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Despite the highly conserved nature of the genetic code, the frequency of usage of each codon can vary significantly. The evolution of codon usage is shaped by two main evolutionary forces: mutational bias and selection pressures. These pressures can be driven by environmental factors, but also by the need for efficient translation, which depends heavily on the concentration of transfer RNAs (tRNAs) within the cell. The data presented here supports the proposal that tRNA modifications play a key role in shaping the overall preference of codon usage in proteobacteria. Interestingly, some codons, such as CGA and AGG (encoding arginine), exhibit a surprisingly low level of variation in their frequency of usage, even across genomes with differing GC content. These findings suggest that the evolution of GC content in proteobacterial genomes might be primarily driven by changes in the usage of a specific subset of codons, whose usage is itself influenced by tRNA modifications.

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Campylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. This zoonotic pathogen colonizes the gastrointestinal tract of a wide range of mammals and birds, with poultry as the most important reservoir for human infections. Apart from its high morbidity rates, the emergence of resistant strains is of global concern. The aims of this work were to determine genetic diversity, presence of antimicrobial resistance determinants and virulence potential of Campylobacter spp. isolated from patients with acute gastrointestinal disease at 'Clinica Alemana', Santiago de Chile. The study considered the isolation of Campylobacter spp., from stool samples during a 20-month period (January 2020 to September 2021). We sequenced (NextSeq, Illumina) and performed an in-depth analysis of the genome sequences of 88 Campylobacter jejuni and 2 Campylobacter coli strains isolated from clinical samples in Chile. We identified a high genetic diversity among C. jejuni strains and the emergence of prevalent clonal complexes, which were not identified in our previous reports. While ~40% of strains harbored a mutation in the gyrA gene associated with fluoroquinolone resistance, no macrolide-resistance determinants were detected. Interestingly, gene clusters encoding virulence factors such as the T6SS or genes associated with long-term sequelae such as Guillain-Barré syndrome showed lineage-relatedness. In addition, our analysis revealed a high degree of variability regarding the presence of fT3SS and T6SS effector proteins in comparison to type strains 81-176, F38011, and NCTC 11168 and 488. Our study provides important insights into the molecular epidemiology of this emerging foodborne pathogen. In addition, the differences observed regarding the repertoire of fT3SS and T6SS effector proteins could have an impact on the pathogenic potential and transmissibility of these Latin American isolates, posing another challenge in characterizing the infection dynamics of this emergent and neglected bacterial pathogen.

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Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, type III secretion system (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host-cell processes, critical for V. parahaemolyticus to colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness of V. parahaemolyticus in its interaction with bacterivorous protists; hence, it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes in Vibrio and non-Vibrio species, suggesting that the T3SS2 gene cluster is not restricted to the Vibrionaceae and can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from 8 bacterial genera, 5 bacterial families and 47 bacterial species. A hierarchical clustering analysis allowed us to define six T3SS2 subgroups (I-VI) with different repertoires of effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of the T3SS2 gene clusters (subgroup VI) that lacks most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond the family Vibrionaceae and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of each bacterium that has acquired the Vibrio T3SS2 gene cluster.

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Introducción: las revistas científicas son el instrumento perfecto para comunicar resultados del proceso de investigación y transmitir el conocimiento. El comité editorial es un equipo de expertos de vital importancia en el funcionamiento de una revista científica. Sin embargo, una frecuente práctica editorial es la publicación de manuscritos en las revistas que editan. Por ello, se buscó determinar cuál es la frecuencia de la endogamia editorial en las revistas peruanas del área de la salud. Métodos: se realizó una revisión de los artículos publicados por miembros del comité editorial de 26 revistas peruanas entre el 2016 y 2019. Se realizó una evaluación de los manuscritos provenientes del comité editorial, así como un análisis de asociación entre el estado de indexación en dos bases de datos regionales; además, cómo esta influye en la frecuencia de endogamia de cada revista. Resultados: durante el periodo evaluado se publicaron 2.885 manuscritos, de los cuales 520 tenían como autores a miembros del comité editorial. El tipo de contribución más frecuente fue el artículo original. La endogamia en los años 2016 al 2018, así como un mayor porcentaje de endogamia por fascículo, fue estadísticamente mayor en las revistas pertenecientes al directorio Latindex. Conclusión: las revistas peruanas del área de la salud tienen frecuencias heterogéneas de endogamia editorial. Las revistas incluidas en el directorio Latindex presentan una mayor frecuencia de esta práctica editorial frente a las revistas que pertenecen a la base de datos SciELO-Perú.

SUMMARY Introduction: Scientific journals are the perfect instrument to communicate results of the research process and transmit knowledge. The editorial board is a team of experts of vital importance in the operation of a scientific journal, however, a frequent editorial practice is the publication of manuscripts in the journals they edit; therefore, we sought to determine the frequency of editorial inbreeding in Peruvian journals in the health area. Methods: A review of the articles published by members of the editorial board of 26 Peruvian journals between 2016 and 2019 was performed, evaluating the manuscripts from the editorial board, as well as analysis of association between the status of indexation in two regional databases and how this influences the frequency of inbreeding in each journal. Results: During the period evaluated, 2885 manuscripts were published, of which 520 had authors of the editorial board as authors. The most frequent type of contribution was the original article. Inbreeding in the years 2016 to 2018, as well as a higher percentage of inbreeding per issue, was statistically higher in the journals belonging to the Latindex directory. Conclusion: Peruvian journals in the health area have heterogeneous frequencies of editorial inbreeding. The journals included in the Latindex directory present higher frequency in editorial inbreeding, compared to journals included in the SciELO-Peru database.

