Protocol for the selection of Mycobacterium tuberculosis spontaneous resistant mutants to d-cycloserine

Mycobacterium tuberculosis (MTB) is known for its adaptive capability in developing resistance to antibiotics, through the selection of spontaneous mutations that arise during treatment. Generating spontaneous antibiotic-resistant mutants in vitro is challenging but necessary for studying this phenomenon. A protocol was designed and tested to select stable, MTB spontaneous, d-cycloserine (DCS) resistant mutants. Twenty-four colonies resistant to DCS were selected, demonstrating an increase between 1 and 4 times the Minimum Inhibitory Concentration (MIC) set for Mycobacterium tuberculosis H37Rv ATCC 27294 reference strain.

Genome-Wide Association Studies (GWAS) Approaches for the Detection of Genetic Variants Associated with Antibiotic Resistance: A Systematic Review

Antibiotic resistance is a significant threat to public health worldwide. Genome-wide association studies (GWAS) have emerged as a powerful tool to identify genetic variants associated with this antibiotic resistance. By analyzing large datasets of bacterial genomes, GWAS can provide valuable insights into the resistance mechanisms and facilitate the discovery of new drug targets. The present study aimed to undertake a systematic review of different GWAS approaches used for detecting genetic variants associated with antibiotic resistance. We comprehensively searched the PubMed and Scopus databases to identify relevant studies published from 2013 to February 2023. A total of 40 studies met our inclusion criteria. These studies explored a wide range of bacterial species, antibiotics, and study designs. Notably, most of the studies were centered around human pathogens such as Mycobacterium tuberculosis, Escherichia coli, Neisseria gonorrhoeae, and Staphylococcus aureus. The review seeks to explore the several GWAS approaches utilized to investigate the genetic mechanisms associated with antibiotic resistance. Furthermore, it examines the contributions of GWAS approaches in identifying resistance-associated genetic variants through binary and continuous phenotypes. Overall, GWAS holds great potential to enhance our understanding of bacterial resistance and improve strategies to combat infectious diseases.

Implementation of an integrated care strategy for child contacts of tuberculosis patients: a quasi-experimental study protocol

BACKGROUND

Childhood tuberculosis continues to be a major public health problem. Although the visibility of the epidemic in this population group has increased, further research is needed.

OBJECTIVE

To design, implement and evaluate an integrated care strategy for children under five years old who are household contacts of bacteriologically confirmed pulmonary tuberculosis patients in Medellín and the Metropolitan Area.

METHODS

A quasi-experimental study in which approximately 300 children who are household contacts of bacteriologically confirmed pulmonary tuberculosis patients from Medellín and the Metropolitan Area will be evaluated and recruited over one year. A subgroup of these children, estimated at 85, who require treatment for latent tuberculosis, will receive an integrated care strategy that includes: some modifications of the current standardized scheme in Colombia, with rifampicin treatment daily for four months, follow-up under the project scheme with nursing personnel, general practitioners, specialists, professionals from other disciplines such as social work, psychology, and nutritionist. Additionally, transportation and food assistance will be provided to encourage treatment compliance. This strategy will be compared with isoniazid treatment received by a cohort of children between 2015 and 2018 following the standardized scheme in the country. The study was approved by the CIB Research Ethics Committee and UPB.

CLINICALTRIALS

gov identifier NCT04331262.

DISCUSSION

This study is expected to contribute to the development of integrated care strategies for the treatment of latent tuberculosis in children. The results will have a direct impact on the management of childhood tuberculosis contributing to achieving the goals proposed by the World Health Organization's End TB Strategy.

TRIAL REGISTRATION

ClinicalTrials.gov identifier NCT04331262 . Implementation of an Integrated Care Strategy for Children Contacts of Patients with Tuberculosis. Registered 2 April 2020.

Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia

Mycobacterium tuberculosis (Mtb) lineage 4 is responsible for the highest burden of tuberculosis (TB) worldwide. This lineage has been the most prevalent lineage in Colombia, especially in the North-Eastern (NE) area of Medellin, where it has been shown to have a high prevalence of LAM9 SIT42 and Haarlem1 SIT62 sublineages. There is evidence that regardless of environmental factors and host genetics, differences among sublineages of Mtb strains play an important role in the course of infection and disease. Nevertheless, the genetic basis of the success of a sublineage in a specific geographic area remains uncertain. We used a pan-genome-wide association study (pan-GWAS) of 47 Mtb strains isolated from NE Medellin between 2005 and 2008 to identify the genes responsible for the phenotypic differences among high and low prevalence sublineages. Our results allowed the identification of 12 variants in 11 genes, of which 4 genes showed the strongest association to low prevalence (mmpL12, PPE29, Rv1419, and Rv1762c). The first three have been described as necessary for invasion and intracellular survival. Polymorphisms identified in low prevalence isolates may suggest related to a fitness cost of Mtb, which might reflect a decrease in their capacity to be transmitted or to cause an active infection. These results contribute to understanding the success of some sublineages of lineage-4 in a specific geographical area.

Changes in Antimicrobial Resistance and Etiology of Blood Culture Isolates: Results of a Decade (2010-2019) of Surveillance in a Northern Region of Colombia

Background

Bloodstream infections (BSI) are important causes of morbidity and mortality worldwide. Antimicrobial surveillance is essential for identifying emerging resistance and generating empirical treatment guides, the purpose of this study is to analyze trends in antimicrobial susceptibility of BSI from 2010 to 2019 in healthcare institutions from Medellin and nearby towns in Colombia.

Methods

A Whonet database was analyzed from the GERMEN antimicrobial surveillance network; frequency and antibiotic susceptibility trends were calculated on more frequent microorganisms using Mann Kendall and Sen’s Slope Estimator Test.

Results

61,299 isolates were included; the three microorganisms more frequent showed a significant increasing trend through time E. coli (Sen’s Slope estimator = 0.7 p = <0.01) S. aureus (Sen’s Slope estimator = 0.60 p = <0.01) and K. pneumonia (Sen’s Slope estimator = 0.30 p = <0.01). E. coli showed a significant increase trend in cefepime and ceftazidime resistance, while K. pneumoniae showed a significant increase in resistance to cefepime, ciprofloxacin, and gentamicin. P. aeruginosa increases its susceptibility to all analyzed antibiotics and S. aureus to oxacillin. No increasing trend was observed for carbapenem resistance.

Conclusion

An upward trends was observed in more frequent microorganisms and resistance to third and fourth-generation cephalosporins for E. coli and K pneumoniae; in contrast, not increasing trends in antibiotic resistance was observed for P. aeruginosa and S. aureus. The essential role of AMR-surveillance programs is to point out and identify these trends, which should improve antibiotic resistance control.

Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment

Approximately 85 000 deaths globally in 2019 were due to drug-resistant tuberculosis (TB), which corresponds to 7% of global deaths attributable to bacterial antimicrobial resistance [1]. Yet concerns have been mounting that drug-resistant TB was being underestimated because the approaches to define susceptibility and resistance to anti-TB agents had not kept up with those used for other major bacterial pathogens [2–9]. Here, we outline the recent, evidence-based initiatives spearheaded by the World Health Organization (WHO) and others to update breakpoints (traditionally referred to as critical concentrations (CCs)) that are used for phenotypic antimicrobial susceptibility testing (AST), also called drug susceptibility testing in the TB literature.

Inappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance. https://bit.ly/3i43wb6

Resultados de uma técnica modificada de reconstrução assistida por artroscopia para instabilidade lateral do tornozelo

Objective  The present study assesses the results of a minimally invasive surgical technique for acute and chronic ankle instability management.

Methods  The present case series study retrospectively evaluated 40 patients undergoing arthroscopic-assisted percutaneous ankle ligament reconstruction from 2013 to 2019.

