Characterization of the Proportion of Clustered Tuberculosis Cases in Guatemala: Insights from a Molecular Epidemiology Study, 2010-2014.

There is little information about the amount of recent tuberculosis transmission in low-income settings. Genetic clustering can help identify ongoing transmission events. A retrospective observational study was performed on Mycobacterium tuberculosis isolates from persons living with HIV (PLHIV) and HIV-seronegative participants who submitted samples to a referral tuberculosis laboratory in Guatemala City, Guatemala from 2010 to 2014. Genotyping results were classified according to the international spoligotyping database, SITVIT2. Spoligotype patterns were categorized as clustered or nonclustered depending on their genotype. The proportion of clustering and the index of recent transmission index (RTIn-1) were estimated. In the RTIn-1 method, clustered cases represent recent transmission, whereas nonclustered cases represent reactivation of older tuberculosis infections. As a secondary aim, the potential risk factors associated with clustering in isolates from the subset of participants living with HIV were explored. From 2010 to 2014, a total of 479 study participants were confirmed as culture-positive tuberculosis cases. Among the 400 available isolates, 71 spoligotype patterns were identified. Overall, the most frequent spoligotyping families were Latin American-Mediterranean (LAM) (39%), followed by T (22%) and Haarlem (14%). Out of the 400 isolates, 365 were grouped in 36 clusters (range of cluster size: 2-92). Thus, the proportion of clustering was 91% and the RTIn-1 was 82%. Among PLHIV, pulmonary tuberculosis was associated with clustering (OR = 4.3, 95% CI 1.0-17.7). Our findings suggest high levels of ongoing transmission of M. tuberculosis in Guatemala as revealed by the high proportion of isolates falling into genomic clusters.

Análisis filogenético de variantes de VIH-1, mediante la subtipificación de las secuencias de la región pol de VIH-1, período 2010-2015 / Phylogenetic analysis of HIV-1 variants of a comprehensive HIV clinic in Guatemala, through the subtyping of the pol-HIV-1 region sequences obtained during the period 2010-2015

El genoma del VIH contiene nueve genes, tres de estos genes (gag, pol y env) codifican proteínas estructurales. Existen dos variantes principales de este virus, VIH-1 y VIH-2. El primero es el causante de la mayoría de las infecciones a nivel mundial, actualmente se han identificado nueve subtipos de VIH-1 y 58 formas recombinantes circulantes (FRC). En Centroamérica, el subtipo B del VIH-1 es el causante de la mayoría de los casos de VIH positivo; en Guatemala se ha reportado la presencia de subtipo B, de formas recombinantes BF1 y del subtipo C; sin embargo, actualmente no existen análisis filogenéticos que indiquen las variantes de este subtipo. Debido a lo anterior, el objetivo del estudio fue llevar a cabo la subtipificación de 400 secuencias de la región pol del VIH-1 obtenidas de 400 pacientes VIH-1 positivos, en una clínica de atención integral de Guatemala del 2010 al 2015. Para determinar los distintos subtipos de VIH-1 presentes en Guatemala se realizó la subtipificación de las secuencias obtenidas por la prueba de genotipo en formato FASTA, con la herramienta REGA HIV-1 Subtyping Tool Version 3.0. Con el fin de determinar la relación entre las variantes de VIH-1, se realizó un alineamiento de secuencias y árboles filogenéticos utilizando el método Neighbor Joining y Máxima Verosimilitud con 100 réplicas bootstrap, con el programa MEGA 7.0.21. Se determinó que el subtipo con mayor frecuencia de las secuencias analizadas es el subtipo B con un 71.5 %, seguido de la forma recombinante BD (16.75 %) y el subtipo B-like (7.75 %)

