Host population structure and species resolution reveal prophage transmission dynamics.

Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages (4,152 prophages + 122 virulent phages, distributed in 46 countries in the world), we show that 91% (875 out of 963) of the prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are not only cosmopolitan but also the most abundant species. We also noted that polylysogens had very divergent prophages, belonging to different prophage species, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. Our study highlights how integrating the host population structure and a solid operational definition of phage species allows us to better appreciate phage diversity and its transmission dynamics. IMPORTANCE: Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages, we show that most prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are cosmopolitan and the most abundant species. Prophages in the same bacterial genome are very divergent, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. This study shows how integrating the host population structure and clustering at the species level allows us to better appreciate phage diversity and its transmission dynamics.

Enhancing Escherichia coli abiotic stress resistance through ornithine lipid formation.

Escherichia coli is a common host for biotechnology and synthetic biology applications. During growth and fermentation, the microbes are often exposed to stress conditions, such as variations in pH or solvent concentrations. Bacterial membranes play a key role in response to abiotic stresses. Ornithine lipids (OLs) are a group of membrane lipids whose presence and synthesis have been related to stress resistance in bacteria. We wondered if this stress resistance could be transferred to bacteria not encoding the capacity to form OLs in their genome, such as E. coli. In this study, we engineered different E. coli strains to produce unmodified OLs and hydroxylated OLs by expressing the synthetic operon olsFC. Our results showed that OL formation improved pH resistance and increased biomass under phosphate limitation. Transcriptome analysis revealed that OL-forming strains differentially expressed stress- and membrane-related genes. OL-producing strains also showed better growth in the presence of the ionophore carbonyl cyanide 3-chlorophenylhydrazone (CCCP), suggesting reduced proton leakiness in OL-producing strains. Furthermore, our engineered strains showed improved heterologous violacein production at phosphate limitation and also at low pH. Overall, this study demonstrates the potential of engineering the E. coli membrane composition for constructing robust hosts with an increased abiotic stress resistance for biotechnology and synthetic biology applications. KEY POINTS: • Ornithine lipid production in E. coli increases biomass yield under phosphate limitation. • Engineered strains show an enhanced production phenotype under low pH stress. • Transcriptome analysis and CCCP experiments revealed reduced proton leakage.

Acinetobacter junii: an emerging One Health pathogen.

Acinetobacter junii is an opportunistic human and animal pathogen severely understudied. Here, we conducted the largest genomic epidemiological study on this pathogen to date. Our data show that this bacterium has spread globally. Also, we found that some human and non-human isolates are not well differentiated from one another, implying transmission between clinical and non-clinical, non-human settings. Remarkably, human but also some non-human isolates have clinically important antibiotic resistance genes, and some of these genes are located in plasmids. Given these results, we put forward that A. junii should be considered an emerging One Health problem. In this regard, future molecular epidemiological studies about this species will go beyond human isolates and will consider animal-, plant-, and water-associated environments. IMPORTANCE: Acinetobacter baumannii is the most well-known species from the genus Acinetobacter. However, other much less studied Acinetobacter species could be important opportunistic pathogens of animals, plants and humans. Here, we conducted the largest genomic epidemiological study of A. junii, which has been described as a source not only of human but also of animal infections. Our analyses show that this bacterium has spread globally and that, in some instances, human and non-human isolates are not well differentiated. Remarkably, some non-human isolates have important antibiotic resistance genes against important antibiotics used in human medicine. Based on our results, we propose that this pathogen must be considered an issue not only for humans but also for veterinary medicine.

Acinetobacter baumannii from grass: novel but non-resistant clones.

Acinetobacter baumannii is one the most worrisome nosocomial pathogens, which has long been considered almost mainly as a hospital-associated bacterium. There have been some studies about animal and environmental isolates over the last decade. However, little effort has been made to determine if this pathogen dwells in the grass. Here, we aim to determine the evolutionary relationships and antibiotic resistance of clones of A. baumannii sampled from grass to the major human international clones and animal clones. Two hundred and forty genomes were considered in total from four different sources for this study. Our core and accessory genomic epidemiology analyses showed that grass isolates cluster in seven groups well differentiated from one another and from the major human and animal isolates. Furthermore, we found new sequence types under both multilocus sequence typing schemes: two under the Pasteur scheme and seven for the Oxford scheme. The grass isolates contained fewer antibiotic-resistance genes and were not resistant to the antibiotics tested. Our results demonstrate that these novel clones appear to have limited antibiotic resistance potential. Given our findings, we propose that genomic epidemiology and surveillance of A. baumannii should go beyond the hospital settings and consider the environment in an explicit One Health approach.