Results  The present study included 17 males and 23 females with an average age of 38.3 years old. Postintervention follow-up using American Orthopaedic Foot and Ankle Society (AOFAS) Ankle-Hindfoot scores identified improvement of > 30 points in function and pain control. The most frequently occurring associated injuries were osteochondral (35%). No patient required reintervention or had infection during follow-up.

Conclusion  The technique in the present study is easy and achieves satisfactory results for function and pain control.

Level of Evidence IV.

Contribución del uso de XPERT MTB/RIF y su costo-efectividad en el diagnóstico de tuberculosis pulmonar y la resistencia a rifampicina: una comparación con métodos diagnósticos no moleculares

Introducción: La tuberculosis es un problema de salud pública; su control requiere diagnóstico temprano y tratamiento oportuno. Xpert MTB/RIF® es una tecnología diagnóstica basada en PCR en tiempo real, detecta el Complejo Mycobacterium tuberculosis y la susceptibilidad a rifampicina. Objetivo: Determinar la contribución del Xpert MTB/RIF y su costo-efectividad en la detección de tuberculosis y la resistencia a rifampicina en muestras respiratorias al compararlo con métodos de diagnóstico no moleculares. Materiales y Métodos: Se analizaron 1.574 muestras de pacientes con sospecha de tuberculosis pulmonar que fueron procesadas para microscopía con coloración fluorescente de auramina-rodamina, Xpert MTB/RIF y cultivo en BACTEC MGIT 960. Los resultados obtenidos se compararon entre los métodos no moleculares y los moleculares para la detección de M. tuberculosis y susceptibilidad a rifampicina y se realizó un análisis comparativo de costos y costo efectividad. Resultados: 19,2% de las muestras fueron positivas por alguna de las técnicas usadas. Xpert MTB/RIF detectó M. tuberculosis en 90,4% del total de muestras positivas con un índice Kappa de 0,77 (IC95%: 0,74-0,82) comparado con el cultivo. La resistencia a rifampicina por Xpert fue 8,1%, sensibilidad 94,1% (IC95%: 73,0–99,0%), especificidad 98,4% (IC95%: 95,5–99,5%) y Kappa de 0,88 (IC95%: 0,76-1,00). La razón incremental de costo efectividad (RICE) fue menor en Xpert MTB/RIF comparada con el cultivo. Conclusión: Xpert MTB/RIF es una prueba eficiente y costo efectiva en la detección de casos de M. tuberculosis en muestras pulmonares comparado con los métodos de diagnóstico basados en cultivo, sin embargo y a diferencia del Xpert MTB/RIF, estos pueden aportar en el diagnóstico con el aislamiento de especies de micobacterias no tuberculosas y la susceptibilidad a isoniazida y otros medicamentos.

Mycobacterium abscessus complex: A Review of Recent Developments in an Emerging Pathogen

Mycobacterium abscessus complex (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.

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

Advancements that occurred during the last years in the diagnosis of Mycobacterium tuberculosis (Mtb), 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 Mtb, 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^-1 and a limit of quantification (LOQ) of 2.12 ng mL^-1. 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^-1) compared with non-tuberculosis infected patients (values below the LOQ of the assay).

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

Toxin-antitoxin systems shows variability among Mycobacterium tuberculosis lineages

The toxin-antitoxin (TA) systems are operons involved in the formation of persistent cells and in stress situations in microorganism. TA systems are widely distributed in Mycobacterium tuberculosis (MTB). The objective of this study was to determine the distribution and variability of protein sequences of TA systems in seven MTB lineages. Protein prediction on 73 genomes of different lineage was made using Prodigal, and profile hidden Markov models (PHMMs) of 225 reference TA proteins were constructed with HMMER. An homology search was made comparing the predicted proteins to PHMMs. Consecutive proteins that matched PHMMs (forming an operon) were selected. Thereafter, clustering of orthologous genes was made for further mutation scanning through multiple alignments. All proteins found belong to TA types II and IV, and 45 proteins were found completely conserved. Six uncharacterized antitoxins homologous to VapB11, VapB5, VapB45, VapB13, ParD1 and RelB were found. Multiple alignments revealed differences among lineages with specific mutations suitable for genotyping. Significant changes in amino acid sequences caused by frameshift mutations were found in 46 TA proteins.

