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Attacking failure of antibiotic treatment by targeting antimicrobial resistance enabler cell-states

Award Number: U19AI158076
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/12/2022
PERIOD OF PERFORMANCE END DATE: 06/30/2026

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Attacking failure of antibiotic treatment by targeting antimicrobial resistance enabler cell-states - SUMMARY Deployment of new antimicrobials is promptly circumvented by the rapid evolution of resistance, underscoring the critical need for new strategies to stay ahead in the arms-race against bacterial pathogens. Developing a detailed understanding of the circumstances as well as genetic and mechanistic basis for which antibiotic resistance develops provides opportunities for pre-emptively subverting this process. While infections caused by organisms harboring antimicrobial resistance (AMR) genes are a major cause of antibiotic treatment failure (ATF), ATF frequently occurs when the etiological agents are not AMR by traditional susceptibility testing. It is becoming increasingly recognized that transient cell-states such as tolerance, persistence and hetero-resistance are critical drivers underlying treatment failure. However, there is a paucity of data with regards to the genetic and mechanistic basis for these cell-states as well as a lack of diagnostic-detection approaches. ATF cell-states initially exist as minority variants within a population and display a transient phenotype that tends to dissipate as the stress subsides, making them challenging to detect and consequently missed in current diagnostic assays. These enabler cell-states remain mechanistically poorly understood and seem to preferentially arise during fluctuating treatment regimens, for instance caused by a drug’s PK/PD characteristics, whereby ATF cell-states can drive the re-emergence of the (susceptible) bacterial infection after antibiotic pressure wanes. Importantly, this creates opportunities where multi-step high-level resistance mutations are given an extended opportunity to emerge. Therefore, because antibiotic resistant variants often follow closely on the heels of the occurrence of ATF cell-states, these cell-states can be viewed as enablers of antibiotic treatment failure and AMR. This proposal focuses on untangling the importance of ATF cell-states in the emergence of antibiotic resistance and treatment failure, and designs new approaches and strategies to identify, track and target them. The main team consists of 4 principal investigators that have a very successful collaboration history. Together they will work on 5 challenges distributed across 3 projects and supported by an administrative and a genomics and bioinformatics core. In Challenge: 1) the full profile of possible genetic pathways that can induce ATF cell-states is determined; 2) treatment regimens that drive the emergence of ATF-cell states are determined; 3) it is determined how ATF cell-states enable the emergence of AMR; 4) drugs and compounds are screened for, that target ATF cell-state collateral sensitivities; 5) a computational deconvolution approach is developed that predicts the presence and frequency of ATF cell-states in a complex bacterial population. Overall this proposal contains a collection of conceptually and technically innovative aspects that are geared towards understating the genetic mechanisms and evolutionary forces that sit at the root of the emergence of resistance, with the ultimate goal to design new diagnostics and antimicrobial strategies that can slow or even stop the current endless arms-race “that takes all the running we can do, to keep in the same place”.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $2,470,464 )
2025	2025	CHILDREN'S HOSPITAL CORPORATION, THE	300 LONGWOOD AVE	BOSTON	MA	02115	SUFFOLK	USA	Allergy and Infectious Diseases Research	003	4	6/27/2025	NON-COMPETING CONTINUATION	$2,470,464
2025	2024	CHILDREN'S HOSPITAL CORPORATION, THE	300 LONGWOOD AVE	BOSTON	MA	02115	SUFFOLK	USA	Allergy and Infectious Diseases Research	001	3	1/23/2025	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$2,012,232
2025	2024	CHILDREN'S HOSPITAL CORPORATION, THE	300 LONGWOOD AVE	BOSTON	MA	02115	SUFFOLK	USA	Allergy and Infectious Diseases Research	002	3	4/23/2025	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$0
2025	2023	THE BROAD INSTITUTE, INC	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Allergy and Infectious Diseases Research	000	2	1/23/2025	NON-COMPETING CONTINUATION	-$2,012,232
														Subtotal = $2,470,464

Issue Date FY: 2024 ( Subtotal = $2,588,682 )
2024	2024	CHILDREN'S HOSPITAL CORPORATION, THE	300 LONGWOOD AVE	BOSTON	MA	02115	SUFFOLK	USA	Allergy and Infectious Diseases Research	002	3	6/14/2024	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$2,588,682
2024	2023	THE BROAD INSTITUTE, INC	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Allergy and Infectious Diseases Research	001	2	6/13/2024	NON-COMPETING CONTINUATION	$0
2024	2023	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Allergy and Infectious Diseases Research	000	2	2/23/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $2,588,682

Issue Date FY: 2023 ( Subtotal = $2,571,561 )
2023	2023	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Allergy and Infectious Diseases Research	001	2	9/7/2023	NON-COMPETING CONTINUATION	$193,067
2023	2023	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Allergy and Infectious Diseases Research	000	2	8/22/2023	NON-COMPETING CONTINUATION	$2,378,494
														Subtotal = $2,571,561

Issue Date FY: 2022 ( Subtotal = $2,362,994 )
2022	2022	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Allergy and Infectious Diseases Research	000	1	9/12/2022	NEW	$2,362,994
														Subtotal = $2,362,994

Grand Total All Awards = $9,993,701

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Attacking failure of antibiotic treatment by targeting antimicrobial resistance enabler cell-states

Award Number: U19AI158076

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/12/2022

PERIOD OF PERFORMANCE END DATE: 06/30/2026

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