Plasmids of the incompatibility group FIBK occur in Klebsiella variicola from diverse ecological niches.

Plasmids play a fundamental role in the evolution of bacteria by allowing them to adapt to different environments and acquire, through horizontal transfer, genes that confer resistance to different classes of antibiotics. Using the available in vitro and in silico plasmid typing systems, we analyzed a set of isolates and public genomes of K. variicola to study its plasmid diversity. The resistome, the plasmid multilocus sequence typing (pMLST), and molecular epidemiology using the MLST system were also studied. A high frequency of IncF plasmids from human isolates but lower frequency from plant isolates were found in our strain collection. In silico detection revealed 297 incompatibility (Inc) groups, but the IncFIBK (216/297) predominated in plasmids from human and environmental samples, followed by IncFIIK (89/297) and IncFIA/FIA(HI1) (75/297). These Inc groups were associated with clinically important ESBL (CTX-M-15), carbapenemases (KPC-2 and NDM-1), and colistin-resistant genes which were associated with major sequence types (ST): ST60, ST20, and ST10. In silico MOB typing showed 76% (311/404) of the genomes contained one or more of the six relaxase families with MOBF being most abundant. We identified untypeable plasmids carrying blaKPC-2, blaIMP-1, and blaSHV-187 but for which a relaxase was found; this may suggest that novel plasmid structures could be emerging in this bacterial species. The plasmid content in K. variicola has limited diversity, predominantly composed of IncFIBK plasmids dispersed in different STs. Plasmid detection using the replicon and MOB typing scheme provide a broader context of the plasmids in K. variicola. This study showed that whole-sequence-based typing provides current insights of the prevalence of plasmid types and their association with antimicrobial resistant genes in K. variicola obtained from humans and environmental niches.

Descriptive Morphology of Male and Female Genitalia of the Long-horned Grasshopper in the Tribe Aphractini (Orthoptera: Tettigoniidae), with a Key to the Genera.

The male and female genital morphologies of the tribe Aphractini are presented in this study. Four species are included: Aphractus acuminatus, Paraphractus abbreviatus, Polycleptidella chilensis and Polycleptis scutellifera. A dichotomous key to the genera is provided. The lengths between the female spermathecal duct and titillatory articulated processes are similar within species but differ between them. Therefore, we propose that the function of these organs could be associated with the sperm removal strategy.

Adaptación y evidencia de validez de la escala de Florecimiento para la población argentina / Adaptation and evidence of validity of the flourishing scale for the Argentine population

El presente trabajo se ocupa de evaluar las propiedades psicométricas de la Escala de florecimiento (EF) en Argentina, para ello se realizó un proceso de traducción/adaptación para el contexto local. Participaron del estudio 363 adultos con edades comprendidas entre 18 y 68 años y de ambos sexos (Mujeres = 73%, Hombres= 27%). El CFA del modelo (NNFI= .9; CFI= .95; RMSEA= .053)y la consistencia interna(α=.89; ω=.91)arrojaron resultados aceptables para la EF. Por otro lado, la validación externa se realizó estudiando la correlación con los instrumentos MHC-SF y SWLS, obteniendo valores significativos. A su vez, la validación cruzada se realizó dividiendo la muestra en mujeres y hombres, hallándose resultados que confirman la validez del instrumento. En conclusión, se considera a partir de los resultados que la escala EF es un instrumento fiable para el estudio del bienestar en población argentina AU

The present work deals with evaluating the psychometric properties of the Flourishing Scale (EF) in Argentina, for which a translation/adaptation process was carried out for the local context. The study included 363 adults aged between 18 and 68 years and of both sexes (Women = 73%, Men = 27%). The CFA of the model (NNFI= .9; CFI= .95; RMSEA= .053) and internal consistency (α =.89; ω=.91) showed acceptable results for the EF. On the other hand, the external validation was carried out studying the connection with the MHC-SF and SWLS instruments, obtaining significant values. In turn, the cross-validation was carried out by dividing the sample into women and men, finding results that confirm the validity of the instrument. In conclusion, it is considered from the results that the EF scale is a reliable instrument for the study of well-being in the Argentine population AU

Molecular and Genomic Insights of mcr-1-Producing Escherichia coli Isolates from Piglets.

