ABSTRACT
We report the draft genome of a clinical multi-resistant Klebsiella pneumoniae (24Kpn33) isolate, whose genome (5.7 Mbp) harbored 17 antibiotic resistance genes, including blaKPC-2. Notably, this gene was mobilized within the IncP-6 pCOL-1 plasmid, the first genetic platform related to the acquisition and dissemination of the blaKPC-2 in Pseudomonas aeruginosa.
ABSTRACT
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.
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Resistance to carbapenems in Klebsiella pneumoniae has been mostly related with the worldwide dissemination of KPC, largely due to the pandemic clones belonging to the complex clonal (CC) 258. To unravel blaKPC post-endemic clinical impact, here we describe clinical characteristics of 68 patients from a high complexity hospital, and the molecular and genetic characteristics of their 139 blaKPC-K. pneumoniae (KPC-Kp) isolates. Of the 26 patients that presented relapses or reinfections, 16 had changes in the resistance profiles of the isolates recovered from the recurrent episodes. In respect to the genetic diversity of KPC-Kp isolates, PFGE revealed 45 different clonal complexes (CC). MLST for 12 representative clones showed ST258 was present in the most frequent CC (23.0%), however, remaining 11 representative clones belonged to non-CC258 STs (77.0%). Interestingly, 16 patients presented within-patient genetic diversity of KPC-Kp clones. In one of these, three unrelated KPC-Kp clones (ST258, ST504, and ST846) and a blaKPC-K. variicola isolate (ST182) were identified. For this patient, complete genome sequence of one representative isolate of each clone was determined. In K. pneumoniae isolates blaKPC was mobilized by two Tn3-like unrelated platforms: Tn4401b (ST258) and Tn6454 (ST504 and ST846), a new NTEKPC-IIe transposon for first time characterized also determined in the K. variicola isolate of this study. Genome analysis showed these transposons were harbored in different unrelated but previously reported plasmids and in the chromosome of a K. pneumoniae (for Tn4401b). In conclusion, in the blaKPC post-endemic dissemination in Colombia, different KPC-Kp clones (mostly non-CC258) have emerged due to integration of the single blaKPC gene in new genetic platforms. This work also shows the intra-patient resistant and genetic diversity of KPC-Kp isolates. This circulation dynamic could impact the effectiveness of long-term treatments.
Subject(s)
Bacterial Proteins/genetics , Carbapenems/pharmacology , Drug Resistance, Bacterial , Klebsiella pneumoniae/genetics , Multilocus Sequence Typing/instrumentation , beta-Lactamases/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Colombia , Female , Genetic Variation , Genome, Bacterial , Genomics , Hospitalization , Hospitals , Humans , Klebsiella Infections , Male , Microbial Sensitivity Tests , Middle Aged , Retrospective Studies , Whole Genome Sequencing , Young AdultABSTRACT
ABSTRACT 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.
RESUMEN La producción y el comercio de cultivos es una de las actividades económicas más importantes para el país. Las enfermedades causadas por virus ocasionan graves pérdidas económicas en el sector, por lo tanto, la detección, diagnóstico y diseño de estrategias para su control y manejo es crucial. Las tecnologías de secuenciación masiva (NGS por sus siglas en ingles) y las ciencias Ómicas constituyen hoy, una herramienta para el descubrimiento de nuevos virus y para el estudio de la interacción entre los virus y su hospedero vegetal. Este conocimiento no solo permite el desarrollo de nuevos métodos de diagnóstico, sino también permite el descubrimiento de componentes claves en la infección, los cuales podrían usarse para obtener plantas resistentes a los virus. En el mundo, el manejo de cultivos se está trabajando con ese enfoque. Por lo tanto, en esta revisión se presentan las diferentes aplicaciones de las tecnologías ómicas en la virología de plantas y el avance que ha alcanzado Colombia. Adicionalmente, se muestran los diferentes recursos y programas usados para el análisis bioinformático de datos ómicos. Debido a su costo cada vez más reducido, las tecnologías NGS son una excelente oportunidad para explorar fitopatologías en una gran diversidad de productos agrícolas y para mejorar su potencial comercial.
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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.
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BACKGROUND: Pseudomonas aeruginosa Sequence Type 235 is a clone that possesses an extraordinary ability to acquire mobile genetic elements and has been associated with the spread of resistance genes, including genes that encode for carbapenemases. Here, we aim to characterize the genetic platforms involved in resistance dissemination in blaKPC-2-positive P. aeruginosa ST235 in Colombia. RESULTS: In a prospective surveillance study of infections in adult patients attended in five ICUs in five distant cities in Colombia, 58 isolates of P. aeruginosa were recovered, of which, 27 (46.6%) were resistant to carbapenems. The molecular analysis showed that 6 (22.2%) and 4 (14.8%) isolates harboured the blaVIM and blaKPC-2 genes, respectively. The four blaKPC-2-positive isolates showed a similar PFGE pulsotype and belonged to ST235. Complete genome sequencing of a representative ST235 isolate shows a unique chromosomal contig of 7097.241 bp with eight different resistance genes identified and five transposons: a Tn6162-like with ant(2â³)-Ia, two Tn402-like with ant(3â³)-Ia and blaOXA-2 and two Tn4401b with blaKPC-2. All transposons were inserted into the genomic islands. Interestingly, the two Tn4401b copies harbouring blaKPC-2 were adjacently inserted into a new genomic island (PAGI-17) with traces of a replicative transposition process. This double insertion was probably driven by several structural changes within the chromosomal region containing PAGI-17 in the ST235 background. CONCLUSION: This is the first report of a double Tn4401b chromosomal insertion in P. aeruginosa, just within a new genomic island (PAGI-17). This finding indicates once again the great genomic plasticity of this microorganism.
