skip to main content

Search for: All records

Creators/Authors contains: "Harris, Angela"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Elkins, Christopher A. (Ed.)
    ABSTRACT Low- and middle-income countries (LMICs) bear the largest mortality burden of antibiotic-resistant infections. Small-scale animal production and free-roaming domestic animals are common in many LMICs, yet data on zoonotic exchange of gut bacteria and antibiotic resistance genes (ARGs) in low-income communities are sparse. Differences between rural and urban communities with regard to population density, antibiotic use, and cohabitation with animals likely influence the frequency of transmission of gut bacterial communities and ARGs between humans and animals. Here, we determined the similarity in gut microbiomes, using 16S rRNA gene amplicon sequencing, and resistomes, using long-read metagenomics, between humans, chickens, and goats in a rural community compared to an urban community in Bangladesh. Gut microbiomes were more similar between humans and chickens in the rural (where cohabitation is more common) than the urban community, but there was no difference for humans and goats in the rural versus the urban community. Human and goat resistomes were more similar in the urban community, and ARG abundance was higher in urban animals than rural animals. We identified substantial overlap of ARG alleles in humans and animals in both settings. Humans and chickens had more overlapping ARG alleles than humans and goats. All fecal hostsmore »from the urban community and rural humans carried ARGs on chromosomal contigs classified as potentially pathogenic bacteria, including Escherichia coli , Campylobacter jejuni , Clostridioides difficile , and Klebsiella pneumoniae . These findings provide insight into the breadth of ARGs circulating within human and animal populations in a rural compared to urban community in Bangladesh. IMPORTANCE While the development of antibiotic resistance in animal gut microbiomes and subsequent transmission to humans has been demonstrated in intensive farming environments and high-income countries, evidence of zoonotic exchange of antibiotic resistance in LMIC communities is lacking. This research provides genomic evidence of overlap of antibiotic resistance genes between humans and animals, especially in urban communities, and highlights chickens as important reservoirs of antibiotic resistance. Chicken and human gut microbiomes were more similar in rural Bangladesh, where cohabitation is more common. Incorporation of long-read metagenomics enabled characterization of bacterial hosts of resistance genes, which has not been possible in previous culture-independent studies using only short-read sequencing. These findings highlight the importance of developing strategies for combatting antibiotic resistance that account for chickens being reservoirs of ARGs in community environments, especially in urban areas.« less
    Free, publicly-accessible full text available July 26, 2023
  2. Effective mosquito surveillance and control relies on rapid and accurate identification of mosquito vectors and confounding sympatric species. As adoption of modified mosquito (MM) control techniques has increased, the value of monitoring the success of interventions has gained recognition and has pushed the field away from traditional ‘spray and pray’ approaches. Field evaluation and monitoring of MM control techniques that target specific species require massive volumes of surveillance data involving species-level identifications. However, traditional surveillance methods remain time and labor-intensive, requiring highly trained, experienced personnel. Health districts often lack the resources needed to collect essential data, and conventional entomological species identification involves a significant learning curve to produce consistent high accuracy data. These needs led us to develop MosID: a device that allows for high-accuracy mosquito species identification to enhance capability and capacity of mosquito surveillance programs. The device features high-resolution optics and enables batch image capture and species identification of mosquito specimens using computer vision. While development is ongoing, we share an update on key metrics of the MosID system. The identification algorithm, tested internally across 16 species, achieved 98.4 ± 0.6% % macro F1-score on a dataset of known species, unknown species used in training, and species reservedmore »for testing (species, specimens respectively: 12, 1302; 12, 603; 7, 222). Preliminary user testing showed specimens were processed with MosID at a rate ranging from 181-600 specimens per hour. We also discuss other metrics within technical scope, such as mosquito sex and fluorescence detection, that may further support MM programs.« less
  3. In September 2018, Hurricane Florence caused extreme flooding in eastern North Carolina, USA, a region highly dense in concentrated animal production, especially swine and poultry. In this study, floodwater samples (n=96) were collected as promptly post-hurricane as possible and for up to approx. 30 days, and selectively enriched for Campylobacter using Bolton broth enrichment and isolation on mCCDA microaerobically at 42°C. Only one sample yielded Campylobacter , which was found to be Campylobacter jejuni with the novel genotype ST-2866. However, the methods employed to isolate Campylobacter readily yielded Arcobacter from 73.5% of the floodwater samples. The Arcobacter isolates failed to grow on Mueller-Hinton agar at 25, 30, 37 or 42°C microaerobically or aerobically, but could be readily subcultured on mCCDA at 42°C microaerobically. Multilocus sequence typing of 112 isolates indicated that all were Arcobacter butzleri. The majority (85.7%) of the isolates exhibited novel sequence types (STs), with 66 novel STs identified. Several STs, including certain novel ones, were detected in diverse waterbody types (channel, isolated ephemeral pools, floodplain) and from multiple watersheds, suggesting the potential for regionally-dominant strains. The genotypes were clearly partitioned into