Search

Background: The genus Borrelia is composed of two well-defined monophyletic groups, the Borrelia burgdorferi sensu lato complex (Bb) and the relapsing fever (RF) group borreliae. Recently, a third group, associated with reptiles and echidnas, has been described. In general, RF group borreliae use rodents as reservoir hosts; although neotropical bats may also be involved as important hosts, with scarce knowledge regarding this association. The objective of this study was to detect the presence of Borrelia spp. DNA in bats from the department of Córdoba in northwest Colombia., Methods: During September 2020 and June 2021, 205 bats were captured in six municipalities of Córdoba department, Colombia. Specimens were identified using taxonomic keys and DNA was extracted from spleen samples. A Borrelia-specific real-time PCR was performed for the 16S rRNA gene. Fragments of the 16S rRNA and flaB genes were amplified in the positive samples by conventional PCR. The detected amplicons were sequenced by the Sanger method. Phylogenetic reconstruction was performed in IQ-TREE with maximum likelihood based on the substitution model TPM3+F+I+G4 with bootstrap values deduced from 1000 replicates., Results: Overall, 10.2% (21/205) of the samples were found positive by qPCR; of these, 81% (17/21) and 66.6% (14/21) amplified 16S rRNA and flaB genes, respectively. qPCR-positive samples were then subjected to conventional nested and semi-nested PCR to amplify 16S rRNA and flaB gene fragments. Nine positive samples for both genes were sequenced, and seven and six sequences were of good quality for the 16S rRNA and flaB genes, respectively. The DNA of Borrelia spp. was detected in the insectivorous and fruit bats Artibeus lituratus, Carollia perspicillata, Glossophaga soricina, Phyllostomus discolor, and Uroderma sp. The 16S rRNA gene sequences showed 97.66-98.47% identity with "Borrelia sp. clone Omi3," "Borrelia sp. RT1S," and Borrelia sp. 2374; the closest identities for the flaB gene were 94.02-98.04% with "Borrelia sp. Macaregua." For the 16S rRNA gene, the phylogenetic analysis showed a grouping with "Candidatus Borrelia ivorensis" and "Ca. Borrelia africana," and for the flaB gene showed a grouping with Borrelia sp. Macaregua and Borrelia sp. Potiretama. The pathogenic role of the Borrelia detected in this study is unknown., Conclusions: We describe the first molecular evidence of Borrelia spp. in the department of Córdoba, Colombia, highlighting that several bat species harbor Borrelia spirochetes., (© 2023. The Author(s).)

Hepatitis C virus (HCV) infection is one of the leading risk factors for end-stage liver disease development worldwide. This RNA virus displays high genetic diversity with 8 genotypes and 96 subgenotypes with heterogeneous geographical distribution around the world. In this study, we carried out an active case finding of individuals with a history of transfusion events before 1996 in three cities in Colombia. Then, the characterization of the HCV genotypes, subgenotypes, and resistance associate substitutions (RAS) was performed in samples positives for antibodies anti-HCV + from this study population. In addition, samples from PWID and patients with end-stage liver disease submitted to liver transplantation were included in the phylogenetic and RAS analysis. The 5'UTR, NS5A, and NS5B regions of the HCV genome were amplified in serum or liver explants samples. After the edition, assembly, and alignment of the sequences, genotyping through phylogenetic analysis was performed using IQTREE V2.0.5 based on the maximum likelihood approach. The identification of RAS was carried out by alignments based on the reference sequence (GenBank NC_004102). Two hundred sixty individuals with blood transfusion events before 1996 were recruited. The seroprevalence of antibodies anti-HCV was 2.69% in this population. The HCV genotypes 1, 2, and 4 and subgenotypes 1a, 1b, 2a, 4a and 4d were characterized in samples of the study populations. Three RAS (Q30R, C316N, and Y93H) were identified in samples obtained from 2 individuals who received blood transfusion before 1996 and without previous antiviral treatment and 6 samples obtained from patients with end-stage liver disease. Among the 20 samples analyzed, the HCV genotype 1, subgenotype 1b, was the most frequent (60%). We report the first characterization of HCV subgenotypes 4a and 4d and the first RAS identification in patients in Colombia., (Copyright © 2022. Published by Elsevier B.V.)

