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Whole genome sequencing (WGS) has become the main tool for studying the transmission of Mycobacterium tuberculosis complex (MTBC) strains; however, the clonal expansion of one strain often limits its application in local MTBC outbreaks. The use of an alternative reference genome and the inclusion of repetitive regions in the analysis could potentially increase the resolution, but the added value has not yet been defined. Here, we leveraged short and long WGS read data of a previously reported MTBC outbreak in the Colombian Amazon Region to analyze possible transmission chains among 74 patients in the indigenous setting of Puerto Nariño (March to October 2016). In total, 90.5% (67/74) of the patients were infected with one distinct MTBC strain belonging to lineage 4.3.3. Employing a reference genome from an outbreak strain and highly confident single nucleotide polymorphisms (SNPs) in repetitive genomic regions, e.g., the proline-glutamic acid/proline-proline-glutamic-acid (PE/PPE) gene family, increased the phylogenetic resolution compared to a classical H37Rv reference mapping approach. Specifically, the number of differentiating SNPs increased from 890 to 1,094, which resulted in a more granular transmission network as judged by an increasing number of individual nodes in a maximum parsimony tree, i.e., 5 versus 9 nodes. We also found in 29.9% (20/67) of the outbreak isolates, heterogenous alleles at phylogenetically informative sites, suggesting that these patients are infected with more than one clone. In conclusion, customized SNP calling thresholds and employment of a local reference genome for a mapping approach can improve the phylogenetic resolution in highly clonal MTBC populations and help elucidate within-host MTBC diversity. IMPORTANCE The Colombian Amazon around Puerto Nariño has a high tuberculosis burden with a prevalence of 1,267/100,000 people in 2016. Recently, an outbreak of Mycobacterium tuberculosis complex (MTBC) bacteria among the indigenous populations was identified with classical MTBC genotyping methods. Here, we employed a whole-genome sequencing-based outbreak investigation in order to improve the phylogenetic resolution and gain new insights into the transmission dynamics in this remote Colombian Amazon Region. The inclusion of well-supported single nucleotide polymorphisms in repetitive regions and a de novo -assembled local reference genome provided a more granular picture of the circulating outbreak strain and revealed new transmission chains. Multiple patients from different settlements were possibly infected with at least two different clones in this high-incidence setting. Thus, our results have the potential to improve molecular surveillance studies in other high-burden settings, especially regions with few clonal multidrug-resistant (MDR) MTBC lineages/clades., Competing Interests: The authors declare no conflict of interest.

Mycobacterium tuberculosis (MTB) lineage 2/Beijing is associated with high virulence and drug resistance worldwide. In Colombia, the Beijing genotype has circulated since 1997, predominantly on the pacific coast, with the Beijing-Like SIT-190 being more prevalent. This genotype conforms to a drug-resistant cluster and shows a fatal outcome in patients. To better understand virulence determinants, we performed a transcriptomic analysis with a Beijing-Like SIT-190 isolate (BL-323), and Beijing-Classic SIT-1 isolate (BC-391) in progressive tuberculosis (TB) murine model. Bacterial RNA was extracted from mice lungs on days 3, 14, 28, and 60. On average, 0.6% of the total reads mapped against MTB genomes and of those, 90% against coding genes. The strains were independently associated as determined by hierarchical cluster and multidimensional scaling analysis. Gene ontology showed that in strain BL-323 enriched functions were related to host immune response and hypoxia, while proteolysis and protein folding were enriched in the BC-391 strain. Altogether, our results suggested a differential bacterial transcriptional program when evaluating these two closely related strains. The data presented here could potentially impact the control of this emerging, highly virulent, and drug-resistant genotype.

