GARLRN Performance Measurement Tool Changes Crosswalk_July2025_for PRA

GARLRN Performance Measurement Tool Changes Crosswalk_July2025_for PRA.docx

[OADPS] The Performance Measures Project: Improving Performance Measurement and Monitoring by CDC Programs

GARLRN Performance Measurement Tool Changes Crosswalk_July2025_for PRA

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Global Antimicrobial Resistance Laboratory and Response Network Performance Measurement Tool Crosswalk

Change #

Form #

QID

Section Name

Original Question

New Question

Change

Justification

1.

N/A

N/A

Tool Instructions

Please complete the tool using information that will be included in your organization's Year 3 performance narrative submission.  Please answer as many questions as possible. 


FORM 1: RECIPIENT INFORMATION

- This form is to be completed at recipient level. Please complete based on project activities during the current budget period BP4. If any recipients are implementing multiple projects, they will be asked to kindly complete Sections 1-3 of this form for each additional Strategy 2-5 projects.

- For any questions where recipient is not aware or unsure of response, please enter ‘N/A’ or ‘Unknown’ where applicable

Please complete the tool using information that will be included in [recipname_bp4]'s performance narrative submission for the current reporting period.


FORM 1: RECIPIENT INFORMATION

Please answer the following questions related to [recipname_bp4]’s Global AR Lab and Response Network project implementation, laboratory activities, and workforce development activities during the current reporting period. This form is to be completed at the recipient level.

Any recipients implementing multiple projects during the current reporting period are kindly requested to complete FORM 1 for each Strategy 2-5 project(s).

For any questions where recipient is not aware or unsure of response, please enter ‘Does not apply’ where applicable

  • your organization” changed to name of variable which will autofill text with name of recipient when form completed on data collection platform

  • Section names updated

  • Changed instructions for repeating the form

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • No change to reporting burden

2.

N/A

N/A

Entire tool

Present tense used in some questions

Past tense for all questions in tool

  • Throughout tool, where appropriate, all questions reworded to past tense

  • No change to reporting burden

3.

1 & 2

N/A

N/A

The reporting period for responses was specified in previous version

All reporting period references changed to “during this reporting period” to allow for specifying at a later time

  • All reporting period references changed to “during this reporting period”

  • Unnecessary to specify reporting period for the purposes of this review or if sharing the tool internally with colleagues

  • No change to reporting burden

4.

1

5.

Recipient Information

Please select the pathogen(s) of interest for this project:

(select all that apply)


  1. Carbapenem-resistant Acinetobacter

  2. Candida auris

  3. Clostridioides difficile

  4. Carbapenem-resistant Enterobacterales

  5. Drug-resistant Neisseria gonorrhoeae

  6. Drug-resistant Campylobacter

  7. Drug-resistant Candida

  8. ESBL-producing Enterobacteriaceae

  9. Haemophilus influenzae

  10. Vancomycin-resistant Enterococci

  11. Multidrug-resistant Pseudomonas aeruginosa

  12. Drug-resistant nontyphoidal Salmonella

  13. Drug-resistant Salmonella serotype Typhi

  14. Drug-resistant Shigella

  15. Methicillin-resistant Staphylococcus aureus

  16. Neisseria meningitidis

  17. Drug-resistant Streptococcus pneumoniae

  18. Drug-resistant Tuberculosis

  19. Erythromycin-resistant group A Streptococcus

  20. Clindamycin-resistant group B Streptococcus

  21. Azole-resistant Aspergillus fumigatus

  22. Drug-resistant Bordetella pertussis

  23. Other (please specify as many as needed):

5. Select the pathogen(s) of interest for this project:

(select all that apply)


  1. Aspergillus fumigatus

  2. Bordetella pertussis

  3. Campylobacter spp.

  4. Candida auris

  5. Candida spp. (excluding Candida auris)

  6. Carbapenem-resistant Acinetobacter

  7. Carbapenem-resistant Enterobacterales

  8. Clostridioides difficile

  9. Cronobacter spp.

  10. Extended-spectrum beta-lactamase-producing Enterobacterales

  11. Escherichia coli

  12. Group A Streptococcus (Streptococcus pyogenes)

  13. Group B Streptococcus (Streptococcus agalactiae)

  14. Haemophilus influenzae

  15. Listeria monocytogenes

  16. Methicillin-resistant Staphylococcus aureus

  17. Multidrug-resistant Pseudomonas aeruginosa

  18. Mycobacterium tuberculosis

  19. Neisseria gonorrhoeae

  20. Neisseria meningitidis

  21. Non-typhoidal Salmonella spp.

  22. Salmonella serotype Typhi

  23. Shigella spp.

  24. Streptococcus pneumoniae

  25. Vancomycin-resistant Enterococci

  26. Vibrio spp.

  27. Other (please specify):


  • Slight wording change in question

  • Additional pathogen options included in new question

  • More comprehensive list of pathogens that minimizes need for respondents to provide open-ended responses

  • Decrease in reporting burden

5.

