Isolation, sequencing, and characterization of four transmissible antibiotic resistance plasmids captured from bacteria in stream sediments

Self-transmissible plasmids are key vectors in the transfer of resistance, catabolic, and other genes among bacteria native to environments such as streams and wetlands. The evolution of antibiotic resistance in particular is known to be powerfully affected by conjugative plasmid transfer due to the ease in which some plasmids can be horizontally transferred into a broad range of host bacteria and their ability to exchange mobile genetic elements that often contain antibiotic resistance genes. In this study, we captured tetracycline resistance plasmids from stream sediments impacted by agricultural runoff. We selected for resistance plasmids using tetracycline, an antibiotic commonly used in agricultural operations, due to the numerous neighboring cattle pastures and poultry farms. We hypothesized that stream sediment is a “hot spot” for horizontal gene transfer due to the use of antibiotics in agricultural operations combined with runoff into streams. Selective pressures exerted on gut and fecal bacteria of farm animals may select for antibiotic resistance genes that can be horizontally transferred to native stream sediment bacteria when runoff events occur. We characterized four transmissible, tetracycline resistance plasmids: the 71 kb IncP-1β plasmid pEG1-06, the 121 kb IncA/C2 plasmid pCCRT11-6, and the 59 kb IncP-9 plasmids pCCP1 and pCCP2. We built upon and improved the methods developed for the preparation of plasmid DNA for sequencing using 2nd and 3rd generation DNA sequencers, hybrid genome assembly, annotation, and analysis. We demonstrated this process by assembling the four plasmid genomes into single, circular contiguous sequences and compared them to the closest related plasmids allowing us to classify their respective incompatibility groups, reveal the essential backbone and accessory genes present on the plasmid genomes including antibiotic resistance genes, and determine their similarity to the closest related known, existing plasmids

Facilitating the Role of Fathers in the Neonatal Intensive Care Unit: Identifying Barriers to Paternal-Infant Bonding

Thesis advisor: Catherine ReadThe purpose of this paper is to identify and examine the sources of paternal stress related to the NICU experience and the supports currently available. Once identified, the possible sources of stress will be incorporated into a checklist that will allow NICU staff to assess barriers to bonding and further personalize the interventions to facilitate the relationship between the parent and infant.Thesis (BS) — Boston College, 2013.Submitted to: Boston College. Connell School of Nursing.Discipline: College Honors Program.Discipline: Connell School of Nursing

Development of an amplicon-based sequencing approach in response to the global emergence of mpox

The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.This publication was made possible by CTSA Grant Number UL1 TR001863 from the National Center for Advancing Translational Science (NCATS), a component of the National Institutes of Health (NIH) awarded to CBFV. INSA was partially funded by the HERA project (Grant/ 2021/PHF/23776) supported by the European Commission through the European Centre for Disease Control (to VB).info:eu-repo/semantics/publishedVersio

The Complementary Roles for Plant-Source and Animal-Source Foods in Sustainable Healthy Diets

There are approximately 100 countries with food-based dietary guidelines throughout the world, each of which aims to encompass the cultural, geographical, and health considerations unique to their country of origin. Common themes throughout these guides emphasize diverse and balanced intake of food groups from both plant- and animal-sources. With the globally recognized need to shift to more sustainable food systems, several countries and international food and health organizations have begun to incorporate sustainability recommendations into their dietary guidance. These sustainability recommendations are often based on food source (i.e., eat more plant-source and fewer animal-source foods), yet food source may not be the only useful or informative comparator for assessing healthy and sustainable diets. The purpose of this narrative review is to examine the roles of plant-source foods and animal-source foods in the context of sustainable healthy diets—with an emphasis on the contributions of the most commonly recommended food groups from global food-based dietary guidelines (i.e., fruits, vegetables, and dairy foods). Overall, plant and animal agriculture have complementary and symbiotic roles in healthy and sustainable food systems, and these abilities are largely dependent on various contextual factors (e.g., geography, production practices, processing methods, consumption patterns)—not just on whether the food originated from the plant or animal kingdom

MinION Sequencing of a captured Antibiotic Resistance Plasmid

<p>MinION and Ion Torrent sequencing of a captured environmental antibiotic resistance plasmid. </p