Multidrug-resistant tuberculosis (isoniazid/rifampin[RIF]-resistant TB) ravages developing countries. Fitness is critical in clinical outcomes. Previous studies on RIF-resistant TB (RR-TB) showed competitive fitness gains and losses, with rpoB-S450L as the most isolated/fit mutation. This study measured virulence/resistance genes, phthiocerol dimycocerosate (PDIM) levels and their relationship with rpoB S450L ATCC25618 RR-TB strain fitness. After obtaining 10 different RR-TB GenoType MTBDRplus 2.0-genotyped isolates (with nontyped, S441, H445 and S450 positions), only one S450L isolate (R9, rpoB-S450L ATCC 25618, RR 1 μg/mL) was observed, with H445Y being the most common. A competitive fitness in vitro assay with wild-type (wt) ATCC 25618: R9 1:1 in 50 mL Middlebrook 7H9/OADC was performed, and generation time (G) in vitro and relative fitness were obtained. mRNA and PDIM were extracted on log and stationary phases. Fitness decreased in rpoB S450L and H445Y strains, with heterogeneous fitness cues in three biological replicas of rpoB-S450L: one high and two low fitness replicas. S450L strain had significant pknG increase. Compared with S450L, wt-rpoB showed increased polyketide synthase ppsA expression and high PDIM peak measured by HPLC-MS in log phase compared to S450L. This contrasts with previously increased PDIM in other RR-TB isolates., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Introduction: Tuberculosis affects vulnerable groups to a greater degree, indigenous population among them., Objective: To determine molecular epidemiology of clinical isolates of Mycobacterium tuberculosis circulating in an indigenous population through Spoligotyping and 24-loci MIRU-VNTR., Methodology: A descriptive cross-sectional study was conducted in 23 indigenous communities of Puerto Nariño-Amazonas, Colombia. Recovered clinical isolates were genotyped. For genotyping analyzes global SITVIT2 database and the MIRU-VNTRplus web portal were used., Results: 74 clinical isolates were recovered. Genotyping of clinical isolates by spoligotyping determined 5 different genotypes, all of them belonged to Euro-American lineage. By MIRU-VNTR typing, a total of 14 different genotypes were recorded. Furthermore, polyclonal infection was found in two patients from the same community. The combination of the two methodologies determined the presence of 19 genotypes, 8 formed clusters with 63 clinical isolates in total. Based on epidemiological information, it was possible to establish a potential chain of active transmission in 10/63 (15.9%) patients., Conclusions: High genomic homogeneity was determined in the indigenous population suggesting possible chains of active transmission. The results obtained showed that specific genotypes circulating among the indigenous population of Colombia are significantly different from those found in the general population., Competing Interests: The authors have declared that no competing interests exist.

Emergence of multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) isolates is a major public health problem that threatens progress made in tuberculosis (TB) care and control worldwide. In Colombia, the prevalence of MDR tuberculosis (MDR-TB) has increased slowly but steadily since 2001. However, the population structure of the MDR-TB strains circulating in Colombia is sparsely known. In this work, 203 MDR isolates isolated in 2012-2013 were collected, and characterized by spoligotyping, followed by 24-loci MIRU-VNTR (data available for 190 isolates). The most prevalent genotypes corresponded to SIT42/LAM9 (12.81%), SIT62/H1 (10.34%), and SIT190/Beijing (10.34%). A fine analysis showed that although the MDR strains came from 29 of the 33 departments of Colombia, the distribution of these main lineages was not at random and depended on the city of isolation (p-value <0.000001). Both LAM and Beijing lineage strains were significantly associated with MDR-TB (p-value <0.0001): LAM lineage was associated with 2 patterns of MDR, namely combined resistance to INH + Rifampin (HR), and to SHRE (Streptomycin + INH + Rifampin + Ethambutol), while the Beijing lineage strains were essentially associated with MDR (SHRE). Interestingly, distribution of genotypic lineages in function of drug resistance information (e.g. pansusceptible vs. MDR) was different in our setting as compared to other countries in Latin America. However, MIRU-VNTR patterns were unique for all strains, an observation that did not support active transmission of circulating MDR clones., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Introduction: Tuberculosis continues to be a public health priority. Indigenous peoples are vulnerable groups with cultural determinants that increase the risk of the disease., Objective: To determine molecular epidemiology and phenotypical features and of Mycobacterium tuberculosis isolates from indigenous people in Colombia during the period from 2009 to 2014., Materials and Methods: We conducted an analytical observational study; we analyzed 234 isolates to determine their patterns of sensitivity to antituberculosis drugs and their molecular structures by spoligotyping., Results: The isolates came from 41 indigenous groups, predominantly the Wayúu (13.10%) and Emberá Chamí (11.35%). We found 102 spoligotypes distributed among seven genetic families (37.2% LAM, 15.8% Haarlem, 8.1% T, 3.4% U, 2.6% S, 2.1% X, and 0.9%, Beijing). The association analysis showed that the non-clustered isolates were related to prior treatment, relapse, orphan spoligotypes, and the Beijing family. The H family presented an association with the Arhuaco and Camëntŝá indigenous groups, the U family was associated with the Wounaan group, and the T family was associated with the Motilón Barí group., Conclusions: This is the first national study on M. tuberculosis characterization in indigenous groups. The study evidenced that diagnosis in indigenous people is late. We described 53% of orphan patterns that could be typical of the Colombian indigenous population. The high percentage of grouping by spoligotyping (62%) could indicate cases of active transmission, a situation that should be corroborated using a second genotyping marker. A new Beijing spoligotype (Beijing-like SIT 406) was identified in Colombia.

