Identification and “in silico” structural analysis of the glutamine-rich protein Qrp (YheA) in staphylococcus aureus

Background: YlbF and YmcA are two essential proteins for the formation of biofilm, sporulation, and competence in Bacillus subtilis. In these two proteins, a new protein domain called com_ylbF was recently discovered, but its role and protein function has not yet been established. Objective: In this study, we identified and performed an “in silico” structural analysis of the YheA protein, another com_ylbF-containing protein, in the opportunistic pathogen Staphylococcus aureus. Methods: The search of the yheA gene was performed using BLAST-P and tBLASn algorithms. The three-dimensional (3D) models of YheA, as well as YlbF and YmcA proteins, were built using the I-TASSER and Quark programs. The identification of the native YheA in Staphylococcus aureus was carried out through chromatography using the FPLC system. Results: We found that YheA protein is more widely distributed in Gram-positive bacteria than YlbF and YmcA. Two new and important characteristics for YheA and other com_ylbF-containing proteins were found: a highly conserved 3D structure and the presence of a putative conserved motif located in the central region of the domain, which could be involved in its function. Additionally, we established that Staphylococcus aureus expresses YheA protein in both planktonic growth and biofilm. Finally, we suggest renaming YheA as glutamine-rich protein (Qrp) in S. aureus. Conclusion: The Grp (YheA), YlbF, and YmcA proteins adopt a highly conserved three-dimensional structure, harboring a protein-specific putative motif within the com_ylbF domain, which possibly favors the interaction with their substrates. Finally, Staphylococcus aureus expresses the Grp (YheA) protein in both planktonic and biofilm growth

First report and comparative genomics analysis of a blaoxa-244-haarboring escherichia coli isolate recovered in the American continent

The carbapenemase OXA-244 is a derivate of OXA-48, and its detection is very difficult in laboratories. Here, we report the identification and genomic analysis of an Escherichia coli isolate (28Eco12) harboring the blaOXA-244 gene identified in Colombia, South America. The 28Eco12 isolate was identified during a retrospective study, and it was recovered from a patient treated in Colombia. The complete nucleotide sequence was established using the PacBio platform. A comparative genomics analysis with other blaOXA-244–harboring Escherichia coli strains was performed. The 28Eco12 isolate belonged to sequence type (ST) 38, and its genome was composed of two molecules, a chromosome of 5,343,367 bp and a plasmid of 92,027 bp, which belonged to the incompatibility group IncY and did not harbor resistance genes. The blaOXA-244 gene was chromosomally encoded and mobilized by an ISR1-related Tn6237 composite transposon. Notably, this transposon was inserted and located within a new genomic island. To our knowledge, this is the first report of a blaOXA-244–harboring Escherichia coli isolate in America. Our results suggest that the introduction of the OXA-244-producing E. coli isolate was through clonal expansion of the ST38 pandemic clone. Other isolates producing OXA-244 could be circulating silently in America

Determination in vitro protein participation in the activation hypothetical Sausa300_0063 operon ARC present in the mobile element for catabolism of arginine (ACME) in clone Usa300 pandemic

