UIC Research Helps Create New Antibiotic that Evades Bacterial Resistance

Doxy-PEP, HIV Vaccines and Community-Engaged Research: Discussions with Carl Dieffenbach and LaRon Nelson at CROI 2024 (VIDEO)

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This blog is adapted and cross-posted from HIV.gov. 

During the first full day of presentations at the 2024 Conference on Retroviruses and Opportunistic Infections (CROI), HIV.gov spoke with Carl Dieffenbach, Ph.D., director of NIAID’s Division of AIDS, about research presented on Doxy-PEP for sexually transmitted infections (STIs) and HIV vaccines. He spoke with Louis Shackelford of the HIV Vaccine Trials NetworkWatch their conversation.

Louis also spoke with LaRon Nelson, Ph.D., R.N., F.N.P., F.N.A.P., F.N.Y.A.M., F.A.A., about community-engaged research, HIV prevention at CROI, and a new study (HPTN 096) he is leading to reduce HIV rates among Black men who have sex with men (inclusive of cisgender and transgender men) in the southern United States. Dr. Nelson is a professor and the associate dean at the Yale School of Nursing. Watch their conversation.

Insights from Doxy-PEP Use in Real World Settings

At last year’s CROI, researchers presented results from an NIH-supported study on using a preventive dose of the antibiotic doxycycline as post-exposure prophylaxis within 72 hours after condomless sex to prevent bacterial STIs, an approach that has become known as Doxy-PEP. (View last year’s Doxy-PEP discussion with Dr. Dieffenbach.) Here at CROI 2024, Dr. Annie Luetkemeyer of the University of California, San Francisco, shared additional findings from the open-label extension of that original study, which found sustained reduction of bacterial STIs among men who have sex with men and transgender women living with HIV or on PrEP in Seattle and San Francisco. The San Francisco AIDS Foundation (SFAF) was one of the first organizations in the United States to roll out Doxy-PEP, beginning in late 2022 when it was offered to all active PrEP clients at their visits at the Magnet clinic. SFAF medical director Dr. Hyman Scott reported that there was high uptake among clients and that bacterial STIs decreased by nearly 60% in less than a year at SFAF’s clinic. The decline was highest for syphilis (78%) and chlamydia (67%). 

The San Francisco Department of Public Health (SFDPH) presented the first findings to measure the effect of Doxy-PEP at the population level. Their analysis, presented by epidemiologist Madeline Sankaran, showed a substantial and sustained decline in the number of chlamydia and early syphilis infections in San Francisco among men who have sex with men and transgender women over the 13 months after the Department released guidelines for the use of Doxy-PEP. As in the other studies presented, SFDPH did not see corresponding significant declines in gonorrhea. Doxy-PEP is not recommended for cis-gender women because there is not yet evidence to suggest it is effective for them.

HIV Vaccine Trials Continue

Dr. Dieffenbach also discussed ongoing research to find a vaccine to prevent HIV, the topic of several presentations at the conference so far. Since there are a number of Phase I HIV vaccine trials currently underway, he and Louis spoke about what those smaller trials do. Then they discussed what some of the HIV vaccine trials currently underway are exploring.

Other Studies of Interest Presented on Monday

Some of the other studies presented centered on broadly neutralizing antibodies (bNAbs), including bNAbs as part of HIV therapy and how different HIV variants can affect bNAb efficacy as a treatment method. A new analysis from the pivotal HVTN 083 study of long-acting PrEP with cabotegravir found no significant risk of hypertension in people using the method, which had been a concern in some previous clinical studies of the same class of antiretroviral drugs.

Community-Engaged Research

The importance and significant benefits of involving community in all aspects of HIV research was the first topic Dr. Nelson and Louis discussed. “If we don’t have community voices or engaged communities, we aren’t going to be asking the right questions or designing the studies in the best ways that will produce the outcome that we need, and we won’t end up with answers that are as relevant as they could be,” Dr. Nelson observed. He pointed to the dapivirine vaginal ring as an example of better outcomes because communities were involved in research. He said he hopes that community engagement in research continues to become more and more common, but it requires that researchers be willing to listen and, when needed, change their plans based on what they hear from community.

HIV Prevention Research at CROI

Dr. Nelson highlighted some of the HIV prevention topics at CROI that have caught his attention, such as increasing equitable use of long-acting injectable forms of HIV PrEP and treatment among different populations and in different countries. Other discussions of interest have included early studies on potentially very long-acting forms of HIV PrEP and exploration of possible dual prevention tools that would provide users with both HIV PrEP and contraception.