Subject(s)
Chromosomes, Bacterial , DNA Transposable Elements , Drug Resistance, Multiple, Bacterial/genetics , Genome, Bacterial , Genomic Islands , Pseudomonas aeruginosa/genetics , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/genetics , Bacterial Typing Techniques , Carbapenems/pharmacology , Colombia , DNA, Bacterial/genetics , Humans , Intensive Care Units/statistics & numerical data , Microbial Sensitivity Tests , Multilocus Sequence Typing , Prospective Studies , Pseudomonas aeruginosa/enzymology , Whole Genome Sequencing , beta-Lactamases/geneticsABSTRACT
Schizophrenia is a multifactorial disease with high genetic heterogeneity and complex inheritance. In Boyacá, Colombia, we studied a group of 20 schizophrenic patients (16 men and 4 women) to establish their sociodemographic and clinical characteristics as well as their genetic and precipitating factors. The patients were analyzed using cytogenetic studies and a descriptive analysis of qualitative and quantitative variables. The disease frequently first manifested in young adults (average age of initiation: 22.5 years). The predominant subtype (8/20) was paranoid schizophrenia, and the onset was typically gradual (14/20). Precipitating factors were found in 15 patients: physical factors in nine patients, social factors in five patients and economic factor in one patient. All karyotypes were normal. Clinical features did not associate with either the sociodemographic characteristics or the genetic and predisposing factors, supporting the clinical heterogeneity of schizophrenia. Patients and their families received genetic counseling and explanations of the study's results, the possibility of recurrences and the risk of suffering the disease given an affected relative. Further and larger studies are required to determine if the factors evaluated in this study influence the development of the disease.
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 sociodemográficas y clínicas y los factores genéticos y precipitantes. Se hicieron estudio citogenético y un análisis descriptivo de las variables cualitativas y cuantitativas. Hubo predominio del comienzo de la enfermedad en adultos 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.
Subject(s)
Humans , Schizophrenia , Multifactorial Inheritance , Genetic Background , Epidemiology, DescriptiveABSTRACT
Introducción: La esquizofrenia es un trastorno mental que afecta a la población mundial, con una prevalencia del 1% y con heredabilidad hasta del 80%. Se han postulado cuatro enfoques para identificar genes de susceptibilidad y establecer marcadores moleculares asociados con la enfermedad: estudios de ligamiento genético, convergencia genómica, asociación y anormalidades cromosómicas. Objetivo: Mostrar anormalidades cromosómicas reportadas en pacientes con esquizofrenia como parte de los factores genéticos hallados en esta patología. Método: Se hizo una selección estratégica de 68 artículos publicados desde 1954 hasta 2008 en bases de datos científicas, clasificando las alteraciones de tipo numérico, estructural y mosaicos, tomando en cuenta sus contribuciones al estudio y relevancia. Resultados: Los cromosomas principalmente involucrados fueron, en orden de mayor a menor frecuencia, 18, 9, 11, 1, X, 22 y 21. En cuanto al tipo de anormalidad se encontraron alteraciones estructurales, mosaicismos, numéricas y también polimorfismos. Las anormalidades estructurales principalmente fueron translocaciones recíprocas balanceadas. Conclusiones: Con esta revisión no solamente se logró un acercamiento hacia la estimación de la frecuencia de estos hallazgos, sino tener un referente del tipo y frecuencia de estas alteraciones para evaluar el factor genético de la esquizofrenia, encaminados a comprender su patogenia...
Introduction: Schizophrenia is a mental disorder that affects the world population with a prevalence of 1% and a hereditability of up to 80% . Four approaches have been postulated to identify susceptibility genes and to establish molecular markers associated with the disease: Genetic linkage studies, genomic convergence, association, and chromosomal abnormalities. Objective: To show chromosomal abnormalities reported in patients with schizophrenia as part of the genetic factors found in this condition. Methods: A strategic selection was made of 68 articles published from 1954 to 2008 in scientific databases, and numerical, structural and mosaical type alterations were classified, taking into account their contributions to the study and relevance. Results: The mainly involved chromosomes were, in order of frequency, 18, 9, 11, 1, X, 22 and 21. As to type of abnormalities, structural and numerical alterations were found, as well as mosaicims and polymorphisms. Conclusions: With this review not only the calculation of the frequency of these findings was made more possible, but it also provided a reference of the type and frequency of these alterations to evaluate the genetic factor of schizophrenia, aimed at understanding its pathogeny...