The aim of this article is to identify the determinants of the differences in the labor supply rates between the women with and without children in Colombia and its Caribbean Coasty. In order to achieve this, Probit models about the determinants of the labor supply rate for each group of women were estimated and the microeconometric decomposition method was applied to the binary models. The results suggest that in the Caribbean Coast of Colombia —as well as in the rest of the country— the main variables to explain such differences are: education, being single and wealth in a lesser degree. [ABSTRACT FROM AUTHOR]

Canine Circovirus (CanineCV) is an emerging virus which since its first report in USA in 2012, it has been described worldwide. It was the second mammalian circovirus species identified in dogs and its role in canine enteritis is still being uncertain as much as its association in disease with the Canine Parvovirus-2 (CPV-2). Here, we aim to confirm for the first time the presence of CanineCV in Colombia and to develop phylogenetic evolutive analyses of CanineCV in CPV-2 positive animals. DNA from samples were extracted and PCR, full genome sequencing and phylogenetic analysis was performed to detect and characterize CanineCV. From a total of 30 CPV-2 positive samples, 16.6% (n = 5) were positives for CanineCV. Sequencing analysis of Colombian CanineCV wild-type strains displayed high identity to each other (99.5-99.7% nt; 99.7% aa). The full genome phylogenetic analysis confirmed that worldwide reported CanineCV strains were separated into four distinct genotypes in addition to a European origin of the South American CanineCV strains. This study demonstrated the importance of continue surveillance of emerging viruses in canine populations and confirm for the first time the circulation and origin of CanineCV in Colombia.

Human mobility, both short and long term, are important considerations in the study of numerous systems. Economic and technological advances have led to a more interconnected global community, further increasing the need for considerations of human mobility. While data on human mobility are better recorded in many developed countries, availability of such data remains limited in many low- and middle-income countries around the world, particularly at the fine temporal and spatial scales required by many applications. In this study, we used 5-year census-based internal migration microdata for 32 departments in Colombia (i.e., Admin-1 level) to develop a novel spatial interaction modeling approach for estimating migration, at a finer spatial scale, among the 1,122 municipalities in the country (i.e., Admin-2 level). Our modeling approach addresses a significant lack of migration data at administrative unit levels finer than those at which migration data are typically recorded. Due to the widespread availability of census-based migration microdata at the Admin-1 level, our modeling approach opens up for the possibilities of modeling migration patterns at Admin-2 and Admin-3 levels across many other countries where such data are currently lacking., Competing Interests: The authors have declared that no competing interests exist.

Piaractus orinoquensis, a new species of serrasalmid fish, is described from the Orinoco River basin. The new species differs from congeners by having a slenderer body, relatively smaller head and snout, more compressed mid-body, fewer scales above and below the lateral line and diagnostic molecular characters in the coI mitochondrial gene region. We also provide a re-description of Piaractus brachypomus, restricting its geographic distribution to the Amazon River basin. Both species are economically important in their respective basins and need to be independently managed as distinct species., (© 2019 The Fisheries Society of the British Isles.)

The recent Zika virus outbreak has been spreading rapidly all over the world, expanding its traditionally geographical affected regions, making it a global public health hazard and endangering millions of people. One unique property of the Zika virus compared to most vector-borne diseases is the fact that the virus is transmitted both by mosquitoes and by direct sexual contact. In the present manuscript, we formulate and analyze five mathematical compartmental models of Zika transmission. We model both transmission routes (i.e., vector-borne and sexual transmission). In order to make the model more realistic, heterogeneity in the sexual transmission is modeled in several ways. We fitted the five different models to data, inferred the parameters and selected the most appropriated model, which describes the Zika outbreak in Columbia. For all the models, we estimate the reproduction numbers, namely direct (sexual) transmission, vector transmission and the basic reproduction number [Formula: see text]. The analysis revealed that the sexual transmission contribution to [Formula: see text] is highest [15.36% (95% CI 12.83-17.4)] for the model which stratifies each gender to high-risk and low-risk individuals in their sexual behavior. For this model, the estimated [Formula: see text] is 1.89 (95% CI 1.21-2.13), the direct transmission reproduction number is 0.42 (95% CI 0.29-0.64), and the vector transmission reproduction number is 1.51 (95% CI 1.23-1.87). The sensitivity analysis demonstrated that the value of [Formula: see text] depends on three controllable parameters: the biting rate, the sexual transmission rate and the average ratio of mosquito to human.

