Tetracycline resistance in Listeria monocytogenes and L. innocua from wild black bears (Ursus americanus) in the United States is mediated by novel transposable elements.

IMPORTANCE: Listeria monocytogenes causes severe foodborne illness and is the only human pathogen in the genus Listeria. Previous surveys of AMR in Listeria focused on clinical sources and food or food processing environments, with AMR in strains from wildlife and other natural ecosystems remaining under-explored. We analyzed 185 sequenced strains from wild black bears (Ursus americanus) from the United States, including 158 and 27 L. monocytogenes and L. innocua, respectively. Tetracycline resistance was the most prevalent resistance trait. In L. monocytogenes, it was encountered exclusively in serotype 4b strains with the novel Tn916-like element Tn916.1039. In contrast, three distinct, novel tetracycline resistance elements (Tn5801.UAM, Tn5801.551, and Tn6000.205) were identified in L. innocua. Interestingly, Tn5801.551 was identical to elements in L. monocytogenes from a major foodborne outbreak in the United States in 2011. The findings suggest the importance of wildlife and non-pathogenic Listeria species as reservoir for resistance elements in Listeria.

Sarcocystis sp. infection (Apicomplexa: Sarcocystidae) in invasive California kingsnake Lampropeltis californiae (Serpentes: Colubridae) in Gran Canaria.

Invasive species pose a threat not only to biodiversity because they displace or compete with native fauna, but also because of the pathogens they can host. The Canary Islands are an Atlantic biodiversity hotspot threatened by increasing numbers of invasive species, including the California kingsnake Lampropeltis californiae, which was recently introduced to Gran Canaria. Seventy-seven snakes were examined for gastrointestinal parasites in 2019­2020. Sporocysts of Sarcocystis sp. were detected in 10 of them; detection of gamogonia stages in histological sections of 3 snakes confirmed the snake as a definitive host. Partial ssrDNA was amplified using SarcoFext/SarcoRext primers; an additional sequence of Sarcocystis was obtained from the tail muscle of the endemic Gran Canaria giant lizard Gallotia stehlini for a comparison. Identical ssrDNA sequences of unknown Sarcocystis sp. were obtained from 5 different snakes. Phylogenetic analysis showed that Sarcocystis sp. isolated from invasive California kingsnakes is unrelated to Sarcocystis provisionally considered S. stehlini from the endemic lizard. The dixenous coccidia are rarely reported to invade new predator­prey systems. However, the present data suggest that previously unknown Sarcocystis sp. is circulating among invasive snakes and as yet unknown vertebrate intermediate hosts, with undetermined consequences for the Gran Canaria ecosystem.

Small islands as potential model ecosystems for parasitology: climatic influence on parasites of feral cats.

The influence of climate on parasite distribution has been demonstrated in different regions worldwide. Despite its small size, Gran Canaria (Canary Islands, Spain) constitutes a 'biodiversity laboratory' due to the huge climatic differences between municipalities. Feral cats may represent a threat to biodiversity due to their predatory behaviour. In addition, they may be a source of pathogens zoonotic to humans. To study the climatic/seasonal influence and prevalence of feral cat parasites throughout the island, a total of 290 stool samples from 29 feral cat colonies were analysed following standard concentration protocols (sodium chloride, formol-ether and zinc sulphate). In total, 13 feline parasitic taxa were found, with the most common species being Ancylostoma spp., which, together with Toxocara spp., Toxoplasma gondii and Giardia spp., are considered a concern for human health. Nematodes were the most common parasites in all areas. Nematodes and protozoans were significantly more prevalent in temperate mild (75.0% and 30.0%) than in dry desert areas (29.3% and 18.7%). In contrast, cestodes were significantly more prevalent in dry desert than in temperate mild areas (26.0% and 13.3%). Only protozoans exhibited statistically significant seasonal patterns, mostly in the wet season. Data reported in this study endorse the usage of small and diverse islands such as Gran Canaria to study the climatic influence on parasitic communities in wild/feral animals. Cat colonies require better management to reduce their threat to endemic wildlife, domestic animals and public health, being invasive species that harbour zoonotic parasites.