1

3.

Project Implementation

1.i. What is the number of sites (laboratories, hospitals, healthcare facilities, etc.) that were supported as part of the project? Please answer for each country.

1.ii. How many sites received direct material support (i.e., lab reagents/diagnostics, other lab equipment, IT material, printed SOPs, etc.) from this organization during this budget period as part of the project? Please answer for each country.

3. How many sites (laboratories, hospitals, healthcare facilities, etc.) were supported as part of the project across all countries during this reporting period?


N/A

  • QID 1.i. now 3.

  • QID 1.ii. deleted

  • Wording changed to clarify question

  • Question 1.ii. was duplicative and removed

  • Form restructured slightly to avoid duplication and to facilitate ease of responding

  • Decrease in reporting burden

6.

1

2., 2.a., 2.b., 2.b.i. & 2.b.ii.

Project Implementation

1.a. Please select the countries in which this project was implemented during BP3.


2. Is this project contributing to achieving the goals of a country’s national action plan (NAP) on antimicrobial resistance?


2.a/b. If yes, please list all countries and describe supporting activities of NAP (Open-ended)


2.c. If no, please list barriers to participation and/or support of the NAP (Open-ended)

2. Select the countries this project was implemented in during this reporting period.

2.a. In [selected country], did this project directly collaborate with: (select all that apply)

  1. Ministry of Health

  2. National Reference Laboratory

  3. National AMR Coordination Center

  4. None of the above

  5. Does not apply

2.b. Did this project contribute to this country’s NAP? (Y/N/DK/Does not apply)

2.b.i. If Yes, please describe how project activities contributed to supporting the country’s NAP

2.b.ii. If No, please list barriers to participation and/or support of the NAP

  • QID 1.a. now 2.

  • Question added as QID 2.a.

  • QID 2. now 2.b.

  • QID 2.a./b. now 2.b.i.;

  • QID 2.c. now 2.b.ii.

  • Each country selected in question 2. will have follow up questions 2.a. and 2.b.

  • Questions streamlined to capture the same information across recipients and countries, rather than open-ended responses that require more analysis

  • Wording changed to clarify question

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • Slight increase in reporting burden

7.

1

4.

Project Implementation

N/A

Select the phase that best describes this partner’s and/or site’s implementation, for the current reporting period:

a) Exploration;

b) Initiation;

c) Initial Implementation;

d) Full Implementation and Maintenance;

e) Expansion/ Scale-Up;

f) Reduction/ Scale-Down

g) Close Out

  • Added question 4. about what phase of implementation recipients’ project(s) were in


  • Provides clarity of project status at the recipient level

  • Slight increase in reporting burden

8.

1

5.

Project Implementation

3. List any major product(s) (e.g., SOPs, job aids, manuscripts, posters, trainings, etc.) developed within this budget period and specify location (if applicable).


If none, enter N/A

5. What major product(s) (e.g., SOPs, job aids, manuscripts, posters, trainings, etc.) were developed within this budget period? How many of each were developed?

(Select all that apply)

  1. Communications products (e.g., website, promotional articles) (à 5.a.)

  2. Conference presentations or posters (à 5.a.)

  3. Non-conference presentations (à 5.a.)

  4. Peer-reviewed publications (à 5.a.)

  5. Standard Operating Procedures (SOPs) and Job Aids (à 5.a.)

  6. Workshop or training materials (e.g., curriculum, modules) (à 5.a.)

  7. Other (à 5.a.)

Does not apply

5.a. Provide links to any major products developed within this reporting period that are publicly available.

  • QID 3 now 5.

  • Question will no longer be open ended and instead will have answer options/categories based on previous year’s responses to facilitate standardized responses

  • Each category selected will have a follow up text box for the number of products developed

  • Removed “and specify location (if applicable)” from original open-ended question and instead added question 5a. requesting links to major products where available


  • No longer necessary for recipients to specify location for this response.

  • No change to reporting burden

9.

1

6.

Project Implementation

4. Have any CDC Subject Matter Experts (SMEs) reviewed the major products listed in question #5?

a) Yes

b) No

c) Don’t Know

d) Does not apply

6. Did any CDC Subject Matter Experts (SMEs) review the major products listed in question #5?

a) Yes, all major products were reviewed by CDC SMEs

b) Yes, some major products were reviewed by CDC SMEs ( 6.a.)

c) No, major product were not reviewed by CDC SMEs ( 6.a.)

d) Don’t know

e) Does not apply

  • QID 4. now 6.