The HIV genome contains nine genes, three of these genes (gag, pol, and env) encode structural proteins. There are two main variants of this virus, HIV-1 and HIV-2. The first one (HIV-1) is the cause of most infections worldwide, of which nine subtypes and 58 circulating recombinant forms (CRF) have been identified. In Central America, subtype B of HIV-1 is the cause of the majority of HIV positive cases. In Guatemala, it has been reported the presence of subtype B, recombinant forms BF1 and subtype C. However, no phylogenetic analysis has been performed to indicate the variants of this subtype. The aim of the study was to subtype 400 sequences of the pol region of HIV-1, of samples that were obtained from a care clinic during the period 2010 to 2015. To determine the different subtypes of HIV-1 present in Guatemala, the subtyping of the sequences obtained by the genotype test, in FASTA format, was performed with REGA HIV-1 Subtyping Tool - Version 3.0. In order to determine the relationship between HIV-1 variants, an alignment of sequences and phylogenetic trees was performed using the Neighbor Union and Maximum Likelihood method with 100 bootstrap replicas, with the MEGA 7.0.21 program. It was determined that the subtypes with the highest prevalence of the studied sequences are the subtype B (71.5 %), recombinant BD (16.75 %), and subtype B-like (7.75 %)

Annotated Genome Sequences of 16 Lineage 4 Mycobacterium tuberculosis Strains from Guatemala.

Whole-genome sequencing has resulted in new insights into the phylogeography of Mycobacterium tuberculosis However, only limited genomic data are available from M. tuberculosis strains in Guatemala. Here we report 16 complete genomes of clinical strains belonging to the Euro-American lineage 4, the most common lineage found in Guatemala and Central America.

High Mortality and Coinfection in a Prospective Cohort of Human Immunodeficiency Virus/Acquired Immune Deficiency Syndrome Patients with Histoplasmosis in Guatemala.

Histoplasmosis is one of the most common and deadly opportunistic infections among persons living with human immunodeficiency virus (HIV)/acquired immune deficiency syndrome in Latin America, but due to limited diagnostic capacity in this region, few data on the burden and clinical characteristics of this disease exist. Between 2005 and 2009, we enrolled patients ≥ 18 years of age with suspected histoplasmosis at a hospital-based HIV clinic in Guatemala City. A case of suspected histoplasmosis was defined as a person presenting with at least three of five clinical or radiologic criteria. A confirmed case of histoplasmosis was defined as a person with a positive culture or urine antigen test for Histoplasma capsulatum. Demographic and clinical data were also collected and analyzed. Of 263 enrolled as suspected cases of histoplasmosis, 101 (38.4%) were confirmed cases. Median time to diagnosis was 15 days after presentation (interquartile range [IQR] = 5-23). Crude overall mortality was 43.6%; median survival time was 19 days (IQR = 4-69). Mycobacterial infection was diagnosed in 70 (26.6%) cases; 26 (25.7%) histoplasmosis cases were coinfected with mycobacteria. High mortality and short survival time after initial symptoms were observed in patients with histoplasmosis. Mycobacterial coinfection diagnoses were frequent, highlighting the importance of pursuing diagnoses for both diseases.

Detección de los genes de carbapenemasas blaKPC y blaNDM en aislamientos de Klebsiella pneumoniae del Hospital General San Juan de Dios de la ciudad de Guatemala

La resistencia a los antibióticos constituye uno de los problemas más relevantes de salud pública en todo el mundo. Las enterobacterias productoras de carbapenemasas representan la mayor amenaza. Las carbapenemasas son potentes enzimas que inactivan los antibióticos carbapenémicos y en general, a todos los antibióticos betalactámicos. Las consecuencias para el tratamiento de las infecciones causadas por estas bacterias son relevantes, ya que los carbapenemes son de las últimas opciones disponibles para bacterias multirresistentes. Esta investigación tuvo como objetivos determinar por medio de la reacción en cadena de la polimerasa (PCR) punto final, la presencia de los genes de carbapenemasas blaKPC (Klebsiella pneumoniae carbapenemasa) y blaNDM (New Delhi Metalobetalactamasa) en aislamientos de K. pneumoniae del Hospital General San Juan de Dios de la ciudad de Guatemala, caracterizar el tipo de muestra y definir el servicio del hospital donde se aislaron este tipo de bacterias. Se analizaron 54 aislamientos de K. pneumoniae resistentes a carbapenemes (imipenem y/o meropenem), 49 (91%) fueron portadoras del gen blaNDM. Estas bacterias se aislaron con más frecuencia en muestras de sangre (37%) y orina (14%). En esta investigación, el 53% de aislamientos se obtuvieron de pacientes de servicios de intensivos. Los resultados de este estudio indican que K. pneumoniae portadora del gen blaNDM se ha diseminado dentro del Hospital General San Juan de Dios, desde el primer caso reportado hace cinco años, poniendo en riesgo de muerte a los pacientes, especialmente a los hospitalizados en los servicios de intensivos.