Introduction: Active tuberculosis (TB) and latent tuberculosis infection (LTBI) are a public health threat in prisons around the world. The objectives of the study were to estimate the prevalence of LTBI and TB as well as to investigate TB transmission inside one prison, in Colombia., Methods: A Cross-sectional study was conducted in inmates who agreed to participate. Inmates with respiratory symptoms (RS) of any duration underwent to medical evaluation and three sputum samples were taken for smear microscopy and culture for TB diagnosis. Drug susceptibility was analyzed using BACTEC MGIT 960 and GenoType MTBDRplus. Molecular genotyping of Mycobacterium tuberculosis isolates was performed by 24-Locus MIRU-VNTR and spoligotyping. LTBI was evaluated according to the result of the tuberculin skin test (TST). Close contact investigation was conducted inside the prison for inmates that shared the cell with the index TB case., Results: Among 301/2,020 (15%) inmates with RS of any duration, 8% were diagnosed with active TB. The prevalence of active TB was 1,026 cases/100,000 inmates. We isolated M. tuberculosis in 19/24 (79%) TB cases, 94.7% were susceptible to first line drugs and only one was monoresistant to isoniazid. The most prevalent sub-lineage was Haarlem (68.4%), followed by LAM (26.3%) and T superfamily (5.3%). 24-Locus MIRU-VNTR typing results alone or in combination with spoligotyping identified three clusters containing two isolates each. Two clusters corresponded to inmates that shared the same cell, but each one was located in different blocks of the prison. Inmates from the last cluster were in the same block in nearby cells. TST reading was performed in 95.6% inmates, and 67.6% had a positive reaction., Conclusions: The prevalence of LTBI and TB was higher in prison than in the general population. Molecular genotyping suggests that TB in this prison is mainly caused by strains imported by inmates or endogenous reactivation., Competing Interests: The authors have declared that no competing interests exist.

Tumor necrosis factor-α (TNF-α) is an important fundamental cytokine during the immune response against cancer and infections such as tuberculosis. This molecule also plays a key pathogenic role in complex and difficult-to-treat diseases such as rheumatoid arthritis, ankylosing spondylitis, Crohn's disease, psoriasis and ulcerative colitis. The treatment of these diseases frequently needs TNF-α antagonists, which has been related to an increased risk of developing tuberculosis, mycoses, and other severe infections.We report the case of a 68-year-old man with Crohn's disease, who developed  disseminated tuberculosis due to anti-TNF-α immunosuppressive therapy. The diagnosis was based on the histopathological findings and molecular biology assays.We discuss the clinical presentation and workup of this case, and we present a comparative analysis of tuberculosis cases associated with anti-TNF-α reported in Colombia during the last 10 years emphasizing on the diagnosis and treatment of latent tuberculosis.

Introduction: Tuberculosis is one of the most widely distributed infectious diseases worldwide. It is the most common cause of mortality among AIDS patients. In Colombia, 12,918 tuberculosis cases were notified, and 926 deaths were reported in 2015., Objective: To determine the prevalence and risk factors associated to mycobacterial infections in HIVpositive patients in two public hospitals from Bogotá., Materials and Methods: A prospective and descriptive study was carried out by an active search for tuberculosis cases and non-tuberculous mycobacterial infections in HIV-positive patients. We considered demographic, social, clinical, and personal habits as variables. Statistical analyses were done using Stata 13™ software., Results: Three hundred and fifty six patients were included, 81.2% were men and 18.8% were women; the mean age was 36.5 years. Tuberculosis infection had a frequency of 19.9% (95% CI: 15.9-24.5%) and non-tuberculous mycobacterial infection had a 3.9% frequency (95% CI: 2.16-6.5%). Bivariate analysis showed a statistically significant association between tuberculosis infection and CD4+ T cell counts (p=0.003), viral load (p=0.008), antiretroviral therapy (p=0.014), and body mass index (BMI) <18 kg/m2 (p=0.000). In non-tuberculous mycobacterial infections there was a statistically significantassociation with BMI (p=0.027) and CD4+ T cell counts (p=0.045)., Conclusion: Factors associated with an impaired immune system caused by HIV infection are an important risk factor for developing tuberculosis. The lack of antiretroviral therapy and the BMI were also important risk factors for tuberculosis.