  • Answer options changed to capture most accurate information

  • Additional option enhances clarity of question and removes potential confusion for respondents

  • No change to reporting burden

10.

1

7.

Project Implementation

5. What strategies or activities has [pilot_recipname] implemented to address sustainability of the efforts and progress made with this project beyond the current budget period? 

7. How did [recipname_bp4] ensure sustainability of project activities, during this reporting period? 

(Consider all project activities, including those related to workforce development, laboratories, and surveillance and response.)

  • QID 5. now 7.

  • Question reworded and clarified

  • Corrected autofill variable name

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • No change to reporting burden

11.

1

N/A

All Sections

Please use this space to include any additional information related to implementation of this project

(Respondents are prompted to add additional information or context at the end of each section)

Please use this space to include any additional information related to [section name] for this project, including notable successes or challenges, during this reporting period?

  • Added “including notable successes or challenges” to each additional info prompt

  • Open-ended responses and option to leave comments can facilitate identification of success stories, case studies , or challenges

  • No change to reporting burden

12.

1

N/A

Laboratory Activities

Section 3 Instructions:

Please answer the following questions based on this organization’s current laboratory enhancement activities for this Global AR Lab & Response Network project. Please use information that will be included in this organization’s Year 3 performance narrative submission and please be as thorough as possible.

Section 3 Instructions:

Please answer the following questions related to laboratory activities for [recipname_bp4]’s Global AR Lab and Response Network project during the current reporting period. We recommend using information that will be reported in the performance narrative submission.

  • Instruction wording changed slightly

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • No change to reporting burden

13.

1

1.

Laboratory Activities

1. Is there a national or central laboratory which performs quality assurance testing for this project?


1. Does the recipient directly provide or collaborate with another organization to provide external quality assessment (EQA) to laboratories for this project?


  • Word change in question language

    • Assurance assessment

    • Performs provides

    • Removed word “testing”

    • Added “to subnational labs”

  • QID 1.b. now 1.

  • Question wording changed to reflect accurate language for subject matter

  • No change to reporting burden

14.

1

1.a.

Laboratory Activities

1.a. If yes:

  1. List the number of labs that External Quality Assessment (EQA) was provided to, by country (Open ended)

  2. Describe the EQA (pathogens included, number of isolates or samples submitted, and frequency), by country. (Open ended)

1.a. If yes:

Describe EQA; organization(s) providing EQA; pathogen(s) included; number of isolates or samples submitted; and frequency), by country

List as follows:

1. [Country A Name], [Number of laboratories], [details about EQA];

2. [Country B Name], [Number of laboratories], [details about EQA];

3. [Country C Name], [Number of laboratories], [details about EQA]; etc.

  • Question wording changed and two sub-questions consolidated into one sub-question

  • Added answer format to guide responders

  • Response template added to facilitate response

  • Follow-up questions consolidated to simplify responses, including deduplicating reporting countries in two related questions

  • No change to reporting burden

15.

1

2.-6

Laboratory Activities

What is the total number of labs where training or other activities for performing [TEST] were implemented?

How many laboratories received training or support for [TEST METHOD] during this reporting period?


  • QID 2.a.-6.a. now 2.-6.

  • Changed overall wording of question to simplify


  • More accurate/ understandable wording

  • No change to reporting burden

16.

1

5. & 6.

Laboratory Activities

5.a.) What is the total number of labs where training or other activities for performing antimicrobial susceptibility testing (AST) were implemented?


6.a.) What is the total number of labs at which training or other activities for performing whole genome sequencing (WGS) were implemented?

5. How many laboratories received training or support for antimicrobial susceptibility testing (AST), including antifungal susceptibility testing (AFST), of any pathogen(s) during this reporting period?

6. How many laboratories received training or support for sequencing of any pathogen(s) during this reporting period?

  • QID 5.a. now 5.

  • QID 6.a. now 6.

  • of any pathogen(s)” added to question

  • Question wording changed to reflect accurate language for subject matter

  • No change to reporting burden

17.

1

N/A

Workforce Development Activities

Section 2 Instructions

The following questions cover current education and training activities for different personnel targeted by this Global AR Lab & Response Network project. Do not answer questions based on future efforts, only established or current opportunities during budget period 3.

Section 2 Instructions:

Please answer the following questions related to Workforce Development activities for [recipname_bp4]’s Global AR Lab and Response Network project during the current reporting period. We recommend using information that will be reported in the performance narrative submission.

  • Instruction wording changed slightly

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • No change to reporting burden

18.

1

1.

Workforce Development
Activities

N/A

  1. How many personnel received training from [recipname_bp4] during this reporting period?

  • Question added for total number of personnel trained by recipient

  • Slight increase in reporting burden

19.

