associated with laboratory and epidemiology coordination and outreach efforts related to the Influenza Virologic Surveillance Right Size Roadmap (Right Size Roadmap). Activities to consider include efforts to improve laboratory and epidemiology coordination (e.g., table top meetings and strategic planning meetings), specimen submitter outreach, and flow of alternative data from providers. A suggestion would be to collaborate with other states in the region and all list this in your proposals to show cross-state coordination .APHLs Right Size webpage has several new resources on the use of alternative data and example practices on establishing partnerships with sentinel providers. All ELR Activities should be requested under Activity C. Requests for support for LIMS upgrades or enhancements may be requested under Activity B.

Attachment C: Health Information Systems Capacity (p. 27 -32)

64 awards; average of $400,000 per award 1. Enhance Health Information Systems Workforce Consider requesting funds to hire a laboratory interoperability specialist as the PHL lead for interoperability efforts. This person liaises with the information technology department, system vendors, data exchange partners, national standards groups and organizations, as well as internal subject matter experts (laboratory and epidemiology stakeholders). Examples of affected interactions and projects include:

Laboratory Information Management Systems (LIMS)

Electronic Disease Surveillance Systems (DSS)

Integration of electronic information for parsing and aggregating data

Data use and data exchange agreements

Service level agreements (SLA)

Instrument interfacing approaches and quality control measures

Training and/or negotiations with external data messaging partners

Cloud computing providers/solutions Consider requesting funds to hire a laboratory interoperability Project Manager as the PHL liaison with the legal department, information security groups, and senior leadership/political leaders. This project manager/program manager would be responsible for coordinating the plan of action for integrating and/or establishing laboratory data exchange between the LIMS, DSS, integration engines, other external data exchange partners etc., and would direct the work of the interoperability specialist outlined above. This position could be a shared resource between the public health agency and laboratory to ensure continuity of epi-lab synergy. Examples of affected interactions and stakeholders include:

Local and State data systems stakeholders

General Counsel (support of HIPAA and CLIA regs, sharing agreements)

State CIOs office/representatives

NEDSS coordinator

https://www.aphl.org/aboutAPHL/publications/Documents/ID_July2013_Influenza-Virologic-Surveillance-Right-Size-Roadmap.pdfhttps://www.aphl.org/programs/infectious_disease/influenza/Influenza-Virologic-Surveillance-Right-Size-Roadmap/pages/default.aspx

Page 5 of 19

CTO/Decision makers at local providers (clinical labs, hospitals, etc.)

Office of the National Coordinator for Health IT

Jurisdictional Health Information Exchange (HIE) technical staff

APHL, ASTHO, NACCHO, CSTE and other national membership organizations and advisors.

Examples of skill sets associated with these positions:

High level of comfort with information technology systems.

Strong project management skills.

Strong oral and written communication skills.

Strong interpersonal skills and an ability to articulate highly complex approaches to data exchange in an easy to understand manner.

Experience working in the public health sector required; experience working in a public health laboratory desired.

Familiarity with national interoperability standards (i.e. HL7, LOINC, SNOMED, etc.).

Familiarity with national meaningful use standards and their effect on certified health technology.

Familiarity with epidemiology terms, laboratory workflows, and national surveillance strategies.

Understanding of

Experience working in roles requiring multi agency coordination and influence.

Experience with integration engine technology such as Rhapsody, Mirth, Cloverleaf or similar.

Familiarity with use of commonly used resources such as the Reportable Conditions Mapping Table and other related resources.

http://www.cdc.gov/ehrmeaningfuluse/rcmt.html Consider requesting training funds to learn or refresh education on various standards such as LOINC, SNOMED, and HL7 (2.5.1 and possibly FHIR) Some Links below to paid and free resources:

HL7 v2 Certification, HL7 FHIR Institute & Meaningful Use Standards Implementation Workshops http://www.hl7.org/implement/training.cfm?ref=nav http://www.hl7.org/implement/certification.cfm

SNOMED CT http://ihtsdo.org/fileadmin/user_upload/doc/elearning.html

LOINC: http://loinc.org/slideshows

To better integrate health information system components, LIMS, DSS, etc. through the use of integration engines or brokers, consider requesting travel funding and support to augment in-house information technical capabilities by attending online, in-person, or other Orion Rhapsody certification trainings found here: http://go.orionhealth.com/l/3942/2015-06-29/3c3f4w To learn more about trainings available for Mirth integration engines, review trainings available here: https://www.mirth.com/Products-and-Services/Training To request customized, one-on-one, integration broker training through the APHL Informatics Technical Assistance Team, submit a request through the electronic data exchange, edx@cdc.gov.

http://www.cdc.gov/ehrmeaningfuluse/rcmt.htmlhttp://www.hl7.org/implement/training.cfm?ref=navhttp://www.hl7.org/implement/certification.cfmhttp://ihtsdo.org/fileadmin/user_upload/doc/elearning.htmlhttp://loinc.org/slideshowshttp://go.orionhealth.com/l/3942/2015-06-29/3c3f4whttps://www.mirth.com/Products-and-Services/Trainingmailto:edx@cdc.gov

Page 6 of 19

2. Advance Electronic Information Exchange Implementation

Consider requesting project funding to assess informatics core capabilities using the APHL Informatics Self-Assessment Tool, this online tool allows a laboratory to weigh current informatics capabilities based on a gold standard. The project could have the following components:

Assess Informatics Capabilities across the organization or test the functionality for a single product or lab section.

