SOW_081524.docx
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- Attached to
- CARBi - Genotype-Phenotype Project
- Solicitation number
- 75F401-24-Q-1277597
About this file
This document is a Statement of Work (SOW) for a federal contract opportunity. The objective is to support the Center for Devices and Radiological Health (CDRH) in advancing the review of devices for detection of antimicrobial resistance and the National Strategy for Combating Antibiotic-Resistant Bacteria (CARB) initiative. The scope includes measuring the production of target enzymes, such as plasmid-encoded beta-lactamases and outer membrane proteins, in Gram-negative bacteria like E. coli and K. pneumoniae, and correlating protein levels to antimicrobial susceptibility profiles. The contractor will use well-characterized clinical isolates and specific organisms from the CDC & FDA Antibiotic Resistance Isolate Bank. Key tasks include project management, a pilot study, and deliverables. This is a continuation of a previous 2021-2023 project, with the focus on expanding testing to additional K. pneumoniae isolates.
The related federal contract opportunity is a solicitation for the "CARBi - Genotype-Phenotype Project 2024-2025." It is a combined synopsis/solicitation for commercial items, with a one-year base period and two 12-month option periods. The requirement is for "Evaluating the Association Between the Expression of Beta-lactamase Enzymes and Other Proteins and Antimicrobial Resistance (AMR) in Gram-Negative Bacterial Pathogens." Offers are due via email by 8/28/2024. The contracting agency is the Department of Health and Human Services Food and Drug Administration Office of Acquisition and Grant Services.
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STATEMENT OF WORK
CENTER FOR DEVICES AND RADIOLOGICAL HEALTH (CDRH) FURTHER ELUCIDATION OF THE ASSOCIATION BETWEEN THE EXPRESSION OF β-LACTAMASE ENZYMES AND OTHER PROTEINS AND ANTIMICROBIAL RESISTANCE (AMR) BY STUDYING ADDITIONAL GRAM-NEGATIVE BACTERIAL ISOLATES.
STATEMENT OF WORK
CENTER FOR DEVICES AND RADIOLOGICAL HEALTH (CDRH) FURTHER ELUCIDATION OF THE ASSOCIATION BETWEEN THE EXPRESSION OF β-LACTAMASE ENZYMES AND OTHER PROTEINS AND ANTIMICROBIAL RESISTANCE (AMR) BY STUDYING ADDITIONAL GRAM-NEGATIVE BACTERIAL ISOLATES Contents
| 1 | Background | 2 |
| 2 | Objective | 2 |
| 3 | Scope | 3 |
| 4 | TASKS | 3 |
| 4.1 | TASK ONE: PROJECT MANAGEMENT | 3 |
| 4.1.1 | Kick-Off Meeting | 3 |
| 4.1.2 | Status Report | 4 |
| 4.1.3 | Project Work Plan | 4 |
| 4.2 | Task Two: Conduct Pilot Study | 4 |
| 4.2.1 | Subtask One: Evaluate the Level of Cmy-2 Beta-Lactamase | 5 |
| 4.2.2 | Subtask Two: Conduct Experiments to Assess Specific Protein Levels | 6 |
| 5 | Deliverables | 8 |
| 5.1 | Format Of Deliverables | 9 |
| 5.2 | Deliverables Submission Procedure | 9 |
| 5.3 | Summary Of Deliverables | 9 |
| 6 | Contract Type and Source | 10 |
| 7 | Place Of Performance | 10 |
| 8 | Period Of Performance | 10 |
| 9 | Government Contacts | 10 |
| 10 | Holidays and Government Closures | 11 |
| 11 | 508 Compliance | 11 |
| 12 | Appendix. Proposed Isolates and Controls for Evaluation | 14 |
Background The Food and Drug Administration (FDA) is responsible for protecting the public health by assuring the safety, efficacy, and security of human and veterinary drugs, biological products, medical devices, our nation’s food supply, cosmetics, and products that emit radiation. The FDA is also responsible for advancing the public health by helping to speed innovations that make medicines and foods more effective, safer, and more affordable, and helping the public get the accurate, science-based information they need to use medicines and foods to improve their health.
The mission of the Center for Devices and Radiological Health (CDRH) is to protect and promote the public health. CDRH assure that patients and providers have timely and continued access to safe, effective, and high-quality medical devices and safe radiation-emitting products. CDRH provides consumers, patients, their caregivers, and providers with understandable and accessible science-based information about the products we oversee. The Center facilitates medical device innovation by advancing regulatory science, providing industry with predictable, consistent, transparent, and efficient regulatory pathways, and assuring consumer confidence in devices marketed in the U.S.
