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1. Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg

   https://doi.org/10.1128/mSystems.00729-21  

   Oladeinde, Adelumola ; Abdo, Zaid ; Press, Maximilian O. ; Cook, Kimberly ; Cox, Nelson A. ; Zwirzitz, Benjamin ; Woyda, Reed ; Lakin, Steven M. ; Thomas, Jesse C. ; Looft, Torey ; et al ( August 2021 , mSystems)

   Garrido, Daniel (Ed.)

   ABSTRACT The overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg, a model food pathogen, to test if chicks raised antibiotic free harbor transferable AR. We challenged chicks with an antibiotic-susceptible S . Heidelberg strain using various routes of inoculation and determined if S . Heidelberg isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole-genome sequencing (WGS) to show that chicks grown without antibiotics harbored an antimicrobial resistant S . Heidelberg population at 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing, we found that S . Heidelberg infection perturbed the microbiota of broiler chicks, and we used metagenomics and WGS to confirm that a commensal Escherichia coli population was the main reservoir of an IncI1 plasmid acquired by S . Heidelberg. The carriage of this IncI1 plasmid posed no fitness cost to S . Heidelberg but increased its fitness when exposed to acidic pH in vitro . These results suggest that HGT of plasmids carrying AR shaped the evolution of S . Heidelberg and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella enterica . IMPORTANCE The reported increase in antibiotic-resistant bacteria in humans has resulted in a major shift away from antibiotic use in food animal production. This shift has been driven by the assumption that removing antibiotics will select for antibiotic susceptible bacterial taxa, which in turn will allow the currently available antibiotic arsenal to be more effective. This change in practice has highlighted new questions that need to be answered to assess the effectiveness of antibiotic removal in reducing the spread of antibiotic resistance bacteria. This research demonstrates that antibiotic-susceptible Salmonella enterica serovar Heidelberg strains can acquire multidrug resistance from commensal bacteria present in the gut of neonatal broiler chicks, even in the absence of antibiotic selection. We demonstrate that exposure to acidic pH drove the horizontal transfer of antimicrobial resistance plasmids and suggest that simply removing antibiotics from food animal production might not be sufficient to limit the spread of antimicrobial resistance. 

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2. Comparison of Antimicrobial-Resistant Escherichia coli Isolates from Urban Raccoons and Domestic Dogs

   https://doi.org/10.1128/AEM.00484-21  

   Worsley-Tonks, Katherine E. ; Gehrt, Stanley D. ; Miller, Elizabeth A. ; Singer, Randall S. ; Bender, Jeff B. ; Forester, James D. ; McKenzie, Shane C. ; Travis, Dominic A. ; Johnson, Timothy J. ; Craft, Meggan E. ( July 2021 , Applied and Environmental Microbiology)

   Elkins, Christopher A. (Ed.)

   ABSTRACT Wildlife can be exposed to antimicrobial-resistant bacteria (ARB) via multiple pathways. Spatial overlap with domestic animals is a prominent exposure pathway. However, most studies of wildlife-domestic animal interfaces have focused on livestock and little is known about the wildlife-companion animal interface. Here, we investigated the prevalence and phylogenetic relatedness of extended-spectrum cephalosporin-resistant (ESC-R) Escherichia coli from raccoons ( Procyon lotor ) and domestic dogs ( Canis lupus familiaris ) in the metropolitan area of Chicago, IL, USA. To assess the potential importance of spatial overlap with dogs, we explored whether raccoons sampled at public parks (i.e., parks where people and dogs could enter) differed in prevalence and phylogenetic relatedness of ESC-R E. coli to raccoons sampled at private parks (i.e., parks where people and dogs could not enter). Raccoons had a significantly higher prevalence of ESC-R E. coli (56.9%) than dogs (16.5%). However, the richness of ESC-R E. coli did not vary by host species. Further, core single-nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that isolates did not cluster by host species, and in some cases displayed a high degree of similarity (i.e., differed by less than 20 core SNPs). Spatial overlap analyses revealed that ESC-R E. coli were more likely to be isolated from raccoons at public parks than raccoons at private parks, but only for parks located in suburban areas of Chicago, not urban areas. That said, ESC-R E. coli isolated from raccoons did not genetically cluster by park of origin. Our findings suggest that domestic dogs and urban/suburban raccoons can have a diverse range of ARB, some of which display a high degree of genetic relatedness (i.e., differ by less than 20 core SNPs). Given the differences in prevalence, domestic dogs are unlikely to be an important source of exposure for mesocarnivores in urbanized areas. IMPORTANCE Antimicrobial-resistant bacteria (ARB) have been detected in numerous wildlife species across the globe, which may have important implications for human and animal health. Wildlife can be exposed to ARB via numerous pathways, including via spatial overlap with domestic animals. However, the interface with domestic animals has mostly been explored for livestock and little is known about the interface between wild animals and companion animals. Our work suggests that urban and suburban wildlife can have similar ARB to local domestic dogs, but local dogs are unlikely to be a direct source of exposure for urban-adapted wildlife. This finding is important because it underscores the need to incorporate wildlife into antimicrobial resistance surveillance efforts, and to investigate whether certain urban wildlife species could act as additional epidemiological pathways of exposure for companion animals, and indirectly for humans. 