Develop an assessment report showing strengths, weaknesses and vulnerabilities based on assessment outcome

Develop action plans to address weaknesses and vulnerabilities. For more information on the Self-assessment tool, please email vanessa.holley@aphl.org Virtual and/or field based technical assistance is available under the broad based APHL Informatics Technical Assistance Team managed by CDC/APHL. Consider coordinating with EPI ELC program coordinator for technical assistance to develop and/or enhance Meaningful Use (MU) compliant HL7 ELR capabilities within the PHA and/or PHL. Consider including funds for local staff to work with the ELR TA team to implement ELR in the local jurisdiction and to maintain the ELR system upon completion of the ELR TA project using HL7 messaging standards. https://www.aphl.org/programs/informatics/Documents/INF_2013May30_ELR-Overview.pdf Consider reviewing your current access to and availability of shared data integration engines (Rhapsody, Mirth, Biz Talk, Pilotfish, Cloverleaf or similar). If the laboratory currently shares this tool with their surveillance/epidemiology department, the lab should reassess their data exchange needs and upcoming projects to determine if they should request funding for a laboratory specific license of the integration tool to support their efforts. PHLs can consider the following options: - If following a shared services model, the lab should determine and outline the appropriate

maintenance and support structure and all technical needs (including number of communication points and routes) to support laboratory data integration initiatives (not just ELR related needs).

- Review current functionality and upgrade to the most recent version of the tool, again, taking into account the PHLs data exchange and integration efforts

- Budget for ongoing training or certification for PHL staff or appropriate personnel to bolster in-house capabilities to message laboratory data and interact with other system outputs.

Consider requesting funds to expand message transport options, outside of PHINMS, to include web services, Direct, SFTP, VPN and/or other protocols as appropriate. Technical assistance to support these different transport options may be available upon request.

Consider requesting funds to review and possibly enhance infrastructure to support exchange/transmission of large data files (such as genomic sequencing and/or advanced molecular detection results) with cloud based data exchange platforms (such as APHL Informatics Messaging Services (AIMS) and/or directly with CDC. Partners already engaged with AIMS can also be considered for data exchange and sharing to further the needs of the public health laboratory community.

mailto:vanessa.holley@aphl.orghttps://www.aphl.org/programs/informatics/Documents/INF_2013May30_ELR-Overview.pdf

Page 7 of 19

Consider requesting funding to support a detailed evaluation and possible pilot of standardized Electronic Test Order and Resulting capabilities at the lab. Sample activities may be:

Identify and survey capabilities of external trading partners

Assess ETOR capability and need in light of test sharing services approach with other PHLs

Evaluate current national standards for ETOR such as the Laboratory Order Interface (LOI) and Laboratory Results Interface (LRI). http://wiki.siframework.org/Laboratory+Orders+Interface+Initiative

Review and possibly implement new transport options to support hospitals and other providers not using PHINMS.

Consider funding for moving existing systems to a secure cloud based architecture for more efficient utilization of IT resources.

3. Sustain and/or Enhance Integrated Surveillance Information Systems

Consider funding to implement/upgrade and maintain CDC influenza surveillance reporting to Meaningful Use compliant HL7 v2.5.1 format via Public Health Laboratory Interoperability Project (PHLIP) Electronic Laboratory Surveillance Messaging (ELSM). Consider funding to consolidate laboratory surveillance reporting for influenza antiviral resistance testing and/or other respiratory conditions via the PHLIP ELSM. Consider working with local influenza coordinator to integrate epidemiological information with surveillance data and align reporting streams. The APHL Informatics Technical Assistance Team may be available to assist local staff onsite or virtually with updating and validating ELSM implementations and enhancements for a number of diseases. For more information about technical assistance and integration of surveillance systems, please email the electronic data exchange inbox, edx@cdc.gov

Attachment D: Advanced Molecular Detection (p. 33-37)

Total funding of $2,000,000 to support 3 funding components. Funding for PulseNet Whole Genome Sequencing must be included under PulseNet USA (Attachment I4). Workforce Training Component: Training Lab Lead: (5-10 awards; $20,000-$150,000/ award) Training Participant: (20-40 award: $5,000-$20,000/award) CDC is asking public health laboratories to form self-identified regional networks to facilitate training in AMD and/or bioinformatics. One of the laboratories in the network should apply to serve as the Training Lab Lead and plan to partner with local universities and/or biotech companies to develop and deliver training for other public health laboratories in the self-identified region. If you would like assistance in coordinating with other public health laboratories or would like to be included in a region as a training participant, contact APHL

http://wiki.siframework.org/Laboratory+Orders+Interface+Initiativemailto:edx@cdc.gov