En las últimas dos décadas se ha reportado la emergencia y rápida diseminación del Staphylococcus aureus resistente a meticilina clon USA300 con una amplia distribución y patogenicidad, causando al ser humano infecciones no solo en el hospital sino en la comunidad. El elemento genético móvil para el catabolismo de la arginina (ACME) fue identificado exclusivamente en este clon y dentro de este elemento se encuentra un operón arc que tiene la misma función catabólica de ACME suministrando ATP en condiciones anaerobias y que en ambientes ácidos aumenta el pH del medio favoreciendo la capacidad para colonizar. Estudios previos en nuestro laboratorio mostraron que una sobreexpresión del operón arcACME en el clon USA300 es dada posiblemente por el gen sausa300_0063 inserto dentro de este operón que codifica para un regulador transcripcional. Determinar la participación de la proteína hipotética SAUSA300_0063 en la activación del operón arc presente en ACME en el clon pandémico USA300. Mediante el sistema de expresión pET303/CT-His en BL21 (DE3) se produjo la proteína recombinante SAUSA300_0063 del operón arcACME la cual se purificó mediante electroelución. Se determinó la unión in vitro de la proteína recombinante SAUSA300_0063 a la secuencia promotora del operón arcACME mediante ensayos de retardamiento en gel y por PCR en tiempo real se analizó la transcripción relativa de los genes sausa300_0063, arcCACME, arcCcons y arcR en condiciones de anaerobiosis en presencia o ausencia de arginina. La evidencia experimental mostró que la proteína SAUSA300_0063 establece su unión en el promotor del operón arcACME sugiriendo una aproximación acerca de su función como regulador transcripcional perteneciente a la familia de proteínas CRP/FNR. Adicionalmente se observó una relación directa en el aumento de la transcripción de los genes sausa300_0063 y arcC del operón arcACME indicando la posible participación de la proteína SAUSA300_0063 en la autoactivación del operón arcACME, dada a esta nueva estructura del operón facilitando su regulación. La proteína SAUSA300_0063 participa en la activación del operón arcACME a través de la unión a su región promotora y esta activación es mayor que la encontrada en el operón arc constitutivo. Estos resultados sugieren que el cambio estructural encontrado en el operón arcACME facilita la participación de la proteína SAUSA300_0063 en la auto-activación de este operón ya que dada a esta nueva estructura se podría regular en modo cis considerándose un sistema altamente ventajoso.Magíster en Ciencias Básicas BiomédicasMaestríaIn the last two decades has reported the emergence and rapid spread of methicillinresistant Staphylococcus aureus USA300 clone with a wide distribution and pathogenicity, causing human infections not only in the hospital but in the community. The mobile genetic element for catabolism of arginine (ACME) was identified only in this clone and inside this element is one arc operon having the same catabolic function ACME providing ATP under anaerobic conditions and in acidic environments increases pH medium favoring the ability to colonize. Previous studies in our laboratory showed that overexpression arcACME operon in clone USA300 is possibly given by the insert sausa300_0063 within this operon gene encoding a transcriptional regulator. Determine the participation SAUSA300_0063 hypothetical protein in the activation of arcACME operon in the USA300 clone pandemic. Using the system pET303 / CT-His expression in BL21 (DE3) recombinant protein produced SAUSA300_0063 arcACME operon which was purified by electroelution. In vitro binding of recombinant protein SAUSA300_0063 to the promoter sequence of the arcACME operon determined by assays retarding gel and real-time PCR the relative transcription sausa300_0063, arcCACME, arcCcons and arcR genes it was analyzed in anaerobiosis in presence or absence of arginine. Experimental evidence showed that establishes its binding protein SAUSA300_0063 in arcACME operon promoter suggesting an approach about its function as a transcriptional regulator belonging to the family of proteins CRP / FNR. Additionally a direct relationship in the increased transcription of sausa300_0063 genes and arcC operon arcACME indicating the possible participation SAUSA300_0063 protein self-activation arcACME operon given to this new structure operon facilitating regulation. SAUSA300_0063 protein participes in the activation arcACME operon across binding to its promoter region and this activation is greater than that found in the constituent arc operon. These results suggest that the structural change in the arcACME operon found facilitates participation SAUSA300_0063 self-protein in the activation of this operon and given to this new structure could be regulated in cis mode considered a highly advantageous system

Next generation sequencing and proteomics in plant virology: how is Colombia doing?

Crop production and trade are two of the most economically important activities in Colombia, and viral diseases cause a high negative impact to agricultural sector. Therefore, the detection, diagnosis, control, and management of viral diseases are crucial. Currently, Next-Generation Sequencing (NGS) and ‘Omic’ technologies constitute a right-hand tool for the discovery of novel viruses and for studying virus-plant interactions. This knowledge allows the development of new viral diagnostic methods and the discovery of key components of infectious processes, which could be used to generate plants resistant to viral infections. Globally, crop sciences are advancing in this direction. In this review, advancements in ‘omic’ technologies and their different applications in plant virology in Colombia are discussed. In addition, bioinformatics pipelines and resources for omics data analyses are presented. Due to their decreasing prices, NGS technologies are becoming an affordable and promising means to explore many phytopathologies affecting a wide variety of Colombian crops so as to improve their trade potential

Participation of the arcRACME protein in self-activation of the arc operon located in the arginine catabolism mobile element in pandemic clone USA300

Staphylococcus aureus pandemic clone USA300 has, in addition to its constitutive arginine catabolism (arc) gene cluster, an arginine catabolism mobile element (ACME) carrying another such cluster, which gives this clone advantages in colonisation and infection. Gene arcR, which encodes an oxygen-sensitive transcriptional regulator, is inside ACME and downstream of the constitutive arc gene cluster, and this situation may have an impact on its activation. Different relative expression behaviours are proven here for arcRACME and the arcACME operon compared to the constitutive ones. We also show that the artificially expressed recombinant ArcRACME protein binds to the promoter region of the arcACME operon; this mechanism can be related to a positive feedback model, which may be responsible for increased anaerobic survival of the USA300 clone during infection-related processes