Resistance to antibiotics is one of the most important public health problems worldwide. Enterobacteriaceae producing carbapenemases pose the greatest threat. The carbapenemases are powerful enzymes that inactivate carbapenem antibiotics and generally all beta-lactam antibiotics. The consequences for the treatment of infections caused by these bacteria are important because carbapenems are the latest options available for multidrug-resistant bacteria. This research aimed to determine through endpoint polymerase chain reaction (PCR), the presence of the carbapenemases encoding genes blaKPC (Klebsiella pneumoniae carbapenemase) and blaNDM (New Delhi metallolactamase) in K. pneumoniae isolates from San Juan de Dios General Hospital located in Guatemala City; and to characterize the sample type and define the service of the hospital where such bacteria were isolated 54 K. pneumoniae isolates resistant to carbapenems (imipenem and / or meropenem), were analyzed. From these, 49 (91 %) were detected as blaNDM gene carriers. These bacteria were isolated more frequently in blood samples (37%) and urine (14%). In this research, 53% of isolates were obtained from patients hospitalized in intensive care units. This study demonstrates that K. pneumoniae carrying the blaNDM gene has spread within San Juan de Dios General Hospital, since the first reported case five years ago, risking the life of patients, especially of those hospitalized in intensive care services.

Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak.

Limited data are available regarding the molecular epidemiology of Mycobacterium tuberculosis (Mtb) strains circulating in Guatemala. Beijing-lineage Mtb strains have gained prevalence worldwide and are associated with increased virulence and drug resistance, but there have been only a few cases reported in Central America. Here we report the first whole genome sequencing of Central American Beijing-lineage strains of Mtb. We find that multiple Beijing-lineage strains, derived from independent founding events, are currently circulating in Guatemala, but overall still represent a relatively small proportion of disease burden. Finally, we identify a specific Beijing-lineage outbreak centered on a poor neighborhood in Guatemala City.

Evaluación de resistencia genotípica del VIH-1 en pacientes con fallo virológico de Guatemala / Evaluation of genotypic resistance of HIV-1 in patients with virologic failure Guatemala

La resistencia a la terapia antirretroviral (TARV) es un factor determinante para el fallo virológico en pacientes con VIH. El objetivo de este estudio fue identificar los patrones genotípicos de resistencia en pacientes con fallo virológico. Fueron incluidos pacientes de las diferentes unidades de atención integral de VIH en Guatemala, de quienes se sospechaba resistencia y que necesitaban cambios en la TARV por fallo virológico, se requirió haber evaluado la adherencia y una carga viral ≥1,000 copias/ml. La información clínica y demográfica fue recolectada a través de la forma de solicitud. El análisis de resistencia se realizó a través de la metodología TRUGENE® HIV-1. La muestra se restringió a 25 pacientes por motivos de accesibilidad. El 68% de las muestras analizadas presentaron resistencia; por familia de ARV la resistencia fue de 88.2% para ITINN, 70.5% para ITIAN y 17.6% para IP. Se identificaron 79 mutaciones entre el grupo de estudio, el 46.8% de fueron asociadas a ITINN, 76.6% a ITIAN y 26.6% a IP. Para ITIAN las mutaciones más frecuentes fueron la M184V 43%, M184I 14% y K219E 10%; el 23.8% fueron mutaciones TAMs. Para ITINN fueron la V179D 16%, K103N 14%, G190A 14% y Y181C 14%. Para los IP la mutación más frecuente fue la M36I con 29%. La resistencia identificada en este grupo, fue menor a lo reportado en otros países latinoamericanos; sin embargo es similar a lo reportado por OMS en países con bajo o medio ingreso económico.