Page 8 of 19

(christin.hanigan@aphl.org) to assist. OAMD anticipates continuing the current training networks, but is also open to new networks. CDC has developed a sample curriculum to get applicants started. APHL has a working group for the selected Training Lab Lead laboratories to facilitate consistency in content across the regions and allow for sharing of tools, resources and ideas. Training should be more general and not be focused on any one particular pathogen or program. (i.e. should not be a repeat of PulseNet training.) Laboratories interested in serving as Training Lab Leads should include costs associated with holding the training (facilities, AV, computer rental, printing, academic partnerships, staff time for coordination and curriculum development) as well as costs for relevant staff to attend the training. Training participant laboratories should plan to request funds required for relevant staff members to attend the training. APHL suggests requesting support for the attendance of several relevant staff members. Bioinformatics Resource Support Component: (2-5 awards; $50,000-$150,000) The goal of this new component is to begin to build bioinformatics capabilities at the state level in various regions. While the PulseNet regions will be used, this work will be independent of PulseNet and any state within the region is eligible to apply for to host the bioinformatics support. These networks will not necessarily be the same as the training networks above. Evidence of prior collaborations, support, and participation in trainings to other states in your region should be noted in your application. Laboratories should request partial or full salary support along with travel for collaboration with other laboratories in their network. CDC does not anticipate funding Bioinformatics support for all regions this year, but hopes to expand in the coming years. AMD Capacity Component: (5-15 awards; $20,000- $100,000/ award) APHL suggests laboratories focus on developing the capacity to sequence for pathogens for which AMD fund are not available through alternative mechanisms (e.g. do not request funds to develop capacity to sequence foodborne pathogens in this section). Consider collaborating closely with your epidemiologists to identify which applications of AMD technologies would be most useful to your jurisdiction. Laboratories should consider requesting funds for equipment and reagent needs and may consider staff time associated to develop the program. Equipment costs for building IT and data storage, streaming, and analysis can also be considered in this request.

Attachment H: Cross-Cutting Outbreak Investigation Response and Reporting Outbreak #1 and Outbreak #2 (p. 45-48)

Funds available on condition of local or national outbreak; $500,000/ jurisdiction All proposals should plan for and request $500,000 but funding will only be released in the event of an outbreak. This request will likely be marked approved but unfunded in your initial budget

mailto:christin.hanigan@aphl.orghttp://www.aphl.org/Materials/Sample-curriculum-PHL-Bioinformatics-Course-Options.pdfhttps://www.aphl.org/Materials/AMD_FY16_Maps.pdf

Page 9 of 19

markup, but it will expedite the release of funds should outbreak conditions warrant. It is acceptable to use the same language that was submitted in the last request.

Section 2: Diseases Specific ELC Activities (Note: this tool includes only sections relevant to the laboratory) NEW -- Attachment I0: Enteric Disease Detection, Investigation, Control, and Reporting Program Overview application template

Applicants should collaborate across enteric disease organizational units to create an executive summary of your jurisdictions enteric disease detection, investigation, control, and reporting program. The executive summary should not exceed two pages and should include an organization chart showing all enteric disease programs. Clearly and succinctly describe your overarching programmatic approach to detect, investigate, control, and report enteric disease cases and outbreaks. Be comprehensive and do not limit the summary to the portion of your enteric work that is federally funded. Inclusion of waterborne disease, environmental health and other programs (e.g., EHS-Net, norovirus, and legionellosis, etc.) when applicable is strongly encouraged. Additionally, applicants should describe current or planned efforts to work across programmatic units (e.g., OutbreakNet, NARMS, PulseNet, FoodCORE, NORS, etc.) to encourage participation, cooperation, and reduce duplicative efforts and describe current or planned efforts to access available resources (e.g., CDC technical assistance, Integrated Food Safety Centers of Excellence, Peer-to-peer mentorship/assistance, etc.) to enhance jurisdictional food safety capacity. The purpose of the executive summary is to reduce the need to repeat background information in each subcomponent sections (I1-16).