Dispersion of adeleid oocysts by vertebrates in Gran Canaria, Spain: report and literature review.

Within the family Adeleidae, Adelina spp. belong to a group of arthropod pathogens. These parasites have been reported to have a wide geographic distribution, however, there are no reports of these protists in the Canary Islands, Spain. One of the peculiarities of the life cycle of Adelina spp. is the participation of a predator, because fecundation and sporulation occur inside the body cavity, and so necessitate destruction of the definitive host. The involvement therefore of a 'dispersion host', which eats the definitive host and spreads the oocysts through its faeces, is critical for the maintenance of certain Adelina spp. On the island of Gran Canaria, adeleid oocysts have been found in stool samples from four animals, three California kingsnakes (Lampropeltis californiae), and one feral cat. These animals were part of a larger coprological study of vertebrate parasites (117 snakes, 298 cats), where pseudoparasitic elements were also recorded. L. californiae and feral cats are invasive species which are widespread across the island and this novel finding of Adelina spp. oocysts in their faeces suggests that they could also serve as potential sentinel species for arthropod parasites.

Parasitological findings in the invasive California kingsnake (Lampropeltis californiae) in Gran Canaria, Spain.

The California kingsnake (Lampropeltis californiae), native to North America, is a significant threat to the conservation of endemic species in the Spanish Macaronesian island of Gran Canaria. However, its role disseminating potential invasive parasites, such as zoonotic pentastomids, has not been proven. Among its parasitic fauna, only protistans have been documented, in contrast to other Lampropeltis spp., which are known to carry pentastomids. Thus, a parasitological study is urgently required. Between 2016 and 2018, a total of 108 snakes were necropsied and stool samples examined. A single snake was infested with Ophionyssus natricis, and another individual with Serpentirhabdias sp. Only this latter snake presented gross lesions, characterized by granulomatous pneumonia. No Pentastomida were found. By contrast, almost the entire population (98.5%) was infested with larval helminths (three different nematode and two cestode species), characterized by granulomatous gastrointestinal serositis. This suggests the snake poses a 'dead end' host for local parasites. Based on these findings, snakes in Gran Canaria carry potential zoonotic mites, which along with Serpentirhabdias sp. could represent a threat to endemic lizards. The presence of metazoan parasites and their lesions are reported for the first time in the California kingsnake.

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.

RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep RegulonDB up to date, and initiated curation of ChIP and gSELEX experiments. We estimate that current knowledge describes between 10% and 30% of the expected total number of transcription factor- gene regulatory interactions in E. coli. RegulonDB provides datasets for interactions for which there is no evidence that they affect expression, as well as expression datasets. We developed a proof of concept pipeline to merge binding and expression evidence to identify regulatory interactions. These datasets can be visualized in the RegulonDB JBrowse. We developed the Microbial Conditions Ontology with a controlled vocabulary for the minimal properties to reproduce an experiment, which contributes to integrate data from high throughput and classic literature. At a higher level of integration, we report Genetic Sensory-Response Units for 200 transcription factors, including their regulation at the metabolic level, and include summaries for 70 of them. Finally, we summarize our research with Natural language processing strategies to enhance our biocuration work.

Probing the Functional Topology of a pH-Dependent Triple Helix DNA Nanoswitch Family through Gaussian Accelerated MD Simulation.

The topology of a pH-dependent triple helix DNA nanoswitch family has been characterized through simulative analysis to evaluate the efficiency of the switching mechanism varying the length of the loop connecting the two strands forming the double helix portion. In detail, the system is formed by a double helix made by two six base complementary sequences, connected by one loop having an increasing number of thymidines, namely 5, 7, or 9. The triplex-forming sequence made by six bases, connected to the double helix through a constant 25 base loop, interacts at pH 5.0 through Hoogsteen hydrogen bonds with one strand of the double helical region. We demonstrate, through molecular dynamics simulation, that the thymidine loop length exerts a fine regulatory role for the stability of the triple helix structure and is critical in modulating the switching mechanism triggered by the pH increase.

