Taxonomic considerations on Aerococcus urinae with proposal of subdivision into Aerococcus urinae, Aerococcus tenax sp. nov., Aerococcus mictus sp. nov., and Aerococcus loyolae sp. nov.

Average nucleotide identity analysis, based on whole genome sequences of 115 strains previously identified as Aerococcus urinae, an emerging uropathogen, discriminates at least six unique genomic taxa. The whole genome analysis affords clearer species boundaries over 16S rRNA gene sequencing and traditional phenotypic approaches for the identification and phylogenetic organization of Aerococcus species. The newly described species can be differentiated by matrix-assisted laser desorption ionization time-of-flight analysis of protein signatures. We propose the emendation of the description of A. urinae (type strain ATCC 51268T = CCUG 34223T=NCFB 2893) and the names of Aerococcus tenax sp. nov. (ATCC TSD-302T = DSM 115700T = CCUG 76531T=NR-58630T), Aerococcus mictus sp. nov. (ATCC TSD-301T = DSM 115699T = CCUG 76532T=NR-58629T), and Aerococcus loyolae sp. nov. (ATCC TSD-300T = DSM 115698T = CCUG 76533T=NR-58628T) for three of the newly identified genomic taxa.

Coliphages of the human urinary microbiota.

Due to its frequent association with urinary tract infections (UTIs), Escherichia coli is the best characterized constituent of the urinary microbiota (urobiome). However, uropathogenic E. coli is just one member of the urobiome. In addition to bacterial constituents, the urobiome of both healthy and symptomatic individuals is home to a diverse population of bacterial viruses (bacteriophages). A prior investigation found that most bacterial species in the urobiome are lysogens, harboring one or more phages integrated into their genome (prophages). Many of these prophages are temperate phages, capable of entering the lytic cycle and thus lysing their bacterial host. This transition from the lysogenic to lytic life cycle can impact the bacterial diversity of the urobiome. While many phages that infect E. coli (coliphages) have been studied for decades in the laboratory setting, the coliphages within the urobiome have yet to be cataloged. Here, we investigated the diversity of urinary coliphages by first identifying prophages in all publicly available urinary E. coli genomes. We detected 3,038 intact prophage sequences, representative of 1,542 unique phages. These phages include both novel species as well as species also found within the gut microbiota. Ten temperate phages were isolated from urinary E. coli strains included in our analysis, and we assessed their ability to infect and lyse urinary E. coli strains. We also included in these host range assays other urinary coliphages and laboratory coliphages. The temperate phages and other urinary coliphages were successful in lysing urinary E. coli strains. We also observed that coliphages from non-urinary sources were most efficient in killing urinary E. coli strains. The two phages, T2 and N4, were capable of lysing 83.5% (n = 86) of strains isolated from females with UTI symptoms. In conclusion, our study finds a diverse community of coliphages in the urobiome, many of which are predicted to be temperate phages, ten of which were confirmed here. Their ability to infect and lyse urinary E. coli strains suggests that urinary coliphages may play a role in modulating the E. coli strain diversity of the urobiome.

When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages.

High-throughput sequencing of microbial communities has uncovered a large, diverse population of phages. Frequently, phages found are integrated into their bacterial host genome. Distinguishing between phages in their integrated (lysogenic) and unintegrated (lytic) stage can provide insight into how phages shape bacterial communities. Here we present the Prophage Induction Estimator (PIE) to identify induced phages in genomic and metagenomic sequences. PIE takes raw sequencing reads and phage sequence predictions, performs read quality control, read assembly, and calculation of phage and non-phage sequence abundance and completeness. The distribution of abundances for non-phage sequences is used to predict induced phages with statistical confidence. In silico tests were conducted to benchmark this tool finding that PIE can detect induction events as well as phages with a relatively small burst size (10×). We then examined isolate genome sequencing data as well as a mock community and urinary metagenome data sets and found instances of induced phages in all three data sets. The flexibility of this software enables users to easily include phage predictions from their preferred tool of choice or phage sequences of interest. Thus, genomic and metagenomic sequencing now not only provides a means for discovering and identifying phage sequences but also the detection of induced prophages.

virMine 2.0: Identifying Viral Sequences in Microbial Communities.