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3. Arsinothricin, an arsenic-containing non-proteinogenic amino acid analog of glutamate, is a broad-spectrum antibiotic

   https://doi.org/10.1038/s42003-019-0365-y  

   Nadar, Venkadesh Sarkarai ; Chen, Jian ; Dheeman, Dharmendra S. ; Galván, Adriana Emilce ; Yoshinaga-Sakurai, Kunie ; Kandavelu, Palani ; Sankaran, Banumathi ; Kuramata, Masato ; Ishikawa, Satoru ; Rosen, Barry P. ; et al ( April 2019 , Communications Biology)

   The emergence and spread of antimicrobial resistance highlights the urgent need for new antibiotics. Organoarsenicals have been used as antimicrobials since Paul Ehrlich’s salvarsan. Recently a soil bacterium was shown to produce the organoarsenical arsinothricin. We demonstrate that arsinothricin, a non-proteinogenic analog of glutamate that inhibits glutamine synthetase, is an effective broad-spectrum antibiotic against both Gram-positive and Gram-negative bacteria, suggesting that bacteria have evolved the ability to utilize the pervasive environmental toxic metalloid arsenic to produce a potent antimicrobial. With every new antibiotic, resistance inevitably arises. ThearsN1gene, widely distributed in bacterial arsenic resistance (ars) operons, selectively confers resistance to arsinothricin by acetylation of the α-amino group. Crystal structures of ArsN1N-acetyltransferase, with or without arsinothricin, shed light on the mechanism of its substrate selectivity. These findings have the potential for development of a new class of organoarsenical antimicrobials and ArsN1 inhibitors.

    

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4. Examining the Literacy Practices of Engineers to Develop a Model of Disciplinary Literacy Instruction for K-12 Engineering (Work in Progress)

   Green, Theresa ; Minichiello, Angela ; Wilson-Lopez, Amy ( June 2018 , ASEE Annual Conference proceedings)

   Despite efforts to diversify the science, technology, engineering, and mathematics (STEM) workforce, engineering remains a White, male-dominated profession. Often, women and underrepresented students do not identify with STEM careers and many opt out of STEM pathways prior to entering high school or college. In order to broaden participation in engineering, new methods of engaging and retaining those who are traditionally underrepresented in engineering are needed. This work is based on a promising approach for encouraging and supporting diverse participation in engineering: disciplinary literacy instruction (DLI). Generally, teachers use DLI to provide K-12 students with a framework for interpreting, evaluating, and generating discipline-specific texts. This instruction provides students with an understanding of how experts in the discipline read, engage, and generate texts used to solve problems or communicate information. While models of disciplinary literacy have been developed and disseminated in several humanities and science fields, there is a lack of empirical and theoretical research that examines the use of DLI within the engineering domain. It is thought that DLI can be used to foster diverse student interest in engineering from a young age by removing literacy-based barriers that often discourage underrepresented students from entering and pursuing careers in STEM fields. This work-in-progress paper describes a new study underway to develop and disseminate a model of disciplinary literacy in engineering. During this project, researchers will observe, interview, and collect written artifacts from engineers working across four sub-disciplines of engineering: aerospace/mechanical, biological, civil/environmental, and electrical/computer. Data that will be collected include interview transcripts, observation field notes, engineer logs of literacy practices, and photographs of texts that the engineers read and write. Data will be analyzed using constant comparative analytic (CCA) methods. CCA will be used to generate theoretical codes from the data that will form the basis for a model of disciplinary literacy in engineering. As a primary outcome of this research, the engineering DLI model will promote the use of DLI practices within K-12 engineering instruction in order to assist and encourage diverse, underrepresented students to engage in engineering courses of study and pursue STEM careers. Thus far, the research team has begun collecting and analyzing data from two electrical engineers. This work in progress paper will report on preliminary findings, as well as implications for K-12 classroom instruction. For instance, this study has shed insights on how engineers use texts as part of the process of conducting failure analysis, and the research team has begun to conceptualize how these types of texts might be used with K-12 students to help them conduct failure analyses during design testing. Ultimately, this project will result in a list of grade-appropriate texts, evaluative frameworks, and activities (e.g., failure analysis in testing) that K-12 engineering teachers can use to prepare their diverse students to think, act, read, and write like engineers. 

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5. Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide

   https://doi.org/10.1038/s41467-023-42998-6  

   Diebold, Peter J. ; Rhee, Matthew W. ; Shi, Qiaojuan ; Trung, Nguyen Vinh ; Umrani, Fayaz ; Ahmed, Sheraz ; Kulkarni, Vandana ; Deshpande, Prasad ; Alexander, Mallika ; Thi Hoa, Ngo ; et al ( November 2023 , Nature Communications)

   The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinaseCTX-Mand carbapenemasesKPC,IMP,NDM, andVIM, remain taxonomically restricted to Proteobacteria. EvencfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted toBacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted toBacteroidesspecies, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.

    

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