The use of colistin in food-producing animals favors the emergence and spread of colistin-resistant strains. Here, we investigated the occurrence and molecular mechanisms of colistin resistance among E. coli isolates from a Mexican piglet farm. A collection of 175 cephalosporin-resistant colonies from swine fecal samples were recovered. The colistin resistance phenotype was identified by rapid polymyxin test and the mcr-type genes were screened by PCR. We assessed the colistin-resistant strains by antimicrobial susceptibility test, pulse-field gel electrophoresis, plasmid profile, and mating experiments. Whole-Genome Sequencing data was used to explore the resistome, virulome, and mobilome of colistin-resistant strains. A total of four colistin-resistant E. coli were identified from the cefotaxime-resistant colonies. All harbored the plasmid-borne mcr-1 gene, which was located on conjugative 170-kb IncHI-2 plasmid co-carrying ESBLs genes. Thus, high antimicrobial resistance rates were observed for several antibiotic families. In the RC2-007 strain, the mcr-1 gene was located as part of a prophage carried on non-conjugative 100-kb-plasmid, which upon being transformed into K. variicola strain increased the polymyxin resistance 2-fold. The genomic analysis showed a broad resistome and virulome. Our findings suggest that colistin resistance followed independent acquisition pathways as clonal and non-genetically related mcr-1-harboring strains were identified. These E. coli isolates represent a reservoir of antibiotic resistance and virulence genes in animals for human consumption which could be potentially propagated into other interfaces.

PCR system for the correct differentiation of the main bacterial species of the Klebsiella pneumoniae complex.

Accurate recognition of the closely related species Klebsiella pneumoniae, Klebsiella quasipneumoniae and Klebsiella variicola by phenotypic, biochemical and automated tests is notoriously unreliable in hospitals' diagnostic laboratories. A comparative genomics approach was conducted for the correct differentiation of the main bacterial species in the K. pneumoniae complex. Analysis of the deduced proteomes of 87 unique genomes of the Klebsiella in public databases, was used for the identification of unique protein family members. This allowed the design of a multiplex-PCR assay for the correct differentiation of these three species from different origins. This system allowed us to determine the prevalence of K. pneumoniae, K. quasipneumoniae and K. variicola among a collection of 552 clinical isolates. Of these, 87.3% (482/552) isolates corresponded to K. pneumoniae, 6.7% (33/552) to K. quasipneumoniae and 5.9% (33/552) to K. variicola. The multiplex-PCR results showed a 100% accuracy for the correct identification of the three species evaluated, which was validated with rpoB phylogenetic sequence analysis.

Exploring the environmental traits and applications of Klebsiella variicola.

Klebsiella variicola has been found in various natural niches, alone or in association with other bacteria, and causes diseases in animals and plants with important economic and environmental impacts. K. variicola has the capacity to fix nitrogen in the rhizosphere and soil; produces indole acetic acid, acetoin, and ammonia; and dissolves phosphorus and potassium, which play an important role in plant growth promotion and nutrition. Some members of K. variicola have properties such as halotolerance and alkalotolerance, conferring an evolutionary advantage. In the environmental protection, K. variicola can be used in the wastewater treatment, biodegradation, and bioremediation of polluted soil, either alone or in association with other organisms. In addition, it has the potential to carry out industrial processes in the food and pharmaceutical industries, like the production of maltose and glucose by the catalysis of debranching unmodified oligosaccharides by the pullulanase enzyme. Finally, this bacterium has the ability to transform chemical energy into electrical energy, such as a biocatalyst, which could be useful in the near future. These properties show that K. variicola should be considered an eco-friendly bacterium with hopeful technological promise. In this review, we explore the most significant aspects of K. variicola and highlight its potential applications in environmental and biotechnological processes.

RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach.

Basic knowledge of transcriptional regulation is needed to understand the mechanisms governing biological processes, i.e., nitrogen fixation by Rhizobiales bacteria in symbiosis with leguminous plants. The RhizoBindingSites database is a computer-assisted framework providing motif-gene-associated conserved sequences potentially implicated in transcriptional regulation in nine symbiotic species. A dyad analysis algorithm was used to deduce motifs in the upstream regulatory region of orthologous genes, and only motifs also located in the gene seed promoter with a p-value of 1e-4 were accepted. A genomic scan analysis of the upstoream sequences with these motifs was performed. These predicted binding sites were categorized according to low, medium and high homology between the matrix and the upstream regulatory sequence. On average, 62.7% of the genes had a motif, accounting for 80.44% of the genes per genome, with 19613 matrices (a matrix is a representation of a motif). The RhizoBindingSites database provides motif and gene information, motif conservation in the order Rhizobiales, matrices, motif logos, regulatory networks constructed from theoretical or experimental data, a criterion for selecting motifs and a guide for users. The RhizoBindingSites database is freely available online at rhizobindingsites.ccg.unam.mx.

Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach.

Morphology of Phasmatodea eggs is remarkably diverse and highly valuable in taxonomic research. Two alterative hypotheses have been proposed to describe the phylogenetic relationship of the species from the genus Agathemera Stål. Additionally, descriptions of the egg morphology within Agathemera have been done based on the eggs of two species. This small sample size does not represent the diverse egg morphology along the genus, thus we attempt to describe the eggs from all the known Agathemera species. The main goal of the present study is to determine whether the evolution of the eggs occurred through either divergent or convergent evolution. We based our descriptions on morphometrics, morphology and the ultrastructure. For data analysis, principal component analysis (PCA) was performed on morphometric variables and the characters emerged from the morphological and ultrastructure were mapped over the molecular phylogeny. The results show that it is possible to discriminate among species using the morphology of the different egg structures, and furthermore, a divergent event at the base of the tree, differentiate the overall egg shape and the internal micropylar plate shape. Finally, we conclude that both divergent and convergent evolution are shaping the different structures of the Agathemera eggs.

Native bees of high Andes of Central Chile (Hymenoptera: Apoidea): biodiversity, phenology and the description of a new species of Xeromelissa Cockerell (Hymenoptera: Colletidae: Xeromelissinae).

High-altitude ecosystems are found in mountain chains and plateaus worldwide. These areas tend to be underrepresented in insect biodiversity assessments because of the challenges related to systematic survey at these elevations, such as extreme climatic and geographic conditions. Nonetheless, high-altitude ecosystems are of paramount importance because they have been seen to be species pumps for other geographic areas, such as adjacent locations, functioning as buffers for population declines. Moreover, these ecosystems and their biodiversity have been proposed to be fast-responding indicators of the impacts caused by global climate change. Bees have been highlighted among the insect groups that have been affected by these problems. This work used bees as a proxy to demonstrate and reinforce the importance of systematic surveys of high-altitude ecosystems. Here, field collections were undertaken and an updated review was conducted for the native bee biodiversity of the high-altitude ecosystem found at the Andes system of central Chile, including the phenological trends of these insects during the flowering season. Of the 58 species that have been described for this location, we were able to confirm the occurrence of 46 of these species as a result of our sampling. In addition, thanks to these recent collections, a new species of Xeromelissa Cockerell is described in the present work. These findings highlight the need for further high-altitude insect surveys of this biome, which include both temporal and spatial complexity in their design, to allow for accurate assessment of bee species diversity and compositional changes in these mountain regions.

Taxonomic study of the genus Araucanioperla Illies 1963 (Plecoptera: Gripopterygidae), with the description of the male genitalia, eggs and the last instar larva for A. brincki.

A comparative study of morphology on the genus Araucanioperla Illies, 1963 is discussed. Two species of Araucanioperla are known, A. bullocki (Navás, 1933) and A. brincki (Froehlich, 1960). For the first time the larva of A. brincki, the male genitalia of A. bullocki and the eggs of the two species are described and illustrated. The results showed that the morphology of the larvae is similar for the genus, definitively rejecting other larval morphotypes proposed for it. Eggs are also similar between the two species. The male genitalia of both species are specifically distinctive.

Molecular epidemiology of Klebsiella variicola obtained from different sources.

Klebsiella variicola is considered an emerging pathogen in humans and has been described in different environments. K. variicola belongs to Klebsiella pneumoniae complex, which has expanded the taxonomic classification and hindered epidemiological and evolutionary studies. The present work describes the molecular epidemiology of K. variicola based on MultiLocus Sequence Typing (MLST) developed for this purpose. In total, 226 genomes obtained from public data bases and 28 isolates were evaluated, which were mainly obtained from humans, followed by plants, various animals, the environment and insects. A total 166 distinct sequence types (STs) were identified, with 39 STs comprising at least two isolates. The molecular epidemiology of K. variicola showed a global distribution for some STs was observed, and in some cases, isolates obtained from different sources belong to the same ST. Several examples of isolates corresponding to kingdom-crossing bacteria from plants to humans were identified, establishing this as a possible route of transmission. goeBURST analysis identified Clonal Complex 1 (CC1) as the clone with the greatest distribution. Whole-genome sequencing of K. variicola isolates revealed extended-spectrum ß-lactamase- and carbapenemase-producing strains with an increase in pathogenicity. MLST of K. variicola is a strong molecular epidemiological tool that allows following the evolution of this bacterial species obtained from different environments.

Along urbanization sprawl, exotic plants distort native bee (Hymenoptera: Apoidea) assemblages in high elevation Andes ecosystem.