In this study, we present an iterative method for delimiting species under the general lineage concept (GLC) based on the multivariate clustering of morphological, ecological and genetic data. Our rationale is that distinct multivariate groups correspond to evolutionarily independent metapopulation lineages because they reflect the common signal of different secondary defining properties (environmental and genetic distinctiveness, phenotypic diagnosability, etc.) that imply the existence of barriers preventing or limiting gene exchange. We applied this method to study a group of endangered poison frogs, the Oophaga histrionica complex. In our study case, we used next-generation targeted amplicon sequencing to obtain a robust genetic data set that we combined with patterns of morphological and ecological features. Our analyses revealed the existence of at least five different species in the histrionica complex (three, new to science), some of them, occurring in small isolated populations outside any protected areas. The lineage delimitation proposed here has important conservation implications as it revealed that some of the Oophaga species should be considered among the most vulnerable of the Neotropical frogs. More broadly, our study exemplifies how multiple-amplicon and multivariate statistical techniques can be integrated to successfully identify species and their boundaries., (© 2018 John Wiley & Sons Ltd.)

Objective: To determine the diagnostic accuracy of Thwaites Index (TI) in a Colombian population to distinguish meningeal tuberculosis (MTB) from bacterial meningitis (BM) and from non-tuberculous meningitis. Exploratory analyses were conducted to assess the TI's validity for patients with human immunodeficiency virus (HIV) and children above six-years-old., Methods: The study included 527 patients, the TI was calculated and results compared with those of a reference standard established by expert neurologists. Sensitivity, specificity, area under the curve of receiver-operator characteristics (AUC-ROC) and likelihood ratios were calculated., Results: The AUC-ROC to distinguish MTB from non-tuberculous meningitis was 0.72 (95% CI: 0.67-0.77) for HIV negative adults. AUC-ROC was 0.62 (95% CI: 0.50-0.74) for HIV positive adults and 0.83 (95% CI: 0.68-0.97) for children. For distinguishing MTB from BM the AUC-ROC was 0.78 (95% CI: 0.73-0.83); furthermore, the AUC-ROC was 0.57 (95% CI: 0.31-0.83) for HIV positive adults and 0.86 (95% CI: 0.73-0.99) for children., Conclusion: The TI was sensitive but not specific when used to distinguish MTB from BM in HIV negative adults. In HIV positive adults the index had low diagnostic accuracy. Moreover, the TI showed discrimination capability for children over 6years; however, research with larger samples is required in these., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Dengue type 3 genotype V viruses have been recently detected in Brazil and Colombia. In this study, we described another Brazilian isolate belonging to this genotype. Phylogenetic analysis including dengue type 3 viruses isolated worldwide showed that Brazilian and Colombian viruses were closely related to viruses isolated in Asia more than two decades ago. The characteristic evolutionary pattern of dengue type 3 virus cannot explain the close similarity of new circulating viruses with old viruses. Further studies are needed to confirm the origin of the new dengue type III genotype circulating in Brazil and Colombia.