1

N/A

Workforce Development Activities

Please select the type of personnel that received training from this organization (can be in collaboration with partners):

(select all that apply)

a) Laboratory

b) Epidemiologist/Data Manager

c) Healthcare Worker

d) Field-based personnel (community interviewer)

e) MOH/NPHL leadership

f) Other (please specify): ____________

g) Trainings that were performed did not document types of personnel in attendance (please provide disaggregated number of personnel)

h) No personnel received training during this budget period (end of form)

2. Please select the type of personnel that received training from this organization (can be in collaboration with partners):

(select all that apply)

a) Epidemiologist/Data Managers

b) Healthcare Workers

c) Laboratory personnel

d) MOH/NPHL leadership

e) Other ( 2.e., then i. &ii.)

f) Personnel type(s) were not captured

g) No personnel received training during this budget period ( skip 2-6)

  • Response wording changed slightly

  • Responses alphabetized

  • Skip logic added to tool

  • Field-based personnel (community interviewer)” answer option removed

  • Original answer option ‘g’ removed


  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • No change to reporting burden

20.

1

2.

Workforce Development Activities

2. Are there any other partnerships (e.g., universities, hospitals, etc.) that provide mentorship for [insert personnel type] personnel targeted by this project?

a) Yes (2.a.)

b) No

c) Don’t Know

2.a. If yes, please list these partnerships.

N/A

  • Question and corresponding open-ended follow-up removed

  • Question unnecessary

  • Decrease in reporting burden

21.

1


Workforce Development Activities

4.a. If yes,

i. Does the curriculum leverage a Train-the-Trainer model? (Yes/No)

ii. What entity is responsible for facilitating the curriculum? (Open ended)

iii. What assessments were conducted to ensure trainings addressed knowledge gaps? (Open ended)

iv.. Do the trainings use a Train-the-Trainer model?


v. What assessments were conducted to ensure trainings objectives were met?

  • QID 4.a.i. now iv.

  • QID 4.a.ii. removed

  • QID 4.a.iii. changed to v.

  • Changed wording - “Does the curriculum leverage” “Do the trainings use…”


  • Questions simplified or deleted

  • Decrease in reporting burden

22.

2

N/A

N/A

Form 2 Instructions:

The following questions are related to project implementation with partners as well as referral network and surveillance practices at EACH hospital, health care facility (HCF) and/or laboratory that is participating in [name of organization autofill]'s Global AR Lab & Response Network project. 

Please complete FORM 2 for EACH partner, HCF/hospital, or laboratory.  Recipients with projects in multiple countries or engaged with multiple partners or HCFS/hospitals/laboratories will be asked to specify country and partner/facility name on each form.

Form 2 Instructions:

Please answer the following questions related to project implementation with partners as well as referral network and surveillance practices for EACH hospital, health care facility (HCF) and/or laboratory that is participating in Global AR Lab and Response Network project during the current budget period. We recommend using information that will be reported in the performance narrative submission.

Please complete FORM 2 for EACH partner, HCF/hospital, and/or laboratory. Recipients with projects in multiple countries or engaged with multiple partners or HCFS/hospitals/laboratories will be asked to specify country and partner/facility name on each form.

For any questions where recipient is not aware or unsure of response, please enter ‘Does not apply’ where applicable.

  • Wording changes to instructions

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • No change to reporting burden

23.

2

2.-6.

Partner or Laboratory Site Information

  1. Partner Name*:

1.a. Is this partner a laboratory or healthcare facility with lab?

  1. Select the option that best describes the level of the health system that the laboratory or healthcare facility site supports

2.a. Is this lab or healthcare site part of an academic institution? Y/N

2.b. Is this lab or healthcare site part of a private organization? Y/N

**Alternative 2. Select the option that best describes this partner: (If No selected above)

  1. Name of partner’s location:

  2. Name of country: – country drop down menu

  3. Project contribution(s) made by this partner

  1. Name of Partner or Laboratory Site:

  2. Name of [partnr1_projsite]’s location (e.g. name of town, city, district, province, etc.):

  3. Name of country:

  4. Is [partnr1_projsite] a laboratory or a healthcare facility with a laboratory? Y/N

  5. Select the option that best describes the level of the health system that [partnr1_projsite] supports:

5.a. Is this lab or healthcare site part of an academic institution? Y/N

5.b. Is this lab or healthcare site part of a private organization? Y/N

**Alternative 5. If answered “No” to question 4., Select the option that best describes this partner:

  • Wording clarified

  • Questions reordered

  • QID 3. now 2.

  • QID 4. now 3.

  • QID 1.a. now 4.

