Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus.

Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, which has led to the assumption that this system is a virulence factor exclusively possessed by L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legionella repeat protein secretion system shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS in Pseudomonas aeruginosa. The Legionella bacteriocin (1-3) secretion systems T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS in Escherichia coli. Of 45 Legionella spp. whole genomes examined, 19 (42%) were determined to possess lssB and lssD homologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a singular virulence factor. Future studies should investigate mechanistic explanations for the association of RtxA with virulence

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

This is the final version of the article. Available from the publisher via the DOI in this record.Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.MRG is supported by the Australian Research Council, AP is supported by the Alfred P Sloan Foundation Microbiology of the Built Environment program and the National Science Foundation RAPID award no. 1402651, KS is supported by the Deutsche Forschungsgemeinschaft (DFG) funding the Research Unit FOR 566 ‘Veterinary Medicines in Soil: Basic Research for Risk Analysis’ (Grant No. SM59/5-3) and by the Umweltbundesamt (3713 63 402), JMT is supported by the US National Science Foundation and Y-GZ is supported by the National Science Foundation of China

Tertiary-Treated Municipal Wastewater is a Significant Point Source of Antibiotic Resistance Genes Into Duluth-Superior Harbor

In this study, the impact of tertiary-treated municipal wastewater on the quantity of several antibiotic resistance determinants in Duluth-Superior Harbor was investigated by collecting surface water and sediment samples from 13 locations in Duluth-Superior Harbor, the St. Louis River, and Lake Superior. Quantitative PCR (qPCR) was used to target three different genes encoding resistance to tetracycline (tet(A), tet(X), and tet(W)), the gene encoding the integrase of class 1 integrons (intI1), and total bacterial abundance (16S rRNA genes) as well as total and human fecal contamination levels (16S rRNA genes specific to the genus Bacteroides). The quantities of tet(A), tet(X), tet(W), intI1, total Bacteroides, and human-specific Bacteroides were typically 20-fold higher in the tertiary-treated wastewater than in nearby surface water samples. In contrast, the quantities of these genes in the St. Louis River and Lake Superior were typically below detection. Analysis of sequences of tet(W) gene fragments from four different samples collected throughout the study site supported the conclusion that tertiary-treated municipal wastewater is a point source of resistance genes into Duluth-Superior Harbor. This study demonstrates that the discharge of exceptionally treated municipal wastewater can have a statistically significant effect on the quantities of antibiotic resistance genes in otherwise pristine surface waters

Arctic plasmidome analysis reveals distinct relationships among associated antimicrobial resistance genes and virulence genes along anthropogenic gradients.

Polar regions are relatively isolated from human activity and thus could offer insight into anthropogenic and ecological drivers of the spread of antibiotic resistance. Plasmids are of particular interest in this context given the central role that they are thought to play in the dissemination of antibiotic resistance genes (ARGs). However, plasmidomes are challenging to profile in environmental samples. The objective of this study was to compare various aspects of the plasmidome associated with glacial ice and adjacent aquatic environments across the high Arctic archipelago of Svalbard, representing a gradient of anthropogenic inputs and specific treated and untreated wastewater outflows to the sea. We accessed plasmidomes by applying enrichment cultures, plasmid isolation and shotgun Illumina sequencing of environmental samples. We examined the abundance and diversity of ARGs and other stress-response genes that might be co/cross-selected or co-transported in these environments, including biocide resistance genes (BRGs), metal resistance genes (MRGs), virulence genes (VGs) and integrons. We found striking differences between glacial ice and aquatic environments in terms of the ARGs carried by plasmids. We found a strong correlation between MRGs and ARGs in plasmids in the wastewaters and fjords. Alternatively, in glacial ice, VGs and BRGs genes were dominant, suggesting that glacial ice may be a repository of pathogenic strains. Moreover, ARGs were not found within the cassettes of integrons carried by the plasmids, which is suggestive of unique adaptive features of the microbial communities to their extreme environment. This study provides insight into the role of plasmids in facilitating bacterial adaptation to Arctic ecosystems as well as in shaping corresponding resistomes. Increasing human activity, warming of Arctic regions and associated increases in the meltwater run-off from glaciers could contribute to the release and spread of plasmid-related genes from Svalbard to the broader pool of ARGs in the Arctic Ocean