Native bees contribute a considerable portion of pollination services for endemic as well as introduced plant species. Their decline has been attributed to several human-derived influences including global warming as well as the reduction, alteration, and loss of bees' habitat. With human expansion comes along the introduction of exotic plant species with negative impacts over native ecosystems. Anthropic effects may even have a deeper impact on communities adapted to extreme environments, such as high elevation habitats, where abiotic stressors alone are a natural limitation to biodiversity. Among these effects, the introduction of exotic plants and urbanization may have a greater influence on native communities. In this work, we explored such problems, studying the relationship between the landscape and its effect over richness and abundance of native bees from the subandean belt in the Andes mountain chain. Furthermore, we investigated the effects of exotic plant abundance on this high-altitude bee assemblage. Despite the landscape not showing an effect over bee richness and abundance, exotic plants did have a significant influence over the native bee assemblage. The abundance of exotic plants was associated with a relative increase in the proportion of small and medium bee species. Moreover, Halictidae was the only family that appeared to be favored by an increase in the abundance of exotic plant species. We discuss these results and the urgent need for further research of high-altitude environments due to their vulnerability and high endemicity.

Austroectobius invunche: new genus and species of Ectobiidae for Chile (Insecta, Blattaria).

We describe a new genus and species of Chilean Blattodea (Ectobiidae), collected on Isla Grande de Chiloé and associated with Fascicularia bicolor (Bromeliaceae). We study the morphology of both sexes with SEM. The new taxon is brachypterous, with tiny ellipsoid tegmina and hind wings absent. The female presents strongly sclerotized genital sclerites and spermathecal plate developed. The male without tergal specializationsand asymmetrical styles. Medium phallomere with modified sclerites, compose a sclerotized complex that includes a long ejaculatory duct.

Distribution, habitat use and plant associations of Moluchia brevipennis (Saussure, 1864) (Blattodea: Ectobiidae): an endemic cockroach from Chilean Mediterranean Matorral biome

ABSTRACT Wild cockroaches are often described as abundant and diverse insects from wet tropical zones; however, they can also be found in arid and semiarid areas. It is proposed that in these drier environments cockroach survival may dependent on its tight association with native plant species. In this work, using bait trapping and active collection methods, we surveyed cockroach species along central Chile coastal scrubland; the southern limit of the semiarid Mediterranean Matorral biome in the Neotropical Region (32° S). Based on morphological and DNA barcoding methods we found that our collected cockroaches belonged to native species Moluchia brevipennis (Saussure, 1864) (Blattodea: Ectobiidae). Furthermore, thanks to field sampling, we noticed for the first time that M. brevipennis predominantly can be found in patches of native vegetation from Matorral biome, for instance, associated to endemic plant species from Puya (Bromeliaceae) genus, where we recorded these wild cockroaches feeding on flowers at dusk. Under the light of these findings, we discuss the relevance of the association between M. brevipennis and native plants for its survival in this semiarid habitat, its potential ecological function and the ongoing hazards for native insect species resulting from nearby urban sprawl in coastal central Chile.

Miedo al Delito, Victimización y Satisfacción con la Vida en México / Fear of Crime, Victimization, and Satisfaction with Live in Mexico

El objetivo del presente estudio es examinar las relaciones existentes entre miedo al delito, victimización y satisfacción con la vida, en función del género. La muestra estuvo conformada por 7535 sujetos de ambos sexos (49.8 % mujeres y 50.2 % hombres) de entre 12 y 70 años, seleccionados a partir de un muestro estratificado proporcional. El instrumento de medida fue una adaptación de la Encuesta Nacional de Victimización y Seguridad Pública de México. A partir de un MANOVA factorial multivariante se observó que el miedo al delito, la victimización y las medidas de protección frente a la delincuencia se relacionaban con una pobre satisfacción con la vida. También se observó, respecto del sexo, que los hombres tenían mayor miedo al delito y realizaban más restricciones en su vida cotidiana. Finalmente, se discuten los resultados y sus implicaciones prácticas.

The aim of this study is to examine how fear of crime, victimization, and satisfaction with life are related and also differ according to gender. 7535 participants of both sexes (49.8% women and 50.2% men) aged from 12 to 70 years old were selected from a proportional stratified sample. The instrument applied was an adaptation of the National Survey of Victimization and Public Security of Mexico. A multivariate factorial MANOVA was carried out. Fear of crime, victimization, and measures of protection against delinquency appear as related to poor satisfaction with life. Regarding to gender, higher scores of men on fear of crime and on restrictions in their daily lives were observed. Finally, the results and their practical implications are discussed.