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Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n = 81), collected in 2017-2019 in Santiago, Chile. This culture collection accounts for more than one third of the available genome sequences from South American clinical strains. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.

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Bacterial oxidative stress responses are generally controlled by transcription factors that modulate the synthesis of RNAs with the aid of some sRNAs that control the stability, and in some cases the translation, of specific mRNAs. Here, we report that oxidative stress additionally leads to inactivation of tRNAGly in Escherichia coli, inducing a series of physiological changes. The observed inactivation of tRNAGly correlated with altered efficiency of translation of Gly codons, suggesting a possible mechanism of translational control of gene expression under oxidative stress. Changes in translation also depended on the availability of glycine, revealing a mechanism whereby bacteria modulate the response to oxidative stress according to the prevailing metabolic state of the cells.

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Campylobacter species are the leading cause of gastroenteritis worldwide and an emerging threat in developing countries. Here, we report the draft whole-genome sequences of 51 Campylobacter jejuni and 12 Campylobacter coli strains isolated from patients with gastroenteritis in Santiago, Chile.

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INTRODUCTION: E. coli is a ubiquitous bacterium commonly used as a sentinel in antimicrobial resistance studies. Here, E. coli was isolated from three groups (sick calves, healthy calves and bedding material), to assess the presence of antimicrobial resistance, describe resistance profiles, and compare these resistances among groups. MATERIAL AND METHODS: Samples were collected from calves and calving pens from 20 dairy farms. Using the disc diffusion method, E. coli isolates were screened for antimicrobial resistance against seven antimicrobials: Amoxicillin, Ceftiofur, Gentamicin, Enrofloxacin, Trimethoprim-sulfamethoxazole, Florfenicol and Oxytetracycline. Isolates resistant to all these seven antimicrobials were tested again against an extended 19 antimicrobial drug panel and for the presence of the most common E. coli pathogenicity genes through PCR. RESULTS & DISCUSSION: Three hundred forty-nine E. coli isolates were obtained; most isolates were resistant to a single antimicrobial, but 2.3% (8) were resistant to 16 to 19 of the antimicrobials tested. The group with the highest percentage of multiresistant isolates was the calves with diarrhea group. Younger calves provided samples with higher antimicrobial resistance levels. CONCLUSIONS: There is a high rate of antimicrobial resistance in dairy farms calving pens. These bacteria could not only be a resistance gene reservoir, but also could have the potential to spread these determinants through horizontal gene transfer to other susceptible bacteria. Measures should be taken to protect colonization of younger calves, based on hygienic measures and proper management.

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RESUMEN Introducción: La miocardiopatía del cirrótico es la disfunción sistólica y/o diastólica del ventrículo izquierdo en reposo o estrés, en ausencia de otras condiciones cardiovasculares que lo explique, y que empeora el pronóstico post trasplante u otros procedimientos quirúrgicos hepáticos. Objetivo: El objetivo del estudio fue caracterizar la función auricular izquierda con speckle tracking en pacientes cirróticos. Material y métodos: Se incluyeron 99 pacientes consecutivos con cirrosis hepática de diferente etiología. A todos pacientes se les realizó estudio ecocardiográfico en reposo con medición de la función ventricular y auricular isquierda con técnicas tradicionales, mediciones tridimensionales y speckle tracking. Resultados: La mediana de edad fue de 50.9 años y 40% de los pacientes fueron hombres. No se observaron alteraciones de la función sistólica del ventrículo izquierdo. El 27% de los pacientes presentó disfunción diastólica y dilatación de la aurícula izquierda, está última con incremento significativo según el estadío Child y se observaron alteraciones de la función de bomba de la aurícula izquierda en el 29% de los casos. Conclusión: Los pacientes cirróticos presentan disfunción diastólica ventricular izquierda y alteraciones de la función sistólica de la aurícula izquierda medida por speckle tracking.

ABSTRACT Background: Cirrhotic cardiomyopathy is the systolic and/or diastolic dysfunction of the left ventricle at rest or stress, in the absence of other cardiovascular conditions, and worsens the prognosis after transplant or other liver surgical procedures. Objective: The aim of the study was to characterize left atrial function with speckle tracking in cirrhotic patients. Methods: Ninety-nine consecutive patients with liver cirrhosis of different etiology were included in the study. All patients underwent rest echocardiographic evaluation with measurement of left ventricular and atrial function using traditional techniques, three-dimensional measurements and speckle tracking. Results: Median age was 50.9 years and 40% were men. No alterations of left ventricular systolic function were observed. Twenty-seven percent of patients had diastolic dysfunction and dilatation of the left atrium, the latter with a significant increase according to the Child stage and left atrial pump function was altered in 29% of cases. Conclusion: Cirrhotic patients present left ventricular diastolic dysfunction and alterations of left atrial systolic function measured by speckle tracking.