Quail IV: Proceedings of the Fourth National Quail Symposium (May 6-9, 1997 : Florida State University, Tallahassee, Florida)

Fourth Herbert L. Stoddard, Sr. Memorial Game Bird Lecturer: Dr. G. R. Potts, Leonard A. Brennan FOURTH STODDARD MEMORIAL GAME BIRD LECTURE Using the Scientific Method to Improve Game Bird Management and Research: Time, G. R. Potts QUAIL POPULATION RESPONSES TO HABITAT MANAGEMENT AND CHANGE Habitat Use by Breeding Northern Bobwhites in Managed Old-Field Habitats in Mississippi, Jimmy D. Taylor, II and Loren W. Burger, Jr. Habitat Management for Northern Bobwhites in Wisconsin: A Long-Term Assessment, LeRoy R. Petersen, Robert T. Dumke, and Barbara F. Duerksen Effects of Filter Strips on Habitat Use and Home Range of Northern Bobwhites on Alligator River National Wildlife Refuge, K. Marc Puckett, William E. Palmer, Peter T. Bromley, John R. Anderson, Jr., and Terry L. Sharpe Vegetation Response to Disking on a Longleaf Pine Site in Southeastern Louisiana, Michael W. Olinde Influence of Food Plots on Northern Bobwhite Movements, Habitat Use, and Home Range, L. Andrew Madison, Robert J. Robel, and David P. Jones The Status of Masked Bobwhite Recovery in the United States and Mexico, William P. Kuvlesky, Jr., Sally A. Gall, Steve J. Dobrott, Susan Tolley, Fred S. Guthery, Stephen A. DeStefano, Nina King, Kenneth R. Nolte, Nova J. Silvy, James C. Lewis, George Gee, Gustavo Camou Luders, and Ron Engel-Wilson Vegetation and Thermal Characteristics of Bobwhite Nocturnal Roost Sites in Native Warm-Season Grass (Abstract), Eliodora Chamberlain, Ronald D. Drobney, and Thomas V. Dailey Effects of Disking Versus Feed Patch Management on Northern Bobwhite Brood Habitat and Hunting Success, Leonard A. Brennan, Jeffrey M. Lee, Eric L. Staller, Shane D. Wellendorf, and R. Shane Fuller Bird Use of Bobwhite Brush Shelters on a Conservation Reserve Program Field, Louis A. Harveson, Nick I. Kassinis, and Fred S. Guthery Effects of Seasonal Fire Applications on Northern Bobwhite Brood Habitat and Hunting Success, Leonard A. Brennan, Jeffrey M. Lee, Eric L. Staller, Shane D. Wellendorf, and R. Shane Fuller Bobwhite Brood Ecology in Relation to Fallow Field Management Techniques and Prescribed Fire Regime (Abstract), A. Vincent Carver, Loren W. Burger, Jr., and Leonard A. Brennan Seed Availability Within Food Plots and Native Vegetation Areas on a Longleaf Pine Site in Southeastern Louisiana (Abstract), Michael W. Olinde Food Plot Use by Juvenile Northern Bobwhites in East Texas, D. Scott Parsons, R. Montague Whiting, Jr., Xiangwen Liu, and Donald R. Dietz Long-Term Trends of Northern Bobwhite Populations and Hunting Success on Private Shooting Plantations in Northern Florida and Southern Georgia, Leonard A. Brennan, Jeffrey M. Lee, and R. Shane Fuller ANALYZING THE EFFECTS OF PREDATION AND HUNTING Theory of the Hunter-Covey Interface, Andrew A. Radomski and Fred S. Guthery Survival Rates of Northern Bobwhite Chicks in South-Central Iowa, Willie J. Suchy and Ronald J. Munkel Is Quail Hunting Self-Regulatory? Northern Bobwhite and Scaled Quail Abundance and Quail Hunting in