Antimicrobial drug resistance is assessed by FDA during the preclinical and clinical evaluations of a new antimicrobial drug. Drug resistance is operationally defined as a breakpoint, i.e., a standardized measure of drug susceptibility/resistance for specific bacteria. Breakpoints refer to a phenotypic expression of growth that can be inhibited by exposure at a specific concentration of antibiotics (minimum inhibitory concentration (MIC)). It is anticipated that there is a high likelihood of treatment success of a bacterial infection if the bacteria are ‘susceptible’ to that drug, i.e., has a MIC below the breakpoint for that drug. Breakpoints are initially determined during FDA review of a new antimicrobial agent by analyzing in vitro derived phenotypic MIC distributions, pharmacokinetic and pharmacodynamics drug information from animal, human, and in vitro models, and information derived from prospective human clinical studies comparing outcomes for subjects with different drug exposures.
There is accumulating knowledge on the enzymatic and molecular (e.g., gene presence or genetic mutation) basis of antimicrobial resistance. There are multiple sources of information on various resistance mechanisms and tools that can help in determining and confirming associations between phenotype and genotype; however, there for certain organism/drug combinations, the relevance/correlation of certain markers to the role they play in resistance is not well-defined or established particularly for certain enzymes and other proteins.
There is a major need to enhance our existing knowledge about antimicrobial resistance, particularly to enhance our understanding of the scientific basis that associates targeted proteins from plasmid-mediated β-lactamases and other relevant proteins with resistance. This knowledge will advance CDRH’s priority to facilitate review of new diagnostic devices that address the threat of antimicrobial resistance, as outlined in the National Strategy for Combating Antibiotic-Resistant Bacteria (CARB) initiative.
There is a need to enhance our understanding through correlations between phenotypic susceptibility/resistance and the large number of resistance mechanisms that can occur in bacterial human pathogens against various antimicrobial agents. Equally important, the resources that exist are static and do not allow easy analysis to assess the strength of the association between phenotype and genotype. Therefore, a continuation of the current project is essential to substantiate the associations between resistance phenotype and protein expression. This additional data will assist FDA to support regulatory decision making with regards to assessing the potential benefits of using genotypic-phenotypic relationships to assist manufacturers in developing devices that complement results of traditional AST for patient management.
The CDRH requires contractor support to continue and advance the review of devices for detection of resistance and the CARB initiative.
Current progress for the 2021-2023 project is summarized below:
· AST and RNA analysis have been completed for all the targeted β-lactamases and outer membrane proteins for the E. coli and K. pneumoniae strains for both the 2021-2022 and 2022-2023 contract. There are some repeat MICs that need to be finished.
· A summary of all the data (2021-2022) compared to susceptibility data was presented in an excel sheet with separate sheets for the data generated for E. coli or K. pneumoniae.
· The Contractor’s group is in the process of cloning those genes for some of the β-lactamases analyzed that did not have control isolates (i.e., DHA, NDM, OXA-1, OXA-48, or TEM-1).
· On-going studies
· AST repeats on some isolates and completion of a few control strains.
· Whole genome sequencing to determine the level of modifications in the porin genes for the Contractor’s Isolates.
· Once all the isolates have been evaluated in triplicate for both enzymes and porins, one isolate each will be run on the same gels to produce a more accurate relative fold difference among strains (reproducibility of the Western).
Objective The objective of this acquisition is to support the Center for Devices and Radiological Health (CDRH) in advancing the review of devices for detection of resistance and the National Strategy for Combating Antibiotic-Resistant Bacteria (CARB) initiative.
Given the predictive nature of molecular diagnostics and the potential to replace certain traditional phenotypic AST in the clinical workflow, we are working to generate a database of relational associations between genotypic markers, resistance phenotypes, and RNA/protein expression patterns. While the number of AMR markers can be extensive, we will build upon existing information (e.g., literature, clinical studies, pre-market submissions) to identify and define correlations supported by data from well-known AMR markers in select organisms.
Therefore, in this project, we plan to incorporate the characterization of new isolates to strengthen the basis on which the levels of evidence are built regarding genotypic/phenotypic relationships giving more confidence in using this information in our regulatory decision-making process or in communications to stakeholders to assist in the development of rapid medical devices.
