Juan Carlos Bravata-Alcántara

Background/Objectives: This study evaluated variation in nodal support for provisional HIV-1 subtype B compatibility across pol, gag, vif, tat and vpr in an institutional cohort from central Mexico. Methods: We performed a secondary descriptive bioinformatics reanalysis of 60 treatment-naïve adults. Paired FASTQ files were available for 58 samples, and 42 were retained across all five regions. Robust support required SH-aLRT ≥ 80 and UFBoot ≥ 95. Additional analyses varied reference-composition thresholds, reselected assignment nodes, harmonized the reference panel and subsampled alignment columns. Results: At the originally recorded nodes, 18/210 sample–region records (8.6%) were robust; 25/42 samples had no robust region, 16 had one and one had two. Node reselection at the 60% composition threshold retained all 18 records and added S42/pol and S29/tat, yielding 20/210 (9.5%). Neither analysis identified robust support in three or more regions. With a common reference panel, the ordering of contextual internal-branch support between pol and vif changed. Conclusions: Support depended on the evaluated node and analytical dataset. Fixed-node threshold stability did not establish stability under node reselection. Differences among regional analyses could not be attributed independently to genomic region. Single-fragment assignments remain provisional and do not establish whole-genome subtype classifications. V3 and ViReMa analyses were exploratory.

Human immunodeficiency virus type 1 exhibits extensive genetic diversity, which has important implications for molecular epidemiology, recombinant-pattern assessment, and antiretroviral resistance surveillance. In Mexico, HIV-1 molecular surveillance has historically relied mainly on partial pol gene sequencing, limiting the ability to compare lineage assignments across gag, pol, and env regions. We analyzed plasma samples from 40 treatment-naïve adults receiving care at a tertiary-care hospital in Mexico using a commercial amplicon-based multiregion HIV-1 genomic sequencing workflow. DeepChek^® was used as the primary workflow for read processing, mutation calling, region-level subtype assignment, and antiretroviral resistance interpretation. Resistance interpretation was restricted to antiretroviral target regions with sufficient coverage, mainly reverse transcriptase, protease, integrase, and capsid, when available. Drug resistance mutations were identified in 6/40 participants (15.0%) when mutation-level resistance findings in RT, PR, and IN were considered; one additional sample showed a capsid inhibitor-nonsusceptible NGS call. NNRTI-associated findings were identified in 2/40 patients (5.0%), whereas NRTI- and PI-associated findings were identified in 1/40 patients (2.5%). Accessory or secondary INSTI-associated substitutions were detected in 2/40 patients (5.0%). Region-level subtype analysis revealed frequent discordant assignments across amplified segments, which is consistent with complex mosaic profiles; however, these findings are interpreted as region-level subtypes and recombinant-pattern assignments rather than continuous whole-genome recombination maps. One sample had insufficient RT/PROT/INT coverage for drug resistance interpretation in the complete DeepChek report and was retained only for regions meeting quality thresholds. These findings support the value of multiregion HIV-1 sequencing for local molecular surveillance while emphasizing the need for transparent region-level coverage reporting, cautious interpretation of recombinant-pattern calls, and transparent repository reporting.

Human immunodeficiency virus type 1 exhibits extensive genetic diversity, which has important implications for transmission dynamics, disease progression, and the effectiveness of antiretroviral therapy. In Mexico, molecular surveillance has largely relied on partial pol gene sequencing, limiting the detection of recombination events and resistance mutations outside canonical regions. In this study, we performed near-full-length whole-genome sequencing of HIV-1 from 40 treatment-naïve adults receiving care at a tertiary-care hospital in Mexico to characterize drug-resistance mutations, viral genetic diversity, and recombinant forms. Viral RNA was extracted from plasma and sequenced on an Illumina platform, followed by bioinformatic processing and interpretation using the DeepChek pipeline for subtype classification, recombinant profiling, and identification of drug-resistance mutations. Drug-resistance mutations were identified in 6/40 (15.0%) participants. NNRTI-associated DRMs were identified in 2/40 patients (5.0%), whereas NRTI- and protease inhibitor-associated DRMs were each identified in 1/40 patient (2.5%). In addition, accessory INSTI-associated substitutions were detected in 2/40 patients (5.0%). No statistically significant differences were observed between patients with and without DRMs with respect to age, sex, or plasma viral load. Furthermore, DRMs were distributed across all recombinant categories, with no significant association between recombinant profile and DRM presence (p = 0.97). Non-B subtypes and recombinant forms predominated (82.5%), while subtype B accounted for 17.5% of cases. Extensive intergenic recombination was observed, with discordant subtype assignments across gag, pol, and env regions, consistent with mosaic viral genomes. Multiple circulating recombinant forms, including CRF03_AB, CRF07_BC, CRF28_BF, and CRF39_BF, were identified, alongside a predominance of BF-related recombinants. In addition, several unique recombinant forms with complex mosaic structures were detected, reflecting ongoing recombination and viral evolution. These findings highlight the high genetic complexity of HIV-1 in this population, characterized by a predominance of recombinant forms and extensive genomic mosaicism. The detection of DRMs across diverse genetic backgrounds supports the value of baseline resistance testing and suggests that broader genomic surveillance may improve HIV-1 molecular epidemiology monitoring in Mexico.

