Publications by authors named "Jaime Robledo"

39 Publications

: A Review of Recent Developments in an Emerging Pathogen.

Front Cell Infect Microbiol 2021 26;11:659997. Epub 2021 Apr 26.

Laboratory of Bacteriology and Mycobacteria, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia.

(MABC is one of the most clinically relevant species among nontuberculous mycobacteria. MABC's prevalence has increased over the last two decades. Although these changes can be explained by improvements in microbiological and molecular techniques for identifying species and subspecies, a higher prevalence of chronic lung diseases may contribute to higher rates of MABC. High rates of antimicrobial resistance are seen in MABC, and patients experience multiple relapses with low cure rates. This review aims to integrate existing knowledge about MABC epidemiology, microbiological identification and familiarize readers with molecular mechanisms of resistance and therapeutic options for pulmonary infections with MABC.
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http://dx.doi.org/10.3389/fcimb.2021.659997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8108695PMC
July 2021

Adverse treatment outcomes in multidrug resistant tuberculosis go beyond the microbe-drug interaction: Results of a multiple correspondence analysis.

Biomedica 2020 12 2;40(4):616-625. Epub 2020 Dec 2.

Unidades de Bacteriología y Micobacterias y Micología Médica y Experimental, Corporación para Investigaciones Biológicas, Medellín, Colombia; Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana, Medellín, Colombia.

Introduction: Multidrug-resistant tuberculosis treatment is effective in 50% of patients due to several factors including antibiotic susceptibility of the microorganism, adverse treatment reactions, social factors, and associated comorbidities.

Objectives: In this study, we describe the demographics, clinical characteristics, and factors associated with treatment outcomes in multidrug-resistant tuberculosis (MDR-TB) patients in Medellín, Colombia.

Materials And Methods: We conducted a retrospective analysis using data from patients diagnosed with MDR-TB attending Hospital La María in Medellín, Colombia, for treatment between 2010 and 2015. Patients were categorized as having successful (cured) or poor (failure, lost to follow-up, and death) treatment outcomes. Associations between demographic, clinical factors, laboratory results, treatment outcomes, and follow-up information were evaluated by univariate, multivariate, and multiple correspondence analyses.

Results: Of the 128 patients with MDR-TB, 77 (60%) had successful outcomes. Of those with poor outcomes, 26 were lost to follow-up, 15 died, and 10 were treatment failures. Irregular treatment, the presence of comorbidities, and positive cultures after more than two months of treatment were associated with poor outcomes compared to successful ones (p<0.05 for all). The multiple correspondence analyses grouped patients who were lost to follow-up, had HIV, and drug addiction, as well as patients with treatment failure, irregular treatment, and chronic obstructive pulmonary disease.

Conclusion: The recognition of factors affecting treatment is essential and was associated with treatment outcomes in this series of patients. Early identification of these factors should increase the rates of treatment success and contribute to MDR-TB control.
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http://dx.doi.org/10.7705/biomedica.5072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7808767PMC
December 2020

Characterization of Mycobacterium tuberculosis var. africanum isolated from a patient with pulmonary tuberculosis in Brazil.

Infect Genet Evol 2020 11 11;85:104550. Epub 2020 Sep 11.

Laboratório de Biologia Molecular Aplicada em Micobacterias, Instituto Oswaldo Cruz, Fiocruz. Av. Brasil 4365, Manguinhos, 21040-360 Rio de Janeiro, RJ, Brazil. Electronic address:

Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC), including Mycobacterium tuberculosis var. tuberculosis (MTB) and Mycobacterium tuberculosis var. africanum (MAF). While MTB is isolated worldwide, MAF is almost completely restricted to the African continent, and despite the historical proximity between Brazil and Africa during the slave trade, no case of TB being caused by MAF has been reported in Brazil to date. We hereby describe the first case of TB caused by MAF in Brazil comparing its genome against the published ones. A female patient who had never visited Africa presented with clinical symptoms typical of pulmonary TB. Based on 16S rRNA gene sequencing, the cultured isolate was identified as belonging to MTBC and partial sequence of the hsp65 gene was identical to that of MAF. This was confirmed by genotyping based on detection of Single Nucleotide Polymorphism (SNP), Region of Difference (RD) and spoligotyping. The isolate presented the Shared International Typing (SIT) 181. In the whole-genome comparison against MAF genomes available on published EMBL-EBI European Nucleotide Archive (ENA), the Brazilian genome (MAFBRA00707) was identified as belonging to Lineage 6 and clustered with isolates from The Gambia. This is the first report of the isolation of MAF from a patient from Brazil, without evidence of having any contact with an African index case.
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http://dx.doi.org/10.1016/j.meegid.2020.104550DOI Listing
November 2020

Risk of infection and disease progression in children exposed to tuberculosis at home, Colombia.

Colomb Med (Cali) 2019 Dec 30;50(4):261-274. Epub 2019 Dec 30.

Universidad de Antioquia, Grupo de Epidemiología, Medellín, Colombia.

Aim: To assess the risk of tuberculosis (infection and disease) in children less than 15 years' old who are household contacts of pulmonary tuberculosis patients in three Colombian cities (Medellín, Cali, and Popayán).

Methods: A cohort of 1,040 children household contacts of 380 adults with smear-positive pulmonary tuberculosis was followed up for 24 months. Study period 2005-2009.