Scope The purpose of this procurement is to obtain experimental data to develop and strengthen the evidence that associates targeted proteins from plasmid-mediated β-lactamases and other relevant proteins with resistance. The study will require using well characterized clinical isolates from the contractor’s well-established biorepository and specific organisms from the CDC & FDA Antibiotic Resistance (AR) Isolate Bank (CDC-AR Bank) to evaluate and determine the level of protein production associated with a specific enzyme (either plasmid or chromosomally encoded) and/or outer membrane proteins (porins or effux) involved in the permeability of an antibiotic with a given β-lactam susceptibility pattern.
More specifically, this study will evaluate the level of protein production for:
1) the plasmid-encoded β-lactamases CTX-M-15, CTX-M-14, CMY-2, NDM, KPC, IMP, OXA-1, OXA-181, OXA-48, and DHA
2) chromosomally encoded proteins including SHV-1 of K. pneumoniae, and
3) the protein production of outer membrane proteins including OmpF, OmpC, and TolC of E. coli as well as OmpK35, OmpK36, PhoE, and TolC of K. pneumoniae using custom-designed polyclonal antibodies.
Protein levels will be correlated to β-lactam susceptibility profiles to determine what level of protein production is required for the organism to present a resistant breakpoint for a given β-lactam antibiotic.
The studies required by this SOW will use a biorepository of highly characterized clinical Gram-negative bacterial isolates with known susceptibility patterns that have been collected from various geographical locations. The focus will be on evaluating the association between β-lactamase protein levels, specifically CTX-M, CMY-2, KPC, NDM, IMP, OXA-1, OXA-181, OXA-48, DHA, and SHV-1 β-lactamases, outer membrane porin/efflux production, and antimicrobial resistance phenotypes. These studies will compliment FDA review of protein-based diagnostics that aim to predict/infer an antimicrobial resistance phenotype from protein expression data started with the 2021-2023 project under contract 75F40121P00591. This information will contribute to our understanding of how protein levels influence resistance to specific β-lactams as well as other drug classes that are impacted by permeability. Further, these data will enhance our understanding of how specific plasmid-mediated β-lactamase protein levels and common outer membrane porins influence susceptibility/resistance in Gram-negative isolates of public health importance.
To expand upon past analyses of the expression of plasmid encoded β-lactamases, chromosomally encoded proteins, membrane proteins, KPC and IMP RNA, and protein levels in gram-negative bacilli will also be evaluated based on preliminary data from the Contractor’s laboratory. Evidence has shown that isolates that contain a KPC gene do not always produce the protein despite resistance to ertapenem. For IMP, expression of IMP β-lactamases are not well defined in Enterobacterales. These protein levels will be correlated to β-lactam susceptibility profiles to determine what level of protein production is required for the organism to present a resistant breakpoint for a given β-lactam.
Because this is a continuation of the 2021-2023 project, the study focus will remain the same but will simply expand testing with additional isolates focusing on K. pneumoniae species to strengthen the knowledge database. Activities for the project include measuring the production of target enzymes of extended spectrum β-lactamases (CTX-M, OXA-1), selected carbapenemases (NDM, OXA-48, OXA-181, KPC, IMP), and plasmid-encoded AmpC β-lactamases (CMY-2 and DHA) that are a predominant cause of β-lactam resistance in Gram-negative bacilli. Members of the Enterobacteriaceae, including E. coli and K. pneumoniae that harbor these enzymes, often cause potentially serious infections in both the hospital and community settings.
TASKS
TASK ONE: PROJECT MANAGEMENT
The Contractor shall work with the FDA’s Contracting Officer Representative (COR), Technical Point of Contact (POC), to provide contracted deliverables for review and approval to CDRH to ensure that the tasks are performed accurately, on time, and in compliance with the requirements of this SOW.
The Contractor shall coordinate with the COR and Technical POC to ensure that the tasks are managed consistently in accordance with overall Contract requirements.
The Contractor shall ensure timely and accurate submission of invoices.
Kick-Off Meeting Within ten (10) business days after the effective date of the contract, the Contractor shall participate in a Kick-Off Meeting with the Technical POC, the COR and other involved FDA staff. The Contractor shall provide meeting materials and agenda two (2) days prior to the Kick-off meeting. The kick off meeting will consist of introductions, roles and responsibilities, the performance work plan, along with questions and clarification. The Contractor shall prepare summary meeting minutes, detailing the discussion held, and provide a copy of the minutes to the COR and the Technical POC within five (5) business days after the meeting.
Status Report The Contractor shall provide a brief (1-2 page) status report every three months, as agreed upon with the COR and Technical POC, to track the status of the assigned tasks.