Texas, Markus J. Peterson and Robert M. Perez Survival of Northern Bobwhites on Areas with and without Liberated Bobwhites, D. Clay Sisson, Dan W. Speake, and H. Lee Stribling Predators and Prickly Paradigms: Nesting Ecology of Bobwhites and Scaled Quail in West Texas (Abstract), Dale Rollins, Fidel Hernandez, Philip L. Carter, and Stacey A. Slater Depredation Patterns of Northern Bobwhite Nest Predators in Virginia, Michael L. Fies and K. Marc Puckett Seasonal Survival and Cause-Specific Mortality of Northern Bobwhites in Mississippi, Jimmy D. Taylor II, Loren W. Burger, Jr., Scott W. Manley, and Leonard A. Brennan Preliminary Findings on the Foraging Ecology of a Northern Bobwhite Predator in North Florida: The Cooper\u27s Hawk (Accipiter cooperii) (Abstract), Brian A. Millsap, Timothy Breen, and Lora Silvmania Efficiency of Pointing Dogs in Locating Northern Bobwhite Coveys (Abstract), D. Clay Sisson, H. Lee Stribling, and Dan W. Speake Influence of Habitat Type and Prescribed Burning on Feral Swine Depredation of Artificial Quail Nests (Abstract), Douglas R. Tolleson, William E. Pinchak, Dale Rollins, and R. James Ansley GENETICS, SURVIVAL, REPRODUCTION, AND POPULATION RESTORATION Comparative Morphology and Phylogenetic Relatedness Among Bobwhites in the Southern U.S. and Mexico, Shirley L. White, Kenneth R. Nolte, William P. Kuvlesky, Jr., and Fred S. Guthery Restocking Northern Bobwhites in East Texas: A Genetic Assessment (Abstract), Michael A. Nedbal, Steven G. Evans, Rodney L. Honeycutt, R. Montague Whiting, Jr., and Donald R. Dietz Temperature and Humidity Relationships of Scaled Quail Nests in Southern New Mexico, Carol A. Evans and Sanford D. Schemnitz Survival and Causes of Mortality of Relocated and Resident Northern Bobwhites in East Texas, Xiangwen Liu, R. Montague Whiting, Jr., Brad S. Mueller, D. Scott Parsons, and Donald R. Dietz Reproductive Effort of Female Mountain Quail Induced by Dietary Xanthophyll (Abstract), David Delehanty The Effects of Endophyte-Infected KY 3 1 Tall Fescue Seed on Northern Bobwhite Reproduction (Abstract), Thomas G. Barnes, James S. Lane, Anthony Pescatore, and Austin Cantor Effects of Feed Restriction on Lipid Dynamics and Reproduction in Northern Bobwhites (Abstract), Thomas V. Dailey and Terrance R. Callahan Effects of Supplemental Feeding on Home Range Size and Survival of Northern Bobwhites in South Georgia, D. Clay Sisson, H. Lee Stribling, and Dan W. Speake Reproduction of Relocated and Resident Northern Bobwhites in East Texas, D. Scott Parsons, R. Montague Whiting, Jr., Xiangwen Liu, Brad S. Mueller, and Stanley L. Cook Habitat Use by Reintroduced Mountain Quail (Abstract), Michael Pope and John A. Crawford Brain Cholinesterase Depression and Mortality of Bobwhite Chicks Exposed to Granular Chlorpyrifos or Fonofos Applied to Peanut Vines (Abstract), William E. Palmer, John R. Anderson, Jr., and Peter T. Bromley Exposure of Captive Bobwhites to an At-Planting Application of Terbufos (Counter® 1 5G) to Corn (Abstract), William E. Palmer, John R. Anderson, Jr., and Peter T. Bromley Survival Rates for Northern Bobwhites on