Stenotrophomonas maltophilia is considered one of the emerging bacterial agents causing healthcare-associated infections (HAIs) in hospital environments. This microorganism has been identified as multidrug-resistant, capable of forming mature biofilms—an ability that promotes adherence to surfaces and invasive medical devices, favoring persistence in hospital environments and the potential to generate outbreaks. The aim of this study was to characterize S. maltophilia strains isolated from HAI cases at the Hospital Juárez de México and to determine the presence of hidden outbreaks. Antibiotic resistance profiles were determined, along with the typing of 20 genes associated with virulence factors and the assessment of the ability to form mature biofilms on inert surfaces. Finally, sequence type (ST) was obtained through multilocus sequence typing (MLST) analysis, and a phylogenetic tree was constructed to determine the clonal diversity of the isolates. All strains showed uniform resistance to β-lactam antibiotics tested while remaining sensitive to fluoroquinolones, phenicols, tetracyclines, and trimethoprim/sulfamethoxazole. Some isolates exhibited adherent activity, with the “strong biofilm-former” phenotype predominating. Sixteen virulence-related genes were heterogeneously detected, revealing broad genetic diversity. MLST analysis grouped the isolates into nine ST related to infection cases reported in others countries. Phylogenetic analyses demonstrated the presence of three potential clones distributed across Internal Medicine and the Pediatric Intensive Care Unit. These results highlight the importance of investigating S. maltophilia as an HAI-associated pathogen that remains understudied.

Ovarian cancer (OC) is usually diagnosed at an advanced stage, contributing to its high mortality rate. The presence of concurrent bacterial infections in these patients is a common clinical observation, and the mechanisms by which this coinfection influences tumor progression are still not fully understood. This study investigates the role of polydisperse extracellular vesicles (PEVs) secreted by OC cells in response to bacterial components, aiming to elucidate a potential communication pathway between OC and the bacterial microenvironment. We stimulated a human OC cell line in vitro with a fraction of E. coli. Our results show that this bacterial stimulation significantly increases the secretion of PEVs by cancer cells. A subsequent proteomic analysis of these PEVs revealed an enrichment of proteins, including filamin A, filamin B, alpha-enolase, and heat shock cognate 71 kDa protein. In addition, the PEVs displayed protease activity (on fibronectin and gelatin) and phosphatase activity against para-nitrophenyl phosphate, indicating their capacity to alter cellular signaling. This represents a novel mechanism through which bacterial coinfection may influence the biological behavior of OC if bacteria interact with tumor cells, potentially contributing to their aggressiveness and the challenges associated with their treatment. Our work highlights the importance of studying the interplay between the tumor and its associated microbiota to better understand ovarian cancer progression and identify new therapeutic targets.

Cervical cancer remains a significant public health priority, particularly in low- and middle-income countries. In this context, liquid biopsy has emerged as a minimally invasive method for detecting and monitoring molecular biomarkers, offering advantages over traditional screening approaches. This systematic review included 21 studies published between 2015 and 2025 and was conducted in accordance with the PRISMA 2020 statement. The analysis examined the role of serum cytokines, circulating microRNAs (miRNAs), and circulating cell-free HPV DNA (cfHPV-DNA) in patients with cervical cancer or high-grade intraepithelial lesions. Circulating miRNAs—particularly miR-21, miR-29a, and miR-34a—are consistently associated with recurrence, tumor progression, and reduced survival. However, their immediate clinical translation remains limited by methodological variability and the lack of universal normalizers. In contrast, cfHPV-DNA, especially with ddPCR, exhibited the best study-level performance, with a specificity of 100% and a sensitivity of approximately 80–88%, across heterogeneous endpoints and analytic conditions. Consequently, cfHPV-DNA represents a promising tool for post-treatment surveillance and early detection of recurrence. Serum cytokines, such as TNF-α, IL-6, and IL-10, reflect inflammation and the tumor microenvironment. Nevertheless, their lack of standardization and variability across detection platforms restricts their reproducibility, positioning them as complementary rather than stand-alone markers. In conclusion, the evidence supports liquid biopsy as a promising tool in cervical cancer management; nonetheless, only cfHPV-DNA is currently ready for clinical application, whereas miRNAs and cytokines require multicenter validation and technical standardization before implementation.