Results: Tuberculin skin test was positive (≥10 mm) in 43.7% (95% CI: 39.2-48.2). Tuberculin skin test positivity was associated with age 10-14 years (Prevalence Ratio -PR= 1.43, 95% CI: 1.1-1.9), having a BCG vaccine scar (PR= 1.52, 95% CI: 1.1-2.1), underweight, closer proximity to the index case and exposure time >3 months. The annual risk of infection (tuberculin skin test induration increase of 6 mm or more per year) was 17% (95% CI: 11.8-22.2) and was associated with a bacillary load of the adult index case (Relative Risk -RR= 2.12, 95% CI: 1.0-4.3). The incidence rate of active tuberculosis was 12.4 cases per 1,000 persons-year. Children <5 years without BCG vaccine scar had a greater risk of developing active disease (Hazard Ratio -HR= 6.00, 95% CI: 1.3-28.3) than those with scar (HR= 1.33, 95% CI: 0.5-3.4). The risk of developing active tuberculosis augmented along with the increase from initial tuberculin skin test (tuberculin skin test 5-9 mm HR= 8.55, 95% CI: 2.5-29.2; tuberculin skin test ≥10 mm HR= 8.16, 95% CI: 2.0-32.9).

Conclusions: There is a need for prompt interruption of adult-to-children tuberculosis transmission within households. Conducting proper contact investigation and offering chemoprophylaxis to infected children could reduce tuberculosis transmission.
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http://dx.doi.org/10.25100/cm.v50i4.4185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7232949PMC
December 2019

Detection and Quantification of HspX Antigen in Sputum Samples Using Plasmonic Biosensing: Toward a Real Point-of-Care (POC) for Tuberculosis Diagnosis.

ACS Infect Dis 2020 05 14;6(5):1110-1120. Epub 2020 Apr 14.

Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER-BBN and BIST, Campus UAB, 08193 Barcelona, Spain.

Advancements that occurred during the last years in the diagnosis of (), the causative agent of tuberculosis infection, have prompted increased survival rates of patients. However, limitations related to the inefficiency of an early detection still remain; some techniques and laboratory methods do not have enough specificity and most instruments are expensive and require handling by trained staff. In order to contribute to a prompt and effective diagnosis of tuberculosis, we report the development of a portable, user-friendly, and low-cost biosensor device for its early detection. By using a label-free surface plasmon resonance (SPR) biosensor, we have established a direct immunoassay for the direct detection and quantification of the heat shock protein X (HspX) of , a well-established biomarker of this pathogen, directly in pretreated sputum samples. The method relies on highly specific monoclonal antibodies that are previously immobilized on the plasmonic sensor surface. This technology allows for the direct detection of the biomarker without amplification steps, showing a limit of detection (LOD) of 0.63 ng mL and a limit of quantification (LOQ) of 2.12 ng mL. The direct analysis in pretreated sputum shows significant differences in the HspX concentration in patients with tuberculosis (with concentration levels in the order of 116-175 ng mL) compared with non-tuberculosis infected patients (values below the LOQ of the assay).
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http://dx.doi.org/10.1021/acsinfecdis.9b00502DOI Listing
May 2020

[Control de la tuberculosis multirresistente a fármacos: un objetivo posible].

Authors:
Jaime Robledo

Biomedica 2019 Sep 1;39(3):431-433. Epub 2019 Sep 1.

Unidad de Bacteriología y Micobacterias, Corporación para Investigaciones Biológicas, Medellín, Colombia; Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana, Medellín, Colombia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357360PMC
September 2019

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.

Nat Genet 2018 02 22;50(2):307-316. Epub 2018 Jan 22.

National Mycobacterium Reference Laboratory, Porto, Portugal.

To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.
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http://dx.doi.org/10.1038/s41588-017-0029-0DOI Listing
February 2018

Comparative study of Candida spp. isolates: Identification and echinocandin susceptibility in isolates obtained from blood cultures in 15 hospitals in Medellín, Colombia.

J Glob Antimicrob Resist 2018 06 26;13:254-260. Epub 2017 Nov 26.

Corporación para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia; Laboratorio Médico de Referencia, Calle 63 No. 41-27, Medellín, Colombia; School of Health Sciences, Universidad Pontificia Bolivariana (UPB), Calle 78b No. 72a-109, Medellín, Colombia.

Objectives: Invasive candidiasis has a high impact on morbidity and mortality in hospitalised patients. Accurate and timely methods for identification of Candida spp. and determination of echinocandin susceptibility have become a priority for clinical microbiology laboratories.

Methods: This study was performed to compare matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS) identification with sequencing of the D1/D2 region of the rRNA gene complex 28 subunit in 147 Candida spp. isolates obtained from patients with candidaemia. Antimicrobial susceptibility testing was performed by broth microdilution (BMD) and Etest. Sequencing of the FKS1 and FKS2 genes was performed.

Results: The most common species isolated were Candida albicans (40.8%), followed by Candida parapsilosis (23.1%) and Candida tropicalis (17.0%). Overall agreement between the results of identification by MALDI-TOF/MS and molecular identification was 99.3%. Anidulafungin and caspofungin susceptibility by the BMD method was 98.0% and 88.4%, respectively. Susceptibility to anidulafungin and caspofungin by Etest was 93.9% and 98.6%, respectively. Categorical agreement between Etest and BMD was 91.8% for anidulafungin and 89.8% for caspofungin, with lower agreements in C. parapsilosis for anidulafungin (76.5%) and C. glabrata for caspofungin (40.0%). No mutations related to resistance were found in the FKS genes, although 54 isolates presented synonymous polymorphisms in the hotspots sequenced.