Identificación directa de microorganismos a partir de muestras de orina y hemocultivos utilizando MALDI-TOF

Objetivo: evaluar la utilidad de la identificación directa de microorganismos en muestras de orina y hemocultivos empleando la tecnología MALDI-TOF MS, me­diante el análisis de concordancia en la identificación, tiempo necesario para la obtención de un resultado y costos asociados a cada método de identificación.Materiales y métodos: estudio descriptivo de febrero de 2017 a octubre de 2017. Se seleccionaron a conveniencia 180 muestras de orinas y 129 hemocultivos de pacientes de la Clínica El Rosario, Medellín, se realizó identificación del microorganismo directamente de la muestra y a partir del cultivo por MALDI-TOF (Vitek® MS‚ bioMérieux). Se analizaron los costos y tiempo, para determinar la utilidad de esta tecnología en los procesos del laboratorio de microbiología.Resultados: En el 79,6% de las orinas positivas y en el 76% de los hemocultivos se obtuvo una identificación de microorganismos directamente por MALDI-TOF MS. El tiempo de identificación directa tuvo una media de 6 horas y por cultivo una media de 29 horas. El costo total por aislamiento identificado de forma directa (sin incluir el valor del equipo) fue de $8.200 (2,58 USD) en muestras de orina y de $9.720 (3,06 USD) en hemocultivos positivos. El equipo introduce un costo variable en cada identificación de acuerdo con el número de identificaciones que se realicen en el laboratorio.Conclusiones: Estos resultados confirman la utilidad del MALDI-TOF MS para generar identificaciones más rápidas cuando se utiliza directamente en muestras clínicas, sin embargo, tiene un bajo desempeño en la identificación directa de bacterias gram positivas, siendo necesario evaluar otros protocolos que mejoren la identificación directa. El costo de los consumibles es bajo, pero la adquisición de esta tecnología introduce un costo variable que depende del volumen de muestras identificadas en el laboratorio. 

Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

In the version of this article initially published, the URL listed for TubercuList was incorrect. The correct URL is https://mycobrowser.epfl.ch/. The error has been corrected in the HTML and PDF versions of the article.

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

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.

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

La espectrometría de masas MALDI-TOF en el laboratorio de microbiología clínica

Los métodos fenotípicos empleados para la identificación de microorganismos dependen de procesos metabólicos que requieren de tiempos de incubación mínimos para alcanzar resultados confiables. La espectrometría de masas MALDI-TOF (desorción/ionización láser asistida por una matriz con detección de masas por tiempo de vuelo) se ha instaurado como una metodología relevante para la identificación de microorganismos mediante el análisis de proteínas, a través de la creación de un espectro de masas específico de género y especie. En esta revisión, se presenta MALDI-TOF MS como una tecnología precisa para la identificación de bacterias, levaduras, mohos, en incluso de virus, que además, permite la reducción del tiempo para obtener un resultado de identificación, que puede impactar los costos de atención y duración de la estancia hospitalaria. La identificación de microorganismos directamente de muestras biológicas y la detección de mecanismos de resistencia a antimicrobianos, prometen un mayor impacto clínico y epidemiológico con el desarrollo e implementación de esta tecnología en los laboratorios de microbiología clínica.