Here, we present virMine 2.0, the next generation of the virMine software tool. virMine 2.0 uses an exclusion technique to remove nonviral data from sequencing reads and scores the remaining data based on relatedness to viral elements, eliminating the sole dependency on homology identification.

Multidrug-Resistant Klebsiella variicola Isolated in the Urine of Healthy Bovine Heifers, a Potential Risk as an Emerging Human Pathogen.

Klebsiella variicola, a member of Klebsiella pneumoniae complex, is found to infect plants, insects, and animals and is considered an emerging pathogen in humans. While antibiotic resistance is often prevalent among K. variicola isolates from humans, this has not been thoroughly investigated in isolates from nonhuman sources. Prior evidence suggests that K. variicola can be transmitted between agricultural products as well as between animals, and the use of antibiotics in agriculture has increased antibiotic resistance in other emerging pathogens. Furthermore, in animals that contain K. variicola as a normal member of the rumen microbiota, the same bacteria can also cause infections, such as clinical mastitis in dairy cows. Here, we describe K. variicola UFMG-H9 and UFMG-H10, both isolated from the urine of healthy Gyr heifers. These two genomes represent the first isolates from the urine of cattle and exhibit greater similarity with strains from the human urinary tract than isolates from bovine fecal or milk samples. Unique to the UFMG-H9 genome is the presence of flagellar genes, the first such observation for K. variicola. Neither of the sampled animals had symptoms associated with K. variicola infection, even though genes associated with virulence and antibiotic resistance were identified in both strains. Both strains were resistant to amoxicillin, erythromycin, and vancomycin, and UFMG-H10 is resistant to fosfomycin. The observed resistances emphasize the concern regarding the emergence of this species as a human pathogen given its circulation in healthy livestock animals. IMPORTANCE Klebsiella variicola is an opportunistic pathogen in humans. It also has been associated with bovine mastitis, which can have significant economic effects. While numerous isolates have been sequenced from human infections, only 12 have been sequenced from cattle (fecal and milk samples) to date. Recently, we discovered the presence of K. variicola in the urine of two healthy heifers, the first identification of K. variicola in the bovine urinary tract and the first confirmed K. variicola isolate encoding for flagella-mediated motility. Here, we present the genome sequences and analysis of these isolates. The bovine urinary genomes are more similar to isolates from the human urinary tract than they are to other isolates from cattle, suggesting niche specialization. The presence of antibiotic resistance genes is concerning, as prior studies have found transmission between animals. These findings are important to understand the circulation of K. variicola in healthy livestock animals.

Diversity of Pseudomonas aeruginosa Temperate Phages.

Modern sequencing technologies have provided insight into the genetic diversity of numerous species, including the human pathogen Pseudomonas aeruginosa. Bacterial genomes often harbor bacteriophage genomes (prophages), which can account for upwards of 20% of the genome. Prior studies have found P. aeruginosa prophages that contribute to their host's pathogenicity and fitness. These advantages come in many different forms, including the production of toxins, promotion of biofilm formation, and displacement of other P. aeruginosa strains. While several different genera and species of P. aeruginosa prophages have been studied, there has not been a comprehensive study of the overall diversity of P. aeruginosa-infecting prophages. Here, we present the results of just such an analysis. A total of 6,852 high-confidence prophages were identified from 5,383 P. aeruginosa genomes from strains isolated from the human body and other environments. In total, 3,201 unique prophage sequences were identified. While 53.1% of these prophage sequences displayed sequence similarity to publicly available phage genomes, novel and highly mosaic prophages were discovered. Among these prophages, there is extensive diversity, including diversity within the functionally conserved integrase and C repressor coding regions, two genes responsible for prophage entering and persisting through the lysogenic life cycle. Analysis of integrase, C repressor, and terminase coding regions revealed extensive reassortment among P. aeruginosa prophages. This catalog of P. aeruginosa prophages provides a resource for future studies into the evolution of the species. IMPORTANCE Prophages play a critical role in the evolution of their host species and can also contribute to the virulence and fitness of pathogenic species. Here, we conducted a comprehensive investigation of prophage sequences from 5,383 publicly available Pseudomonas aeruginosa genomes from human as well as environmental isolates. We identified a diverse population of prophages, including tailed phages, inoviruses, and microviruses; 46.9% of the prophage sequences found share no significant sequence similarity with characterized phages, representing a vast array of novel P. aeruginosa-infecting phages. Our investigation into these prophages found substantial evidence of reassortment. In producing this, the first catalog of P. aeruginosa prophages, we uncovered both novel prophages as well as genetic content that have yet to be explored.