Conclusions: MALDI-TOF/MS is a good alternative for routine identification of Candida spp. isolates. DNA sequencing of the FKS genes suggested that the isolates analysed were susceptible to echinocandins; alternatively, unknown resistance mechanisms or limitations related to antifungal susceptibility tests may explain the resistance found in a few isolates.
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http://dx.doi.org/10.1016/j.jgar.2017.11.010DOI Listing
June 2018

[Diagnostic accuracy of three technologies for the diagnosis of multi-drug resistant tuberculosis].

Biomedica 2017 Sep 1;37(3):397-407. Epub 2017 Sep 1.

Grupo de Investigación en Economía de la Salud, Universidad de Cartagena, Cartagena, Colombia Observatorio Nacional de Salud, Instituto Nacional de Salud, Bogotá, D.C., Colombia.

Introduction: Multi-drug resistant (MDR-TB) and extensively drug-resistant (XDR-TB) tuberculoses are a global public health problem. Their timely detection might reduce the burden of the disease and the economic impact on health systems worldwide.

Objective: To conduct a literature review of the diagnostic accuracy of three molecular tests to detect multi-drug resistant and extensively drug-resistant tuberculoses.

Materials And Methods: A systematic literature review following Cochrane methodology was carried out to study the diagnostic accuracy of three molecular tests to detect MDR-TB and XDR-TB in previous studies among immunocompetent population. Articles indexed in Medline and Embase were reviewed starting in 2007. Diagnostic accuracy was reported by sensitivity, specificity, and positive and negative predictive values of each test.

Results: In total, 8, 12 and 13 studies were included to assess the diagnostic accuracy of GeneXpert MTB/RIF®, GenoType MTBDRplus® and GenoType MTBDRsl®, respectively. The specificity of GeneXpert MTB/RIF® ranged between 91 and 100%, and its sensitivity between 33.3 and 100%. The sensitivity of GenoType® MTBDRplus® ranged between 88 and 100%. The sensitivity and specificity of GenoType MTBDRsl® to evaluate drug resistance ranged between 56 and 100% and 21 and 100%, respectively.

Conclusion: The three diagnostic tests evaluated have shown an adequate diagnostic accuracy to detect MDR and XDR tuberculoses.
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http://dx.doi.org/10.7705/biomedica.v37i3.3437DOI Listing
September 2017

Some Synonymous and Nonsynonymous Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDR Assays.

Antimicrob Agents Chemother 2017 04 24;61(4). Epub 2017 Mar 24.

Department of Medicine, University of Cambridge, Cambridge, United Kingdom

In this study, using the Hain GenoType MTBDR assays (versions 1 and 2), we found that some nonsynonymous and synonymous mutations in in result in systematic false-resistance results to fluoroquinolones by preventing the binding of wild-type probes. Moreover, such mutations can prevent the binding of mutant probes designed for the identification of specific resistance mutations. Although these mutations are likely rare globally, they occur in approximately 7% of multidrug-resistant tuberculosis strains in some settings.
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http://dx.doi.org/10.1128/AAC.02169-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5365657PMC
April 2017

Tuberculous Lymphadenitis and Parotitis.

Microbiol Spectr 2016 12;4(6)

Section of Mycobacteria Research, Corporación para Investigaciones Biológicas and Universidad Pontificia Bolivariana, Medellín, Colombia.

Tuberculous lymphadenitis is the most common extrapulmonary manifestation of disseminated tuberculosis (TB). It is considered to be the local manifestation of the systemic disease that has disseminated to local lymph nodes, but a high index of suspicion is needed for the diagnosis, because there are several infectious and noninfectious diseases that can mimic the same clinical picture. In recent years, different diagnostic methods have been introduced, including fine-needle aspiration cytology, which has emerged as a simple outpatient diagnostic procedure that replaced the complete excisional node biopsy, and a number of molecular methods which have greatly improved diagnostic accuracy. This chapter covers the most actual knowledge in terms of epidemiology, clinical manifestations, pathogenesis, and treatment and emphasizes current trends in diagnosis of tuberculous lymphadenitis. TB parotid gland involvement is extremely rare, even in countries in which TB is endemic. Because of the clinical similarity, parotid malignancy and other forms of parotid inflammatory disease always take priority over the rarely encountered TB parotitis when it comes to differential diagnosis. As a result, clinicians often fail to make a timely diagnosis of TB parotitis when facing a patient with a slowly growing parotid lump. This chapter highlights the most important features of this uncommon disease.
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http://dx.doi.org/10.1128/microbiolspec.TNMI7-0008-2016DOI Listing
December 2016

[GenoType MTBDR plus 1.0® for the detection of cross-resistance between isoniazide and ethionamide in isolates of multidrug-resistant Mycobacterium tuberculosis].

Biomedica 2015 Oct-Dec;35(4):541-8

Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana.

Introduction: A variable proportion of isolates of multidrug-resistant Mycobacterium tuberculosis also presents resistance to ethionamide. It is important to determine whether resistance to isoniazid is independent or crossed with resistance to ethionamide, given that this could lead to the re-evaluation of second-line anti-tuberculosis treatment. The GenoType MTBDR plus ® molecular test is used for the detection of MDR-MTB, as it identifies mutations associated with resistance to isoniazide and could detect cross-resistance with ethionamide.

Objective: To evaluate the performance of GenoType MTBDR plus ® in comparison with sequencing in the detection of mutations in gene katG and promotor inhA in clinical isolates of multidrug-resistant M. tuberculosis .