Project Work Plan The contractor shall develop a proposed schedule and high-level Project Work Plan (PWP). The Contractor shall ensure the PWP defines and details timelines and deliverables as well as any dependencies or associated constraints.
The contractor shall present the draft PWP at the Kick-Off Meeting. The COR will have fifteen (15) business days to review the draft PWP and provide feedback; the contractor shall have ten (10) days to revise the proposed approach and workplan based on feedback from FDA before submitting a final PWP within a month after the Kick-off meeting.
The Contractor shall ensure the final PWP includes the timeline for all tasks and subtasks alongside detailed descriptions of deliverables and their respective due dates.
The Contractor shall update the PWP no more than quarterly with submission and COR review periods defined in the initial approved PWP.
Task Two: Conduct Study The contractor shall conduct a continuation of the study from 2021-2023, contract 75F40121P00591 focused on measuring the production of target enzymes for: 1) the plasmid-encoded β-lactamases TEM-1, CTX-M-15, CTX-M-14, CMY-2, NDM, KPC, IMP, OXA-1, OXA-48, and DHA 2) chromosomally encoded proteins including SHV-1 of K. pneumoniae, and 3) the protein production of outer membrane proteins including OmpF, OmpC, and TolC (of E. coli), as well as OmpK35, OmpK36, PhoE, and TolC (of K. pneumoniae) in Gram-negative bacilli. Members of the Enterobacteriaceae including E. coli and K. pneumoniae that harbor these enzymes often cause potentially serious infections in both the hospital and community settings. To date, more than 240 CTX-M types have been identified and described (https://www.ncbi.nlm.nih.gov/pathogens/refgene/#gene_family:(blaCTX-M%20blaKLUC), with CTX-M-15 and CTX-M-14 types being the most commonly isolated variants worldwide. In general, the CTX-M type enzymes exhibit higher levels of affinity and activity against third generation cephalosporins such as cefotaxime and ceftriaxone and in the case of CTX-M-15, ceftazidime. The presence of a CTX-M producing organism is often associated with co-resistance phenotypes such as to the fluoroquinolones and aminoglycosides, as well as to tetracycline, and trimethoprim/sulfamethoxazole. OXA-1 is another extended spectrum β-lactamase that will be measured in select isolates described in this proposal. OXA-1 hydrolyzes cefepime and could impact the new β-lactam/β-lactamase inhibitor, cefepime/zidebactam.
From preliminary studies, it is clear that K. pneumoniae isolates are unique in the ability to emerge resistant to ß-lactam antibiotics in ways not represented by E. coli. This observation can be difficult to understand when evaluating AST results only. Additional characterizations may elucidate resistance mechanism differences between K. pneumoniae and E. coli. We propose to expand testing of 10 additional K. pneumoniae isolates to be evaluate the expression of RNA and proteins, as well as AST profiles.
Subtask One: Evaluate the Level of Cmy-2 Beta-Lactamase The contractor shall evaluate the level of CMY-2 β-lactamase which is the most prevalent and widely disseminated plasmid-mediated AmpC β-lactamase. Bacteria that produce a CMY-2 β-lactamase are commonly resistant to all β-lactam antibiotics, except for cefepime, cefpirome, and the carbapenems, resulting in a multidrug resistant phenotype and limited therapeutic options. Resistance to the carbapenems is also achievable when strains harboring CMY-2 exhibit porin deficiencies. DHA is another particularly concerning plasmid-encoded AmpC β-lactamase as it can result in a derepressed phenotype in isolates that do not possess a chromosomally encoded AmpC. New isolates will be included in the analysis.
The presence of carbapenemases such as NDM, OXA-48, OXA-181, and KPC contribute to carbapenem resistant phenotypes. However, the contribution of these enzymes to the resistant phenotype has only been correlated with the presence of the gene as determined by molecular analysis. Work from Contractor’s lab (unpublished data before beginning 1st contract) has shown in carbapenem resistant E. coli carrying the KPC gene that upon analysis of KPC protein production, very little and in some cases no detection of the protein was present using Western analysis. NDM genes have been associated with elevated cefiderocol MICs; however, strains evaluated for the presence of NDM have also been shown to be susceptible. These data indicate that varying levels of the NDM protein occur in these isolates. However, no data correlating the level of NDM protein with a β-lactam susceptibility pattern are available. Isolates that possess OXA-48 and OXA-181 also show variability in susceptibility patterns indicating that the protein levels required for the carbapenem resistance varies. It is also possible that the carbapenem resistance observed in these isolates could be associated with porin or efflux modifications in addition to the low-level production of the carbapenemases.