Descriptive study of 20 patients with schizophrenia in Boyacá, Colombia Schizophrenia = Estudio descriptivo de una muestra de pacientes con esquizofrenia residentes en el departamento de Boyacá, Colombia Zayda Lorena Corredor Rozo1 , Mayely Paola Sánchez Espinosa1 , Milena Rondón Lagos2 , Paola Liliana Páez Rojas3 , Carolina Cortés Duque4 , Ruth Maribel Forero Castro5 RESUMEN

Schizophrenia is a multifactorial disease with high genetic heterogeneity and complex inheritance. In Boyacá, Colombia, we studied a group of 20 schizo- phrenic patients (16 men and four women) in order to establish their socio-demographic and clinical characteristics, and the genetic and predisposing factors. Cytogenetic studies and a descriptive anal- ysis of qualitative and quantitative variables were done. More often the disease started in young adults (average age of initiation: 22.5 years). The predomi- nant subtype (8/20) was paranoid schizophrenia, with progressive start (14/20). Predisposing factors were found in 15 patients, namely: physical in nine, social in five and economic in one. All cariotypes were normal. Clinical features did not associate with either the sociodemographic characteristics or the genetic and predisposing factors; this is evidence of the clinical heterogeneity of schizophrenia. Patients and their families received genetic counseling and explanations on the results, the possibility of recur- rences and the risk of suffering the disease when a relative is affected by it. Further and larger studies are required in order to determine if the factors eval- uated in this work have influence on the develop- ment of the disease

Descriptive study of 20 patients with schizophrenia in Boyacá, Colombia

La esquizofrenia, enfermedad multifactorial, tiene gran heterogeneidad genética y herencia compleja. En Boyacá, Colombia, se estudió un grupo de 20 pacientes esquizofrénicos (16 hombres y cuatro mujeres) y se establecieron las características sociodemográfica- cas y clínicas y los factores genéticos y precipitantes. Se hicieron estudio citogenética y un análisis descriptivo de las variables cualitativas y cuantitativas. Hubo predominio del comienzo de la enfermedad en adul-tos jóvenes (promedio de edad en el momento de la aparición: 22,5 años). Predominaron la esquizofrenia paranoide (8/20) con modo de aparición progresivo (14/20). Se hallaron factores precipitantes en 15 pacientes: físicos en nueve, sociales en cinco y económicos en uno. Todos los cariotipos fueron normales. Los rasgos clínicos no se asociaron con las características sociodemográficas ni con los factores genéticos y precipitantes, lo que evidencia gran heterogeneidad en las formas de manifestación de la enfermedad. Se dio asesoría genética a los pacientes y sus familias y se les explicaron los resultados, el riesgo de recurrencias y el de padecer la enfermedad cuando se tiene un pariente afectado. Es necesario analizar una serie mayor de casos, para poder determinar si los factores evaluados influyen en el desarrollo de la enfermedad

Worldwide Dissemination of <i>bla</i>_KPC Gene by Novel Mobilization Platforms in <i>Pseudomonas aeruginosa</i>: A Systematic Review

The dissemination of blaKPC-harboring Pseudomonas aeruginosa (KPC-Pa) is considered a serious public health problem. This study provides an overview of the epidemiology of these isolates to try to elucidate novel mobilization platforms that could contribute to their worldwide spread. A systematic review in PubMed and EMBASE was performed to find articles published up to June 2022. In addition, a search algorithm using NCBI databases was developed to identify sequences that contain possible mobilization platforms. After that, the sequences were filtered and pair-aligned to describe the blaKPC genetic environment. We found 691 KPC-Pa isolates belonging to 41 different sequence types and recovered from 14 countries. Although the blaKPC gene is still mobilized by the transposon Tn4401, the non-Tn4401 elements (NTEKPC) were the most frequent. Our analysis allowed us to identify 25 different NTEKPC, mainly belonging to the NTEKPC-I, and a new type (proposed as IVa) was also observed. This is the first systematic review that consolidates information about the behavior of the blaKPC acquisition in P. aeruginosa and the genetic platforms implied in its successful worldwide spread. Our results show high NTEKPC prevalence in P. aeruginosa and an accelerated dynamic of unrelated clones. All information collected in this review was used to build an interactive online map

First Report and Comparative Genomics Analysis of a blaOXA-244-Harboring Escherichia coli Isolate Recovered in the American Continent