Mycobacterium avium complex (MAC) contains clinically important nontuberculous mycobacteria worldwide and is the second largest medical complex in the Mycobacterium genus after the Mycobacterium tuberculosis complex. MAC comprises several species that are closely phylogenetically related but diverse regarding their host preference, course of disease, virulence and immune response. In this study we provided immunologic and virulence-related insights into the M. colombiense genome as a model of an opportunistic pathogen in the MAC. By using bioinformatic tools we found that M. colombiense has deletions in the genes involved in p-HBA/PDIM/PGL, PLC, SL-1 and HspX production, and loss of the ESX-1 locus. This information not only sheds light on our understanding the virulence mechanisms used by opportunistic MAC pathogens but also has great potential for the designing of species-specific diagnostic tools.

Tuberculosis is a serious public health problem worldwide. In 2012, the World Health Organization estimated 8.6 million new cases and 1.3 million deaths due to the disease. In 2011, the incidence in Colombia was 24 cases per 100,000 inhabitants. There is little information about tuberculosis in pregnant women, and congenital infection is considered a rare disease that is difficult to diagnose, leads to high mortality, and may be confused with tuberculosis acquired after birth. In addition, it has been associated with HIV infection in mothers and infants. Moreover, there is increasing incidence of congenital syphilis in the world. In Colombia, the prevalence is 2.5 cases per 1,000 births and its frequency in the Instituto Materno Infantil-Hospital La Victoria is one case per 57 births. We report the case of a newborn under treatment for congenital syphilis and in whom microcalcifications were found in a transfontanelar ultrasound. This finding warned about the existence of another infectious agent. PCR was negative for cytomegalovirus, and IgM titers for toxoplasma, rubella and herpes I and II were also negative. After learning about a history of incomplete treatment for tuberculosis in the mother, we suspected the presence of an infection by the tubercle bacillus in the newborn. No acid-fast bacilli were demonstrated in three gastric juice samples. The IS6110 PCR assay was found positive in cerebrospinal fluid and urine, but not in blood. The newborn was treated with crystalline penicillin for 10 days along with isoniazid, rifampicin, pyrazinamide and streptomycin. The patient is currently under clinical monitoring.

Approximately 2 million people die each year from tuberculosis. One third of the world´s population is estimated to be infected with the tuberculosis bacillus, although only 5-10% will develop the disease in their lifetime. The disease progression risk depends on endogenous and exogenous factors. Indigenous communities are a high-risk group for infection and development of tuberculosis. In addition to factors such as geographical isolation, social and cultural neglect and malnutrition, susceptibility to genetic polymorphisms has been identified in them. Spinal tuberculosis is the most destructive form of the disease, which represents approximately half of all cases of skeletal tuberculosis. The case of an HIV negative, indigenous Colombian man is presented. His diagnosis was done based on clinical and image findings, and it was confirmed with the rapid molecular assay Genotype MTBDRplus® and IS6110 PCR.The culture in solid media was negative after 16 weeks. We briefly discuss the pathogenesis, diagnosis and treatment. Finally, we comment on some aspects of the situation of tuberculosis among indigenous Colombian communities.

We report here the whole-genome sequence of the multidrug-resistant Beijing-like strain Mycobacterium tuberculosis 323, isolated from a 15-year-old female patient who died shortly after the initiation of second-line drug treatment. This strain is representative of the Beijing-like isolates from Colombia, where this lineage is becoming a public health concern., (Copyright © 2015 Rodríguez et al.)

Tuberculosis is the single most frequent cause of death by an infectious agent worldwide. Diagnosis of extra-pulmonary tuberculosis is not always possible through conventional methods, due to the long time required for cultures and the paucibacillary nature of samples; hence the need of rapid molecular methods. HIV infection increases the risk of tuberculosis, and HIV/tuberculosis coinfection is associated with higher mortality. We describe the case of a 56-year old mestizo male patient suspected of having tuberculosis who consulted the San Ignacio Hospital in Bogotá with a two-month history of a painful ulcerated lesion over the distal third area of the right forearm and in whom HIV coinfection was confirmed. Bone and pulmonary histological examination evidenced multiple granulomas, giant cells and fibrosis. Cultures and IS6110-PCR from lung and bone tissues were positive for Mycobacterium tuberculosis complex. Mycobacterium tuberculosis isolates were sensitive to first line drugs.

The following article arises from the study "Representaciones sociales en el campo de la salud mental" (Social Representations in the Mental Health Field), in which the objective was to address the social representations in the family context; concerning caring, as well as the burden it implies using a qualitative method. The corpus was built based on the analysis and interpretation gathered from families with mental illness members. There were 17 individual interviews, 13 group interviews and one family group of three generations, held regarding the clinical care of the family member. These interviews were held at three different hospitals in Bogota. The representation of "a family" constitutes the structuring of the meanings of family relationships that cope with mental illness built upon the social and historical life of its members. The three comprehensive categories were: a) Family in good times and bad times; b) mental illness in family interactions, and c) Care and burden. Socially speaking, mental illness can lead to dehumanization, in that it discriminates and stigmatizes, even within the family unit. Caring for a family member with mental illness comes about by hierarchical order, self assignation, and by institutionalization. This latter occurs due to lack of caregivers or because the family does not consider their home the best place to care for such a patient., (Copyright © 2013 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.)