In addition to plasmid-mediated resistance such as with the CTX-Ms, CMY-2, and carbapenemases, the chromosomal β-lactamase SHV-1 of K. pneumoniae combined with other β-lactamases and/or decreased production of a porin and/or an increase in the production of an efflux pump can also contribute to β-lactam resistance. The primary outer membrane proteins implicated in the decreased permeability are OmpC and OmpF for E. coli and OmpK35, OmpK36, and PhoE for K. pneumoniae. These porins are non-specific and allow the diffusion of hydrophilic molecules including β-lactams. Therefore, it is important to examine the production of plasmid-mediated β-lactamases and chromosomal-mediated β-lactamases in combination with porin production. Strains producing the plasmid-encoded β-lactamases (i.e., CTX-M-15/14, OXA-1, CMY-2, NDM, OXA-48, OXA-181, KPC) will also be evaluated for porin production. In the case of K. pneumoniae, the level of chromosomal protein production of SHV will also be examined. As controls, knockouts of these specific porins will be assessed in this pilot study to gain an understanding of the interplay between β-lactamase production, porin expression or lack thereof, and a resistant phenotype.
Subtask Two: Conduct Experiments to Assess Specific Protein Levels The contractor shall use the experimental methods outlined below to assess specific protein levels with a focus on the following classes/subclasses of β-lactamase enzymes and/or porins (See Table 1: Associated Organisms) in the associated organisms that could play a role in resistance. The Contractor shall examine AST profiles for isolates tested. The Contractor shall include new isolates (Table 3, Appendix) in the analysis.
Methods Isolates/CDC & FDA Antibiotic Resistance (AR) Isolate Bank Panels The Contractor shall recommend isolates, and the COR shall provide final approval of the organisms to be incorporated in the upcoming 2024-2025 study based on the identified need to further knowledge of the association between enzyme expression and AMR and to strengthen the evidence available for genotypic-phenotypic relationships. The COR will select a total of 10 isolates to expand 2021-2023 study. The Contractor shall expand the number of K. pneumoniae isolates evaluated by RNA, protein, and AST (Appendix, Table 3).
Common Procedures for Evaluating Isolates The Contractor shall use the same testing methods to yield genotypic and phenotypic results for evaluation as those previously used for the 2021-2023 project. These include:
· Susceptibility testing
· Molecular characterization of β-lactamase genes
· Protein isolation and Western blot analysis using Polyclonal Peptide Antibodies
· RNA Isolation and mRNA steady-state expression levels
Table 1: Associated Organisms
| Organism |
| Target Protein |
| Drug/Drug Classes, Subclasses of Critical/Serious Concern |
| E. coli/Klebsiella spp. |
| CTX-M-15 or CTX-M-14, NDM, OXA-1, OXA-48, OXA-181, KPC |
| cephalosporins (3rd-4th generation)/β-lactam-β-lactamase inhibitor combinations/ carbapenems/ fluoroquinolones |
| E.coli/Klebsiella spp. |
| CMY-2, DHA |
| cephalosporins (3rd-4th generation, specifically cefepime)/β-lactam-β-lactamase inhibitor combinations/carbapenems/aztreonam |
| K. pneumoniae |
| SHV hyperproduction |
| cephalosporins (3rd-4th generation)/β-lactam-β-lactamase inhibitor combinations |
| E. coli |
| OmpF/OmpC, TolC outer membrane protein |
| cephalosporins (3rd-4th generation)/β-lactam-β-lactamase inhibitor combinations/ carbapenems |
| K. pneumoniae |
| OmpK35/OmpK36, PhoE, TolC outer membrane protein |
| cephalosporins (3rd-4th generation)/β-lactam-β-lactamase inhibitor combinations/ carbapenems |
Organisms and controls to be evaluated in this study A list of 10 suggested isolates with appropriate characteristics and profiles will be approved by COR prior to the initiation of the study. Please see the appendix for a proposed list of organisms presented in Tables 3 in the Appendix.
Susceptibility testing The Contractor shall purchase Frozen broth microdilution MIC panels, prepared according to CLIS M7 (and ISO 20776-1), from IHMA and use them to confirm the susceptibility of each isolate according to current breakpoints. The Contractor shall ensure the drug ranges for piperacillin/tazobactam, ceftazidime, imipenem, meropenem, imipenem/relebactam, ceftolozane/tazobactam, ceftazidime/avibactam, and cefepime/zidebactam are 0.0625 to 64 µg/ml with fixed concentrations of tazobactam and avibactam at 4 µg/ml. The drug range for cefiderocol will be 0.03 to 32 µg/ml.