Caracterización de los procedimientos para la realización de hemocultivos en pacientes adultos, en instituciones hospitalarias del Área Metropolitana del Valle de Aburrá

Objetivo: Caracterizar procedimientos para la toma, análisis, reporte y aseguramiento de la calidad en hemocultivos en pacientes adultos, en instituciones hospitalarias.Material y método: Estudio descriptivo en 15 hospitales de Medellín y alrededores. Se empleó un formulario semiestructurado para recolectar la información, se utilizó SPSS® para el análisis.Resultados: Todas las instituciones tienen protocolos basados en fuentes de autoridad reconocida; con diferencias importantes en procesos pre-analíticos y postanalíticos. Los productos más empleados para la antisepsia fueron gluconato de clorhexidina al 2-4% (66,7%) y alcohol isopropílico o etílico al 70% (20,0%), con discrepancias en los tiempos de acción. El 73,3% emplea guantes estériles y la misma proporción usa sistema abierto (jeringa) para la venopunción. En el 46,6% se toman dos botellas aerobias y una anaerobia por episodio y en 33,3% dos botellas aerobias. El 66,6% lleva un indicador de contaminación, 53,3% de positividad y 26,6% de volumen de sangre. La tasa promedio de hemocultivos contaminados durante el semestre de seguimiento fue 1,61%.Conclusión: Se observa heterogeneidad en los procedimientos, especialmente en fases pre-analítica y post-analítica. En la búsqueda de la excelencia y la seguridad del paciente son necesarios protocolos estandarizados e indicadores para medir y controlar el desempeño de los hemocultivos.

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

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.

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

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.

Rapid diagnosis of pulmonary tuberculosis

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.

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

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.

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

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

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.

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

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.

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

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.

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

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.

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

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.

Assessment of mycobacteremia detection as a complementary method for the diagnosis of tuberculosis in HIV-infected patients

The purpose of this investigation was to assess the usefulness of mycobacteremia detection in human immunodeficiency virus (HIV) patients with suspected tuberculosis. The study included 47 patients with suspected tuberculosis and confirmed HIV infection. A first blood sample was incubated in a BACTEC 9050 MB system, while white blood cells isolation was performed on a second blood specimen before incubation in a BACTEC MGIT 960 system. The third specimen was taken from the affected organs of each patient according to their clinical profile. Twelve (25.5%) patients were positive for mycobacterial infection identified by any of the methods used. Ten (21.2%) were positive for Mycobacterium tuberculosis and 2 (4.3%) for M. avium. Six patients were diagnosed by the culture of specimen from affected organs only, whilst three other patients were positive exclusively for blood cultures. Three additional patients were diagnosed by both methods. Four patients with negative cultures were ultimately diagnosed with tuberculosis by measuring the adenosine deaminase levels. Mycobacteremia detection can be used to increase the sensitivity of the diagnosis of tuberculosis and other mycobacteria in patients with HIV. However, it cannot be used as the sole diagnostic method. Clinical specimen cultures do not provide 100% diagnostic accuracy and it is, therefore, critical to further improve the mycobacteria detection sensitivity.

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

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 </=2 days. However, qPCR identification of resistant isolates, particularly for isolates with mixed RIF-susceptible and RIF-resistant bacteria, is reader dependent and limits its clinical use. The aim of this study was to develop an objective, reader-independent method to define rpoB mutants using beacon qPCR. This would facilitate the transition from a research protocol to the clinical setting, where high-throughput methods with objective interpretation are required. For this, DNAs from 107 M. tuberculosis clinical isolates with known susceptibility to RIF by culture-based methods were obtained from 2 regions where isolates have not previously been subjected to evaluation using molecular beacon qPCR: the Texas-Mexico border and Colombia. Using coded DNA specimens, mutations within an 81-bp hot spot region of rpoB were established by qPCR with 5 beacons spanning this region. Visual and mathematical approaches were used to establish whether the qPCR cycle threshold of the experimental isolate was significantly higher (mutant) compared to a reference wild-type isolate. Visual classification of the beacon qPCR required reader training for strains with a mixture of RIF-susceptible and RIF-resistant bacteria. Only then had the visual interpretation by an experienced reader had 100% sensitivity and 94.6% specificity versus RIF resistance by culture phenotype and 98.1% sensitivity and 100% specificity versus mutations based on DNA sequence. The mathematical approach was 98% sensitive and 94.5% specific versus culture and 96.2% sensitive and 100% specific versus DNA sequence. Our findings indicate the mathematical approach has advantages over the visual reading, in that it uses a Microsoft Excel template to eliminate reader bias or inexperience, and allows objective interpretation from high-throughput analyses even in the presence of a mixture of RIF-resistant and RIF-susceptible isolates without the need for reader training.

