Miguel Ángel Martínez

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI (sequence-based ultrarapid pathogen identification), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7-500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.

Discovery of a Novel Polyomavirus in Acute Diarrheal Samples from Children

Polyomaviruses are small circular DNA viruses associated with chronic infections and tumors in both human and animal hosts. Using an unbiased deep sequencing approach, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. The ∼5.0 kB viral genome exhibits little overall homology (<46% amino acid identity) to known polyomaviruses, and, due to phylogenetic variation among its individual proteins, cannot be placed in any existing taxonomic group. PCR-based screening detected MXPyV in 28 of 834 (3.4%) fecal samples collected from California, Mexico, and Chile, and 1 of 136 (0.74%) of respiratory samples from Mexico, but not in blood or urine samples from immunocompromised patients. By quantitative PCR, the measured titers of MXPyV in human stool at 10% (weight/volume) were as high as 15,075 copies. No association was found between the presence of MXPyV and diarrhea, although girls were more likely to shed MXPyV in the stool than boys (pu200a=u200a0.012). In one child, viral shedding was observed in two stools obtained 91 days apart, raising the possibility of chronic infection by MXPyV. A multiple sequence alignment revealed that MXPyV is a closely related variant of the recently reported MWPyV and HPyV10 polyomaviruses. Further studies will be important to determine the association, if any, of MXPyV with disease in humans.

Gangliosides have a functional role during rotavirus cell entry.

ABSTRACT Cell entry of rotaviruses is a complex process, which involves sequential interactions with several cell surface molecules. Among the molecules implicated are gangliosides, glycosphingolipids with one or more sialic acid (SA) residues. The role of gangliosides in rotavirus cell entry was studied by silencing the expression of two key enzymes involved in their biosynthesis—the UDP-glucose:ceramide glucosyltransferase (UGCG), which transfers a glucose molecule to ceramide to produce glucosylceramide GlcCer, and the lactosyl ceramide-α-2,3–sialyl transferase 5 (GM3-s), which adds the first SA to lactoceramide-producing ganglioside GM3. Silencing the expression of both enzymes resulted in decreased ganglioside levels (as judged by GM1a detection). Four rotavirus strains tested (human Wa, simian RRV, porcine TFR-41, and bovine UK) showed a decreased infectivity in cells with impaired ganglioside synthesis; however, their replication after bypassing the entry step was not affected, confirming the importance of gangliosides for cell entry of the viruses. Interestingly, viral binding to the cell surface was not affected in cells with inhibited ganglioside synthesis, but the infectivity of all strains tested was inhibited by preincubation of gangliosides with virus prior to infection. These data suggest that rotaviruses can attach to cell surface in the absence of gangliosides but require them for productive cell entry, confirming their functional role during rotavirus cell entry.

Impact of Laboratory Cross-Contamination on Molecular Epidemiology Studies of Tuberculosis

ABSTRACT Laboratory cross-contamination by Mycobacterium tuberculosis is known to be responsible for the misdiagnosis of tuberculosis, but its impact on other contexts has not been analyzed. We present the findings of a molecular epidemiology analysis in which the recent transmission events identified by a genotyping reference center were overestimated as a result of unnoticed laboratory cross-contamination in the original diagnostic laboratories.

DNA Microarray for Detection of Gastrointestinal Viruses

ABSTRACT Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 × 103 virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n = 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant virus. The microarray described in this work should help in understanding the etiology of gastroenteritis in humans and animals.

A theoretical and experimental evaluation of imidazolium-based ionic liquids for atmospheric mercury capture

AbstractIn this work, the capacity of three different imidazolium-based ionic liquids (ILs) for atmospheric mercury capture has been evaluated. Theoretical calculations using monomer and dimer models of ILs showed that [BMIM]+[SCN]− and [BMIM]+[Cl]− ionic liquids capture gaseous Hg0, while [BMIM]+[PF6]− shows no ability for this purpose. These findings are supported by experimental data obtained using particle induced X-ray emission (PIXE) trace element analysis. Experimental and theoretical infrared data of the ILs were obtained before and after exposure to Hg. In all cases, no displacement of the bands was observed, indicating that the interaction does not significantly affect the force constants of substrate bonds. This suggests that van der Waals forces are the main forces responsible for mercury capture. Since the anion-absorbate is the driving force of the interaction, the largest charge-volume ratio of [Cl]− could explain the higher affinity for mercury sequestration of the [BMIM]+[Cl]− salt.n FigureMercury capture by [BMIM]+[PF6]−, [BMIM]+[SCN]−and [BMIM]+[Cl]−double pair ionic liquids

Malaria Hidden in a Patient with Diffuse Large-B-Cell Lymphoma and Sickle-Cell Trait

ABSTRACT We report a case of an African patient with sickle cell trait who was diagnosed in Spain with B-cell lymphoma. Blood smears were negative for malaria, and no plasmodium antigens were detected in the blood. To treat his lymphoma, the patient underwent chemotherapy and autologous stem cell transplantation. Following a splenectomy due to a worsening condition, he developed clinical malaria with detectable parasitemia. This case suggests that the humoral response and parasite removal by the spleen may afford protection from overt disease and may even help maintain subclinical human reservoirs of the disease.

Mating modifies apoptosis pattern in epithelial cells of the rat uterus

Estrous cycle in mammals includes marked epithelial changes in reproductive tract, regulated by sex steroid hormones. In the present work we studied the activation of caspases and apoptotic pattern in uterine epithelial cells during proestrus and estrus, and the effect of mating in this process. In addition, we investigated the role of seminal vesicle secretions on apoptosis of uterine epithelia. Apoptotic index was evaluated by TUNEL assay, caspases‐8, ‐9, and ‐3 activation was detected by Western blot and active caspase‐3 expression was detected by immunohistochemistry. Our results show that mating during proestrus and estrus transition induced changes in the apoptotic pattern of uterine luminal epithelium during estrus, characterized by a delay in the onset of apoptosis as compared with that observed in nonmated rats. No differences in the apoptotic pattern in the glandular epithelium between mated and nonmated rats were observed. Seminal vesicle secretions inhibited luminal epithelium apoptosis, while no changes in glandular epithelium apoptosis were observed. We also demonstrate that activation of caspases‐8, ‐9, and ‐3 occurred in both mated and nonmated rats. Active caspase‐3 was detected in the luminal and glandular epithelium in both nonmated and mated rats. The overall results indicate that mating delays but does not prevent the cellular death of the rat uterine luminal epithelium and seminal vesicle secretions are involved in this delay. Finally, the activation of both the mitochondrial and the membrane receptor pathways of cell death are implicated in the molecular mechanism of uterine apoptosis. Mol. Reprod. Dev. 76: 564–572, 2009.