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.

RegulonDB (http://regulondb.ccg.unam.mx) is one of the most useful and important resources on bacterial gene regulation,as it integrates the scattered scientific knowledge of the best-characterized organism, Escherichia coli K-12, in a database that organizes large amounts of data. Its electronic format enables researchers to compare their results with the legacy of previous knowledge and supports bioinformatics tools and model building. Here, we summarize our progress with RegulonDB since our last Nucleic Acids Research publication describing RegulonDB, in 2013. In addition to maintaining curation up-to-date, we report a collection of 232 interactions with small RNAs affecting 192 genes, and the complete repertoire of 189 Elementary Genetic Sensory-Response units (GENSOR units), integrating the signal, regulatory interactions, and metabolic pathways they govern. These additions represent major progress to a higher level of understanding of regulated processes. We have updated the computationally predicted transcription factors, which total 304 (184 with experimental evidence and 120 from computational predictions); we updated our position-weight matrices and have included tools for clustering them in evolutionary families. We describe our semiautomatic strategy to accelerate curation, including datasets from high-throughput experiments, a novel coexpression distance to search for 'neighborhood' genes to known operons and regulons, and computational developments.

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date the knowledge from the published literature regarding transcriptional regulation in Escherichia coli K-12. We have maintained and expanded our curation efforts to improve the breadth and quality of the encoded experimental knowledge, and we have implemented criteria for the quality of our computational predictions. Regulatory phrases now provide high-level descriptions of regulatory regions. We expanded the assignment of quality to various sources of evidence, particularly for knowledge generated through high-throughput (HT) technology. Based on our analysis of most relevant methods, we defined rules for determining the quality of evidence when multiple independent sources support an entry. With this latest release of RegulonDB, we present a new highly reliable larger collection of transcription start sites, a result of our experimental HT genome-wide efforts. These improvements, together with several novel enhancements (the tracks display, uploading format and curational guidelines), address the challenges of incorporating HT-generated knowledge into RegulonDB. Information on the evolutionary conservation of regulatory elements is also available now. Altogether, RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available.

Antimicrobial and Virus Adsorption Properties of Y-Zeolite Exchanged with Silver and Zinc Cations.

The antimicrobial activity of silver and zinc exchanged cations in Y-zeolite (Ag/CBV-600, Zn/CBV-600) is evaluated against Staphylococcus aureus (gram (+)) and Escherichia coli (gram (-)) bacteria along with their adsorption capacity for viruses: brome mosaic virus (BMV), cowpea chlorotic mottle virus (CCMV), and the bacteriophage MS2. The physicochemical properties of synthesized nanomaterials are characterized by inductively coupled plasma optical emission spectroscopy (ICP-OES), UV-Vis spectroscopy, X-ray diffraction (XRD), and scanning electron microscopy (SEM). According to the obtained results, the main species associated with the exchanged ions are Ag+ and Zn2+ cations with the concentration of around 1 atomic %. The incorporation of cations does not modify the Y-zeolite framework. The Ag/CBV-600 and Zn/CBV-600 materials show an inactivation of 90% for both gram (+) and gram (-) bacteria at 16 h at a relatively low concentration of nanomaterial (0.5 mg/mL). Moreover, the samples present good adsorption capacity for BMV, CCMV, and MS2 viruses showing adsorption higher than 40% after 2 h of interaction with the viruses. These prominent results allow the further usage of nanomaterials as an effective remedy to inhibit and reduce the spread of viruses such as SARS-CoV-2 or other gram (+) or gram (-) bacteria.

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).

RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database of the best-known regulatory network of any free-living organism, that of Escherichia coli K-12. The major conceptual change since 3 years ago is an expanded biological context so that transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. We call these genetic sensory response units, or Gensor Units. We have initiated their high-level curation, with graphic maps and superreactions with links to other databases. Additional connectivity uses expandable submaps. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. Several DNA-binding motifs and their sizes have been redefined and relocated. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.

Usefulness of Inhaled Sedation in Patients With Severe ARDS Due to COVID-19.

BACKGROUND: Sedation in intensive care is fundamental for optimizing clinical outcomes. For many years the world has been facing high rates of opioid use, and to combat the increasing opioid addiction plans at both national and international level have been implemented.1 The COVID-19 pandemic posed a major challenge for health systems and also increased the use of sedatives and opioid analgesia for prolonged periods of time, and at high doses, in a significant proportion of patients. In our institutions, the shortage of many drugs for intravenous (IV) analgosedation forces us to alternatives to replace out-of-stock drugs or to seek sedation goals, which are difficult to obtain with traditional drugs at high doses.2 METHODS: This was an analytical retrospective cohort study evaluating the follow-up of subjects with inclusion criteria from ICU admission to discharge (alive or dead). Five end points were measured: need for high-dose opioids (≥ 200 µg/h), comparison of inhaled versus IV sedation of opioid analgesic doses, midazolam dose, need for muscle relaxant, and risk of delirium. RESULTS: A total of 283 subjects were included in the study, of whom 230 were administered IV sedation and 53 inhaled sedation. In the inhaled sedation group, the relative risks (RRs) were 0.5 (95% CI 0.4-0.8, P = .045) for need of high-dose fentanyl, 0.3 (95% CI 0.20-0.45, P < .001) for need of muscle relaxant, and 0.8 (95% CI 0.61-1.15, P = .25) for risk of delirium. The median difference of fentanyl dose between the inhaled sedation and IV sedation groups was 61 µg/h or 1,200 µg/d (2.2 ampules/d, P < .001), and that of midazolam dose was 5.7 mg/h. CONCLUSIONS: Inhaled sedation was associated with lower doses of opioids, benzodiazepines, and muscle relaxants compared to IV sedation. This therapy should be considered as an alternative in critically ill patients requiring prolonged ventilatory support and where IV sedation is not possible, always under adequate supervision of ICU staff.

One Health Approach: Invasive California Kingsnake (Lampropeltis californiae) as an Important Source of Antimicrobial Drug-Resistant Salmonella Clones on Gran Canaria Island.

The increase in the reptile population has led to a rise in the number of zoonotic infections due to close contact with reptiles, with reptile-associated salmonellosis being particularly relevant. California kingsnake invasion not only threatens the endemic reptile population of the island of Gran Canaria (Spain) but also poses serious public health problems by spreading zoonotic pathogens and their antimicrobial resistance (AMR) to the environment. Thus, the aim of this study was to assess the occurrence, genetic diversity, and AMR among Salmonella spp. strains isolated from California kingsnakes in Gran Canaria Island (Spain). Of 73 invasive individuals captured, 20.5% carried Salmonella spp., belonging to different subspecies and serovars, with subsp. salamae as the most abundant. Pulsed-field electrophoresis showed high genetic diversity among subsp. salamae isolates, and among these, 73.3% showed resistance to at least one of the antimicrobials tested. In conclusion, the present study revealed the importance of wild invasive California kingsnakes as reservoirs of drug-resistant Salmonella spp. that could pose a direct threat to livestock and humans. Identification of drug-resistant Salmonella strains in wildlife provides valuable information on potential routes of transmission that involve risks to public and animal health.

Pathogenic determinants of Kingella kingae disease.