Materials And Methods: The GenoType MTBDR plus 1.0® commercial kit and sequencing were used to evaluate mutations in gene katG and promotor inhA in 30 multidrug-resistant M. tuberculosis isolates that were resistant to ethionamide. The laboratory strain H37Rv and three pan-sensitive isolates acted as controls.

Results: The kappa index for the comparison between the results of sequencing and GenoType MTBDR plus® was 1. All the isolates resistant to isoniazid and ethionamide had the mutations detected by GenoTypeMTBDR plus® in the katG gene and 40% of them in promotor inhA. Sequencing also revealed katG mutations in positions different to those detected by GenoType MTBDR plus®.

Conclusion: GenoType MTBDR plus ® is able to detect resistance to isoniazid rapidly. Our results suggest that it could also be used to screen for cross-resistance with ethionamide.
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http://dx.doi.org/10.7705/biomedica.v35i4.2813DOI Listing
December 2016

Ertapenem resistance in 2 tertiary-care hospitals: Microbiology, epidemiology, and risk factors.

Enferm Infecc Microbiol Clin 2017 Oct 6;35(8):511-515. Epub 2016 Jan 6.

Laboratorio Médico de Referencia, Medellín, Colombia; Clínica El Rosario, Medellín, Colombia; Unidad de Bacteriología y Micobacterias, Corporación para Investigaciones Biológicas (CIB), Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana, Medellín, Colombia.

Introduction: Carbapenems resistance is a growing phenomenon and a threat to public health because of the reduced therapeutic options for resistant infections.

Methods: A retrospective case-control study was conducted in 2 tertiary-care hospitals in Medellín, Colombia. Fifty patients infected with ertapenem-resistant enterobacteriaceae were compared with a control group consisting of 100 patients with infections caused by ertapenem susceptible enterobacteriaceae. A multivariate logistic regression model was used to identify factors that best explain ertapenem-resistant enterobacteriaceae infections.

Results: The factors associated with ertapenem-resistant enterobacteriaceae infections were prior exposure to carbapenems (adjusted OR 3.43; 95% IC 1.08-10.87) and prior exposure to cefepime (adjusted OR 6.46; 95% IC 1.08-38.38).

Conclusion: Prior exposure to antibiotics is the factor that best explains the ertapenem-resistant enterobacteriaceae infection in this population, highlighting the importance of antimicrobial stewardship programs in hospitals.
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http://dx.doi.org/10.1016/j.eimc.2015.11.009DOI Listing
October 2017

Genotypic Analysis of Genes Associated with Independent Resistance and Cross-Resistance to Isoniazid and Ethionamide in Mycobacterium tuberculosis Clinical Isolates.

Antimicrob Agents Chemother 2015 Dec 14;59(12):7805-10. Epub 2015 Sep 14.

Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana (UPB), Medellín, Colombia Unidad de Bacteriología y Micobacterias, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia.

Ethionamide (ETH) is an antibiotic used for the treatment of multidrug-resistant (MDR) tuberculosis (TB) (MDR-TB), and its use may be limited with the emergence of resistance in the Mycobacterium tuberculosis population. ETH resistance in M. tuberculosis is phenomenon independent or cross related when accompanied with isoniazid (INH) resistance. In most cases, resistance to INH and ETH is explained by mutations in the inhA promoter and in the following genes: katG, ethA, ethR, mshA, ndh, and inhA. We sequenced the above genes in 64 M. tuberculosis isolates (n = 57 ETH-resistant MDR-TB isolates; n = 3 ETH-susceptible MDR-TB isolates; and n = 4 fully susceptible isolates). Each isolate was tested for susceptibility to first- and second-line drugs using the agar proportion method. Mutations were observed in ETH-resistant MDR-TB isolates at the following rates: 100% in katG, 72% in ethA, 45.6% in mshA, 8.7% in ndh, and 33.3% in inhA or its promoter. Of the three ETH-susceptible MDR-TB isolates, all showed mutations in katG; one had a mutation in ethA, and another, in mshA and inhA. Finally, of the four fully susceptible isolates, two showed no detectable mutation in the studied genes, and two had mutations in mshA gene unrelated to the resistance. Mutations not previously reported were found in the ethA, mshA, katG, and ndh genes. The concordance between the phenotypic susceptibility testing to INH and ETH and the sequencing was 1 and 0.45, respectively. Among isolates exhibiting INH resistance, the high frequency of independent resistance and cross-resistance with ETH in the M. tuberculosis isolates suggests the need to confirm the susceptibility to ETH before considering it in the treatment of patients with MDR-TB.
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http://dx.doi.org/10.1128/AAC.01028-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649173PMC
December 2015

[Trends in antibiotic resistance in Medellín and municipalities of the Metropolitan Area between 2007 and 2012: Results of six years of surveillance].

Biomedica 2014 Jul-Sep;34(3):433-46

Unidad de Bacteriología y Micobacterias, Corporación para Investigaciones Biológicas.

Introduction: Bacterial resistance is a global phenomenon, but it presents geographic and temporal variations; this is the importance of local surveillance programs.

Objective: To determine trends in antibiotic resistance in hospitals between 2007 and 2012 in Medellín and its Metropolitan Area.

Materials And Methods: Percentages of antibiotic resistance between 2007 and 2012 in 22 institutions were obtained using WHONET 5.6 program. For interpretation of susceptibility results, CLSI standards of 2009 and 2012 were used. Using the Epi-Info 6.04 program a trends analysis of antibiotic resistance was done using the chi-square for linear trend with a confidence level of 95%, a value of p=0.05 was considered significant.