Introduction: The early detection of resistance in Mycobacterium tuberculosis is of primary importance for both patient management and infection control., Objective: To evaluate nitrate reductase assay (NRA) performance for the testing of Mycobacterium tuberculosis drug-resistance against first-line anti-tuberculosis drugs, such as rifampicin (RIF), isoniazid (INH), streptomycin (STR) and ethambutol (EMB)., Materials and Methods: Fifty isolates were tested by using both the proportion method and the nitrate reductase assay., Results: RIF, INH, STR and EMB sensitivity was found to be 92%, 91%, 63% and 80% and 100%, respectively, and a corresponding specificity of 100%, 100%, 100% and 98% by comparing NRA results to those obtained with the gold standard (i.e., the proportion method). The positive predictive values for RIF, INH, STR and EMB were 100%, 100%, 100% and 80% and the negative predictive values were 97%, 93%, 73% and 98%, respectively. The mean time for obtaining results was shorter when using the nitrate reductase assay (10 days) compared to using the proportion method (28 days). Excellent agreement was observed between both phenotypic tests: 98%, 96%, 81% and 96% for RIF, INH, STR and EMB, respectively ., Conclusions: The results showed that the nitrate reductase assay is suitable for the early determination of multidrug-resistant tuberculosis (MDR-TB) and is a useful tool for the quick and accurate determination of a rapid M. tuberculosis drug-sensitivity test in countries having low resources.

The genus Mycobacterium comprises more than 150 species, including important pathogens for humans which cause major public health problems. The vast majority of efforts to understand the genus have been addressed in studies with Mycobacterium tuberculosis. The biological differentiation between M. tuberculosis and nontuberculous mycobacteria (NTM) is important because there are distinctions in the sources of infection, treatments, and the course of disease. Likewise, the importance of studying NTM is not only due to its clinical significance but also due to the mechanisms by which some species are pathogenic while others are not. Mycobacterium avium complex (MAC) is the most important group of NTM opportunistic pathogens, since it is the second largest medical complex in the genus after the M. tuberculosis complex. Here, we evaluated the virulence and immune response of M. avium subsp. avium and Mycobacterium colombiense, using experimental models of progressive pulmonary tuberculosis and subcutaneous infection in BALB/c mice. Mice infected intratracheally with a high dose of MAC strains showed high expression of tumor necrosis factor alpha (TNF-α) and inducible nitric oxide synthase with rapid bacillus elimination and numerous granulomas, but without lung consolidation during late infection in coexistence with high expression of anti-inflammatory cytokines. In contrast, subcutaneous infection showed high production of the proinflammatory cytokines TNF-α and gamma interferon with relatively low production of anti-inflammatory cytokines such as interleukin-10 (IL-10) or IL-4, which efficiently eliminate the bacilli but maintain extensive inflammation and fibrosis. Thus, MAC infection evokes different immune and inflammatory responses depending on the MAC species and affected tissue.

Mycobacterium avium complex (MAC) consists of 9 species of slow-growing mycobacteria with differing degrees of pathogenicity, host preference and environmental distribution. Mycobacterium colombiense is a novel member of MAC that is responsible for disseminated infections in HIV-infected patients in Colombia and lymphadenopathy cases in Europe. At present, methods to easily differentiate novel members of MAC are lacking. In this study, we identified possible biomarkers that are potentially useful for the detection of M. colombiense by PCR or chromatography. The Randomly Amplified Polymorphic DNA (RAPD) technique was used to amplify genomic fragments of M. colombiense CECT 3035 that were subsequently used in the development of a direct colony-specific PCR assay using specific primers. The designed primers amplified a 634-bp fragment of DNA from M. colombiense, which included a 450-bp genomic region that encodes a hypothetical protein of 149 amino acids that is exclusive to M. colombiense. Bioinformatic analyses revealed that this hypothetical protein had no signal peptide, active sites or functional domains to aid its identification or classification. In addition, using thin-layer chromatography, we identified a different profile of mycolates for M. colombiense strains. The test developed in this study has potential applications in the routine identification of M. colombiense and in molecular assays designed for the surveillance of MAC strains., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

We report a case of granulomatous mastitis caused by Mycobacterium tuberculosis in an immunocompetent woman with chronic inflammatory lesions of the breast. It was diagnosed by detection of mycobacteria DNA using polymerase chain reaction technique targeting IS6110 insertion element of M. tuberculosis complex in a paraffin-embedded histological specimen. The primary breast tuberculosis is rare, even in countries where the incidence and prevalence of pulmonary and extra pulmonary tuberculosis are high. It should be suspected in female patients with chronic granulomatous mastitis with no apparent cause. The cornerstone of treatment is antituberculous chemotherapy, and surgery is rarely required.