ARV drug resistance is one of the leading causes of virologic failure among HIV patients on HAART. Theobjective of this study was to determine genotypic resistance profiles among HIV patients on virologic failure. Patients from one HIV clinic in Guatemala on whom ARV drug resistance was suspected and needed a change in their ARV regimen due to virologic failure were included. In order to perform the genotype, the patient had to demonstrate good adherence to therapy and a confirmed viral load ≥1,000 copies/ml. Demographics andclinical data were collected through the resistance-testing questionnaire. The TRUGENE® HIV-1 methodology was used for resistance analysis. The patient sample was restricted to 25 patients due to accessibility, 68% presented resistance to at least one ARV drug. By ARV class, 88.2% presented resistance to NNRTIs, 70.5% to NRTIs and 17.6% to IPs. We found 79 mutations among the samples analyzed. Of the mutations found, 46.8% were associated with NNRTI resistance, 76.6% to NRTI resistance and the remainder 26.6% to PI resistance. The most frequent NRTI associated mutations were M184V 43%, M184I 14% and K219E 10%; 23.8% were TAM. The NNRTI associated mutations were V179D 16%, K103N 14%, G190A 14% and Y181C 14%. For the PI the most frequent mutation was M36I with 29%. The resistance found in this study was lower to that reported in other Latin American studies, however, it is similar to what is reported by WHO in low and middle income countries.

The wag31 gene of Mycobacterium tuberculosis is positively regulated by the stringent response.

The stringent response of Mycobacterium tuberculosis is coordinated by Rel and is required for full virulence in animal models. A serological-based approach identified Wag31(Mtb) as a protein that is upregulated in M. tuberculosis in a rel-dependent manner. This positive regulation was confirmed by analysis of M. tuberculosis mRNA expression. Mycobacterium smegmatis was used to confirm that the expression of wag31(Mtb) from its native promoter is positively regulated by the stringent response. Furthermore, elevated wag31(Mtb) expression in M. smegmatis drastically alters the cell-surface hydrophobic properties.

Inactivation of lsr2 results in a hypermotile phenotype in Mycobacterium smegmatis.

Mycobacterial species are characterized by the presence of lipid-rich, hydrophobic cell envelopes. These cell envelopes contribute to properties such as roughness of colonies, aggregation of cells in liquid culture without detergent, and biofilm formation. We describe here a mutant strain of Mycobacterium smegmatis, called DL1215, which demonstrates marked deviations from the above-mentioned phenotypes. DL1215 arose spontaneously from a strain deficient for the stringent response (M. smegmatis Delta rel(Msm) strain) and is not a reversion to a wild-type phenotype. The nature of the spontaneous mutation was a single base-pair deletion in the lsr2 gene, leading to the formation of a truncated protein product. The DL1215 strain was complicated by having both inactivated rel(Msm) and lsr2 genes, and so a single lsr2 mutant was created to analyze the gene's function. The lsr2 gene was inactivated in the wild-type M. smegmatis mc(2)155 strain by allelic replacement to create strain DL2008. Strain DL2008 shows characteristics unique from those of both the wild-type and Delta rel(Msm) strains, some of which include a greatly enhanced ability to slide over agar surfaces (referred to here as "hypermotility"), greater resistance to phage infection and to the antibiotic kanamycin, and an inability to form biofilms. Complementation of the DL2008 mutant with a plasmid containing lsr2 (pLSR2) reverts the strain to the mc(2)155 phenotype. Although these phenotypic differences allude to changes in cell surface lipids, no difference is observed in glycopeptidolipids, polar lipids, apolar lipids, or mycolic acids of the cell wall.

The relA homolog of Mycobacterium smegmatis affects cell appearance, viability, and gene expression.

The modification of metabolic pathways to allow for a dormant lifestyle appears to be an important feature for the survival of pathogenic bacteria within their host. One regulatory mechanism for persistent Mycobacterium tuberculosis infections is the stringent response. In this study, we analyze the stringent response of a nonpathogenic, saprophytic mycobacterial species, Mycobacterium smegmatis. The use of M. smegmatis as a tool for studying the mycobacterial stringent response was demonstrated by measuring the expression of two M. tuberculosis genes, hspX and eis, in M. smegmatis in the presence and absence of rel(Msm). The stringent response plays a role in M. smegmatis cellular and colony formation that is suggestive of changes in the bacterial cell wall structure.