Ovarian cancer (OC) is diagnosed at an advanced stage, contributing to its high mortality rate. The presence of concurrent bacterial infections in these patients is a common clinical observation, and the mechanisms by which this coinfection influences tumor progression, still not fully understood. This study investigates the role of extracellular vesicles polydispersity (EVPs) secreted by OC cells in response to bacterial components, aiming to elucidate a potential communication pathway between the OC and the bacterial microenvironment. We stimulated a human OC cell line in vitro with a fraction of E. coli. Our results show that this bacterial stimulation significantly increases the secretion of PEVs by the cancer cells. A subsequent proteomic analysis of these PEVs revealed an enrichment of proteins, including filamin A-B, alpha-enolase, heat shock cognate 71 kDa protein, etc. In addition, the EVPs displayed protease (on fibronectin and gelatin) and phosphatase activity against para-nitrophenyl phosphate, indicating their capacity to alter cellular signaling. This represents a novel mechanism through which bacterial coinfection may influence the biological behavior of OC, potentially contributing to their aggressiveness and the challenges associated with their treatment. Our work highlights the importance of studying the interplay between the tumor and its associated microbiota to better understand ovarian cancer progression and identify new therapeutic targets.

The global emergence of multidrug- and pandrug-resistant Klebsiella pneumoniae poses a critical threat to public health, particularly in hospital settings. This study describes a nosocomial outbreak caused by K. pneumoniae in a tertiary-care hospital in Mexico and provides a comprehensive genomic analysis of six clinical isolates. All isolates exhibited pandrug resistance, including carbapenems and colistin. Whole-genome sequencing identified 37 antimicrobial resistance genes, including blaNDM-1, blaOXA-1, blaCTX-M-15, and a pmrB R256G mutation associated with colistin resistance. Two conjugative plasmids (pAA046 and pAA276) carried multiple resistance genes and mobile genetic elements. Although all isolates harbored CRISPR-Cas type I-E systems, no spacers matched resistance plasmids, suggesting functional inactivity. Capsular typing identified the KL27 locus with the wzi187 allele. Phylogenetic and cgMLST analyses confirmed clonal dissemination and close genetic relatedness to strains from Europe and the USA. Despite the absence of classical hypervirulence markers, the presence of kfu, fimH, and mrkD genes indicates adaptation to the hospital environment. These findings confirm the clonal spread of pandrug-resistant K. pneumoniae ST392-KL27 in a Mexican hospital, underscoring the role of plasmid-mediated resistance and the potential for global dissemination.

B-lineage acute lymphoblastic leukemia (B-ALL) is classified into more than 20 molecular subtypes, and next-generation sequencing has facilitated the identification of these with high sensitivity. Bulk RNA-seq analysis of bone marrow was realized to identify molecular subtypes in Mexican pediatric patients with B-ALL. High hyperdiploidy (27.3%) was the most frequent molecular subtype, followed by DUX4 (13.6%), TCF3::PBX1 (9.1%), ETV6::RUNX1 (9.1%), Ph-like (9.1%), ETV6::RUNX1-like (9.1%), PAX5alt (4.5%), Ph (4.5%), KMT2A (4.5%), and ZNF384 (4.5%), with one patient presenting both the PAX5alt and low hypodiploidy subtypes (4.5%). The genes TYK2, SEMA6A, FLT3, NRAS, SETD2, JAK2, NT5C2, RAG1, and SPATS2L harbor deleterious missense variants across different B-ALL molecular subtypes. The Ph-like subtype exhibited mutations in STAT2, ADGRF1, TCF3, BCR, JAK2, and NRAS with overexpression of the CRLF2 gene. The DUX4 subtype showed mutually exclusive missense variants in the PDGRFA gene. Here, we have demonstrated the importance of using RNA-seq to facilitate the differential diagnosis of B-ALL with successful detection of gene fusions and mutations. This will aid both patient risk stratification and precision medicine.

Background/Objectives: In adults with B-cell acute lymphoblastic leukemia (B-ALL), central nervous system (CNS) involvement represents a significant clinical challenge due to its association with adverse outcomes. Infiltration of blast cells into the CNS is primarily detected via cerebrospinal fluid (CSF) microscopy, the current gold standard diagnostic method, although it has limitations in terms of sensitivity. Quantitative polymerase chain reaction (qPCR) offers higher sensitivity and can support the diagnosis of CNS infiltration. This study assessed the mRNA expression levels of CD79A and IL7R in CSF to evaluate their potential for detecting CNS involvement in adults with B-ALL. Methods: CSF samples were collected from adults with B-ALL. The classification criteria for CNS Leukemia (CNS status) were used to evaluate CNS involvement. RNA was extracted from the CSF, and quantitative reverse transcription PCR (RT-qPCR) was used to measure the CD79A and IL7R mRNA expression levels. Results: A total of 19 treatment-naïve adult patients with B-ALL were enrolled over a 19-month period. Four (21%) patients had CNS3 status. Four (21%) patients had CNS3 status. The results also showed that the expression levels of CD79A and IL7R mRNA were significantly higher (median fold change = 0.62 and 2.12, p < 0.05, respectively) in the group with CNS3. Furthermore, using the Haldane-Anscombe correction and Fisher’s exact test, we demonstrated an association between IL7R and CNS3 expression (odds ratio = ∞, due to zero CNS+ in the IL7R group, p < 0.05). Conclusions: CD79A and IL7R mRNA levels in CSF could be potential biomarkers for detecting CNS involvement in adult patients with B-ALL.