Molecular characterization of β-lactamase genes After discussing options with COR and receiving concurrence on the selected targets, the Contractor shall access whole genome sequencing data for the CDC-AR Bank isolates and available annotations to confirm molecular genetic markers in each isolate. The Contractor shall perform DNA amplification by PCR using the ARM-D β-lactamase molecular assays[footnoteRef:2] and Sanger sequencing to identify/confirm specific mutations. [2: https://www.streck.com/products/molecular/antibiotic-resistance-kits/]
Protein isolation and Western blot analysis using Polyclonal Peptide Antibodies The Contractor shall lyse Cells from cultures grown to mid-logarithmic growth (OD600~0.5) in Mueller–Hinton broth at 37°C using the Bullet Blender (Next Advance). The Contractor shall perform Western blotting as previously described3, 4 and protein normalization and levels of protein targets determined by imaging the blot using the Bio-Rad ChemiDocTM System. Custom, polyclonal peptide antibodies specific for CTX-M-15/CTX-M-14, KPC, SHV, CMY-2, OmpC, OmpF, and TolC for E. coli and OmpK35, OmpK36, PhoE, and TolC for Klebsiella spp. were previously generated by GenScript (Piscataway, NJ, USA). The use of all antibodies has been optimized for the amount of primary and secondary antibody use as well as a linearity curved performed on the optimal amount of protein sample to use. The NDM, DHA, OXA-1, OXA-48, and OXA-181 polyclonal peptide antibodies will be generated by GenScript as previously described[footnoteRef:3], [footnoteRef:4], [footnoteRef:5] . [3: ] [4: ] [5: ]
The Contractor shall normalize the chemiluminescent signal intensity of the target proteins. The Contractor shall use K12 MG1655 (WT E. coli) and clinical isolates that do not encode the target protein as controls for cross-reactivity to proteins other than the target. The Contractor shall use isolates in which the gene for the target protein has been removed (knockouts) as an additional control. The Contractor shall purchase the TolC knockout isolate, JW5503 from the Keio Collection. The Contractor shall include K12 MG1655 and a clinical isolate possessing the target protein but susceptible to 3rd generation cephalosporins, β-lactam/β-lactamase inhibitor combinations, and the carbapenems including ertapenem, imipenem, and meropenem as positive controls. The Contractor’s laboratory has access to all of these control isolates. The Contractor shall present data as the mean of three independent protein isolations and three separate western blots.
RNA Isolation and mRNA steady-state expression levels The Contractor shall grow cultures to mid-logarithmic growth (OD600~ 0.5) in Mueller–Hinton broth at 37°C. The Contractor shall isolate total RNA using TRIzol Max (Invitrogen). The Contractor shall use 150 ng of DNA-free RNA in 25 μL PCR reactions that consist of 1× concentration of QuantiNova® SYBR® Green RT–PCR master mix, and 25 pmol of each primer. The Contractor shall perform RT–PCR on the Rotor Gene Q 5plex high resolution melt system (Qiagen, Valencia, CA, USA) or the 7500 Fast ABI system.
The Contractor shall calculate relative mRNA expression via the 2-ΔΔCt method using a clinical isolate susceptible to 3rd generation cephalosporins, beta-lactam/beta-lactamase inhibitor combinations, and the carbapenems, ertapenem, imipenem, and meropenem as the comparator. The Contractor shall normalize expression data using the single-copy gene frr. The Contractor shall calculate the mean of three independent RNA isolations and three independent real-time RT–PCR assays with a coefficient of variance of <10%.
Deliverables The Contractor shall conduct experimental studies on a new set of well-defined isolates (n=10) from select panels of phenotypically and molecularly characterized organisms chosen from the CDC-AR Bank.
The Contractor shall establish expression data including mRNA and protein levels from experimental studies with the new isolates and the collective data, interpretations, and shall submit conclusions to the COR in an electronic report along with an electronic searchable database (e.g., Excel format).
The Contractor shall deliver a final version of all study reports to the COR prior to the contract expiration date.
Format Of Deliverables The Contractor shall provide deliverables (both in draft and final versions) in an electronic format along with an electronic searchable database using MS Office products. At three month intervals, interim, informal, and working-copy products will be provided by e-mail to the COR. The Contractor shall develop final soft copies of deliverables using Microsoft Office products and/or other standard application software.