The Colombian jaguar population is thought to contain two different subspecies, Panthera onca centralis and Panthera onca onca. The genetic structure of this population was evaluated using 12 microsatellite loci (n = 62 samples). In addition, 22 jaguar DNA samples from Guatemala, Paraguay, Perú, Bolivia, Venezuela and Brazil were analyzed for these microsatellite loci (n = 84 samples). The results of this study indicate six primary themes. First, the levels of gene diversity were very high. Second, the majority of the loci analyzed showed an absence of Hardy-Weinberg equilibrium, probably due to the Wahlund effect (= population subdivision). Third, several microsatellite loci showed significant heterogeneity between the two supposed subspecies in the country. Nevertheless, gene flow was present between them, and heterogeneity was relatively low, although the assignment analyses showed good classification of the jaguars studied into their respective subspecies. Fourth, the long-term historical effective population sizes were calculated through a maximum likelihood procedure for single and multi-step mutation models. Fifth, seven out of twelve DNA microsatellites studied significantly deviated from a single-step mutation model. However, the overall mean multi-step mutation percentage for these 12 DNA microsatellites was only 6%. Therefore, 94% of mutations were uni-step. Sixth, no bottleneck events were detected in the Colombian jaguar population overall.

The 13C-urea breath test (UBT) is currently regarded as one of the most important noninvasive diagnostic methods for detecting Helicobacter pylori (H. pylori) infection in adults and children. However, for infants and young children, the standard for UBT interpretation has not been validated, and its reliability has not been established for diagnosing H. pylori infection in this group. The primary outcome data from UBT consist of mixture data, which come from subjects whose H. pylori infection classifications are unconfirmed. In this paper, we propose the finite mixture distribution method to identify a reliable UBT cut-off value in a large baseline sample in which gastric biopsy is not available to confirm the H. pylori infection in younger children. Maximum likelihood estimators of the parameters in the mixture model were obtained using an expectation maximization (EM) algorithm. The standard deviation of the cut-off point was estimated by bootstrap methods. We applied the same analytical methods to the UBT results yielded from the follow up, as well as the overall UBT results in the longitudinal cohort data. The cut-off points from those UBT data sets are similar. The advantage of the finite mixture model is that it may be used to calculate sensitivity and specificity in the absence of other diagnostic tests., (Copyright 2004 John Wiley & Sons, Ltd.)

Objectives: Estimate under "real life" conditions the operating characteristics of several stool tests for determining whether a diarrheal episode is invasive-inflammatory., Design: Determination of operating characteristics of diagnostic tests against a standard in a prospectively gathered sample., Setting: The emergency room of the largest Social Security Pediatric Hospital in Colombia serving referred and nonreferred patients., Patients: Stool samples from children attending the emergency room because of acute diarrhea (three or more loose stools per day lasting <7 days). Patients receiving antibiotics or antiparasitic medications were excluded., Interventions: Samples were collected in sterile containers and examined immediately for protozoa, fecal leukocytes, occult blood and lactoferrin. Specimens were inoculated onto culture media for common bacterial fecal pathogens except enteroinvasive Escherichia coli and Clostridium difficile., Main Outcome Measure: Sensitivity, specificity and likelihood ratios of several cutoff levels for fecal lactoferrin, fecal leukocytes and occult blood., Results: Stool samples from 500 infants and children with diarrhea were collected. Patients' median age was 2.66 years (range, 0.5 to 13 years), and 261 (52.2%) were males. In 155 (31%) cases enteroinvasive bacteria and/or Entamoeba histolytica were documented. Fecal leukocytes >5 had the best sensitivity (63.2%; 95% confidence interval, 55.4 to 70.5) and specificity (84.3%; 95% confidence interval, 80.2 to 87.9), although not statistically or clinically significantly different from lactoferrin., Conclusions: No single test or combination had satisfactory operating characteristics. Nevertheless the use of likelihood ratios derived here can help clinicians identify invasive-inflammatory diarrheal episodes in many instances.

Treponema denticola and Porphyromonas gingivalis have been associated with human adult severe periodontitis. In this study, we quantified these putative pathogens in subgingival plaque samples collected from 74 Fijians, 74 Colombians and 73 U.S. Americans stationed at the Multinational Force and Observers encampment in the Sinai Desert, Egypt. A contingency table of T. denticola and P. gingivalis frequency revealed a highly significant synergistic relationship. We discovered that the occurrence of T. denticola apparently requires the presence of P. gingivalis. This represents the first observation of a synergistic relationship between these putative oral pathogens associated with adult severe periodontal disease.