Attachment I1-I6: Foodborne Disease Activities (p.49-87) Attachment I1: Enteric Disease Outbreak Surveillance, Response and Reporting Capacity (OutbreakNet, NORS, OutbreakNet Enhanced, and FoodCORE Programs)

For FoodCORE participants, applicants must respond to all three core areas, including enhancement of public health laboratory surveillance. Applicants should describe plans to include all listed activities (D1, a-i) as well as plans for the implementation and reporting of the established measureable performance indicators and metrics. Applicants with existing federal infrastructure provided to conduct enteric disease surveillance and response activities should describe how programmatic activities in each core area will be synergized with the relevant programs. Specifically, consider requesting funds for the following, depending on which program you are applying to participate in:

Consider the costs of working with the CDC NARMS team to submit isolates from every outbreak caused by diarrheagenic Escherichia coli, Salmonella, and Shigella. [NORS B2]

Review FoodCORE isolate/specimen based metrics to guide funding requests for the laboratory component of the FoodCORE program. The following activities are part of FoodCORE (D1):

Consider the costs of transporting bacterial, viral and parasitic specimens (or broths) from clinical laboratories to public health laboratories.

Consider the costs of reagents for traditional or molecular serotyping testing (Luminex xMAP, traditional antisera) and PFGE/WGS to conduct real-time serotyping and

https://www.cdc.gov/foodcore/metrics/ssl-metrics.html

Page 10 of 19

molecular characterization of all Salmonella, Shiga toxin-producing E. coli (STEC) and Listeria isolates.

Consider the costs of supporting IT needs for linking PulseNet laboratory data to epidemiology systems to ensure timely sharing of laboratory data for outbreak investigations and routine surveillance, including the ability to link illnesses to contaminated food products.

Consider costs of obtaining specimens from patients with uncertain foodborne illness diagnoses. The CIFOR Outbreaks of Undetermined Etiology has recommendations on "universal" collection, shipment, testing and retention of foodborne outbreak specimens in the event that an etiology is elusive, even in the early stages of an investigation and may be a useful resource to review.

Consider the costs for real-time video microscopy related to DpDx submission, real-time characterization of norovirus for CaliciNet participation, and collection of serologic samples for Hepatitis A testing may be included here.

Attachment I2: National Antimicrobial Resistance Monitoring System: Surveillance Activities (p.61-66) Proposal should range from $50,000 to $400,000 (54 awards) Submission of Routine and Outbreak Isolates: Consider packaging and shipping costs for sending routine surveillance and outbreak-related isolates to CDC, per the required NARMS performance metrics (5% for non-typhoidal Salmonella, Shigella, and E. coli O157; 100% for Salmonella serotypes Typhi, Paratyphi A, and Paratyphi C; FoodNet site-specific targets for Campylobacter). Additionally, consider the cost to submit 3 representative isolates from single state outbreaks of Salmonella, Shigella, and E. coli reported through NORS and the cost to submit isolates from multistate outbreaks upon request by CDC. Note that you must designate a laboratorian to serve as the primary contact for outbreak response and other program communications. Proposal should range from approximately $1,000 to $18,000 (54 awards) Whole Genome Sequencing (WGS) Activities: NARMS funding is also available to complement WGS of enteric pathogens described in the PulseNet Attachment I4. Consider expenses for maintaining sequencing equipment and infrastructure or costs to purchase lab supplies that will help achieve the goal of performing WGS (using PulseNet methods) on all Salmonella from humans. Additional funds can be requested to sequence a representative sample of Campylobacter and Shigella from humans and to package and ship isolates to CDC when requested.

Funding will be based on the average number of isolates received in the laboratory annually. Target is to sequence 100% of Salmonella isolates and a representative number of Campylobacter and Shigella, as funding allows.

Consider requesting funds to support WGS infrastructure to include: o Sequencers and related equipment. Refer to PulseNet SOPs (PNL32) for WGS supplies

and reagent needs. o Software upgrades (BioNumerics v.7x) o Service agreements for WGS-related equipment, etc. o WGS supplies and reagents. Refer to PulseNet SOPs (PNL32) o Personnel for WGS

Note that FoodNet sites must have the capability to perform WGS on Salmonella isolates and must store all isolates for which the state has collected expanded case exposure ascertainment information.

https://www.aphl.org/programs/food_safety/Pages/CIFOR-Resources-for-Response-to-Foodborne-Outbreaks.aspx

Page 11 of 19

(Note that this year, FoodNet sites can apply for NARMS funding to support the collection and transmission of exposure and outcome epidemiological information associated with antimicrobial resistance as part of expanded case exposure ascertainment (eCEA). Laboratories from FoodNet sites must have the capability to perform WGS on Salmonella and other isolates with eCEA information and must store those isolates for further characterization.) Proposal should range from $50,000 to $400,000 (54 awards) Attachment I4: PulseNet USA (p.72-81)

General PulseNet Laboratories: (Total of $4,000,000 available; Awards will vary; request support for all the activities planned during the performance cycle)