  • QID 2., 2.a., 2.b. and Alternative 2. now 5., 5.a., 5.b., and Alternative 5. Respectively

  • QID 5. now QID 3. In Project Implementation section

  • Wording and order of questions changed to enhance clarity of instructions and to avoid confusion for respondents

  • No change to reporting burden

24.

2

6.

Partner or Laboratory Site Information

N/A

  1. Please select pathogen(s) of interest for [partnr1_projsite] for this project.

(same answer options as QID 5 in Form 1)

  • Question added to ask about pathogen of interest for partner or laboratory site

  • Addition frames Form 2 in appropriate context and helps avoid confusion for respondents

  • Slight increase in reporting burden

25.

2

7.

Project Implementation

  1. Select the implementation phase that best describes this partner’s and/or site’s stage in the project, as it currently stands:

  1. Exploration – Engaging stakeholders to identify 1. need(s); and 2. appropriate steps to address gaps or enhance activities

  2. Initiation – Project planning; consensus reached with stakeholders regarding project sites, objectives, and activities, as well as timeline for implementation

  3. Initial Implementation – Beginning stages of project implementation at selected sites including: 1. collection of baseline data; 2. establishing new practices/protocols; 3. supply/equipment procurement; 4. recruitment/hiring of locally based staff; etc.

  4. Full Implementation – Majority of project activities have been rolled out and routinely monitored

  5. Expansion/Scale-Up – Increasing the number of sites targeted for project activities

  6. Reduction/Scale Down – Decreasing the number of sites targeted for project activities or scaling down scope of activities


  1. Select the phase that best describes this partner’s and/or site’s implementation, for the current reporting period:

  1. Exploration – Engaging stakeholder to identify 1. need(s); and 2. appropriate steps to address gaps or enhance project site’s activities

  2. Initiation – Project planning; consensus reached with stakeholder(s) regarding project site, objectives, and activities, as well as timeline for implementation

  3. Initial Implementation – Beginning stages of project implementation at project site including: 1. collection of baseline data; 2. establishing new practices/protocols; 3. supply/equipment procurement; 4. recruitment/hiring of locally based staff; etc.

  4. Full Implementation and Maintenance – Majority of project site’s activities have been rolled out and routinely monitored

  5. Expansion/Scale-Up – Scaling up scope of project site activities

  6. Reduction/Scale Down – Scaling down scope of project site activities

  7. Close out - Project/funding cycle coming to a close and site activities completed

  8. Institutionalization - Site has taken ownership of project activities with little to no support from the implementing partner

  • Reworked original wording of question and responses

  • Added two more answer options (g. and h.)

  • QID 7. Now QID 1 in Project Implementation section

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • Changes based on feedback and latest data analysis, which showed different interpretations of the prompt when answering

  • No change to reporting burden

26.

2

2.

Project Implementation

N/A

2. What type of assistance did [partr1_projsite] receive during this reporting period?

a) Financial assistance only

b) Technical assistance only

c) Financial and technical assistance

d) Does not apply

- Question added about type of assistance provided to project site


  • Slight increase in reporting burden

27.

2

3.

Project Implementation

5. Project contribution(s) made by this partner (e.g., equipment and supplies procured, trainings provided, isolates collected and submitted, etc.):

3. What contribution(s) did [partnr1_projsite] make for the project during this reporting period? (select all that apply)

a) Epidemiological data collection, management, and reporting

b) Facilitation of or participation in meetings, trainings, or workshops

c) Laboratory testing

d) Project coordination

e) Sample collection

f) Sample submission, including storage, handling, and transport

g) Technical assistance to other project sites

h) Work product development (e.g., SOPs, publications, etc.)

i) Other (Please specify)

j) N/A


  • Reworked original wording of question and provided answer options rather than open-ended responses

  • Question moved from Partner or Laboratory Site Information section to Project Implementation section

  • Wording change and addition of options enhance clarity of instructions and remove potential confusion for respondents

  • Decrease in reporting burden

28.

2

1.a.

Laboratory Activities

N/A

If no, please list barriers to this site’s participation in a laboratory network or referral network.

  • Follow up question added to understand barriers experienced at site level

  • Important to understand some of the factors that hinder participation in or engagement with referral networks or reference laboratories

  • Slight increase in reporting burden

29.

2

8.

Laboratory Activities

  1. Has this site agreed to (or is it required to) submit or forward isolates?

(Only asked of laboratories or HCFs with lab)

a) Yes

b) No (end of form)

c) Don’t know (end of form)

d) Other (Please specify): __________________

N/A

  • Question removed

  • Question was redundant

  • Decrease in reporting burden

30.

2

2.-8.

Laboratory Activities

Which of the following testing methods are routinely performed at this site/laboratory?

