Complexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs.

BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)'s 2013-2017 sample collection. METHODS: A total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10®Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using the pipelines developed collaboratively by the National Institute for Health Research Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance (AMR), and AGROSAVIA. RESULTS: Of the 425 CRKP isolates, 91.5% were carbapenemase-producing strains. The data support a recent expansion and the endemicity of CRKP in Colombia with the circulation of 7 high-risk clones, the most frequent being CG258 (48.39% of isolates). We identified genes encoding carbapenemases blaKPC-3, blaKPC-2, blaNDM-1, blaNDM-9, blaVIM-2, blaVIM-4, and blaVIM-24, and various mobile genetic elements (MGE). The virulence of CRKP isolates was low, but colibactin (clb3) was present in 25.2% of isolates, and a hypervirulent CRKP clone (CG380) was reported for the first time in Colombia. ST258, ST512, and ST4851 were characterized by low levels of diversity in the core genome (ANI > 99.9%). CONCLUSIONS: The study outlines complex CRKP epidemiology in Colombia. CG258 expanded clonally and carries specific carbapenemases in specific MGEs, while the other high-risk clones (CG147, CG307, and CG152) present a more diverse complement of carbapenemases. The specifics of the Colombian situation stress the importance of WGS-based surveillance to monitor evolutionary trends of sequence types (STs), MGE, and resistance and virulence genes.

Draft Genome Sequences of Corynebacterium diphtheriae Clinical Isolates from Colombia.

Since the implementation of the diphtheria-tetanus-pertussis (DTP) vaccine in Colombia, there has been a decrease in the reporting of cases. Here, we report two isolates of Corynebacterium diphtheriae bv. mitis isolated in the reference laboratory at Instituto Nacional de Salud from samples received from Norte de Santander and La Guajira; both areas are located on the northeast border of Colombia.

[National surveillance of clinical isolates of Enterococcus faecalis resistant to linezolid carrying the optrA gene in Colombia, 2014-2019]. / Vigilancia nacional de aislamientos clínicos de Enterococcus faecalis resistentes al linezolid portadores del gen optrA en Colombia, 2014-2019.

OBJECTIVE: To describe the epidemiological, phenotypical and genetic characteristics of clinical isolates carrying the optrA gene identified in antimicrobial resistance surveillance by the laboratory of the National Institute of Health of Colombia. METHODS: Between October 2014 and February 2019, 25 isolates of Enterococcus spp. resistant to linezolid were received. Antimicrobial identification and sensitivity were determined using Vitek 2 and the minimum inhibitory concentration (MIC) to linezolid was established with E-test. The optrA gene was detected by PCR, and the genetic diversity of optrA-positive isolates was tested with Diversilab®. Six isolates were selected to perform whole genome sequencing. RESULTS: The optrA gene was confirmed in 23/25 isolates of E. faecalis from seven departments in Colombia. The isolates presented a MIC to linezolid between 8 and >256µg/mL. Typing by Diversilab® showed a wide genetic variability. All the isolates analyzed by whole genome sequencing showed the resistance genes fexA, ermB, lsaA, tet(M), tet(L) and dfrG in addition to optrA and were negative for other mechanisms of resistance to linezolid. Three type sequences and three optrA variants were identified: ST16 (optrA-2), ST476 (optrA-5) and ST618 (optrA-6). The genetic environment of the optrA-2 (ST16) isolates presented the impB, fex, optrA segment, associated with plasmid, while in two isolates (optrA-6 and optrA-5) the transferable chromosomal element Tn6674-like was found. CONCLUSION: OptrA-positive clinical isolates present a high genetic diversity, with different optrA clones and variants related to two types of structures and different mobile genetic elements.