For PulseNet Laboratories: ELC funding levels to support general PulseNet activities have not been set yet. APHL strongly recommends laboratories to clearly establish project priorities and request the full amount necessary to conduct real-time molecular characterization of all organisms under PulseNet surveillance and confirmatory testing on CIDT positive specimens. There are two separate areas within the ELC FOA which your laboratory can apply to support PulseNet activities. This includes funding to support National Antimicrobial Resistance Monitoring System (NARMS) and PulseNet Project activities, attachments I2 and I4, respectively. This years request for funds to support implementation of WGS laboratory and analysis tools for PulseNet must be included in the PulseNet section of the FOA (not the AMD section). It is important to notice that this years NARMS requests for funding of PulseNet whole genome sequencing (WGS) activities is for equipment, reagents, supplies, contracts, workforce and infrastructure. These requests must be included in the NARMS section (I2) only. Additionally, up to $25,000 can be requested for WGS reagents and supplies under the PulseNet attachment, I4 of the FOA in addition to the standard PulseNet activities (e.g. PFGE, InFORM and/or regional conference attendance, etc.) Note: As always, ELC can only support states up to the limit of their request, i.e. if you do not ask for necessary funds, you will not receive them. Thus, states should request support for everything they need and NOT just for what they think that they likely will get. PulseNet Laboratories:

PulseNet Core Activities (PFGE testing) o Reagents, supplies, personnel, equipment for PFGE testing. Refer to PulseNet SOPs

(PNL01) and other pathogen specific PFGE protocols for reagent and equipment needs.

STEC and Salmonella surveillance o Consider cost to support traditional and molecular serotyping, including commercial

molecular serotyping assays such as the Luminex xMAP kits for Salmonella.

Isolate recovery from Culture-Independent Diagnostic Test (CIDT) positive specimens from clinical laboratories.

o Consider the additional expenses related to transporting, culturing, isolating and characterizing culture-independent diagnostic test (CIDTs) CIDT positive specimens. Be sure to fill out expected number of specimens to culture for Salmonella and STEC due to increasing use of CIDTs in your jurisdiction. If funding is available for this activity it will be based, in part, on what you report.

Consider costs for any personnel that conduct PFGE, WGS, or culturing of primary specimens

Page 12 of 19

Request the follow costs related to implementation of WGS laboratory and analysis tools for PulseNet:

o WGS reagents/supplies, up to $25K o Funding will be based on the average number of isolates received in the laboratory

annually (small, mid, high volume laboratories). o Consider requesting funds to support routine sequencing of 100% of STEC and Listeria

isolates in addition to other isolates not sequenced as part of NARMS/CARB. Refer to PulseNet SOP (PNL32) for supplies and reagent needs.

Travel to attend PFGE, WGS and/or BioNumerics trainings o APHL also strongly recommends requesting funds to attend at least one training per

laboratory per year in WGS, PFGE and/or BioNumerics.

Travel to InFORM Conference o APHL strongly recommends requesting funds for as many people as you need to travel to

the InFORM 2017 Conference, which will be held November 6-9, 2017 in Garden Grove, CA. PulseNet/OutbreakNet Regional Meetings will be held in late 2018-early 2019.

PulseNet Area Laboratories:

PulseNet expects Area Laboratories to sequence >800 isolates during the funding cycle, including isolates submitted by laboratories in the respective regions.

Consider requesting additional funding for anticipated molecular testing of out-of-state isolates or specimens.

Additionally, request funds to support other surveillance activities (PFGE, CIDT isolate recovery) in addition to other Area Laboratory functions such as trainings.

MLVA testing Laboratories:

MLVA testing is no longer supported. Attachment I5: NoroSTAT (p. 82-84) ($50,000/award; 9 awards) Funds are primarily for personnel, including laboratory personnel. Also consider resources for travel, supplies and equipment related to norovirus outbreak investigation. Applicants must already be CaliciNet-certified. Applicants must upload norovirus sequences (at least 2 per outbreak) within 7 days of receipt in the PHL with enough data to link the outbreak to the corresponding NORS report. Importantly, NoroSTAT includes reporting of all norovirus outbreaks, regardless of transmission mode.

Attachment I6: CaliciNet (p. 85-87) ($600,000 total; $2,500-$70,000/award; 25-32 awards) For CaliciNet Laboratories: Consider requesting funds for the required travel to a mandatory annual CaliciNet users group meeting and for personnel, supplies and equipment for norovirus testing. Attachment J1-J3 Sexually Transmitted Disease Activities Attachment J1: Threat of Antibiotic-Resistant Gonorrhea: Rapid Detection and Response (p 88-94) ($660,000/award; 9 awards) Eligibility is limited to public health laboratories that received K8 ELC funding in fiscal year 2016. Public Health Laboratories should request funds for 1 laboratorian to attend an annual resistant GC rapid

Page 13 of 19

detection and response capacity meeting (Atlanta, GA 2017) and other laboratory activities to support AST testing by Etest and rapid electronic reporting. Attachment J2: Enhanced Gonococcal Isolate Surveillance Project (eGISP) (p.95-100)

($60,000/award; 10 awards) Public health laboratories should collaborate with your jurisdictional STD prevention and surveillance programs to determine if you plan to apply. Public health laboratories should contribute to applications by describing current capability and capacity to perform NAAT on pharyngeal and rectal specimens and perform gonorrhea culture, data collection, reporting and storage mechanisms. Laboratories may consider requesting funds to improve culture capability, perform validation of extragenital CT/GC NAAT and or ship specimens or isolates to CDC. Attachment K1-K3 Healthcare Associated Infections/ Antimicrobial Resistance Activities Attachment K1: Detection, Containment and Prevention (p. 108-122) Activity: Detection, Containment and Prevention (Core): (average $400,000/award; 57 awards) Activities previously proposed under K6 should now be proposed here. Work closely with your HAI coordinator to develop this section of your proposal.