With an incidence of 25.6/100,000 in 2008, tuberculosis (TB) remains an important public health problem in Colombia. In this study, a total of 152 Mycobacterium tuberculosis complex strains isolated in Bogotá, Colombia between years 1995 and 2007 were genotyped by spoligotyping and 12-loci MIRU-VNTRs. The various spoligotyping-based genotypic lineages in our sample were: Latin American & Mediterranean (LAM) n=75, 49.34%; Haarlem, n=38, 25.0%; ill-defined T group, n=21, 13.82%; S family, n=5, 3.29%; X clade, n=2, 1.32%; Beijing, n=1, 0.65%, while strains with unknown signatures (n=10) represented 6.58% of isolates. Using spoligotyping as a first molecular marker and MIRU-VNTRs as second marker, we obtained 102 single patterns and 14 clustered patterns (n=52 strains from 49 patients, 2-8 strains per cluster). The MIRU-VNTRs patterns corresponded to 50 MITs for 109 strains and 43 orphan patterns. The most frequent patterns were MIT190 (n=12), MIT45 (n=10), and MIT25 (n=9). The Hunter & Gaston discriminatory index (HGDI) of both methodologies used together showed a value of 0.992. In our setting, the HGDI of five loci subset (MIRU10, 16, 23, 26 and 40) contributed most to the discriminatory power of 12-loci format used (HGDI=0.977). The lineage distribution of M. tuberculosis showed that more than 3/4 of strains in Bogotá are commonly found in Latin America, Caribbean, and Europe. This observation might reflect the shared post-Columbus history of Colombia and its Latin-American neighbors as well as strains brought in by 20th century immigrants from Europe. We also demonstrate the usefulness of MIRU-VNTR to detect suspected links among patients and polyclonal infections., (Copyright © 2011 Elsevier B.V. All rights reserved.)

We report the first whole-genome sequence of the Mycobacterium colombiense type strain, CECT 3035, which was initially isolated from Colombian HIV-positive patients and causes respiratory and disseminated infections. Preliminary comparative analyses indicate that the M. colombiense lineage has experienced a substantial genome expansion, possibly contributing to its distinct pathogenic capacity.

This report describes a first case due to a genetically distinct and relatively rare "Beijing-like" strain of Mycobacterium tuberculosis isolated from a 15 years old female patient who died shortly after the initiation of antituberculous therapy with second-line drugs. Positive cultures obtained from lung, kidney and adrenal glands upon autopsy were identified as Mycobacterium tuberculosis complex characterized by an identical 15-banded IS6110-RFLP pattern, and were found to be resistant to all the 4 first-line antituberculous drugs tested (rifampin, isoniazid, ethambutol and streptomycin). Spoligotyping followed by comparison with the SITVIT2 database revealed that the isolate belonged to a rare pattern identified as Spoligotype International Type SIT190, which represents only 1.7% of all the Beijing strains worldwide. We present data on its worldwide distribution and present an evolutionary scenario based on available MIRU typing data., (Copyright 2010 Elsevier B.V. All rights reserved.)

Objective: Characterising clinical Mycobacterium tuberculosis isolates obtained from 1995 to 2006 in Bogotá , Colombia , using standardised IS6110-based RFLP typing for determining phylogenetic relationships. Calculating cases due to recent infection (grouped cases) cf endogenous reactivation (single patterns)., Methods: This retrospective study characterised 137 clinical Mycobacterium tuberculosis isolates obtained in Bogotá from 1995 to 2006. Study variables consisted of gender, age, HIV status, homelessness, Ziehl Neelsen smear result and date of culture. All isolates were freshly identified by phenotypic methods, confirmed by PRA and evaluated for susceptibility to antimicrobial agents according to the proportional method. Mycobacterium tuberculosis cultures were typed by standardised IS6110-based RFLP., Results: All isolates were confirmed as being M. tuberculosis by phenotypic and genotypic methods. 9,4 % monoresistance and 2,9 % MDR (rifampicin- and isoniazid-resistant) were found. 129 M . tuberculosis isolates were genotyped; 96 (74 %) of them presented unique DNA fingerprints, whilst 35 (26 %) were grouped into 17 clusters consisting of two to four isolates. Direct epidemiological links between patients could not be established in most cases. Only HIV status was a significant predictor of clustering amongst the variables being studied (p<0.05)., Conclusion: The results of our study revealed a high proportion of unique DNA fingerprints, suggesting high genetic variability between M. tuberculosis strains in Bogotá , Colombia , meaning that most cases of TB in this study were attributed to endogenous reactivation.