The carbapenemase OXA-244 is a derivate of OXA-48, and its detection is very difficult in laboratories. Here, we report the identification and genomic analysis of an Escherichia coli isolate (28Eco12) harboring the blaOXA-244 gene identified in Colombia, South America. The 28Eco12 isolate was identified during a retrospective study, and it was recovered from a patient treated in Colombia. The complete nucleotide sequence was established using the PacBio platform. A comparative genomics analysis with other blaOXA-244&ndash;harboring Escherichia coli strains was performed. The 28Eco12 isolate belonged to sequence type (ST) 38, and its genome was composed of two molecules, a chromosome of 5,343,367 bp and a plasmid of 92,027 bp, which belonged to the incompatibility group IncY and did not harbor resistance genes. The blaOXA-244 gene was chromosomally encoded and mobilized by an ISR1-related Tn6237 composite transposon. Notably, this transposon was inserted and located within a new genomic island. To our knowledge, this is the first report of a blaOXA-244&ndash;harboring Escherichia coli isolate in America. Our results suggest that the introduction of the OXA-244-producing E. coli isolate was through clonal expansion of the ST38 pandemic clone. Other isolates producing OXA-244 could be circulating silently in America

Caracterización genética y molecular de Pseudomonas Aeruginosa causante de infecciones en UCI de tres ciudades de Colombia.

Pseudomonas aeruginosa, ubiquitous bacteria that can generate complicated infections in hospital patients, increasing morbidity and mortality rates due to increased antimicrobial resistance in clinical use, especially the last therapeutic option as carbapenems for the acquisition of resistance determinants through mainly mobile genetic elements.OBJECTIVE: To characterize the resistance profile and molecular characteristics of P. aeruginosa isolated from adult patients with a diagnosis of infection in three intensive care units in Colombia. METHODS: Patients with P. aeruginosa infections in adults were analyzed UCI. A bacterial isolates were determined profile of susceptibility to 12 antibiotics and resistance genes were amplified β-lactams, quinolones, sulfonamides and genetic platforms like integron class 1 and 2. The genetic relationship by PFGE and MLST. RESULTS: In the study 40 patients of which 23 (57.5%) analyzed belong to an ICU in the city of Pereira. The main sources of isolating microorganisms are 13 blood cultures (32.5%) and urine-11 (27.5%). Resistance profiles SAM-SAM-FOX and FOX-SXT occurred in 6 (15.0%) and 4 (10.0%) isolates respectively. The β-lactamases frequently were blaTEM type in 8 (20.0%), blaSHV seven (17.5%) and blaCTX-M 3 (7.5%), carbapenemases blaVIM blaKPC-2 and type 4 (9.7%) and 3 (7.5%). Isolates presented a polyclonal behavior pulsotypes 28. The KPC-producing isolates 2 and VIM are associated with the ST235 and ST111 respectively. CONCLUSION: those generated in ICUs participating entities infections are highly variable and moderate resistance to carbapenems associated with the presence of KPC-2 and VIM associated with the pandemic clone ST235 and ST111.Pseudomonas aeruginosa, bacteria ubicua que puede generar infecciones complicadas en pacientes hospitalarios, incrementando los índices de morbimortalidad debido al incremento de resistencia a los antimicrobianos de uso clínico, en especial los de última opción terapéutica como los carbapenémicos por la adquisición de determinantes de resistencia a través de elementos genéticos móviles principalmente. OBJETIVO: Caracterizar el perfil de resistencia y características moleculares de P. aeruginosa, aislada de pacientes adultos con diagnóstico de infección en tres unidades de cuidados intensivos en Colombia.MÉTODOS: Se analizaron pacientes con infecciones por P.aeruginosa en UCI adultos. A los aislamientos bacterianos se les determinó el perfil de susceptibilidad a 12 antibióticos y se amplificaron genes de resistencia a β-lactámicos, quinolonas, sulfonamidas y plataformas genéticas como integrón clase 1 y 2. La relación genética por medio de PFGE y MLST. RESULTADOS: En el estudio se analizaron 40 pacientes de los cuales 23(57,5%) pertenecen a una UCI en la ciudad de Pereira. Las principales fuentes de aislamiento de los microorganismos son hemocultivos 13(32,5%) y urocultivos 11(27,5%). Los perfiles de resistencia SAM-FOX y SAM-FOX-SXT se presentaron en 6(15,0%) y 4(10,0%) aislamientos respectivamente. Las β-lactamasas más frecuentes fueron de tipo blaTEM, en 8(20,0%), blaSHV 7(17.5%) y blaCTX-M 3(7.5%), carbapenemasas de tipo blaKPC-2 y blaVIM en 4(9.7%) y 3(7.5%). Los aislamientos presentan un comportamiento policlonal con 28 pulsotipos. Los aislamientos productores de KPC-2 y VIM se encuentran asociados al ST235 y ST111 respectivamente. CONCLUSIONES: las infecciones generadas en las UCI de las entidades participantes presentan gran variabilidad y con una moderada resistencia a carbapenémicos asociados a la presencia de KPC-2 y VIM asociados al clon pandémico ST235 y ST111