skip to main content

Title: Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes: Mining antimicrobial resistance and biosynthesis
Authors:
 ;  ;  
Publication Date:
NSF-PAR ID:
10036993
Journal Name:
Annals of the New York Academy of Sciences
Volume:
1388
Issue:
1
Page Range or eLocation-ID:
42 to 58
ISSN:
0077-8923
Publisher:
Wiley-Blackwell
Sponsoring Org:
National Science Foundation
More Like this
  1. Antimicrobial resistance is a threat to global health, aggravated by the use of antimicrobials in livestock production. Mitigating the growing economic costs related to antimicrobial use in livestock production requires strong global coordination, and to that end policy makers can leverage global and national food animal trade policies, such as bans and user fees. Evaluation of such policies requires representing the interactions between competing producers in the global meat market, which is usually out of the scope of statistical models. For that, we developed a game-theoretic food system model of global livestock production and trade between 18 countries and aggregatemore »world regions. The model comprises the largest producing and consuming countries, the explicit interconnections between countries, and the use of antimicrobials in food animal production. Our model allows us to provide policy insights beyond standard literature and assess the trade-off between trade, cost of a policy, and antimicrobials-induced productivity. We studied three scenarios: global increased user fees on antimicrobials, a global ban of meat imports from Brazil, and a decrease in China's meat consumption. We found that a user fee that increases the price of antimicrobials by 50% globally leads to a 33% reduction in global antimicrobial use. However, participation of developing and emerging countries in the coordination scheme is jeopardized, since they become less competitive for meat sales compared to developed countries. When meat imports from Brazil are banned globally, importers of Brazil's meat would turn primarily to the U.S. to supplement their demand. Lastly, meeting China's medium-term lower meat consumption target would not affect global antimicrobial use, but could increase China's antimicrobial use by 11%. We highlighted the importance of trade for the outcome of a policy and concluded that global cooperation is required to align the incentives of all countries toward tackling antimicrobial resistance.« less
  2. Bacillus anthracis, the causative agent of anthrax disease, is a worldwide threat to livestock, wildlife and public health. While analyses of genetic data from across the globe have increased our understanding of this bacterium’s population genomic structure, the influence of selective pressures on this successful pathogen is not well understood. In this study, we investigate the effects of antimicrobial resistance, phage diversity, geography and isolation source in shaping population genomic structure. We also identify a suite of candidate genes potentially under selection, driving patterns of diversity across 356 globally extant B. anthracis genomes. We report ten antimicrobial resistance genes andmore »11 different prophage sequences, resulting in the first large-scale documentation of these genetic anomalies for this pathogen. Results of random forest classification suggest genomic structure may be driven by a combination of antimicrobial resistance, geography and isolation source, specific to the population cluster examined. We found strong evidence that a recombination event linked to a gene involved in protein synthesis may be responsible for phenotypic differences between comparatively disparate populations. We also offer a list of genes for further examination of B. anthracis evolution, based on high-impact single nucleotide polymorphisms (SNPs) and clustered mutations. The information presented here sheds new light on the factors driving genomic structure in this notorious pathogen and may act as a road map for future studies aimed at understanding functional differences in terms of B. anthracis biogeography, virulence and evolution.« less
  3. Emerging resistance to all classes of antimicrobials is one of the defining crises of the 21st century. Many advances in modern medicine, such as routine surgeries, are predicated on sustaining patients with antimicrobials during a period when their immune systems alone cannot clear infection. The development of new antimicrobials has not kept pace with the antimicrobial resistance (AR) threat. AR bacteria have been documented in various environments, such as drinking and surface water, food, sewage, and soil, yet surveillance and sampling has largely been from infected patients. The prevalence and diversity of AR bacteria in the environment, and the risksmore »they pose to humans are not well understood. There is consensus that environmental surveillance is an important first step in forecasting and targeting efforts to prevent spread and transmission of AR microbes. However, efforts to date have been limited. The Prevalence of Antibiotic Resistance in the Environment (PARE) is a classroom-based project that engages students around the globe in systematic environmental AR surveillance with the goal of identifying areas where prevalence is high. The format of PARE, designed as short classroom research modules, lowers common barriers for institutional participation in course-based research. PARE brings real-world microbiology into the classroom by educating students about the pressing public health issue of AR, while empowering them to be partners in the solution. In turn, the PARE project provides impactful data to inform our understanding of the spread of AR in the environment through global real-time surveillance.« less