Human clinical isolates of the Mycobacterium avium complex, from hospitals in Bogotá, were studied using a wide range of molecular tests including PCR restriction-enzyme analysis (PRA) of the hsp65 gene. Up to 21 of the isolates were identified as M. avium PRA variant III (Mav III), a variant obtained only from isolates on the American continent. In contrast to previous reports, restriction fragment length polymorphism analysis using IS1245 and IS1311 showed a single copy for each insertion sequence (IS) in the majority (19/21) of the Colombian Mav III isolates under study. In order to analyse whether the ISs were inserted in a relevant genomic region, experimental conditions were established to determine the insertion loci of each single copy of both ISs in the genome. Analysis of genomic insertion loci indicated that both IS1245 and IS1311 were present in areas containing putatively truncated integrases and/or transposases, which may have an influence on the mobility of the inserted IS. In addition, a conserved genomic region was identified for the insertion of IS1311; this region could be part of the IS1311 itself.

Objective: Evaluating the frequency of mycobacterium infection in an HIV-positive population and its influence on medium-term survival, along with clinical and epidemiological factors associated with co-infection., Methods: Several clinical specimens were studied for mycobacteria in a sample of 92 HIV+ patients at the San Juan de Dios teaching-hospital in Bogota, Colombia, during 1996. Factors associated with infection were measured using a prevalence ratio (PR), CI=95%, and logistic regression was used in the multivariable models. The likelihood of survival for three months was measured using Kaplan-Meir curves and factors associated with survival were assessed using Rate ratios and Cox's model., Results: Eight percent of the patients had tuberculosis and 6% of them were found to be infected with atypical mycobacterium. Mycobacterium avium complex (MAC) was the most frequent species, followed by M. fortuitum and M. chelonae. Mixed infections with M. tuberculosis and MAC were diagnosed in one patient and two different species of atypical mycobacterium were isolated in other two cases. Patients suffering from tuberculosis and stages III or IV HIV infection had a 16% survival rate., Conclusions: Tuberculosis-HIV/AIDS frequency and atypical Mycobacterium-HIV/AIDS' association were very similar. The most frequently isolated atypical mycobacterium specie in this study was MAC. Survival rate was lower for patients infected by M. tuberculosis and even lower when a multi-resistant strain was involved. The most important clinical factor associated with M. tuberculosis was the presence of fever and loss of weight with mycobacterial infection. Blood provided the best samples for isolating mycobacteria.

Forty-five mycobacterial strains isolated from 23 Colombian HIV-positive patients were identified as members of the Mycobacterium avium complex (MAC) and were characterized using different molecular approaches. Seven of the isolates showed characteristic features that allowed them to be differentiated from other members of the complex. The isolates had a novel 16S-23S rRNA internal transcribed spacer (ITS 1) gene sequence which is described as a new sequevar, MAC-X. All of the seven novel isolates gave a positive result with the MAC-specific AccuProbe (Gen-Probe), but tested negative for Mycobacterium avium and Mycobacterium intracellulare species-specific probes (64 and 100 % of the isolates, respectively). The novel isolates could be differentiated phenotypically from other members of the MAC on the basis of the production of urease and by a consistent mycolic acid pattern. The novel isolates shared some characteristics with M. avium, such as the avium variant I (av-I) pattern of the hsp65 gene as determined by PCR restriction analysis and a positive PCR result for the mig (macrophage-induced) gene. However, the novel isolates showed a unique 16S rRNA gene sequence. DNA-DNA relatedness values, from 24 to 44 %, confirmed the distinction of the novel isolates from other members of the MAC at the genetic level and their status as members of a separate species. The novel isolates are proposed as representatives of a novel species, Mycobacterium colombiense sp. nov., that is closely related to M. avium within the MAC. The type strain is 10B(T) (=CIP 108962(T)=CECT 3035(T)).