Two Areas with Different Levels of Harvest, Willie J. Suchy and Ronald J. Munkel Releasing Captive-Reared Masked Bobwhites for Population Recovery: A Review, Sally A. Gall, William P. Kuvlesky, Jr., and George Gee LANDSCAPE SCALE EFFECTS ON QUAIL POPULATIONS AND HABITAT Habitat and Weather Effects on Northern Bobwhite Brood Movements, J. Scott Taylor, Kevin E. Church, and Donald H. Rusch The Development of a Gamebird Research Strategy: Unraveling the Importance of Arthropod Populations, Nicolas W. Sotherton Status, Ecology and Management of Scaled Quail in West Texas, Dale Rollins Habitat Characteristics of Northern Bobwhite Quail-Hunting Party Encounters: A Landscape Perspective, William K. Michener, Jimmy B. Atkinson, Don G. Edwards, Jeffrey W. Hollister, Paula F. Houhoulis, Paula M. Johnson, and Robert N. Smith Montezuma Quail Management in Arizona, James R. Heffelfinger and Ronald J. Olding Quails in Mexico: Needs and Opportunities, John P. Carroll and Jack Clinton Eitniear Historic Distribution of Mountain Quail in the Pacific Northwest, John A. Crawford Potential Effects of Global Warming on Quail Populations, Fred S. Guthery, N. David Forrester, Kenneth R. Nolte, Will E. Cohen, and William P. Kuvlesky, Jr. Ontario Ministry of Natural Resources South-Central Region Bobwhite Quail Rehabilitation Program (Abstract), P. Hunter and R. Ludolph How Ecological Disturbances May Influence Mountain Quail in the Pacific Northwest (Abstract), Michael D. Pope and Patricia E. Heekin RESEARCH METHODS Efficiency of Bait Trapping and Night Lighting for Capturing Northern Bobwhites in Missouri, Vicki L. Truitt and Thomas V. Dailey Effects of Radio-Transmitters on Body Condition, Harvest Rate, and Survival of Bobwhites (Abstract), Lori Corteville, Loren W. Burger, Jr., and Leonard A. Brennan Evaluation of Two Marking Methods for 1 -day-old Northern Bobwhite Chicks (Abstract), A. Vincent Carver, Loren W. Burger, Jr., and Leonard A. Brennan Comparison of Two Methods for Quantifying Northern Bobwhite Habitat Use, Scott W. Manley, Jeffrey M. Lee, R. Shane Fuller, John P. Carroll, and Leonard A. Brennan HUMAN DIMENSIONS Demographics of Quail Hunters in Oklahoma, Andrea K. Crews and Stephen J. DeMaso Missouri\u27s Quail Hunter Cooperator Survey (Abstract), Thomas V. Dailey The Bobwhite Brigade: An Innovative Approach to Wildlife Extension Education, Dale Rollins, Don W. Steinbach, and Cristy G. Brown The Future of Quail Hunting in the Southeastern United States (Abstract), Frank B. Barick Strategic Planning Update, Leonard A. Brennan and John P. Carroll SYMPOSIUM WORKSHOP SUMMARIES Workshop Summary, Developing Northern Bobwhite Management Plans: A Habitat-Based Framework, Brad S. Mueller Quail Modeling Workshop Summary, Fred S. Guthery Workshop Summary: Federal Farm Programs-What Can Be Done for Quail? Steve Capel Workshop Summary: Radio Telemetry Applications in Wildlife Research, Loren W. Burger, Jr., and Jimmy D. Taylor II CONFERENCE SUMMARY AND CONCLUDING REMARKS Concluding Remarks: The Research Perspective, John L. Roseberry Concluding Remarks: The Manager\u27s Perspective, Hunter Dre