Deliverables Submission Procedure The Contractor shall submit all deliverables to the COR, unless otherwise stated. The COR will be responsible for the review of all draft and final deliverables to ensure accuracy, functionality, completeness, professional quality, and overall compliance with the guidelines and requirements of the tasks. The Contractor shall ensure the accuracy and completeness of all deliverables in accordance with referenced policy, regulations, laws, and directives. The Contractor shall ensure all reports and presentations are concise and clearly written; errors, misleading or unclear statements, incomplete information shall be considered deficiencies and will be subject to correction by the Contractor at no additional cost to the government. Unless specified otherwise, the COR will have ten (10) working days to complete the review and approve the deliverables. If deficiencies are found or areas require modification, the Contractor will be notified and shall have five (5) calendar days to correct the deficiencies. Upon re-submission by the Contractor, the COR will reapply the same acceptance criteria. If the deliverable does not meet the acceptance criteria a second time, the COR may consider the Contractor as having deficient performance with respect to the subject task.
The tasks and deliverables performed in each option will be the same, a kick-off meeting, final PWP, quarterly Status Report, and written final study report. The only difference is that it will include a new set of 10 isolates.
Summary Of Deliverables Table 2: Deliverables
| Task |
| Deliverables |
| Quantity/Frequency |
| Due Date |
| 1.5.1 |
| Kick-Off Meeting Agenda |
| One / Once |
| Two (2) days prior to Kick-Off Meeting. |
| 1.5.2 |
| Final PWP |
| One |
| Within One Month after the Kick-Off Meeting |
| 1.5.3 |
| Status Report |
| Every 3 Months |
| Due by 12:00 PM EST the last business day of the month |
| 1.5.4 |
| Written Final Study Report |
(electronic report with an electronic searchable database also acceptable)
| TBD |
| No later than 60-days after the contract completion date. |
Contract Type and Source The anticipated award type is Firm-Fixed Price.
Place Of Performance All work shall be performed at the contractor’s facility.
Period Of Performance The services are determined to be non-severable and the expected period of performance is 12 months, beginning on the contract award date. There are two 12 month option periods. Each option period will be performing the same work, but on ten new isolates.
Holidays and Government Closures The Contractor is not required to provide on-site services on the following days that are Federal Holidays or on any other day designated as a Federal holiday, Government closure, or shut down for the Washington, D.C. area:
New Year's Day Martin Luther King Day President 's Day Memorial Day Juneteenth Independence Day Labor Day Columbus Day Veteran 's Day Thanksgiving Day Christmas Day 508 Compliance Section 508 of the Rehabilitation Act of 1973 (29 U.S.C. 794d) requires Federal agencies to purchase information and communication technologies (ICT) that meet specific accessibility standards. This law helps to ensure that federal employees with disabilities have access to, and use of, the information and data they need to do their jobs. Furthermore, this law ensures that members of the public with disabilities have the ability to access government information and services.
There are three regulations addressing the requirements detailed in Section 508. The Section 508 technical and functional standards are codified at 36 CFR Part 1194 and may be accessed through the Access Board’s Web site at http://www.access-board.gov. The second regulation issued to implement Section 508 is the Federal Acquisition Regulation (FAR). FAR Part 39.2 requires that agency acquisitions of Electronic and Information Technology (EIT) comply with the Access Board’s standards. The entire FAR is found at Chapter 1 of the Code of Federal Register (CFR) Title 48, located at http://www.acquisition.gov. The FAR rule implementing Section 508 can be found at http://www.section508.gov. The third applicable regulation is the HHS Acquisition Regulation (HHSAR).
Regardless of format, all Web content or communications materials produced for publication on or delivery via HHS Web sites - including text, audio or video - must conform to applicable Section 508 standards to allow federal employees and members of the public with disabilities to access information that is comparable to information provided to persons without disabilities. All contractors (including subcontractors) or consultants responsible for preparing or posting content intended for use on an HHS-funded or HHS-managed Web site must comply with applicable Section 508 accessibility standards, and where applicable, those set forth in the referenced policy or standards documents below. Remediation of any materials that do not comply with the applicable provisions of 36 CFR Part 1194 as set forth in the SOW, shall be the responsibility of the contractor or consultant retained to produce the Web-suitable content or communications material.
Unless an agency exception to this requirement exists, the Contractor must conform to applicable Section 508 standards and must apply best practices associated with Section 508 compliance during the application design, development, and testing phases. The Contractor shall utilize FDA approved tools to verify the compliance with the Section 508 standards and ensure the delivery of the fully compliant products.
