Isolation, genome analysis and tissue localization of Ceratobasidium theobromae, a new encounter pathogen of cassava in Southeast Asia.

In Southeast Asia (SEA) fastidious fungi of the Ceratobasidium genus are associated with proliferation of sprouts and vascular necrosis in cacao and cassava, crops that were introduced from the tropical Americas to this region. Here, we report the isolation and in vitro culture of a Ceratobasidium sp. isolated from cassava with symptoms of witches' broom disease (CWBD), a devastating disease of this crop in SEA. The genome characterization using a hybrid assembly strategy identifies the fungus as an isolate of the species C. theobromae, the causal agent of vascular streak dieback of cacao in SEA. Both fungi have a genome size > 31 Mb (G+C content 49%), share > 98% nucleotide identity of the Internal Transcribed Spacer (ITS) and > 94% in genes used for species-level identification. Using RNAscope® we traced the pathogen and confirmed its irregular distribution in the xylem and epidermis along the cassava stem, which explains the obtention of healthy planting material from symptom-free parts of a diseased plant. These results are essential for understanding the epidemiology of CWBD, as a basis for disease management including measures to prevent further spread and minimize the risk of introducing C. theobromae via long-distance movement of cassava materials to Africa and the Americas.

Cassava Witches' Broom Disease in Southeast Asia: A Review of Its Distribution and Associated Symptoms.

Cassava witches' broom disease (CWBD) is one of the main diseases of cassava in Southeast Asia (SEA). Affected cassava plants show reduced internodal length and proliferation of leaves (phyllody) in the middle and top part of the plant, which results in reduced root yields of 50% or more. It is thought to be caused by phytoplasma; however, despite its widespread distribution in SEA still little is known about CWBD pathology. The overarching goal of this study was to review and corroborate published information on CWBD biology and epidemiology considering recent field observations. We report the following: (1) CWBD symptoms are conserved and persistent in SEA and are distinct from what has been reported as witches' broom in Argentina and Brazil. (2) In comparison with cassava mosaic disease, another major disease of cassava in SEA, symptoms of CWBD develop later. (3) Phytoplasma detected in CWBD-affected plants belong to different ribosomal groups and there is no association study available indicating phytoplasma as the causing agent of CWBD. These findings are essential clues for designing surveillance and management strategies and for future studies to better understand the biology, tissue localization and spatial spread of CWBD in SEA and other potential risk areas.

Ceratobasidium sp. is associated with cassava witches' broom disease, a re-emerging threat to cassava cultivation in Southeast Asia.

Cassava witches' broom disease (CWBD) is a devastating disease of cassava in Southeast Asia (SEA), of unknown etiology. Affected plants show reduced internodal length, proliferation of leaves and weakening of stems. This results in poor germination of infected stem cuttings (i.e., planting material) and significant reductions in fresh root yields and starch content, causing economic losses for farmers and processors. Using a metagenomic approach, we identified a fungus belonging to the Ceratobasidium genus, sharing more than 98.3-99.7% nucleotide identity at the Internal Transcribed Spacer (ITS), with Ceratobasidium theobromae a pathogen causing similar symptoms in cacao. Microscopy analysis confirmed the identity of the fungus and specific designed PCR tests readily showed (1) Ceratobasidium sp. of cassava is strongly associated with CWBD symptoms, (2) the fungus is present in diseased samples collected since the first recorded CWBD outbreaks in SEA and (3) the fungus is transmissible by grafting. No phytoplasma sequences were detected in diseased plants. Current disease management efforts include adjustment of quarantine protocols and guarantee the production and distribution of Ceratobasidium-free planting material. Implications of related Ceratobasidium fungi, infecting cassava, and cacao in SEA and in other potential risk areas are discussed.

Complete Genome Sequence of the Plant Pathogen Ralstonia solanacearum Strain CIAT-078, Isolated in Colombia, Obtained Using Oxford Nanopore Technology.

Moko is one of the main diseases affecting banana and plantain in Colombia. Here, we report the genome sequence of the causal agent, the bacterium Ralstonia solanacearum (Smith) strain CIAT-078, collected in 2004 from affected plantains in central-west Colombia. The assembled genome was obtained using Oxford Nanopore Technology.

High frequency of toxigenic Clostridium difficile and Clostridium perfringens coinfection among diarrheic patients at health care facility-onset (HCFO) and community-onset (CO) centers in Bogotá, Colombia.

BACKGROUND: The aim of this study was to evaluate the frequency of toxigenic C. difficile and C. perfringens infections at health care facility-onset (HCFO) and community-onset (CO), in two health care centers (HCC) in Bogotá, Colombia. A total of 220 stool samples from patients presenting diarrhea acquired at HCFO or CO were analyzed by several PCR tests. RESULTS: We found that 65.5% (n = 144) of the population had C. difficile infection, followed by toxigenic C. difficile with 57.3% (n = 126), and finally toxigenic C. perfringens with a frequency of 32.7% (n = 72). CONCLUSIONS: This study is the first molecular detection and characterization of C. difficile and C. perfringens in HCFO and CO in Latin America and demonstrates a relevant frequency of these two species, including coinfection and strikingly diverse toxigenic profiles, especially in the CO.