two major clades, one with high representation of human and ruminant isolates and another with anmore »abundance of swine and poultry isolates. Surveillance of environmental waters and food animal production systems in this animal agriculture-dense region is needed to assess potential regional prevalence and temporal stability of the observed A. butzleri strains, as well as their potential association with specific types of food animal production. IMPORTANCE Climate change and associated extreme weather events can have massive impacts on the prevalence of microbial pathogens in floodwaters. However, limited data are available on foodborne zoonotic pathogens such as Campylobacter or Arcobacter in hurricane-associated floodwaters in rural regions with intensive animal production. With high density of intensive animal production as well as pronounced vulnerability to hurricanes, Eastern North Carolina presents unique opportunities in this regard. Our findings revealed widespread incidence of the emerging zoonotic pathogen Arcobacter butzleri in floodwaters from Hurricane Florence. We encountered high and largely unexplored diversity while also noting the potential for regionally-abundant and persistent clones. We noted pronounced partitioning of the floodwater genotypes in two source-associated clades. The data will contribute to elucidating the poorly-understood ecology of this emerging pathogen, and highlight the importance of surveillance of floodwaters associated with hurricanes and other extreme weather events for Arcobacte r and other zoonotic pathogens.« less
  4. First-generation (FG) and/or low-income (LI) engineering student populations are of particular interest in engineering education. However, these populations are not defined in a consistent manner across the literature or amongst stakeholders. The intersectional identities of these groups have also not been fully explored in most quantitative-based engineering education research. This research paper aims to answer the following three research questions: (RQ1) How do students’ demographic characteristics and college experiences differ depending on levels of parent educational attainment (which forms the basis of first-generation definitions) and family income? (RQ2) How do ‘first-generation’ and ‘low-income’ definitions impact results comparing to their continuing-generation and higher-income peers? (RQ3) How does considering first-generation and low-income identities through an intersectional lens deepen insight into the experiences of first-generation and low-income groups? Data were drawn from a nationally representative survey of engineering juniors and seniors (n = 6197 from 27 U.S. institutions). Statistical analyses were conducted to evaluate respondent differences in demographics (underrepresented racial/ethnic minority (URM), women, URM women), college experiences (internships/co-ops, having a job, conducting research, and study abroad), and engineering task self-efficacy (ETSE), based on various definitions of ‘first generation’ and ‘low income’ depending on levels of parental educational attainment and self-reported family income. Ourmore »results indicate that categorizing a first-generation student as someone whose parents have less than an associate’s degree versus less than a bachelor’s degree may lead to different understandings of their experiences (RQ1). For example, the proportion of URM students is higher among those whose parents have less than an associate’s degree than among their “associate’s degree or more” peers (26% vs 11.9%). However, differences in college experiences are most pronounced among students whose parents have less than a bachelor’s degree compared with their “bachelor’s degree or more” peers: having a job to help pay for college (55.4% vs 47.3%), research with faculty (22.7% vs 35.0%), and study abroad (9.0% vs 17.3%). With respect to differences by income levels, respondents are statistically different across income groups, with fewer URM students as family income level increases. As family income level increases, there are more women in aggregate, but fewer URM women. College experiences are different for the middle income or higher group (internship 48.4% low and lower-middle income vs 59.0% middle income or higher; study abroad 11.2% vs 16.4%; job 58.6% vs 46.8%). Despite these differences in demographic characteristics and college experiences depending on parental educational attainment and family income, our dataset indicates that the definition does not change the statistical significance when comparing between first-generation students and students who were continuing-generation by any definition (RQ2). First-generation and low-income statuses are often used as proxies for one another, and in this dataset, are highly correlated. However, there are unique patterns at the intersection of these two identities. For the purpose of our RQ3 analysis, we define ‘first-generation’ as students whose parents earned less than a bachelor’s degree and ‘low-income’ as low or lower-middle income. In this sample, 68 percent of students were neither FG nor LI while 11 percent were both (FG&LI). On no measure of demographics or college experience is the FG&LI group statistically similar to the advantaged group. Low-income students had the highest participation in working to pay for college, regardless of parental education, while first-generation students had the lower internship participation than low-income students. Furthermore, being FG&LI is associated with lower ETSE compared with all other groups. These results suggest that care is required when applying the labels “first-generation” and/or “low-income” when considering these groups in developing institutional support programs, in engineering education research, and in educational policy. Moreover, by considering first-generation and low-income students with an intersectional lens, we gain deeper insight into engineering student populations that may reveal potential opportunities and barriers to educational resources and experiences that are an important part of preparation for an engineering career.« less