Plasmids of the urinary microbiota.

Studies of the last decade have identified a phylogenetically diverse community of bacteria within the urinary tract of individuals with and without urinary symptoms. Mobile genetic elements (MGEs), including plasmids and phages, within this niche have only recently begun to be explored. These MGEs can expand metabolic capacity and increase virulence, as well as confer antibiotic resistance. As such, they have the potential to contribute to urinary symptoms. While plasmids for some of the bacterial taxa found within the urinary microbiota (urobiome) have been well characterized, many urinary species are under-studied with few genomes sequenced to date. Using a two-pronged bioinformatic approach, we have conducted a comprehensive investigation of the plasmid content of urinary isolates representative of 102 species. The bioinformatic tools plasmidSPAdes and Recycler were used in tandem to identify plasmid sequences from raw short-read sequence data followed by manual curation. In total, we identified 603 high-confidence plasmid sequences in 20 different genera of the urobiome. In total, 70 % of these high-confidence plasmids exhibit sequence similarity to plasmid sequences from the gut. This observation is primarily driven by plasmids from E. coli , which is found in both anatomical niches. To confirm our bioinformatic predictions, long-read sequencing was performed for 23 of the E. coli isolates in addition to two E. coli strains that were sequenced as part of a prior study. Overall, 66.95 % of these predictions were confirmed highlighting the strengths and weaknesses of current bioinformatic tools. Future studies of the urobiome, especially concerning under-studied species in the urobiome, should employ long-read sequencing to expand the catalogue of plasmids for this niche.

Sex Work Governance Models: Variations in a Criminalized Context.

BACKGROUND: Under current laws, sex workers are effectively criminalized, which can lead to harmful impacts beyond arrest and prosecution for sex work-specific offenses, including eviction, search and seizure, surveillance, harassment, and deportation. Although these laws are federal, they are realized in and by policy communities at the municipal level. MATERIALS AND METHODS: Based on a qualitative and inductive study of local policy actors affected by or involved in the implementation of prostitution laws, including 65 semistructured interviews in 2014, 2015, and 2016, we identify five different governance models within a shared legal framework of criminalization. We derive these models from an exploration of interactions among actors and organizations based in selected Canadian cities, all of which are bound by federal laws that criminalize the buying of sex thus effectively criminalizing prostitution. RESULTS: Our study surfaces a diversity of traditional and non-traditional policy players who interpret and implement prostitution laws or advocate for and support sex workers. Focusing on equilibrium moments in relationships among these actors, we identify ideational frames that appear to shape dynamics among them and, in turn, give rise to different governance models. CONCLUSIONS: Our findings of different models within the same, overarching legal context are notable because it demonstrates the variability of a single law when it is implemented in local contexts. This is a contribution not just to understanding how prostitution is governed in particular contexts but also to policy and governance theory more generally. Our findings can serve in future, deductive studies that seek to determine the causes and implications of different governance models in the policy area of prostitution and beyond.

Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms.

Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female bladders were sequenced. These isolates were collected from four cohorts, including women: (1) without lower urinary tract symptoms, (2) overactive bladder symptoms, (3) urgency urinary incontinence, and (4) a clinical diagnosis of UTI. Comparative genomic analyses were conducted, including core and accessory genome analyses, virulence and motility gene analyses, and antibiotic resistance prediction and testing. We found that the genomic content of these 66 E. coli isolates does not correspond with the participant's symptom status. We thus looked beyond the E. coli genomes to the composition of the entire urobiome and found that the presence of E. coli alone was not sufficient to distinguish between the urobiomes of individuals with UTI and those with no LUTS. Because E. coli presence, abundance, and genomic content appear to be weak predictors of UTI status, we hypothesize that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition.

Draft Genome Sequences of Two Pseudomonas aeruginosa Isolates from the Female Urogenital Tract.

Pseudomonas aeruginosa is a Gram-negative bacterium that has the ability to survive in and readily adapt to a variety of environmental conditions. Here, we report 2 genome sequences of P. aeruginosa strains, UMB1046 and UMB5686, isolated from the female urogenital tract.

Environmental drivers of paralytic shellfish toxin producing Alexandrium catenella blooms in a fjord system of northern Southeast Alaska.

Paralytic shellfish poisoning (PSP) is a persistent problem that threatens human health and the availability of shellfish resources in Alaska. Regular outbreaks of marine dinoflagellates in the genus Alexandrium produce paralytic shellfish toxins (PSTs) that make shellfish consumption unsafe, and impose economic hardships on Alaska's shellfish industry. Phytoplankton and environmental monitoring spanning 2008-2016, and a pilot benthic cyst survey in 2016, were focused in the Juneau region of Southeast Alaska to investigate Alexandrium catenella distributions and conditions favorable to bloom development. Overwintering Alexandrium cysts were found in near-shore sediments throughout the study region. Alexandrium catenella cells were present in the water column across a range of sea surface temperatures (7-15 °C) and surface salinities (S = 4-30); however, an optimal temperature/salinity window (10-13 °C, 18-23) supported highest cell concentrations. Measurable levels of PSTs were associated with lower concentrations (100 cells L-1) of A. catenella, indicating high cell densities may not be required for shellfish toxicity to occur. Several interacting local factors were identified to support A. catenella blooms: 1) sea surface temperatures ≥7 °C; 2) increasing air temperature; 3) low to moderate freshwater discharge; and 4) several consecutive days of dry and calm weather. In combination, these bloom favorable conditions coincide with toxic bloom events during May and June in northern Southeast Alaska. These findings highlight how integrated environmental and phytoplankton monitoring can be used to enhance early warning capacity of toxic bloom events, providing more informed guidance to shellfish harvesters and resource managers in Alaska.

Draft Genome Sequences of Six Lactobacillus gasseri and Three Lactobacillus paragasseri Strains Isolated from the Female Bladder.

Lactobacilli are dominant members of the healthy female bladder microbiota. Here, we report the complete genome sequences of six Lactobacillus gasseri and three Lactobacillus paragasseri strains isolated from catheterized urine samples. These L. paragasseri genomes are the first publicly available sequences of the species from the bladder.

Complete Genome Sequence of a Pseudomonas aeruginosa Isolate from a Kidney Stone.

Recently, we isolated a temperate bacteriophage, Pseudomonas phage Dobby, from a calcium oxalate kidney stone. Here, we present the complete genome of the bacterial host harboring this phage, Pseudomonas aeruginosa UMB2738. From the analysis of the genome sequence, five additional prophage sequences were identified.

Genome Sequence of Pseudomonas Phage UMP151, Isolated from the Female Bladder Microbiota.

A temperate bacteriophage, designated UMP151, was isolated from a Pseudomonas aeruginosa strain from a catheterized urine sample of a woman with overactive bladder (OAB) symptoms. The 41,303-bp genome sequence of Pseudomonas phage UMP151 exhibits sequence similarity to prophage and lytic phage sequences isolated from other areas of the human body.