The possibility that the strains included within the Mycobacterium avium complex (MAC), but not belonging either to M. avium or to Mycobacterium intracellulare, may be members of undescribed taxa, has already been questioned by several taxonomists. A very homogeneous cluster of 12 strains characterized by identical nucleotide sequences both in the 16S rDNA and in the 16S-23S internal transcribed spacer was investigated. Similar strains, previously reported in the literature, had been assigned either to the species M. intracellulare on the basis of the 16S rDNA similarity or to the group of MAC intermediates. However, several phenotypical and epidemiological characteristics seem to distinguish these strains from all other MAC organisms. The unique mycolic acid pattern obtained by HPLC is striking as it is characterized by two clusters of peaks, instead of the three presented by all other MAC organisms. All of the strains have been isolated from humans and all but one came from the respiratory tract of elderly people. The clinical significance of these strains, ascertained for seven patients, seems to suggest an unusually high virulence. The characteristics of all the strains reported in the literature, genotypically identical to the ones described here, seem to confirm our data, without reports of isolations from animals or the environment or, among humans, from AIDS patients. Therefore, an elevation of the MAC variant was proposed and characterized here, with the name Mycobacterium chimaera sp. nov.; this increases the number of species included in the M. avium complex. The type strain is FI-01069T (=CIP 107892T=DSM 44623T).

Mycobacterium avium complex (MAC) infections are the most frequent systemic infections associated with advanced AIDS. DNA probes for accurate identification of mycobacteria are available but are very expensive in many Latin American settings. Consequently, most Latin American diagnostic laboratories employ inaccurate and outdated tests for mycobacteria identification. Therefore, PCR restriction analysis (PRA) of the hsp65 gene was evaluated for the identification of 163 MAC human isolates originated from Spain and South America. The predominant PRA type in each country was: M. avium type I in Argentina (23/42, 55%) and Brazil (48/72, 67%), M. avium type II in Spain (18/26, 69%) and M. avium type III in Colombia (10/23, 43%). The Colombia frequency is noteworthy, since the PRA type III was quite infrequent in the other three countries. Furthermore, its presence has not been reported outside the Americas. The advantages and disadvantages of PRA in diagnostic mycobacteriology are discussed.

Background: The non invasive diagnosis of amebic liver abscess allows the use of empirical therapy without the requirement of invasive diagnostic procedures., Aim: To determine the discriminatory capacity of clinical, laboratory and ultrasound studies for the etiological diagnosis of liver abscess., Patients and Methods: Sixty one patients were initially included in this prospective study, but 12 did not comply with the inclusion criteria. Of the rest, 29 (59%) had an amebic liver abscess, 16 (33%) had a pyogenic liver abscess and four (8%) had an abscess of mixed etiology. Blood cultures were done in 42 patients. Ultrasound guided needle aspiration was done in 7 patients with amebic liver abscess and 13 patients with non amebic liver abscess., Results: The clinical picture and ultrasound findings were similar in all types of amebic abscess. ELISA test for IgG anti-Entamoeba histolytica antibodies were positive in 100% of patients with amebic liver abscess. Antibodies measured by gel diffusion were positive in 93%. All patients with mixed liver abscess had positive antibodies and some of them positive culture. Blood cultures were positive for anaerobic bacteria in five patients. Cultures of aspirated material were positive in 7 patients (obligate anaerobic bacteria in 3 and facultative anaerobic bacteria in the rest). The most common complications, whatever the etiology, were right pleural effusion and systemic inflammatory response., Conclusions: A final model of binomial regression analysis revealed that age under 40 years, an hematocrit greater than 35% and an elevation in prothrombin time of less than 1.5 seconds had enough discriminatory capacity for the diagnosis of amoebic liver abscess.

A case is reported of a woman who lived in a rural area with a chronic illness that consisted of weight loss and abdominal pain in the epigastrium and upper right quadrant. The initial diagnosis was a mass in the liver, which was later, demonstrated, both by direct and histological examination, to be an abscess caused by Ascaris lumbricoides. Eggs of Ascaris lumbricoides and abundant Charcot-Leyden Crystals were found.

During a study of intestinal parasitic infections in human immunodeficiency virus-positive patients, a parasite belonging to the phylum Myxozoa, recently described from human samples, was identified in one sample. When this parasite was stained by the modified Ziehl-Neelsen staining method, the features of the spores were identified: they were pyriform in shape, had thick walls, and had one suture and two polar capsules, with each one having four or five coils. The suture and two polar capsules were observed with the chromotrope-modified stain. The number of stools passed was more than 30 per day, but oocysts of Isospora belli were also found. Upon reexamination of some formalin- or merthiolate-iodine-formaldehyde-preserved samples an identical parasite was found in another sample from a patient presenting with diarrhea. Strongyloides stercoralis larvae and eggs of Hymenolepis nana and Ascaris lumbricoides were also found in this sample. Given that both patients were also infected with other pathogens that cause diarrhea, the possible pathogenic role of this parasite could not be established. The probable route of infection also could not be established.