Genotyping Klebsiella pneumoniae isolated from hepatic abscesses in three patients from Bogota, Colombia / Genotipificación de Klebsiella pneumoniae aislada de abscesos hepáticos de pacientes de Bogotá, Colombia / Genotipificação de Klebsiella pneumoniae isolada de abscessos hepáticos de pacientes de Bogotá, Colômbia

Pyogenic liver abscess caused by Klebsiella pneumoniae represents an ever increasing entity which has mainly been described as occurring in Asia, even though, on a smaller scale, cases are being more frequently described from the USA and Europe, 13% overall mortality being reached worldwide. Affected patients are severely sick, suffering from fever, sweating, having increased acute phase reactants and risk factors such as Diabetes Mellitus, alcoholism and the inherent characteristics of the bacteria causing the disease. Objective: in this work we used a Multilocus Sequencing Typing (MLST), a nucleotide sequence-based method in order to characterize the genetic relationships among bacterial isolates. Materials and methods: the report is focused on three cases involving patients suffering from pyogenic liver abscess caused by Klebsiella pneumoniae in two hospitals in Bogota, Colombia, where phenotyping and hypermucoviscosity studies were carried out, as well as the genotyping of cultured Klebsiella isolates. Results: it was found that the isolated microorganism in cases I and II corresponded to the same K. pneumoniae strain, having 100% sequence identity for the 5 genes being studied while the strain in Case III was genotypically different. Conclusion: it is important to carry out multidisciplinary studies allowing all pyogenic liver abscess cases reported in Colombia to be complied to ascertain the frequency of microorganisms causing this pathology in our country, as well as a genotyping study of different K. pneumoniae strains to compare them and confirm clonal and pathogenicity relationships through housekeeping gene analysis.

El absceso hepático piógeno causado por Klebsiella pneumoniae representa una entidad descrita con frecuencia en los países asiáticos y, en menor escala, también en Estados Unidos y Europa. En el ámbito mundial su mortalidad alcanza a un 13%. Los pacientes pueden presentar un compromiso severo, el cual cursa con fiebre, sudoración y aumento de reactantes de fase aguda, sobre todo en individuos con factores de riesgo como la diabetes mellitus y el alcoholismo, además de las características inherentes de la bacteria responsable de la infección. Objetivo: a continuación se presentan tres casos de pacientes con absceso hepático piógeno causado por Klebsiella pneumoniae en dos hospitales de Bogotá. Materiales y métodos: se realizó caracterización molecular de los aislados de Klebsiella mediante la técnica de Multilocus Secquence Typing (MLST), análisis fenotípicos y de hipermucoviscosidad. Resultado: se encontró que el microorganismo aislado en los casos I y II corresponde a la misma cepa de K. pneumoniae, que tiene 100% de identidad de secuencia de los 5 genes en estudio mientras que la cepa en Case III fue genotípicamente diferente. Conclusión: es importante llevar a cabo estudios multidisciplinarios que incluyan todos los casos de abscesos hepáticos piógenos reportados en Colombia con el objeto de determinar la frecuencia de los microorganismos causantes de esta patología en nuestro país, así como un estudio de genotipificación de diferentes cepas de K. pneumoniae para confirmar las relaciones clonales y de patogenicidad.

O abscesso hepático piogênico causado por Klebsiella pneumoniae representa uma entidade descrita com frequência nos países asiáticos e, em menor escala, também nos Estados Unidos e na Europa. No âmbito mundial sua mortalidade alcança um 13%. Os pacientes podem apresentar um compromisso severo, o qual cursa com febre, sudoração e aumento de reagentes de fase aguda, especialmente em indivíduos com fatores de risco como a diabetes mellitus e o alcoolismo, além das características inerentes da bactéria responsável da infecção. Objetivo: a continuação apresentamse três casos de pacientes com abscesso hepático piogênico causado por Klebsiella pneumoniae em dois hospitais de Bogotá; Materiais e métodos: realizou-se caracterização molecular dos isolados de Klebsiella mediante a técnica de Multilocus Secquence Typing (MLST), análises fenotípicas e de hipermucoviscosidade. Resultado: encontrou-se que o micro-organismo isolado nos casos I e II corresponde à mesma cepa de K. pneumoniae, que tem 100% de identidade de sequencia dos 5 genes em estudo enquanto a cepa no caso III foi genotipicamente diferente. Conclusão: é importante levar a cabo estudos multidisciplinares que incluam todos os casos de abscessos hepáticos piogênicos reportados na Colômbia com o objeto de determinar a frequência dos micro-organismos causadores desta patologia em nosso país, assim como um estudo de genotipificação de diferentes cepas de K. pneumoniae para confirmar as relações clonais e de patogenicidade.