Kingella kingae is an emerging pediatric pathogen and is increasingly recognized as a leading etiology of septic arthritis, osteomyelitis, and bacteremia and an occasional cause of endocarditis in young children. The pathogenesis of K. kingae disease begins with colonization of the upper respiratory tract followed by breach of the respiratory epithelial barrier and hematogenous spread to distant sites of infection, primarily the joints, bones, and endocardium. As recognition of K. kingae as a pathogen has increased, interest in defining the molecular determinants of K. kingae pathogenicity has grown. This effort has identified numerous bacterial surface factors that likely play key roles in the pathogenic process of K. kingae disease, including type IV pili and the Knh trimeric autotransporter (adherence to the host), a potent RTX-family toxin (epithelial barrier breach), and multiple surface polysaccharides (complement and neutrophil resistance). Herein, we review the current state of knowledge of each of these factors, providing insights into potential approaches to the prevention and/or treatment of K. kingae disease.

Characterization and photocatalytic activity of TiO2 nanoparticles on cotton fabrics, for antibacterial masks.

The in-situ impregnation of two commercial cotton fabrics (lab coat and Indiolino) with TiO2 nanoparticles (TiO2-NPs) was carried out. For this, two commercial cotton fabrics were dipped in titanium isopropoxide, titanium butoxide and titanium tetrachloride solutions to the TiO2-NPs formation and in-situ TiO2-NPs impregnation on the cotton fabric surface by the sonochemical, hydrothermal and solvothermal methods, respectively. The impregnated fabrics were characterized by ATR-FTIR, SEM-EDS, Raman, UV-Vis, DRS and tension tests. The results showed the successful formation and impregnation of TiO2-NPs on both cotton fabrics. The leaching of TiO2-NPs from cotton fabrics was negligible after several washing cycles. The self-cleaning properties and antibacterial activity of TiO2-NPs functionalized cotton fabrics were assessed by photocatalytic and antibacterial tests. The photocatalytic activity was determined by the degradation of methylene blue dye under UV and solar irradiation. The materials showed good photoactivity, since MB was degraded up to 99% under solar and UV irradiations in 60 min. The bactericidal capacity of the TiO2-NPs on fabrics, evaluated in-situ by SEM, showed that Indiolino presented the best antibacterial properties against Escherichia coli and Bacillus pumilus.

Systematic revision of the genus Isodacrys Sharp, 1911 (Coleoptera: Curculionidae: Entiminae: Tanymecini).

The genus Isodacrys Sharp, 1911 is revised. Twenty species of the genus are recognized ranging from south United States of America, Mexico, Guatemala and Honduras of which eight are herein described as new. These species are Isodacrys antrum Cortés-Hernández, new species (Mexico: Tamaulipas, Chiapas; Guatemala: Baja Verapaz); Isodacrys carlae Cortés-Hernández, new species (Mexico: Coahuila, Hidalgo, Nuevo León, San Luis Potosí, Tamaulipas); Isodacrys confusum Cortés-Hernández, new species (Mexico: Tamaulipas); Isodacrys fasciatum Cortés-Hernández, new species (Mexico: Coahuila, Durango, Nuevo León); Isodacrys frontalis Cortés-Hernández, new species (Mexico: Oaxaca; Guatemala: Sacatepéquez, Guatemala); Isodacrys kuchii Cortés-Hernández, new species (Mexico: Puebla); Isodacrys obrienorum Cortés-Hernández, new species (Guatemala: Totonicapán, Jalapa, San Marcos); and Isodacrys okuiltontli Cortés Hernández, new species (Mexico: Oaxaca). Insights into the monophyly of Isodacrys and its phylogenetic relationships with other Tanymecini based on adult morphology are given by implementing a phylogenetic analysis of 43 terminals (21 ingroup, 22 outgroup) coded for 72 adult morphological characters. Characters were discussed and highlighted for the inclusion in the phylogenetic analysis. Final analysis yielded two most-parsimonious cladograms of 242 steps, which support the monophyly of Isodacrys. Isodillex Cortés-Hernández, new genus is here described to accommodate Isodillex minutum (Sharp, 1911), new combination and Isodillex plumosum Cortés-Hernández, new species (Mexico: Zacatecas). Isodillex was recovered as sister group of Isodacrys. Key to separate Isodacrys species, occurrence map and habitus photographs are also provided.

