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.

Brachybacterium conglomeratum, traditionally considered an environmental bacterium, has recently garnered attention for its potential involvement in human health. While prior research hinted at its pathogenic role in humans, our study aims to determine its prevalence and associations in diverse clinical contexts. We examined vaginal swabs from three distinct patient groups: patients with low-grade squamous intraepithelial lesions (LSIL), patients with cervicovaginal infections, and patients with a history of precancerous lesions undergoing follow-up. B. conglomeratum was present in all three patient groups, with the highest prevalence observed in the LSIL group. Statistically significant associations were primarily identified in the LSIL group, where B. conglomeratum was present in 60% of cases. Notably, the LSIL group exhibited coinfections with multiple high-risk oncogenotypes of human papillomavirus (HPV), suggesting potential synergistic effects, and understanding these microbial relationships and their influence on viral persistence, particularly with HPV, holds promise for mitigating HPV-related carcinogenesis. Furthermore, Gardnerella vaginalis and Atopobium vaginae were frequently detected in this group, along with Ureaplasma parvum as the predominant sexually transmitted bacterium. In all cases, B. conglomeratum was found in association with these microorganisms rather than as a sole pathogen. This coexistence underscores the intricate microbial interactions within cervicovaginal infections and precancerous lesions. This study marks the first report of B. conglomeratum prevalence in women with these clinical conditions.

Infertility, both primary and secondary, is strongly influenced by microbiological factors, with the vaginal microbiota playing a key role in reproductive health. Objective: The aim of this study was to characterize the vaginal microbiota of 136 Mexican women diagnosed with infertility—primary (n = 58) and secondary (n = 78)—by evaluating the presence of pathogenic bacterial species and their associations with infertility conditions. Methods: Samples were obtained through cervical swabs, and microorganism identification was performed using qPCR techniques. Results: Analysis revealed a positive correlation between increased age and the likelihood of primary infertility, as well as a negative correlation with secondary infertility. Significant differences in microbial composition were also observed between the two infertility groups. Lactobacillus crispatus and Lactobacillus gasseri were dominant in women with primary infertility, in addition to a high prevalence of Gardnerella vaginalis and Fannyhessea vaginae. Additionally, correlations were found between the presence of human papillomavirus (HPV) and sexually transmitted bacteria, as well as Gardnerella vaginalis. Conclusion: Our findings suggest that the composition of the vaginal microbiota may play a decisive role in infertility, highlighting the need for personalized therapeutic strategies based on microbial profiles.

Progressive immune damage associated with Human Immunodeficiency Virus (HIV) alters mucosal homeostasis, favouring oral microbial imbalance and the development of opportunistic infections. The aim of this study was to characterize the composition and structure of the oral microbiota in different clinical conditions of HIV infection. A cross-sectional study was conducted in 99 Mexican men divided into five groups: HIV-negative controls, newly diagnosed without antiretroviral treatment, virally suppressed, with oral candidiasis, and with HPV infection. Metagenomic DNA was obtained from salivary samples, and the V1–V3 region of the 16S rRNA gene was massively sequenced. Taxonomic profiles, alpha/beta diversity, differential abundance, microbial co-occurrence networks and degree of dysbiosis were analysed. The results showed distinctive profiles between the groups. Alpha and beta diversity was significantly higher in the groups with oral Candida and HPV lesions, reflecting a disturbance of microbial balance. Differential abundance analysis revealed an increase in Streptococcus, Veillonella, Lactobacillus and Actinomyces genera in HIV patients, while healthy subjects showed higher abundance of Neisseria, Treponema, and Rothia, associated with a eubiotico state. The group of patients with HPV lesions had the highest number of taxa with differential abundance, suggesting an ecological environment altered by the lesion. Analysis of co-occurrence networks revealed a progressive pattern of microbial complexity: controls presented simple networks with weak positive correlations, while HIV groups showed increased connection density and appearance of structured nuclei. The group of patients with HPV lesions presented the highest connectivity, with multiple strongly correlated cores and core nodes such as Prevotella melaninogenica and Shuttleworthia. The dysbiosis score increased progressively from healthy subjects to those with HPV lesions, indicating a gradient of oral microbial disruption. These findings suggest that HIV immunosuppression and the presence of oral lesions are associated with enhanced dysbiosis, although their individual contributions could not be independently assessed due to the absence of non-HIV lesion controls. The integration of microbial networks and dysbiosis scores could be useful for assessing mucosal and immune health in people with HIV and used as biomarkers of clinical progression.

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.

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.