Concordancia entre las técnicas de IFD, PCR y ELISA para determinar la frecuencia de Bordetella parapertussis y Bordetella pertussis en un brote de tos ferina en el departamento de Antioquia (Colombia) en 2013 / Correlation among the DIF, PCR and ELISA techniques for determining the frequency of Bordetella parapertussis and Bordetella pertussis in an outbreak of whoopingcough in the department of Antioquia, Colombia, 2013

Objetivo: Obtener la concordancia de técnicas diagnósticas y confirmar el diagnóstico de los casos probables de tos ferina captados por inmunofluorescencia directa (IFD) durante un brote en 2013 en el departamento de Antioquia. Materiales y métodos: Se analizaron los datos demográficos, clínicos, epidemiológicos y de resultados de laboratorio de casos probables de tos ferina confirmados por IFD en un pico de tos ferina en 2013 en el departamento de Antioquia. Las muestras de aspirado nasofaríngeo y suero fueron recolectadas y recibidas entre los periodos epidemiológicos IV - VII de 2013. Todos los pacientes confirmados por IFD fueron confirmados por PCR o ELISA. El análisis de concordancia se realizó por índice kappa. Resultados: De las 180 muestras procesadas en el LSP de Antioquia, 134 (74%) fueron positivas por la técnica de IFD, de las cuales se confirmaron por PCR 109 muestras con 24 (22%) positivas para B. parapertussis , 3 (2,8%) para B. pertussis , 17 (15,6%) para Bordetella spp. y 18 (16,5%) con infección mixta por B. pertussis y B. parapertussis . De 81 casos que se confirmaron por ELISA, 31 (38,3%) fueron positivos. En el municipio de La Estrella la edad media de los casos confirmados fue de 6,6 años y la mediana de 3 años (rango: 2-4 años). Con respecto a los casos del municipio de Medellín, la edad media fue de 28,7 años y la mediana de 25 años (rango: 12-42 años). En su mayoría, en los síntomas no hubo diferencias significativas, excepto para la tos paroxística entre los casos confirmados de B. parapertussis y B. pertussis (p = <0,04) del municipio de La Estrella. De acuerdo con el índice kappa, los resultados mostraron una fuerza de concordancia pobre y sin grado de acuerdo con los resultados de las pruebas de PCR y ELISA comparados con IFD, índice kappa: (IFD/PCR: K = 0,0944) y (IFD/ELISA: K = - 0,4533). Conclusiones: Durante este análisis, en el 2013 la población de Antioquia fue afectada por la circulación de B. parapertussis y B. pertussis en población adolescente y adulta en Medellín y en la población de 2-4 años en La Estrella. Actualmente, la PCR y la ELISA son las técnicas adecuadas para el diagnóstico de tos ferina. La IFD por su subjetividad y baja concordancia se encuentra en desuso.

Objective: To determine the correlation between diagnostic techniques and to confirm the diagnosis of probable cases of whooping cough captured by direct immunofluorescence (DIF) during an outbreak in 2013 in the department of Antioquia. Materials and methods: We analysed the demographic, clinical, and epidemiological data and the laboratory results of probable cases of whooping cough confirmed by DIF at a peak of whooping cough in 2013 in the department of Antioquia. The nasopharyngeal aspirate and serum samples were collected and received between the epidemiological periods IV - VII of 2013. All patients confirmed by DIF were confirmed by polymerase chain reaction (PCR) and/or enzyme-linked immunosorbent assay (ELISA). The analysis of agreement was performed using the kappa index. Results: Of the 180 samples processed in the public health laboratory of Antioquia, 134 (74%) were positive using the DIF technique of which 109 samples were confirmed by PCR, with 24 (22%)samples positive for B. parapertussis , 3 (2.8%) for B. pertussis , 17 (15.6%) for Bordetella spp. and18 (16.5%) for mixed infection by B. pertussis and B. parapertussis . Of the 81 cases confirmed by ELISA, 31 (38.3%) were positive. In the municipality of La Estrella, the mean age of the confirmed cases was 6.6 years, and the median was 3 years (range, 2-4 years). For the municipality of Medellin, the mean age was 28.7 years, and the median was 25 years (range, 12-42 years). For most of the symptoms, there were no significant differences, except for paroxysmal cough among the confirmed cases of B. parapertussis and B. pertussis ( p = <.04) in the municipality of La Estrella. According to the kappa index, the results showed poor correlation strength and no agreement with the results of the PCR and ELISA tests compared with DIF, kappa index: (DIF/PCR: K = 0.0944) and (DIF/ELISA: K = - 0.4533). Conclusions: During this analysis in 2013, Antioquia was affected by the circulation of B. parapertussis and B. pertussis in the adolescent and adult population in Medellin and the 2-4 year-old population in La Estrella. Currently, PCR and ELISA are the recommended techniques for diagnosing whooping cough. Due to its subjectivity and low correlation, DIF is in disuse.