Rapid detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis by the direct thin-layer agar method

We evaluated thin-layer agar (TLA) for the detection of resistance of Mycobacterium tuberculosis to rifampicin (RMP) and isoniazid (INH) as a direct method in patients at risk of multidrug-resistant tuberculosis (MDR-TB). Quadrant TLA plates contain 7H10 Middlebrook growth control, para-nitrobenzoic acid, INH and RMP. Detection of RMP and INH resistance by TLA was compared to that in indirect conventional drug susceptibility testing (DST) and conventional culture media. Median time for growth was respectively 22, 10 and 7.6 days for Löwenstein-Jensen, TLA and the Mycobacterial Growth Indicator Tube. TLA sensitivity, specificity and predictive values for RMP and INH resistance were 100%. Time to resistance detection was respectively 11 and 11.5 days for RMP and INH. TLA showed a rapid turnaround time and performance comparable to conventional DST methods.

Mycobacterium tuberculosis strains of the Beijing genotype are rarely observed in tuberculosis patients in South America

The frequency of the Beijing genotype of Mycobacterium tuberculosis as a cause of tuberculosis (TB) in South America was determined by analyzing genotypes of strains isolated from patients that had been diagnosed with the disease between 1997 and 2003 in seven countries of the subcontinent. In total, 19 of the 1,202 (1.6%) TB cases carried Beijing isolates, including 11 of the 185 patients from Peru (5.9%), five of the 512 patients from Argentina (1.0%), two of the 252 Brazilian cases (0.8%), one of the 166 patients from Paraguay (0.6%) and none of the samples obtained from Chile (35), Colombia (36) and Ecuador (16). Except for two patients that were East Asian immigrants, all cases with Beijing strains were native South Americans. No association was found between carrying a strain with the Beijing genotype and having drug or multi-drug resistant disease. Our data show that presently transmission of M. tuberculosis strains of the Beijing genotype is not frequent in Latin America. In addition, the lack of association of drug resistant TB and infection with M. tuberculosis of the Beijing genotype observed presently demands efforts to define better the contribution of the virulence and lack of response to treatment to the growing spread of Beijing strains observed in other parts of the world.

High prevalence of infections in patients with systemic lupus erythematosus and pulmonary haemorrhage

The main objective of this study is to describe the presence of infections in patients with pulmonary haemorrhage and systemic lupus erythematosus. Patients with systemic lupus erythematosus and pulmonary haemorrhage were thoroughly evaluated in the first 48 hours with imaging plus bronchoscopy and bronchoalveolar fluid analysis. If needed, videoassisted thoracoscopy and lung biopsy were performed too. In all, search for bacterial, mycobacterial and fungal infections proceeded. Appropriate blood, bronchoalveolar fluid and tissue cultures were taken. Patients were treated with antibiotics and corticosteroids in case of infection. Otherwise, they received initial intravenous methylprednsiolone pulses for 3 days as standard therapy for pulmonary haemorrhage in systemic lupus erythematosus. Additional treatment with immunosuppressives was further decided by the treating physicians. Fourteen events in 13 patients were evaluated. In eight events (57%), an infection was demonstrated. Aetiological agents included Pseudomonas sp. and Aspergillus fumigatus. Four patients died, three of them because of the pulmonary infection and one because of cerebral haemorrhage secondary to severe systemic hypertension, 48 hours after methylprednisolone treatment. Patients with systemic lupus erythematosus and pulmonary haemorrhage have a high prevalence of infections. The influence of pulmonary haemorrhage in the setting of systemic lupus erythematosus needs further study to establish adequate treatment and to reduce the high mortality of this complication.