Results: In six years of surveillance of antibiotic resistance we found a decrease of oxacillin resistance in Staphylococcus aureus (p=0.0006) and an increase of vancomycin resistance in Enterococcus faecium (p=0.0000). In Escherichia coli and Serratia marcescens an increase of resistance to ceftazidime was found, in contrast to a decrease in Klebsiella pneumoniae (p=0.0000) and Enterobacter cloacae (p=0.058). K. pneumoniae , S. marcescens and E. cloacae showed an increase of carbapenem resistance in contrast to a reduction of carbapenem resistance in Pseudomonas aeruginosa and Acinetobacter baumannii .

Conclusions: The resistance surveillance identified important findings as the emergence of E. faecium resistant to vancomycin and carbapenem-resistant Enterobacteriaceae . It is essential to determine the antibiotic use in the region to establish their influence on the resistance profiles, as well as ensuring the quality of information and microbiological procedures in the microbiology laboratories.
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http://dx.doi.org/10.1590/S0120-41572014000300013DOI Listing
August 2015

Rapid diagnosis of pulmonary tuberculosis.

Pan Afr Med J 2014 17;18:141. Epub 2014 Jun 17.

School of Health Sciences, Universidad Pontificia Bolivariana (UPB), Medellín, Colombia ; Bacteriology and Mycobacteriology Unit, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia.

Introduction: World Health Organization had estimated 9.4 million tuberculosis cases on 2009, with 1.7 million of deaths as consequence of treatment and diagnosis failures. Improving diagnostic methods for the rapid and timely detection of tuberculosis patients is critical to control the disease. The aim of this study was evaluating the accuracy of the cord factor detection on the solid medium Middlebrook 7H11 thin layer agar compared to the Lowenstein Jensen medium for the rapid tuberculosis diagnosis.

Methods: Patients with suspected tuberculosis were enrolled and their sputum samples were processed for direct smear and culture on Lowenstein Jensen and BACTEC MGIT 960, from which positive tubes were subcultured on Middlebrook 7H11 thin layer agar. Statistical analysis was performed comparing culture results from Lowenstein Jensen and the thin layer agar, and their corresponding average times for detecting Mycobacterium tuberculosis. The performance of cord factor detection was evaluated determining its sensitivity, specificity, positive and negative predictive value.

Results: 111 out of 260 patients were positive for M. tuberculosis by Lowenstein Jensen medium with an average time ± standard deviation for its detection of 22.3 ± 8.5 days. 115 patients were positive by the MGIT system identifying the cord factor by the Middlebrook 7H11 thin layer agar which average time ± standard deviation was 5.5 ± 2.6 days.

Conclusion: The cord factor detection by Middlebrook 7H11 thin layer agar allows early and accurate tuberculosis diagnosis during an average time of 5 days, making this rapid diagnosis particularly important in patients with negative sputum smear.
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http://dx.doi.org/10.11604/pamj.2014.18.141.2295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236790PMC
August 2015

Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis.

Microbiome 2014 25;2:29. Epub 2014 Aug 25.

Molecular Genetics & Biotechnology, Corporación CorpoGen, Carrera 5 No. 66A-34, Bogotá, DC 110231, Colombia.

Background: Changes in respiratory tract microbiota have been associated with diseases such as tuberculosis, a global public health problem that affects millions of people each year. This pilot study was carried out using sputum, oropharynx, and nasal respiratory tract samples collected from patients with pulmonary tuberculosis and healthy control individuals, in order to compare sample types and their usefulness in assessing changes in bacterial and fungal communities.

Findings: Most V1-V2 16S rRNA gene sequences belonged to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria, with differences in relative abundances and in specific taxa associated with each sample type. Most fungal ITS1 sequences were classified as Ascomycota and Basidiomycota, but abundances differed for the different samples. Bacterial and fungal community structures in oropharynx and sputum samples were similar to one another, as indicated by several beta diversity analyses, and both differed from nasal samples. The only difference between patient and control microbiota was found in oropharynx samples for both bacteria and fungi. Bacterial diversity was greater in sputum samples, while fungal diversity was greater in nasal samples.

Conclusions: Respiratory tract microbial communities were similar in terms of the major phyla identified, yet they varied in terms of relative abundances and diversity indexes. Oropharynx communities varied with respect to health status and resembled those in sputum samples, which are collected from tuberculosis patients only due to the difficulty in obtaining sputum from healthy individuals, suggesting that oropharynx samples can be used to analyze community structure alterations associated with tuberculosis.
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http://dx.doi.org/10.1186/2049-2618-2-29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164332PMC
September 2014

[Changes over time in the distribution of dominant clonal complexes of methicillin-resistant Staphylococcus aureus in Medellín, Colombia].

Biomedica 2014 Apr;34 Suppl 1:34-40

Grupo de Investigación en Microbiología Básica y Aplicada, MICROBA, Escuela de Microbiología, Universidad de Antioquia.

Introduction: Part of the success of methicillin-resistant Staphylococcus aureus (MRSA) as a pathogen responds to the rapid spread of pandemic lineages with diverse virulence and antimicrobial susceptibility profiles. In Colombia, several healthcare-associated MRSA (HA-MRSA) clones have been found, including the pediatric clone (CC5-ST5-SCC mec IV), the Brazilian clone (CC8-ST239-SCC mec III), and the Chilean/Cordobés clone (CC5-ST5-SCC mec I). Moreover, the community-associated MRSA (CA-MRSA) clone USA300 has been reported as causing hospital-acquired infections.