Culturing – only in context of project pathogen(s) of interest

  • Enteric bacteria culture

  • Invasive bacteria culture

  • N. gonorrhoeae culture

  • Candida sp. Culture

  • Other fungal culture

  • Other bacterial culture

  • Other (please specify): ;

  • Unknown

AST – only in context of project pathogen(s) of interest

  • Broth microdilution (e.g. Sensititre);

  • Disk diffusion;

  • Gradient test/E test;

  • Agar dilution;

  • Vitek 2

  • Other automated device (e.g. Phoenix, Microscan)

  • Other (please specify):;

  • Unknown

Phenotypic – only in context of project pathogen(s) of interest

  • API (manual)

  • MALDI-TOF (e.g. Bruker, Vitek MS)

  • Vitek 2

  • Chromogenic Media (e.g. CHROMagar)

  • Colormetric Tests (e.g. Carba NP, Blue-Carba)

  • Lateral Flow Assay (e.g. Carba 5)

  • mCIM

  • Serotyping

  • Other biochemical tests

  • Other (please specify): ;

  • Unknown

Genotypic – only in context of project pathogen(s) of interest

  • PCR

  • RT-PCR/qPCR

  • Cepheid Xpert (e.g. Carba-R)

  • LAMP

  • Hologic Panther

  • Other (specify):;

  • Unknown

WGS – only in context of project pathogen(s) of interest

What type of sequencing are you doing?

  • Whole Genome Sequencing

  • Short-read

  • Long-read

  • Direct Amplicon Sequencing

  • Next Generation Sequencing

  • Sanger Sequencing

  • Other, please specify

What instrument(s) are you using?

  • Illumina

    • Please specify machine:

      • MiSeq

      • NextSeq

      • MiniSeq

      • Other, please specify:

  • Pacific Bio (PacBio)

    • Please specify machine:

      • Revio

      • Vega

      • Onso

      • Other, please specify:

  • Oxford Nanopore Technologies

    • Please specify machine:

      • MinION

      • GridION

      • PromethION

      • Other, please specify:

  • Other, please specify


ii. Total testing volume (during budget period) Open ended

iii. Total number of personnel that received training in testing method Integer


Sequencing only

v. Total number of personnel trained to perform bioinformatics analysis of WGS data Integer

vi. Describe the bioinformatics pipelines being utilized to analyze data Open ended

2.-8. Select testing methods performed on project pathogen(s) of interest (Select all that apply).


2. Culture

3. Antimicrobial Susceptibility Testing (AST or ASFT) (e.g., E test, disk diffusion, broth microdilution)

4. Phenotypic Testing (e.g., MALDI-TOF, VITEK 2, API, etc.)

5. Genotypic Testing (e.g., PCR)

6. Sequencing (e.g., WGS, short-read Illumina, long-read ONT, direct amplicon sequencing, NGS, etc.)

7. Other (Please specify):_______________

8. Unknown ( if only Unknown selected, skip to 9.)


2.i.-7.i. For each testing method selected, select the specific tests routinely performed on project pathogen(s) of interest (Select all that apply)


2.i. Culturing – only in context of project pathogen(s) of interest

  • Candida spp. culture

  • Enteric bacteria culture

  • Invasive respiratory bacteria culture

  • N. gonorrhoeae culture

  • Other fungal culture

  • Other bacterial culture

  • Other (please specify):

  • Unknown

3.i. AST – only in context of project pathogen(s) of interest

  • Agar dilution;

  • Broth microdilution (e.g. sinsititre);

  • Disk diffusion;

  • Gradient test/E test;

  • VITEK 2

  • Other automated device (e.g. Phoenix, Microscan)

  • Other (please specify):;

  • Unknown

4.i. Phenotypic – only in context of project pathogen(s) of interest

  • API (manual)

  • Chromogenic Media (e.g. CHROMagar)

  • Colormetric Tests (e.g. Carba NP, Blue-Carba)

  • Lateral Flow Assay (e.g. Carba 5)

  • MALDI-TOF (e.g. Bruker, Vitek MS)

  • mCIM

  • Serotyping

  • VITEK 2

  • Other biochemical tests

  • Other (please specify):

  • Unknown

5.i. Genotypic – only in context of project pathogen(s) of interest

  • Cepheid Xpert (e.g. Carba-R)

  • Hologic Panther

  • LAMP

  • PCR

  • RT-PCR/qPCR

  • Other (specify):;

  • Unknown

6.i. Sequencing – only in context of project pathogen(s) of interest

What type of sequencing are you doing?

