During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages and identify the most common circulating lineages during this period. We defined six different geographical regions with particular dynamics of lineage circulation. The Northeast and Northwest regions were the ones that exhibited the highest lineage diversity, while the Central south and South/Southeast regions presented less diversity with predominance of a certain lineage. Additionally, by late February 2021, lineage B.1.1.519 represented more than 89% of all circulating lineages in the country.

Background: Ventilator-Associated pneumonia (VAP) is one of the leading causes of morbidity and mortality in critically ill COVID-19 patients in lower-and-middle-income settings, where timely access to emergency care and accurate diagnostic testing is not widely available. Therefore, rapid microbiological diagnosis is essential to improve effective therapy delivery to affected individuals, preventing adverse outcomes and reducing antimicrobial resistance. Methods: We conducted a cross-sectional study of patients with suspected VAP and COVID-19, evaluating the diagnostic performance of the BioFire® FilmArray® Pneumonia Panel (FA-PP). Respiratory secretion samples underwent standard microbiological culture and FA-PP assays, and the results were compared. Results: We included 252 samples. The traditional culture method detected 141 microorganisms, and FA-PP detected 277, resulting in a sensitivity of 95% and specificity of 60%, with a positive predictive value of 68% and negative predictive value of 93%. In samples with high levels of genetic material (> 10^5 copies/mL), the panel had a sensitivity of 94% and specificity of 86%. In addition, 40% of the culture-negative samples had positive FA-PP® results, of which 35% had > 10^5 copies/mL of genetic material. The most prevalent bacteria were Gram-negative bacilli, followed by Gram-positive cocci. The panel identified 98 genes associated with antimicrobial resistance, predominantly extended-spectrum beta-lactamases (28%). Conclusion: The FA-PP is a sensitive assay for identifying bacteria causing VAP in patients with COVID-19, with a greater capacity to detect bacteria than the conventional method. The timely microbiological recognition offered by this panel could lead to optimized decision-making processes, earlier tailored treatment initiation, and improved antibiotic stewardship practices.

Characterize the colistin-resistance mechanisms, determine the molecular epidemiology, and genomic traits of the colistin-resistant Klebsiella pneumoniae species complex (ColR-KpSC) clinical isolates in Mexico. In this study, 1,539 KpSC isolates were collected in Mexico from 2016 to 2021. We conducted a comprehensive analysis that included microbiological, genetic, molecular, and genomic approaches. A total of 50 isolates (3.25%) were colistin-resistant; of which 49 (98%) corresponded to K. pneumoniae and 1 (2%) to Klebsiella quasipneumoniae. Whole genome sequencing of these resistant isolates revealed intra- and inter-hospital dissemination, and the mgrB inactivation was the main resistance mechanism. Some KpSC isolates carried plasmid-borne mcr-1 gene found in Escherichia coli from piglets in Mexico. The colistin-resistant isolates presented a high prevalence of ESBL- and NDM-1 genes, and one hypervirulent strain also produced ESBL CTX-M-15. This study provides a comprehensive snapshot of the epidemiology of ColR-KpSC in Mexico, highlighting a high prevalence of NDM-1 carbapenemase among ColR-KpSC isolates; this is in line with previous reports identifying NDM-1 as the most prevalent carbapenemase in K. pneumoniae species complex. This problem is particularly concerning in Mexico because of the lack of therapeutic options.

There has been very limited investigation regarding the genetic diversity of Mycobacterium tuberculosis (MTb) strains isolated from human immunodeficiency virus (HIV)-infected patients in Mexico. In this study, we isolated 93 MTb strains from pulmonary and extrapulmonary samples of HIV-infected patients treated in a public hospital in Mexico City to evaluate the genetic diversity using spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) typing (based on 24 loci). The cohort comprised 80 male and 13 female individuals. There was a positive correlation between a high HIV viral load (>100,000 copies) and extrapulmonary tuberculosis (TB) (r = 0.306, p = 0.008). Lineage 4 was the most frequent lineage (79 strains). In this lineage, we found the H clade (n = 24), including the Haarlem, H3, and H1 families; the T clade (n = 22), including T1 and T2; the X clade (n = 15), including X1 and X3; the LAM clade (n = 14), including LAM1, LAM2, LAM3, LAM6, and LAM9; the S clade (n = 2); Uganda (n = 1); and Ghana (n = 1). We also found 12 strains in the EAI clade belonging to lineage 1, including the EAI2-Manila and EAI5 families. Interestingly, we identified one strain belonging to the Beijing family, which is part of lineage 2. One strain could not be identified. This study reports high genetic diversity among MTb strains, highlighting the need for a molecular epidemiological surveillance system that can help to monitor the spread of these strains, leading to more appropriate measures for TB control in HIV-infected patients.

In April 2024, the Instituto Nacional de Enfermedades Respiratorias of Mexico City identified a case of unsubtypeable Influenza A in a 58-year-old immunocompromised patient with renal failure due to diabetic nephropathy and bacterial peritonitis. Through sequencing the M, NS, NA, NP, and HA complete segments, we identified an H5N2 influenza virus with identity of 99% with avian influenza A(H5N2) from Texcoco, Mexico, in 2024. This case is the first reported with direct evidence of human infection caused by the H5N2 influenza virus; the relationship of the virus with the severity of his condition remains unknown.