Characterization of the ϕCTX-like Pseudomonas aeruginosa phage Dobby isolated from the kidney stone microbiota.

Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37,152 bp genome that closely resembles the temperate P. aeruginosa phage ϕCTX, a member of the P2 phage group. Dobby does not, however, encode for the cytotoxin CTX. Dobby's genome was queried against publicly available bacterial sequences identifying 44 other ϕCTX-like prophages. These prophages are integrated within the genomes of P. aeruginosa strains from a variety of environments, including strains isolated from urine samples and other niches of the human body. Phylogenetic analysis suggests that the temperate ϕCTX phage species is widespread. With the isolation of Dobby, we now have evidence that phages are members of the kidney stone microbiota. Further investigation, however, is needed to determine their abundance and diversity within these communities.

Measures of incentives and confidence in using a social robot.

Measures of incentives and confidence in using a social robot were stable, predictive, and sensitive to changes in robot behaviors.

Internet use and psychological wellness during late adulthood.

An aging population is best served by social, personal, and health support focused on maintaining and maximizing personal independence. The Internet affords numerous opportunities for individuals of all ages to communicate, access information, and engage in recreational activities. A community-based sample of 122 adults over 60 years of age completed a questionnaire which assessed three clusters of characteristics: (a) frequency and patterns of Internet use, (b) well-being (loneliness, life satisfaction, self-efficacy, social support, and depression), and (c) demographics (age, income, education). Significant correlations emerged between the three clusters of measured variables. Controlling for demographic differences, Internet use and self-efficacy remained significantly related. Among the sample of older adults, individuals who used the Internet more had higher perceptions of self-efficacy than those who used the Internet rarely or not at all.

Iron defecation by sperm whales stimulates carbon export in the Southern Ocean.

The iron-limited Southern Ocean plays an important role in regulating atmospheric CO(2) levels. Marine mammal respiration has been proposed to decrease the efficiency of the Southern Ocean biological pump by returning photosynthetically fixed carbon to the atmosphere. Here, we show that by consuming prey at depth and defecating iron-rich liquid faeces into the photic zone, sperm whales (Physeter macrocephalus) instead stimulate new primary production and carbon export to the deep ocean. We estimate that Southern Ocean sperm whales defecate 50 tonnes of iron into the photic zone each year. Molar ratios of C(export):Fe(added) determined during natural ocean fertilization events are used to estimate the amount of carbon exported to the deep ocean in response to the iron defecated by sperm whales. We find that Southern Ocean sperm whales stimulate the export of 4 × 10(5) tonnes of carbon per year to the deep ocean and respire only 2 × 10(5) tonnes of carbon per year. By enhancing new primary production, the populations of 12 000 sperm whales in the Southern Ocean act as a carbon sink, removing 2 × 10(5) tonnes more carbon from the atmosphere than they add during respiration. The ability of the Southern Ocean to act as a carbon sink may have been diminished by large-scale removal of sperm whales during industrial whaling.

Dimensions of online behavior: toward a user typology.

Online behavior refers to organized (e.g., search) and unorganized (e.g., browse) interactions with both human (e.g., chat) and nonhuman (e.g., database) elements in online environments. The salient features of online behavior are conceptualized as sociability (human connection motives), utility (efficiency orientation), and reciprocity (cognitive stimulation and active involvement). Recently published factor analytic studies support the validity of these three dimensions of online behavior. The proposed Brief Test of Online Behavior (BTOB) contains five rating scale items that determine user position on each dimension of online behavior (i.e., 15 items in total). A typology of online behavior emerges as BTOB scores position users in the three-dimensional space created by the intersection of sociability, utility, and reciprocity. Subsequent research may validate the proposed dimensions of online behavior, establish practical applications of the BTOB, and connect type of user with cognitive, social, and emotional outcomes. For example, users who score high on sociability and reciprocity but low on utility may learn best in interactive and stimulating online environments, which necessarily include self-regulating software.