HPTN 096 Study

Finally, Dr. Nelson discussed an example of community-informed research that will soon be underway: the NIH-supported study through the HIV Prevention Trials Network (HPTN) known as HPTN 096. It aims to reduce HIV rates among Black men who have sex with men in the southern United States using a strategy developed based on what communities have told Dr. Nelson and colleagues is needed to do so. As a result, the study includes a package of four interventions which simultaneously address social, structural, institutional, and behavioral barriers to HIV prevention and care. HPTN 096 will soon launch in Atlanta, south Florida, Montgomery, Memphis, and Dallas.

More HIV Research Updates to Follow on HIV.gov

HIV.gov will be sharing additional video interviews from CROI 2024 with Dr. Dieffenbach, CDC’s Dr. Jono Mermin and Dr. Robyn Neblett Fanfair, and others. You can find all of them on HIV.gov’s social media channels and recapped here on the blog.

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Big Opportunity to Join Centers for Excellence in Translational Research

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Since 2014, NIAID’s Centers of Excellence for Translational Research (CETR) have advanced discovery and preclinical development of new or improved medical countermeasures for emerging and re-emerging infectious diseases. 

Through the new notice of funding opportunity (NOFO) Centers of Excellence for Translational Research (CETR) (U19, Clinical Trial Not Allowed), NIAID seeks applications from single institutions or consortia of institutions ready to generate, validate, and advance medical countermeasures (MCMs) against a select list of bacteria or fungi with known or emerging resistance to current therapies.  

Each center will be organized around a theme focused on preclinical development or use of MCMs or technologies that target specified pathogens to translate research results into product development. Successful applicants must propose three or more research projects plus an administrative core, and may propose up to three scientific cores.

Targeted Pathogens 

To start, know that your application must prioritize one or more of the antimicrobial resistant (AMR) pathogens below.  

Bacteria 

  • Acinetobacter baumannii 
  • Campylobacter spp. 
  • Clostridioides difficile 
  • Enterobacter spp. 
  • Enterococcus spp. 
  • Escherichia coli 
  • Klebsiella pneumoniae 
  • Neisseria gonorrhoeae 
  • Non-tuberculous mycobacteria (NTM) 
  • Nontyphoidal Salmonella spp. 
  • Pseudomonas aeruginosa 
  • Salmonella enterica serovar Typhi 
  • Shigella spp. 
  • Staphylococcus aureus 
  • Streptococcus pneumoniae 

Fungi 

  • Aspergillus fumigatus 
  • Candida spp., in particular C. auris 

Though experiments with nonvirulent forms of these pathogens are allowed, you must focus on the virulent form. 

Research Directions 

The CETR program aims to develop MCMs that are effective against a variety of pathogens and toxins, technologies that can be widely applied to improve classes of products, and platforms that can reduce the time and cost of creating new products. To that end, your proposed research projects should focus on therapeutics, immunotherapeutics, vaccines, vaccine technologies, or in vitro diagnostics for the targeted pathogens. 

Therapeutics 

For AMR bacteria, applications should focus on therapeutic discovery in the lead optimization phase with existing lead candidates to support progression through pivotal nonclinical studies required for entry into clinical trials. For AMR fungal pathogens listed above, earlier lead discovery efforts are of interest.  

Therapeutic candidates of interest include small molecule, biotherapeutic, monoclonal antibody, or phage candidates to be used as monotherapy, in combination with other drugs, or as adjunctive therapy. Candidates with broad-spectrum activity are encouraged, though you may also pursue therapeutic candidates with a narrow spectrum that target high-priority pathogens for which no standard clinical treatment exists or for which drug resistance poses a significant public health concern. 

Vaccines 

Vaccines provide an important tool to combat infectious disease, yet the preclinical and clinical pipelines for vaccine candidates against the bacterial and fungal pathogens remain limited. This NOFO will support both antigen identification and development of vaccines (including immunoprophylactics) against one or more of the AMR pathogens. Monovalent, multivalent, or broadly protective vaccines may also be considered. 

Related identification and validation of antigen targets and immunogen design should focus on systems vaccinology approaches and technologies including multi-omics approaches, structural biology, and computational modeling and prediction that elucidate host responses. 

Diagnostics 

This initiative will support coupled development of integrated, sensitive, culture-independent, pathogen identification testing systems with a phenotypic antibiotic or antifungal susceptibility testing system. 