Multicenter evaluation of mycobacteria identification by PCR restriction enzyme analysis in laboratories from Latin America and the Caribbean

The identification of mycobacterial species in clinical isolates is essential for making patient care decisions. Polymerase chain reaction (PCR) restriction enzyme analysis (PRA) is a simple and rapid identification method, based on amplification of 441 bp of the hsp65 gene and restriction with BstEII and HaeIII. As a contribution to the validation of PRA, a multicenter study was performed in eight laboratories located in Argentina, Brazil, Colombia, Chile, and Guadeloupe. Each laboratory received 18 coded isolates from the collection of the Institute of Tropical Medicine (Antwerp, Belgium), representing duplicates of nine laboratory strains: Mycobacterium terrae CIPT 140320001, Mycobacterium scrofulaceum CIPT 140220031, Mycobacterium flavescens ATCC 14474, Mycobacterium triviale ATCC 23292, Mycobacterium nonchromogenicum ATCC 19530, Mycobacterium chitae ATCC 19627, Mycobacterium abscessus ATCC 19977, Mycobacterium kansasii ATCC 12478, and Mycobacterium peregrinum ATCC 14467. A detailed protocol including amplification, enzymatic digestion, and gel preparation was provided to each laboratory. Two laboratories identified correctly all 18 (100%) isolates, one identified correctly 17 (94.5%), two identified 14 (77.7%), one identified 11 (61%), and two identified 8 (44.4%) isolates. Errors detected in laboratories with more than 77% accuracy were associated with electrophoresis running conditions and an unspecific amplicon produced by a single strain. Lower accuracy was mainly related to inappropriate use of DNA markers and insufficient training in interpretation of patterns. In conclusion, the PRA method was readily implemented in some Latin American and Caribbean laboratories of mycobacteria, but improvements in critical points, as gel running conditions and training in interpretiation of patterns, are needed in order to improve accuracy. In others, improvement in critical points is still necessary.

[Five year experience with thin layer agar medium for rapid diagnosis of tuberculosis]

Tuberculosis represents a public health problem worldwide, mainly in developing countries where 95% of the cases occur. New technologies that support rapid diagnosis are not available in these settings because of high cost. New, rapid, and less expensive techniques are necessary before diagnosis can be improved in these areas. The present work compared the performance of a rapid and costly culture media, thin layer agar (CD7H11), with the traditional Lowenstein-Jensen (LJ) culture method. For this comparison, 1,809 clinical specimens were processed for diagnosis of mycobacterial infections. Clinical samples were processed according to standard procedures and cultured concomitantly in LJ and CD7H11. The times required to obtain an isolate were compared for culture media. Sensitivity (S), specificity (Sp), predictive values (PPV, NPV) and agreement (kappa coefficient) were calculated for CD7H11, with LJ serving as the gold standard. CD7H11 showed S to be 73.5% (C.I.95%: 69.6-80.4), Sp to be 99.2% (C.I.95%: 98.8-99.6), PPV 90.4% (C.I.95%: 85.3-95.6) and NPV 97.6% (C.I.95%: 96.8-98.3). Agreement had a kappa coefficient of 0.52. The mean time for CD7H11 was 11 days (SD+/-4.9) compared with 26.5 (SD+/-8.6) days for LJ. Similar results were obtained in a comparison of respiratory and multibacillary clinical samples. In extrapulmonary samples and those with lowered bacillus count, CD7H11 demonstrated a lower sensitivity. The concomitant use of both culture media enhanced sensitivity of detection. CD7H11 proved a simple and rapid technique for culturing mycobacteria and can be combined with traditional methods for improving laboratory capability for diagnosis of tuberculosis.