  • Direct Amplicon Sequencing

  • Next Generation Sequencing

  • Long-read sequencing

  • Short-read sequencing

  • Sanger Sequencing

  • Whole Genome Sequencing

  • Other, please specify

7.i. Other – only in context of project pathogen(s) of interest Please describe the testing method (Open-ended)

2-7.ii. What was the total testing volume for the pathogen(s) of interest for this testing method during this reporting period? Integer

2-7.iii. How many personnel received training in this testing method during this reporting period? Integer


6.iv. What [sequencing] instrument(s) are used?

  • Illumina

    • Please specify machine:

      • MiniSeq

      • MiSeq

      • NextSeq

      • Other, please specify:

  • Pacific Bio (PacBio)

    • Please specify machine:

      • Onso

      • Revio

      • Vega

      • Other, please specify:

  • Oxford Nanopore Technologies

    • Please specify machine:

      • GridION

      • MinION

      • PromethION

      • Other, please specify:

6.v. How many personnel were trained to perform bioinformatic analysis of sequencing data during this reporting period? Integer

6.vi. Please name the bioinformatics pipelines that were utilized to analyze sequencing data. Open ended

- Additional answer options provided, and others removed in follow up questions for each testing method routinely performed

- Changed numbering scheme for easier data management and navigation of the tool

- All sequencing-specific sub-questions (6.iv., 6.v., 6.vi.) are now grouped together in the tool

- Alphabetized options to help respondents more quickly select appropriate responses

- Some overall wording changes to ensure accurate interpretation of questions


  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • Facilitates easier navigation of the tool

  • Decrease in reporting burden

31.

2

N/A

Laboratory Activities

10. Does this site have a program or any activities that focus on retaining staff with institutional and technical knowledge once they are trained on any of the testing methods listed previously?

a) Yes ( 10.a.)

b) No

c) Don’t know

d) Does not apply


10.a. If yes, please describe:

N/A

  • Question 10. removed

  • Question not considered priority for inclusion

  • Decrease in reporting burden

32.

2

9.

Laboratory Activities

11. Describe how laboratory data and results are managed and what platform (e.g., Laboratory Information Management System (LIMS), etc.) is used for data management at this laboratory/facility.

a) Data is managed manually

b) Laboratory Information Management System (LIMS)

c) Sample Management System

d) N/A for this reporting period

e) Unknown

f) Other (please specify):

9. How are laboratory samples and data primarily managed?

a) Laboratory Information Management System (LIMS) - please specify

b) Microsoft Excel

c) Paper

d) Other – please specify

e) N/A

f) Unknown


  • QID 11 now 9.

  • Answer options reworded

  • Formatting and question numbering changes

  • Determined that QID 9 will capture information needed and open-ended question is not a priority

  • Decrease in reporting burden

33.

2

12.

Laboratory Activities

12. If applicable, describe data management in the field or at point of collection (e.g., environmental surveillance sites, etc.) as well as in the lab. Open ended

N/A

  • Question 12 removed

  • Decrease in reporting burden

34.

2

10. & 10.a.

Laboratory Activities

13. Is regular external quality assessment performed for AR testing at this project’s participant laboratories?

a) Yes ( 13.a.)

b) No

c) Don’t Know

d) Does not apply

13.a. If yes, please describe the type and frequency of these EQA activities

(e.g., PulseNet EQA, 2 bacterial specimens/ year for identification and AST, etc.)

10. Was the [partnr1_projsite] participating in any EQA programs for the project’s pathogen(s) of interest?

(NOTE: answer yes even if EQA provided separately from project)

a) Yes ( 10.a.)

b) No

c) Don’t know

d) Does not apply

10.a. Describe EQA (organization[s] providing EQA; pathogens included; number of isolates or samples submitted; and frequency)

List as follows:

1. [Organization providing EQA], [pathogen(s) included], [number of isolates or samples submitted], and [frequency];

2. [Organization providing EQA], [pathogen(s) included], [number of isolates or samples submitted], and [frequency];

  • Changed wording for both questions

  • QID 13. now 10

  • QID 13.a. now 10.a.

  • Response template added to facilitate response

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • Decrease in reporting burden

35.

2

1.a.

Surveillance and Response Activities

1. Are epidemiological data elements collected with samples tested under this project?

a) Yes ( 1.a.)

b) No ( 1.b.)

c) Don’t know

1.a. If yes, please

i. Describe what data elements are being collected. (Open ended)

ii. List each of the sites collecting these elements within the project and indicate if the information is shared with public health for decision making. (Open ended)

1. Were epidemiological data elements collected with samples tested as part of this project?

a) Yes ( 1.a.)

b) No ( 1.b.)

c) Don’t know

1.a. If yes, describe what data elements are being collected and, if applicable, how they are used for public health decision-making.

- Small wording edit in QID 1

- QIDs 1.a.i. and 1.a.ii. consolidated into question 1.a.