All public health laboratories should apply for funds to build or sustain capacity to perform testing on suspected Carbapenem-resistant Enterobacteriaceae (CRE) and carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates. Laboratories should describe the test methods they will use, which can include species identification, confirmatory AST, phenotypic screening for carbapenemase production and/or molecular detection of resistance determinants. Confirmatory AST may be performed by disc diffusion, Etest or broth microdilution using frozen or dried panels. Laboratories performing carbapenemase screening can utilize either the modified carbapenem inactivation method or CarbaNP assay. Laboraolecular detection of AR determinants should be performed using real-time PCR or the Cepheid, with the CRE markers KPC, NDM and OXA-48-like and the CRPA markers KPC, NDM and VIM. APHL strongly advises public health laboratories to implement some level of CRE or CRPA testing. However, public health laboratories are not expected to implement all of the above testing. Consider your laboratory capability and capacity including staff skills and available equipment as well as your jurisdictional needs when developing your proposals. Public health laboratories will be expected to develop and/or enhance their relationships with clinical microbiology laboratories to facilitate the submission of suspected CRE isolates to public health laboratories. APHL suggests looking for opportunities to leverage other efforts to strengthen relationships with clinical laboratory partners such as ongoing biosafety efforts. Training will be provided for each public health laboratory at your designated Antimicrobial Resistance Regional Laboratory which will be selected through a competitive process (see K7). APHL will have funds available to support travel for one laboratory representative to the training. Activity: Data Validation (optional)

Page 14 of 19

Consider funding to hire a trained System Analyst IT resource to implement validation tools for better quality surveillance data, drive enhanced surveillance completeness, timeliness, and specificity. By applying standard definitions and business rules within the logical system architecture via an integration broker (e.g., Rhapsody, Mirth, etc.) a front-end validator can prepopulate tables, ensure data transparency, require that key fields are populated, automatically flag message inaccuracies, and improve the overall quality of processed data. Additional validation artifacts and resources can be found here to improve the robustness of the final data set:

The Message Quality Framework (MQF) is a free, online flexible framework of services and

utilities designed to assist public health partners with preparing and communicating quality,

standard electronic messages as defined by the applicable messaging, vocabulary, and

programmatic standards.

MQF online validator for various types of electronic messages:

https://phinmqf.cdc.gov/default.aspx

7Edit is a productivity tool for browsing, editing, validating HL7 messages and exchanging data with HL7 applications.

7Edit: HL7 message validator application: http://7edit.com/home/index.php

The NIST Electronic Lab Reporting (ELR) Validation Suite is intended for certifying 2014 Edition

Meaningful Use EHR technology. The validation suite provides functionality to test EHR senders.

NIST Electronic Lab Reporting (ELR) Validation Suite: http://hl7v2-elr-testing.nist.gov/mu-elr/.

Attachment K3: Antimicrobial Resistance Regional Laboratory Network (p. 131-141) In 2016 CDC established 1 ARLN Regional Labortory in each of the 7 PulseNet regions through the ELC award. However, candidates are not limited to laboratories that previously received funding. The application process is still open in this years ELC cycle and public health laboratories not currently serving as a Regional Lab are eligible to apply to become one. The ELC FOA Guidance outlines both required and optional activities that candidate ARLN regional laboratories may apply for in Activities 1-9- (p. 134-137). CDC will give preference to laboratories that describe advanced existing capacity and apply for optional as well as required activities. Existing ARLN Regional Laboratories that are reapplying should consider including requests for funds required to maintain existing services as well as provide enhanced testing or other services. Consider requesting equipment or reagents necessary to expand your capacity to perform Next Generation Sequencing (see Activity 5) but note that this is not a required activity.

https://phinmqf.cdc.gov/default.aspxhttp://7edit.com/home/index.phphttp://hl7v2-elr-testing.nist.gov/mu-elr/

Page 15 of 19

As outlined in Activity 2, regional laboratories must establish a network of laboratories willing to submit isolates of certain phenotypes for further characterization. The two phenotypes outlined in Activity 2 that should be focused on are carbapenem-resistant Acinetobacter and third-generation cephalosporin-resistant Escherichia coli or Klebsiella spp. Regional laboratories must work with the jurisdictional public health laboratories to recruit clinical laboratories to submit isolates for Activity 2 testing. The network should include at least 1 laboratory from each state in the region, with preference given to large laboratories that collect isolates from multiple healthcare facilities. Laboratory testing by the regional laboratories should include species identification, AST, phenotypic methods and molecular testing. Regional Laboratories should plan to conduct regular trainings for other public health laboratories in their region. APHL has some funding available to facilitate those trainings but consider requesting additional funds to supplement. Training will be provided for all of the selected ARLN laboratories and is planned for Fall 2017. APHL will have funding available to allow travel to the training.