Objective: To describe the changes over time in the distribution of MRSA clones from a university hospital in Medellín collected at two time points a decade apart.

Materials And Methods: A total of 398 MRSA strains were analyzed. Of these, 67 strains were collected in 1994, while the remaining 331 strains were collected between 2008 and 2010. Species identification and methicillin resistance were confirmed by detection of nuc and mec A genes, respectively. Molecular characterization included spa typing, SCC mec typing, PFGE and MLST.

Results: Analysis of the MRSA strains collected in 1994 revealed that they belonged to a single clone, the CC5-SCC mec IV, whereas among the isolates from 2008-2010, two dominant clones were identified: CC8-SCC mec IVc, which included spa types t008 and t1610 and is closely related to the USA 300 clone, and CC5-SCC mec I ( spa type t149), related to the Chilean clone. The ST5-SCC mec IV clone from 1994 was not detected.

Conclusions: This study identifies temporal dynamics in MRSA clone diversity, and highlights the importance of local surveillance and dissemination of results, especially in countries like Colombia where MRSA is prevalent and knowledge regarding its epidemiology is still insufficient.
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http://dx.doi.org/10.1590/S0120-41572014000500005DOI Listing
April 2014

Population structure among mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Colombia.

PLoS One 2014 18;9(4):e93848. Epub 2014 Apr 18.

Corporación para Investigaciones Biológicas, CIB, Medellín, Colombia; Universidad Pontificia Bolivariana, Medellín, Colombia; Centro Colombiano de Investigación en Tuberculosis, CCITB, Medellín, Colombia.

Background: Phylogeographic composition of M. tuberculosis populations reveals associations between lineages and human populations that might have implications for the development of strategies to control the disease. In Latin America, lineage 4 or the Euro-American, is predominant with considerable variations among and within countries. In Colombia, although few studies from specific localities have revealed differences in M. tuberculosis populations, there are still areas of the country where this information is lacking, as is a comparison of Colombian isolates with those from the rest of the world.

Principal Findings: A total of 414 M. tuberculosis isolates from adult pulmonary tuberculosis cases from three Colombian states were studied. Isolates were genotyped using IS6110-restriction fragment length polymorphism (RFLP), spoligotyping, and 24-locus Mycobacterial interspersed repetitive units variable number tandem repeats (MIRU-VNTRs). SIT42 (LAM9) and SIT62 (H1) represented 53.3% of isolates, followed by 8.21% SIT50 (H3), 5.07% SIT53 (T1), and 3.14% SIT727 (H1). Composite spoligotyping and 24-locus MIRU- VNTR minimum spanning tree analysis suggest a recent expansion of SIT42 and SIT62 evolved originally from SIT53 (T1). The proportion of Haarlem sublineage (44.3%) was significantly higher than that in neighboring countries. Associations were found between M. tuberculosis MDR and SIT45 (H1), as well as HIV-positive serology with SIT727 (H1) and SIT53 (T1).

Conclusions: This study showed the population structure of M. tuberculosis in several regions from Colombia with a dominance of the LAM and Haarlem sublineages, particularly in two major urban settings (Medellín and Cali). Dominant spoligotypes were LAM9 (SIT 42) and Haarlem (SIT62). The proportion of the Haarlem sublineage was higher in Colombia compared to that in neighboring countries, suggesting particular conditions of co-evolution with the corresponding human population that favor the success of this sublineage.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093848PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991582PMC
January 2015

Association of clinical and demographic factors in invasive candidiasis caused by fluconazole-resistant Candida species: a study in 15 hospitals, Medellín, Colombia 2010-2011.

Diagn Microbiol Infect Dis 2014 Jun 22;79(2):280-6. Epub 2014 Feb 22.

Laboratorio Médico de Referencia, Clínica El Rosario, Medellín, Colombia; Grupo GERMEN, Medellín, Colombia.; Unidad de Bacteriología y Micobacterias, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia; Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana (UPB), Medellín, Colombia. Electronic address:

Candida is the most important agent of fungal infections. Several risk factors have been described associated with invasive infection by fluconazole-resistant Candida spp. A prospective cross-sectional study with case-control analysis was conducted. Case group patients with fluconazole-resistant Candida isolate were included; control group were patients with fluconazole-susceptible Candida spp. A multivariate logistic regression model was performed. Three hundred isolates of Candida spp. were analyzed. Most frequent species were Candida albicans/Candida dubliniensis (48.3%) and Candida tropicalis (22.3%). Posaconazole susceptibility was 93.7%; voriconazole, 84%; and fluconazole, 78.7%. Susceptibility to anidulafungin and caspofungin was 92.7% and 92.3%, respectively. Neutropenia (adjusted odds ratio [aOR] 6.5, 95% confidence interval [CI] 1.0-43.1), antifungal exposure (aOR 5.1, 95% CI 2.3-11.2), and antituberculosis therapy (aOR 7.7, 95% CI 1.4-43.2) were associated to fluconazole resistance. Susceptibility results are useful to guide the selection of empiric antifungal treatment and the design of local therapeutic guidelines. Previous antifungal exposure suggests possible resistance to fluconazole, pointing towards the selection of a different class of antifungal agents.
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http://dx.doi.org/10.1016/j.diagmicrobio.2014.02.003DOI Listing
June 2014

Tuberculosis among homeless population from Medellín, Colombia: associated mental disorders and socio-demographic characteristics.