All diagnostics applications should be supported by sufficient proof-of-concept data to establish feasibility and reproducibility and should eventually exceed performance specifications of currently available instruments and systems for reduced turnaround time, breadth of antibiotic or anti-fungal test panels, and test performance. Additionally, applications should adequately describe design and development planning of instrument systems (e.g., assay and hardware prototype development, consumables development, sample preparation, sample processing, system integration, software development, manufacturing, and diagnostic validation). 

Cores for Support 

You must propose an Administrative Core, which will manage, coordinate, and supervise all Center activities. The Administrative Core will include a Scientific Advisory Board (SAB) that will participate in the development and management of the CETR and corresponding activities. Do not propose or contact any SAB members before an award is made (i.e., when applying). 

Optionally, you can create up to three scientific cores, which would provide resources or facilities that are essential for the activities of two or more of your research projects. Scientific Cores are intended to only serve the needs of Center project researchers and they may not conduct research independent of the Center’s research projects. 

Nonresponsive Elements 

NIAID will consider applications that contain the research projects including the following to be nonresponsive and not review them: 

  • Therapeutic projects targeting AMR bacterial pathogens focused on basic discovery (e.g., target identification) 
  • Viral pathogens 
  • Bacterial strains: Mycobacterium tuberculosis, Group A/B Streptococcus, Bordetella pertussis,and Mycoplasma genitalium 
  • Clinical trials (all phases) 
  • Solely focused upon repurposing an FDA-approved drug 
  • Development of surveillance or detection technologies 
  • Activities other than translational activities towards the development of therapeutic, vaccine, or diagnostic countermeasures 

Also, take note: Your application must include a “Product Development Strategy” attachment, and within that attachment you must describe Milestones and Product Development Plans. Only applications solely proposing early translational studies in fungal pathogens are exempt from this requirement. 

Tie It All Together 

Recall that your CETR application must be arranged around a central theme. The NOFO provides examples, such as: 

  • Developing new approaches for a known pathogen target (e.g., gyrase, cell wall) to include broad-spectrum therapeutics with extended activity against more than one AMR pathogen. 
  • Developing a monoclonal antibody, phage, or other technology approach to counter pathogen resistance. 
  • Developing faster phenotypic antibacterial susceptibility test (AST) characterization for better antibiotic stewardship. 

Find additional examples of possible themes in the NOFO, as well as more thorough descriptions of translational research activities. 

Administrative Details 

Application budgets are not expected to exceed $5 million in annual direct costs and must reflect the actual research needs. The scope of the proposed project should determine the project period. The maximum project period is 5 years. 

This NOFO has a single application due date: April 29, 2024, at 5 p.m. local time of the applicant organization. 

Direct scientific or research-related questions to Dr. Candace Kerr at candace.kerr@nih.gov or 301-761-6257. For review-related inquiries, contact Dr. Caitlin Brennan at caitlin.brennan2@nih.gov  or 301-761-7792 or Dr. Lindsey Pujanandez at lindsey.pujanandez@nih.gov or 301-761-7830.

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Emory Team Finds Promising Approach to Treating Multi-Drug Resistant Microbes in Human Gut

NIH Investigates Multidrug-Resistant Bacterium Emerging in Community Settings

New “hypervirulent” strains of the bacterium Klebsiella pneumoniae have emerged in healthy people in community settings, prompting a National Institutes of Health research group to investigate how the human immune system defends against infection. After exposing the strains to components of the human immune system in a laboratory “test tube” setting, scientists found that some strains were more likely to survive in blood and serum than others, and that neutrophils (white blood cells) are more likely to ingest and kill some strains than others.

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Diverse Team Including UMass Amherst Biostatistician Receives $13.7 Million Grant to Address Antibiotic Resistance in Nursing Homes

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NIAID-Funded Study Traces Evolution of Malaria Drug Resistance in E. Africa

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NIAID-Funded Study Traces Evolution of Malaria Drug Resistance in E. Africa – Emergence of Artemisinin Partial Resistance Mutations Found Across Uganda

Emerging resistance to common malaria treatments in Uganda could be connected to inconsistent use of measures to control mosquito populations, according to new findings published in the New England Journal of Medicine. The trend is worrisome, the NIAID-funded scientists state, because resistance mutations they tracked are taking root and spreading. Researchers at the University of California at San Francisco (UCSF), funded in part by NIAID’s International Centers of Excellence for Malaria Research program, led the international collaboration.