Activity 11: TB Public Health Laboratories interested in applying should be able to perform prospective WGS for at least half of the requested volume and be able to either perform MIRU-VNTR or be able to subcontract to another laboratory. PHLs applying for the entire volume should also consider including a budget for half of the volume. Other budget considerations include preparing the budget for the noted lower volume due to the delayed start date (7,500 Isolates for MIRU-VNTR starting December 1, 2017 and 6,000 isolates for TB WGS, with a start date of February 1, 2018). Minor equipment costs (

Page 16 of 19

Attachment N1: Tickborne: Lyme disease ($60,000/award; 16 awards) (p. 156-159) Lyme Disease funding is limited to jurisdictions where the disease is most prevalent. Funding is traditionally distributed primarily to support epidemiology activities. However, public health laboratories in areas with a high prevalence of Lyme disease are encouraged to coordinate with their epidemiology counterparts to discuss testing needs.

Attachment N2 Tickborne: Non-Lyme Disease (p. 204-207)($30,000/award; 12 awards) Purchase reagents, maintain staff and update/ maintain equipment used in the surveillance and identification of tickborne diseases from ticks and clinical specimens. More information on the diagnosis of select tickborne diseases can be found in this 2006 MMWR.

Attachment O: Parasitic Diseases (p. 160-162) Component One: Implementation and Training ($8,000/award; 10 awards) Consider implementing molecular methods for the diagnosis of parasitic diseases. CDC protocols are available upon request. Consider purchasing the equipment (digital cameras, image enhancement software or electronic databases) necessary to develop the capabilities for telediagnosis or real-time digital remote microscopy.

Consider requesting funding to travel to training at CDC or another public health laboratory. Component Two: Enhanced Laboratory Investigation of Cyclosporiasis ($32,500/award; 4 awards) APHL suggests requesting funds for reagents and/or equipment such as additional or upgraded UV microscopes. Consider the costs of obtaining more positive stool samples from clinical partners and for packaging and shipping stools for genotypic analysis. Preference may be given to laboratories that apply more sensitive detection methods, implement confirmatory methods at the species or subspecies level, and/or increase capacity to obtain and confirm suspect cases of cyclosporiasis. Attachment P Influenza Activities (p. 163-168) P1 Influenza Surveillance and Diagnostic Testing ($131,573/award; 57 awards)

APHL strongly suggests that you that you place a high priority on personnel. At a minimum, be sure to include staff that was funded on ELC last year. As most reagents and many consumables used for influenza testing are provided by the International Reagent Resource (IRR), those budget items are not likely to be funded. Laboratories should also consider budgeting for service contracts on their ABI 7500 Fast DX instruments. Consider the new Evaluation and Performance Measurement bullets 10-11 when responding to Strategies and Activities bullet 5.d.

P2 Influenza Outbreak Response (up to $500,000 in the event of an outbreak) Funds will only be available in the event of a local or national influenza outbreak. However, all proposals should plan for and request $500,000 (small jurisdictions may request less while very large jurisdictions may request more). This request will likely be marked approved but unfunded in your

http://www.cdc.gov/mmwr/preview/mmwrhtml/rr5504a1.htm

Page 17 of 19

initial budget markup, but it will expedite the release of funds should outbreak conditions warrant. It is acceptable to use the same language that was submitted in the last request. Attachment Q Non -Influenza Respiratory Disease Activities (p. 169-174) Q1 Non-Influenza Respiratory Diseases: Diagnostics, Reporting and Surveillance ($70,000/ award; 10-12 awards) Consider requesting funds for the maintenance, implementation or expansion of non-influenza respiratory virus tests including reagents and personnel. CDC protocols, including enterovirus D68, are available upon request and commercial respiratory virus panels are also available. See the APHL Respiratory Pathogens page under ID Member Resources for select protocols and lists of commercially available respiratory virus panels. Note that access to the webpage is restricted to APHL members. Also, consider inclusion of transmitting non-influenza respiratory data via the PHLIP ELSM 251 HL7 data feed as a proposal activity and for budget requests (see Q1.v.5b). As noted above, the APHL Informatics Technical Assistance Team may be available to assist local staff onsite or virtually with updating and validating ELSM implementations. For more information about technical assistance and integration of surveillance systems, please email the Electronic Data Exchange Inbox at edx@cdc.gov

Q2 Non-Influenza Respiratory Diseases: Outbreak Response (up to $300,000 in the event of an outbreak) Funds will only be available to provide surge capacity in the event of a local or national outbreak of non-influenza respiratory disease such as MERS-CoV. All proposals should plan for and request $300,000. Consider requesting funds for additional temporary personnel, supplies, and specimen shipping expenses This request will likely be marked approved but unfunded in your initial budget markup, but it will expedite the release of funds should outbreak conditions warrant.