Draft Genome Sequence of Multidrug-Resistant Listeria innocua Strain UAM003-1A, Isolated from a Wild Black Bear (Ursus americanus).

There is currently limited knowledge of the genome sequences of nonpathogenic Listeria species, especially strains from wildlife. Here, we report the draft genome sequence and associated genome information of an antibiotic-resistant Listeria innocua strain, UAM003-1A, isolated from the feces of a black bear in California, USA.

A key to the Mexican genera of Tanymecini (Coleoptera: Curculionidae).

We provide a key to the eight genera of the tribe Tanymecini distributed in Mexico. Habitus photographs of all genera are included as are photographs of various other key characters. A brief synopsis of each genus is included as well as a list of the species recorded for Mexico. The species Minyomerus languidus Horn and Pandeleteius championi Howden are newly recorded for Mexico.

Mild Cognitive Impairment and Dementia Involving Multiple Cognitive Domains in Mexican Urbanites.

Exposures to fine particulate matter PM2.5 and ozone O3 are associated with Alzheimer's disease (AD) risk. Mexico City residents have lifetime exposures to PM2.5 and O3 above annual USEPA standards and their brains contain high redox, combustion, and friction-derived magnetite nanoparticles. AD pathological changes with subcortical pre-tangle stages in infancy and cortical tau pre-tangles, NFT Stages I-II, and amyloid phases 1-2 are identified by the 2nd decade. Given their AD continuum, a reliable identification of cognitive impairment is of utmost importance. The Montreal Cognitive Assessment (MoCA) was administered to 517 urbanites, age 21.60±5.88 years, with 13.69±1.28 formal education years, in Mexican PM2.5 polluted cities. MoCA score was 23.92±2.82, and 24.7% and 30.3% scored ≤24 and ≤22, respectively (MCI≤24, AD≤22). Cognitive deficits progressively targeted Visuospatial, Executive, Language, and Memory domains, body mass index (BMI) impacting total scores negatively (p = 0.0008), aging driving down Executive, Visuospatial, and Language index scores (p < 0.0001, 0.0037, and 0.0045), and males performing better in Executive tasks. Average age for AD MoCA scores was 22.38±7.7 years. Residency in polluted cities is associated with progression of multi-domain cognitive impairment affecting 55% of Mexican seemingly healthy youth. Normal BMI ought to be a neuroprotection goal. MoCA provides guidance for further mandatory neuropsychological testing in young populations. Identifying and lowering key neurotoxicants impacting neural risk trajectories in the developing brain and monitoring cognitive performance would greatly facilitate multidisciplinary early diagnosis and prevention of AD in high risk young populations. Cognitive deficits hinder development of those representing the force moving the country in future years.

Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.

In RegulonDB, for over 25 years, we have been gathering knowledge by manual curation from original scientific literature on the regulation of transcription initiation and genome organization in transcription units of the Escherichia coli K-12 genome. This unit describes six basic protocols that can serve as a guiding introduction to the main content of the current version (v9.4) of this electronic resource. These protocols include general navigation as well as searching for specific objects such as genes, gene products, transcription units, promoters, transcription factors, coexpression, and genetic sensory response units or GENSOR Units. In these protocols, the user will find an initial introduction to the concepts pertinent to the protocol, the content obtained when performing the given navigation, and the necessary resources for carrying out the protocol. This easy-to-follow presentation should help anyone interested in quickly seeing all that is currently offered in RegulonDB, including position weight matrices of transcription factors, coexpression values based on published microarrays, and the GENSOR Units unique to RegulonDB that offer regulatory mechanisms in the context of their signals and metabolic consequences. © 2018 by John Wiley & Sons, Inc.