J Immigr Minor Health 2013 Aug;15(4):693-9

School of Health Sciences, Universidad Pontificia Bolivariana (UPB), Medellín, Colombia.

Homeless people are highly susceptible to tuberculosis. It has been suggested that this population have high rates of mental disorders associated with tuberculosis. We assessed tuberculosis incidence, its transmission patterns and association with socio-demographic factors and mental disorders in Colombian homeless people. Prospective study which socio-demographic characteristics and mental disorders were assessed through interviews. Sputa from patients with respiratory symptoms were processed and clinical isolates analyzed by IS6110-RFLP. Multivariate analysis performed by logistic regression model. From 426 homeless studied, tuberculosis incidence found was 7.9 %. 44 % of isolates were clustering. It was found high risk of having tuberculosis associated with income from drugs trade (OR: 3.40 [95 % CI: 1.28-9.05]), dysthymia (OR: 2.54 [95 % CI: 1.10-5.86]) and receiving food from other homeless (OR: 2.47 [95 % CI: 1.16-5.25]). Tuberculosis incidence and degree of transmission are high in homeless studied. Implementing programs to better control tuberculosis among homeless population must consider socio-demographic factors and mental disorders associated with the disease.
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http://dx.doi.org/10.1007/s10903-013-9776-xDOI Listing
August 2013

Tuberculosis in indigenous communities of Antioquia, Colombia: epidemiology and beliefs.

J Immigr Minor Health 2013 Feb;15(1):10-6

Bacteriology and Mycobacteriology Unit, Corporación para Investigaciones Biológicas, Carrera 72 A No 78 B-141, Medellín, Colombia.

Morbidity and mortality caused by tuberculosis are increased in most of the Latin-American indigenous communities. Factors that could explain this situation are poverty and limited health services access due to social conflicts and geographical isolation. We determined the frequency of tuberculosis in Colombian indigenous communities and described their knowledge related to transmission and control. We developed a descriptive study and health survey. Interviews were performed to find ancestral knowledge about tuberculosis. Sputum samples from patients with respiratory symptoms were analyzed. 10 indigenous communities were studied, which tuberculosis incidence was 291/100,000. Communities believe that tuberculosis is a body and spirit disease, which transmission is by direct contact or by witchcraft. Tuberculosis incidence in the studied communities was ninefold higher than that of the general population from Antioquia Department. Knowledge exchange could facilitate the community empowerment and implementation of educational activities which might improve the control of the disease.
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http://dx.doi.org/10.1007/s10903-012-9688-1DOI Listing
February 2013

IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes.

BMC Genomics 2012 Jun 15;13:249. Epub 2012 Jun 15.

Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St, Louis, MO 63108, USA.

Background: The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium tuberculosis, the etiological agent of human tuberculosis. Although IS 6110 has been used extensively as an epidemiological marker, the identification of the precise chromosomal insertion sites has been limited by technical challenges. Here, we present IS-seq, a novel method that combines high-throughput sequencing using Illumina technology with efficient combinatorial sample multiplexing to simultaneously probe 519 clinical isolates, identifying almost all the flanking regions of the element in a single experiment.

Results: We identified a total of 6,976 IS6110 flanking regions on the different isolates. When validated using reference strains, the method had 100% specificity and 98% positive predictive value. The insertions mapped to both coding and non-coding regions, and in some cases interrupted genes thought to be essential for virulence or in vitro growth. Strains were classified into families using insertion sites, and high agreement with previous studies was observed.

Conclusions: This high-throughput IS-seq method, which can also be used to map insertions in other organisms, extends previous surveys of in vivo interrupted loci and provides a baseline for probing the consequences of disruptions in M. tuberculosis strains.
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http://dx.doi.org/10.1186/1471-2164-13-249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443423PMC
June 2012

Whole genome shotgun sequencing of one Colombian clinical isolate of Mycobacterium tuberculosis reveals DosR regulon gene deletions.

FEMS Microbiol Lett 2012 May 28;330(2):113-20. Epub 2012 Mar 28.

Centro Nacional de Secuenciación Genómica-CNSG, Universidad de Antioquia, Medellin, Colombia.

Several genomes of different Mycobacterium tuberculosis isolates have been completely sequenced around the world. The genomic information obtained have shown higher diversity than originally thought and specific adaptations to different human populations. Within this work, we sequenced the genome of one Colombian M. tuberculosis virulent isolate. Genomic comparison against the reference genome of H37Rv and other strains showed multiple deletion and insertions that ranged between a few bases to thousands. Excluding PPE and PG-PGRS genes, 430 proteins present changes in at least 1 amino acid. Also, novel positions of the IS6110 mobile element were identified. This isolate is also characterized by a large genomic deletion of 3.6 kb, leading to the loss and modification of the dosR regulon genes, Rv1996 and Rv1997. To our knowledge, this is the first report of the genome sequence of a Latin American M. tuberculosis clinical isolate.
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http://dx.doi.org/10.1111/j.1574-6968.2012.02540.xDOI Listing
May 2012

Conspicuous multidrug-resistant Mycobacterium tuberculosis cluster strains do not trespass country borders in Latin America and Spain.

Infect Genet Evol 2012 Jun 21;12(4):711-7. Epub 2011 Jun 21.

Instituto Nacional de Enfermedades Infecciosas ANLIS Carlos Malbrán, Vélez Sarsfield 563, 1281 Buenos Aires, Argentina.