Malaria is one of the most common and serious infectious diseases. The World Health Organization (WHO) estimates that about half of the world’s population is at risk of getting malaria, which is caused primarily by Plasmodium falciparum parasites spread through the bites of female Anopheles mosquitos. In 2021, WHO estimated that about 247 million people contracted malaria in 85 countries; about 619,000 people died. About 95% of cases and deaths were in Africa.

For decades a combination of measures has resulted in effective malaria control in Africa: preventing malaria transmission with bed nets treated with insecticides; spraying insecticides indoors; treating malaria with artemisinin-based combination medicines; and preventing malaria with other drugs.

Artemisinins – originally extracted from the sweet wormwood plant, but also now available synthetically – rapidly eliminate malaria parasites from the bloodstream. They are used in combination with other longer-lasting drugs to effectively treat malaria. Beginning in 2008, however, studies in Southeast Asia identified poor results from artemisinins and eventually from artemisinin-based combination malaria treatments. Scientists soon found the primary reason – a protein (PfK13) in P. falciparum had developed mutations that made it partially resistant to artemisinins.

Since then, scientists in Africa have watched for the same mutations to emerge. The NEJM study identified five of these mutations, each of which may lead to partial resistance, that have emerged in different parts of Uganda. Their work used data from malaria cases and annual patient surveillance throughout Uganda between 2014 and 2022.

They found that two of the five key mutations appeared in far northern Uganda in 2016-17. The mutations then spread across much of northern Uganda and nearby regions, appearing in up to 54% of cases in one district. The other three key mutations emerged in western Uganda in about 2021-22, with prevalence up to 20% to 40% in different districts.

The study notes that in parts of Uganda where indoor spraying stopped between 2014 and 2018, cases of malaria quickly surged. Likewise, the emergence of any of the five key resistance mutations also surged, suggesting that the emergence was aided by malaria epidemics in populations where malaria had previously been well-controlled.

The researchers have different theories about how and why the mutations emerged. Their leading hypothesis, which they have targeted for more study, is that in populations with a low level of immunity to malaria, an epidemic increases the likelihood that resistance will emerge. “In northern Uganda,” the study states, “this scenario occurred after the withdrawal of effective malaria control, leading to high incidence of malaria in a population with relatively low antimalarial immunity.” They also suggest that fluctuating malaria transmission contributed to the emergence of drug resistance in southwestern Uganda. They emphasize the importance of maintaining malaria control interventions, with attention to malaria outbreaks, to decrease the likelihood of emergence or spread of drug resistance.

Others working on the project with UCSF include scientists from the Infectious Diseases Research Collaboration and Makerere University in Uganda; the University of Tubingen in Germany; Brown University in Rhode Island; and Dominican University of California.

Reference: 

M Conrad et al. Evolution of Partial Resistance to Artemisinins in Malaria Parasites in Uganda. New England Journal of Medicine DOI: 10.1056/NEJMoa2211803 (2023).

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UCI Health Team Receives $13.7 Million Federal Grant to Address Antibiotic Resistance in Nursing Homes

Combating Antibiotic-Resistant Bacteria Interdisciplinary Research Units (CARBIRU)

The Combating Antibiotic-Resistant Bacteria Interdisciplinary Research Units (CARBIRUs) are multidisciplinary research centers focused on bacterial pathogens for which antibiotic resistance poses a significant public health concern, as designated by the CDC’s 2019 Report on Antibiotic Resistance Threats in the United States. Each center brings together investigators from multiple disciplines to investigate non-antibiotic alternative treatment and preventive strategies, including bacteriophage, monoclonal antibodies, ligand mimetics, and defined microbial consortia; poorly understood resistance mechanisms contributing to bacterial persistence and antibiotic treatment failure; and identification and validation of novel bacterial targets for antibiotic intervention.

Main Areas of Focus

The CARBIRU program supports fundamental, collaborative research ranging from discovery to early development research activities such as the:

  • Discovery and validation of viable therapeutic, diagnostic, or vaccine targets
  • Identification and characterization of host factors involved in susceptibility or response to infection and/or resistance
  • Elucidation of known or evolving mechanisms of antibiotic resistance and strategies to prevent emergence of resistance
  • Identification and development of novel approaches to combat antibiotic-resistant infections
  • Understanding the role of the microbiome and antibiotic-mediated dysbiosis in the development of resistant infections

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Restricting Antibiotics for Livestock Could Limit Spread of Antibiotic-Resistant Infections in People

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