  • Simpler format for analysis

  • Decrease in reporting burden

36.

2

2., 2.a.-2.e.

Surveillance and Response Activities

2. Are the collected data for this project (e.g., phenotypic, genotypic, and NGS) integrated into subnational, national, or global databases?

a) Yes ( 2.a.)

b) No ( 2.b.)

c) Don’t Know

2.a. If yes, please

i. Describe what database(s) the data were reported to. Please list all. (Open ended)

ii. Indicate the frequency of data sharing with national-level decision makers (e.g., MoHs, NPHIs, etc.)?

a) Daily

b) Weekly

c) Bi-weekly

d) Quarterly

e) Annually

f) Other (please specify):

2.b. If no, please list any barriers to data integration. (Open ended)

2. Were the data (e.g. laboratory, epidemiological, etc.) collected for this project submitted to subnational, national, or global databases?

(select all that apply)

a) Global ( 2.a.)

b) National ( 2.b.)

c) Subnational ( 2.c.)

d) Other ( 2.d.)

e) Not submitted to a database ( 2.e.)

f) N/A

g) Don’t Know

2.a.-2.d. Sub-questions i. and ii. will iteratively repeat for each of the selections above a-d.

i. How often were data submitted to the database(s)

a) Daily

b) Weekly

c) Bi-weekly

d) Quarterly

e) Annually

f) Other (please specify):

ii. Please list and describe database(s) that data were reported to (Open-ended)

List as follows:

  1. [Name of database]; [Description of database]

  2. [Name of database]; [Description of database]

  3. [Name of database]; [Description of database]

2.e. If no, list any barriers to data submission or sharing. (Open ended)



  • Question reformatted to streamline responses and capture the same information for each level of data submission

  • Respondents will answer two follow up questions (i. and ii.) for each level of submission reported (2.a.-2.d.)

  • QID 2.b. is now 2.e.

  • Response template added to facilitate response

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • Reformatting of questions facilitates easier analysis steps required after data collection

  • Potential for increase in reporting burden due to increase in answer options and follow up questions for each database(s) reported to

37.

2

3. & 3.a.

Surveillance and Response Activities

3. Have any alerts or findings from the lab or facility required a local response (e.g., within facility or local area, data sharing, PPS, etc.)?

a) Yes ( 3.a.)

b) No

c) Don’t Know

3.a. If yes, please list the entities involved, response activities, and how data was shared. (Open ended)

3. Did any findings from [partnr1_projsite] lead to an alert notification during this reporting period?

a) Yes ( 3.a.)

b) No

c) Don’t know

d) Does not apply

3.a. If yes, describe the alert, including why an alert was needed, entities and levels of health system involved, and how data were shared.

List as follows:

1. [Alert 1: description and justification], [level(s) of health system involved], [entities involved], and [describe how data were shared];

2. [Alert2: description and justification], [level(s) of health system involved], [entities involved], and [describe how data were shared];


  • Question wording simplified

  • Response template added to facilitate response

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • No change to reporting burden

38.

2

4., 4.a., & 4.b.

Surveillance and Response Activities


4. Have any alerts or findings from the lab or facility been detected which required a sub-national or national response (e.g., new organism/type of resistance or large outbreak)?

a) Yes ( 4.a.)

b) No

4.a. If yes, please list the entities involved, response activities, and how data was shared. (Open ended)


4. Did any findings from [partnr1_projsite] led to the detection of an outbreak that required a response?

a) Yes ( 4.a.)

b) No

c) Don’t know

d) Does not apply

4.a. What level(s) of the health system were involved in the response? (select all that apply)

a) Global

b) National

c) Subnational

d) Other

e) Don’t Know

4.b. Describe the outbreak and response activities, including entities and levels of health system involved,

List as follows:

1. [Outbreak 1: description of outbreak and response activities], [entities involved], and [level(s) of health system involved]

2. [Outbreak 2: description of outbreak and response activities], [entities involved], and [level(s) of health system involved]

  • Question wording simplified

  • Question 4.a. changed to capture level of health system and second follow up question 4.b. with text from original 4.a. question

  • Follow up question wording expanded to ensure necessary information captured

  • Response template added to facilitate response

  • Wording change enhances clarity of instructions and removes potential confusion for respondents

  • Slight increase in reporting burden

39.

2

N/A

Laboratory Activities & Surveillance and Response Activities

Original Section Names:


Section 2: Laboratory Network Activities


Section 3: Surveillance Activities



Section 2: Laboratory Activities


Section 3: Surveillance and Response Activities

  • Changes made to section names

  • No change to reporting burden



40


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AuthorTavitian, Stephanie Victoria (CDC/NCEZID/DHQP/OD)
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