The State of Digital Media Data Research, 2024

The purpose of this report is to reflect on the state of digital media data research in 2024. This is the second in a series of reports on the state of digital media research, which we originally published in 2023. We reflect on changes to digital media research since our report in 2023. Specifically, we highlight the following trends: 1. From 2023 to 2024, access to digital media data changed drastically. Researchers were largely priced out of the Twitter API, and Pushshift–a commonly used archive for Reddit data–went private to comply with Reddit’s API policies. Meta also announced the imminent sunsetting of CrowdTangle, a transparency tool popular amongst researchers and journalists alike. At the same time, however, many platforms announced academic programs for data access, including the YouTube researcher program, TikTok’s Research API, and the Meta Content Library. 2. Federated social media platforms became more popular. Following Elon Musk’s purchase of Twitter, Twitter users flocked to Mastodon, Threads, BlueSky, and other federated (or soon to be federated) platforms. This presents unique challenges for researchers studying digital media data. As new platforms are created, researchers must build new tools to analyze them or wait for third parties or the platforms themselves to make data available. 3. Generative AI’s explosion may change how we study digital media. First, researchers using computational methods to measure social media content have turned to OpenAI’s ChatGPT and other Large Language Models (LLMs) to classify content. Second, researchers and civil society groups are increasingly concerned about the possibility for Generative AI to flood the information environment with fake content. 4. In February 2024, the EU Digital Services Act (DSA) went into effect, mandating that large platforms give researchers near real-time access to public data. We don’t yet know how these policies will impact data access in the United States, and it remains unclear what this data access will look like in practice. In the United States, legislative efforts to mandate researcher access stalled. While the last year brought many welcome and unwelcome changes to digital media data research, the findings in this report renew our encouragement that digital media data research should be guided by collaboration, transparency, preparation, and consistency.Journalism and Medi

Bipolar Ionization Did Not Reduce Airborne Bacteria in a Lecture Hall

Ionization treatment of indoor air has attracted attention for its potential to inactivate airborne pathogens and reduce disease transmission, yet its real-world effectiveness remains unverified. We evaluated the impact of an in-duct, bipolar ionization system on airborne particles, including culturable bacteria, in a lecture hall. The ionizer was off with variable fan speed for 1 week, on with variable fan speed for a second week, and on with high and constant fan speed for a third week. We measured ion concentrations and aerosol particle concentrations, and we collected bioaerosol samples for analysis of 16S rRNA gene copies representing total bacteria and colony forming units (CFUs) on Tryptic Soy Agar representing culturable bacteria. There were no significant differences in positive, in-room ion concentrations between any weeks; however, negative, in-room ion concentrations were significantly lower when the ionizer was on with constant fan speed. To account for day-to-day variability in total bacteria concentrations, related to occupancy and other factors, we examined the ratio of CFUs to 16S rRNA gene copies (CFU gc) and found no significant differences whether the ionizer was on or off. This result indicates that the ionizer was not effective at reducing levels of culturable airborne bacteria in this study

Vaccine Hesitancy Under the Magnifying Glass: A Systematic Review of the Uses and Misuses of an Increasingly Popular Construct

Resistance to vaccines has hindered attempts to contain and prevent outbreaks of infectious diseases for centuries. More recently, however, the term "vaccine hesitancy" has been used to describe not necessarily outright resistance but also a delay in acceptance or uncertainty regarding vaccines. Given concerns about hesitancy and its impact on vaccine uptake rates, researchers increasingly shifted the focus from resistance to vaccines toward vaccine hesitancy. Acknowledging the urgency to accurately assess the phenomenon, it is critical to understand the state of the literature, focusing on issues of conceptualization and operationalization. To carry out this systematic review, we collected and analyzed all published empirical articles from 2000 to 2021 that explicitly included quantitative self-report measures of vaccine hesitancy (k = 86). Using a mixed-method approach, the review demonstrates and quantifies crucial inconsistencies in the measurement of the construct, lack of clarity in regard to the determination of who should or should not be defined as hesitant, and overreliance on unrepresentative samples. Crucially, our analysis points to a potential systematic bias toward exaggerating the level of hesitancy in the population. Modeling a vaccine hesitancy co-citation network, the analysis also points to the existence of insular academic silos that make it harder to achieve a unified measurement tool. Theoretical and practical implications for academics, practitioners, and policymakers are discussed