Attachment R1 Vaccine Preventable Disease Surveillance (p. 175-185) (52 awards; $100,000/award)

Proposals should include funds for shipping isolates (particularly for meningococcal disease) to CDC. However, requests for shipping supplies and services should be limited to no more than $5,000. APHL further suggests coordinating with your epidemiology or immunizations partners to ensure that adequate testing services are in place to meet your jurisdictional surveillance needs. Implementation of molecular assays for detection of diseases you see frequently in your jurisdictions (e.g. mumps, measles) may best serve your jurisdiction. CDC has protocols available upon request. Request funds for reagents and supplies necessary to implement this testing. In order to improve efficiencies and offer a broader range of testing services. Laboratories can consider enrolling in the APHL/CDC VPD Reference Center as a submitting site. The Reference Centers offer molecular testing services for 7 VPDs. A subset of viral specimens and all bacterial specimens/isolates submitted to the reference center are sent to CDC following testing at the Reference Centers. All results of VPD laboratory tests performed at the reference centers are reported to CDC via HL7 messaging. If you are interested in learning more about the Reference Centers please contact Kevin Bradley (Kevin.Bradley@aphl.org).

https://www.aphl.org/programs/infectious_disease/member-resources/Pages/default.aspxmailto:edx@cdc.govhttps://www.aphl.org/programs/infectious_disease/Pages/VPD.aspxhttps://www.aphlweb.org/aphl_departments/public_health_programs/Shared%20Documents/Kevin.Bradley@aphl.org

Page 18 of 19

Attachment W2 Rabies: Laboratory Capacity for National Rabies Surveillance (p. 201-202)($3,500/award; 20 awards) Priority should be given to maintain staff qualifications and proficiency; recommendations can be found in the national standard protocol. This includes travel for attendance at national training course if they have not attended within the last 6 years. Ensure equipment used in DFA is up to date. Consider upgrading fluorescence microscopes. The quality of fluorescence microscopes is critical to the sensitivity of the DFA assay. The national standard protocol contains a discussion on choosing an adequate microscope in Appendix 3. Attachment X Mycotics (p. 203-206) ($65,385/award; 8 awards)

Purchase reagents, maintain staff and update/ maintain equipment used in the identification of Cryptococcus, Coccidioides, Histoplasma, Blastomyces, and Candida spp in clinical and environmental specimens. For those laboratories wishing to apply to serve as a regional laboratory for Candida testing, include funding requests for reagents to perform Candida identification and susceptibility testing in your application for Project K7 AR Regional Laboratories. Laboratories not currently performing testing for mycotic diseases should consider using ELC funds to partner with other public health or university laboratories to deliver testing services for low volume tests.

Attachment Y Legionella Prevention (p. 207-211) ($100,000-$800,000/award; 2-3 awards) APHL recommends submitting proposals that will improve surveillance and testing capacity for Legionella including developing or maintaining proficiency and expertise in Legionella culture methods. Laboratories that are willing to collaborate with CDC to provide clinical isolates and urine from non-serogroup 1 culture confirmed cases for assay development purposes are encouraged to include that in their proposal. Consider budgeting for personnel time and training to demonstrate continued expertise in Legionella test methods particularly culture. Also include laboratory supplies and specimen shipping costs. Laboratories should coordinate with health departments and environmental testing laboratories on a comprehensive approach to improving surveillance and outbreak response in their proposals.

Attachment Z - Waterborne Disease Detection, Investigation, and Reporting (p. 213-217) ($22,500/award; 20 awards) Applicants should utilize funds for personnel, training, travel, supplies, and equipment that help implement strategies that build on current capacity. Consider the costs of implementing standard investigation protocols and tools that utilize laboratory capacity, including collaboration with other states and localities. Applicants should request funds that allow participation in CryptoNet through single gene or WGS subtyping of cryptosporidium specimens. Alternatively, include the cost of packing and shipping isolates to regional CryptoNet centers or to CDC. Include costs associated with participation as a regional

http://www.cdc.gov/rabies/pdf/rabiesdfaspv2.pdfhttp://www.cdc.gov/rabies/pdf/rabiesdfaspv2.pdf

Page 19 of 19

CryptoNet center. You may propose environmental sampling and testing for pathogens or water quality indicators that will aid in outbreak investigations and facilitate interpretation of clinical results. Funds can also support improved methods of sample collection and analysis. Also, consider conducting meetings or attend trainings that improve waterborne disease laboratory expertise.