The following Section 508 provisions apply to the content or communications material identified in this SOW:
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· E101.2 Equivalent Facilitation (Appendix A, Application and Scoping Requirements)
· E203 Access to Functionality (Appendix A, Application and Scoping Requirements)
· E204 Functional Performance Criteria (Appendix A, Application and Scoping Requirements)
· E205 Electronic Content (Appendix A, Application and Scoping Requirements)
· E208 Support Documentation and Services (Appendix A, Application and Scoping Requirements)
· Chapter 6 Support Documentation and Services (Appendix C, Functional Performance Criteria and Technical Requirements)
· 302 Functional Performance Criteria (Appendix C, Functional Performance Criteria and Technical Requirements)
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Appendix. Proposed Isolates for Evaluation Table 3: CDC-AR Bank Isolatesa
| AR Bank # |
| Organism |
| Resistance Mechanisms |
| Biosample Accession # |
| 0047 |
| Klebsiella pneumoniae |
| aac(6')-Ib, aadA2, catA1, dfrA12, EMRD, KDEA, mph(A), Omp35, OmpK35, oqxA, oqxB, qacEdelta1, sul1, TEM-1A, tet(D) |
| SAMN04014888 |
| 0049 |
| Klebsiella pneumoniae |
| aac(3)-IIa, aac(6')-Ib-D181Y, aadA2, aph(3')-Ib, aph(6)-Id, ble-MBL, catB4, CMY-6, CTX-M-15, dfrA14, EMRD, KDEA, mph(A), NDM-1, Omp35, OmpK35, oqxA, oqxB, OXA-1, qacEdelta1, QnrB9, rmtC, SHV-53, sul1, sul2, TEM-1, tet(A), tet(R) |
| SAMN04014890 |
| 0097 |
| Klebsiella pneumoniae |
| aac(6')-Ib, aadA1, aadA2, aph(3")-Ib, aph(6)-Id, dfrA12, dfrA14, EMRD, fosA5, KDEA, KPC-3, oqxA, oqxB, OXA-9, qacEdelta1, SHV-11, sul1, sul2, TEM-1A |
| SAMN04014938 |
| 0140 |
| Klebsiella pneumoniae |
| aac(3)-IId, aadA2, armA, catA1, CTX-M-15, dfrA12, dfrA14, OmpK35, OXA-181, SHV-26, sul1, sul2, tet(A) |
| SAMN04014981 |
| 0347 |
| Klebsiella pneumoniae |
| aac(6')-Ib, aph(3')-Ia, dfrA14, KPC-3, mph(A) |
| SAMN11953775 |
| 0525 |
| Klebsiella pneumoniae |
| aac(6')-Ib, aph(3')-Ia, dfrA1, KPC-11, oqxA, oqxB, SHV-12, sul1 |
| SAMN11953968 |
| 0605 |
| Klebsiella pneumoniae |
| aac(3)-IIa, aadA1, CTX-M-2, OXA-2, SHV-187, sul1, TEM-1B |
| SAMN11953925 |
| 1032 |
| Klebsiella pneumoniae |
| aac(3)-IIa, aac(6')-Ib-cr, aph(3')-Ib, aph(6)-Id, catB4, CTX-M-15, dfrA14, oqxA, OXA-1, QnrB1, SHV-99, sul2, TEM-1B, tet(A), tet(R) |
| SAMN28235855 |
| 1149 |
| Klebsiella pneumoniae |
| aac(3)-IIa, aac(6')-Ib-cr, aacA43, aadA2, aph(3')-Ia, catB4, CTX-M-15, dfrA14, EMRD, erm(42), fosA5, IMP-18, KDEA, KPC-45, mph(A), OXA-1, OXA-2, qacEdelta1, QnrA1, SHV-1, sul1, sul2, tet(D) |
| SAMN34111336 |
| 1163 |
| Klebsiella pneumoniae |
| aac(6')-Ib, aadA2, aph(3")-Ib, aph(3')-VI, aph(6)-Id, ARR-2, ble-MBL, catB, CMY-4, CTX-M-15, dfrA12, EMRD, erm(B), KDEA, KPC-2, mph(A), NDM-1, oqxA, oqxB11, OXA-181, qacEdelta1, rmtF1, rmtF1, SHV-1, sul1, sul2, TEM-1 |
| SAMN34111349 |
a10 isolates of the species K. pneumoniae will be selected and mutually agreed upon.
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