Multidrug-resistant Mycobacterium tuberculosis strain diversity in Ibero-America was examined by comparing extant genotype collections in national or state tuberculosis networks. To this end, genotypes from over 1000 patients with multidrug-resistant tuberculosis diagnosed from 2004 through 2008 in Argentina, Brazil, Chile, Colombia, Venezuela and Spain were compared in a database constructed ad hoc. Most of the 116 clusters identified by IS6110 restriction fragment length polymorphism were small and restricted to individual countries. The three largest clusters, of 116, 49 and 25 patients, were found in Argentina and corresponded to previously documented locally-epidemic strains. Only 13 small clusters involved more than one country, altogether accounting for 41 patients, of whom 13 were, in turn, immigrants from Latin American countries different from those participating in the study (Peru, Ecuador and Bolivia). Most of these international clusters belonged either to the emerging RD(Rio) LAM lineage or to the Haarlem family of M. tuberculosis and four were further split by country when analyzed with spoligotyping and rifampin resistance-conferring mutations, suggesting that they did not represent ongoing transnational transmission events. The Beijing genotype accounted for 1.3% and 10.2% of patients with multidrug-resistant tuberculosis in Latin America and Spain, respectively, including one international cluster of two cases. In brief, Euro-American genotypes were widely predominant among multidrug-resistant M. tuberculosis strains in Ibero-America, reflecting closely their predominance in the general M. tuberculosis population in the region, and no evidence was found of acknowledged outbreak strains trespassing country borders.
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http://dx.doi.org/10.1016/j.meegid.2011.06.006DOI Listing
June 2012

Physiological role and potential clinical interest of mycobacterial pigments.

IUBMB Life 2011 Feb;63(2):71-8

Corporación para Investigaciones Biológicas, Unidad de Bacteriologia, Medellín, Colombia.

The production of pigments by bacterial colonies has sparked interest among bacteriologists since the 19th century, whether for taxonomy or, in the case of carotenoids for their association with antibiotics resistance. Mycobacteria have gained a very special place in the bacterial world due to their clinical importance. Alone, Mycobacterium tuberculosis is responsible for about two million deaths annually worldwide making tuberculosis one of the most influential diseases in the history of mankind. Almost half of the Nontuberculous Mycobacteria species identified are associated with opportunistic infections in animals and humans. Mycobacterial pigmentary characteristics started to be documented about 80 years ago; but to date, their main use has been only for limited taxonomic and identification purposes. While mycobacterial pigments, especially carotenoids have been clearly associated with cellular photoprotection and survival, the regulation of their production and their physiological role have been largely unstudied. Recent advances in deciphering mycobacterial genomes and characterization of carotenoid synthesis genes, combined with an urgent need for innovative approaches to understand Mycobacterium tuberculosis pathogenic properties open new avenues for exciting research opportunities that might lead to new therapeutic strategies against a devastating secular disease.
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http://dx.doi.org/10.1002/iub.424DOI Listing
February 2011

Genomic signatures of the haarlem lineage of Mycobacterium tuberculosis: implications of strain genetic variation in drug and vaccine development.

J Clin Microbiol 2010 Oct 14;48(10):3614-23. Epub 2010 Jul 14.

Corporación Corpogen, Bogotá, DC, Colombia.

Tuberculosis is the world's leading cause of death due to a single infectious agent, and efforts aimed at its control require a better understanding of host, environmental, and bacterial factors that govern disease outcome. Growing evidence indicates that certain Mycobacterium tuberculosis strains of distinct phylogeographic lineages elicit unique immunopathological events. However, identifying the genetic basis of these phenotypic peculiarities has proven difficult. Here we report the presence of six large sequence polymorphisms which, together with two single-nucleotide changes previously described by our group, consistently differentiate Haarlem strains from the remaining M. tuberculosis lineages. The six newly found Haarlem-specific genetic events are four deletions, which altogether involve more than 13 kb, and two intragenic insertions of the element IS6110. The absence of the genes involved in these polymorphisms could have an important physiological impact on Haarlem strains, i.e., by affecting key genes, such as Rv1354c and cyp121, which have been recently proposed as plausible drug targets. These lineage-specific polymorphisms can serve as genetic markers for the rapid PCR identification of Haarlem strains, providing a useful tool for strain surveillance and molecular epidemiology studies. Strain variability such as that described here underscores the need for the definition of a core set of essential genes in M. tuberculosis that are ubiquitously present in all circulating lineages, as a requirement in the development of effective antituberculosis drugs and vaccines.
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http://dx.doi.org/10.1128/JCM.00157-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953103PMC
October 2010

Systematic interpretation of molecular beacon polymerase chain reaction for identifying rpoB mutations in Mycobacterium tuberculosis isolates with mixed resistant and susceptible bacteria.

Diagn Microbiol Infect Dis 2010 May 12;67(1):37-46. Epub 2010 Mar 12.

The University of Texas Health Science Center Houston, School of Public Health at Brownsville, Brownsville, TX 78520, USA.

Detection of multidrug-resistant tuberculosis (MDR-TB), a frequent cause of treatment failure, takes 2 or more weeks to identify by culture. Rifampicin (RIF) resistance is a hallmark of MDR-TB, and detection of mutations in the rpoB gene of Mycobacterium tuberculosis using molecular beacon probes with real-time quantitative polymerase chain reaction (qPCR) is a novel approach that takes
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http://dx.doi.org/10.1016/j.diagmicrobio.2009.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854294PMC
May 2010
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