Acinetobacter baumannii is an opportunistic pathogen responsible for healthcare-associated infections (HAIs) and outbreaks. Antimicrobial resistance mechanisms and virulence factors allow it to survive and spread in the hospital environment. However, the molecular mechanisms of these traits and their association with international clones are frequently unknown in low- and middle-income countries. Here, we analyze the phenotype and genotype of seventy-six HAIs and outbreak-causing A. baumannii isolates from a Mexican hospital over ten years, with special attention to the carbapenem resistome and biofilm formation. The isolates belonged to the global international clone (IC) 2 and the Latin America endemic IC5 and were predominantly extensively drug-resistant (XDR). Oxacillinases were identified as a common source of carbapenem resistance. We noted the presence of the bla_OXA-143-like family (not previously described in Mexico), the bla_OXA-72 and the bla_OXA-398 found in both ICs. A low prevalence of efflux pump overexpression activity associated with carbapenem resistance was observed. Finally, strong biofilm formation was found, and significant biofilm-related genes were identified, including bfmRS, csuA/BABCDE, pgaABCD and ompA. This study provides a comprehensive profile of the carbapenem resistome of A. baumannii isolates belonging to the same pulse type, along with their significant biofilm formation capacity. Furthermore, it contributes to a better understanding of their role in the recurrence of infection and the endemicity of these isolates in a Mexican hospital.

Antimicrobial resistance in healthcare-associated infections represents one of the greatest threats to global health. The COVID-19 pandemic disrupted infection control and antimicrobial stewardship, potentially affecting the prevalence of pathogens and the development of resistance. This study aimed to investigate the prevalence, antimicrobial resistance, and clonal dissemination of ESKAPE pathogens isolated from bloodstream infections during the second year of the COVID-19 pandemic in four tertiary-care hospitals in Mexico. A total of 926 isolates were analyzed: Staphylococcus aureus (22.4%), Klebsiella pneumoniae (22%), Acinetobacter baumannii (21.5%), Pseudomonas aeruginosa (12.5%), Enterobacter cloacae (9.4%), Enterococcus faecalis (8.4%), and Enterococcus faecium (3.8%). High rates of multidrug resistance were observed in A. baumannii (70.9% XDR) and K. pneumoniae (71% XDR plus MDR with 79% ESBL). P. aeruginosa and E. cloacae showed the highest susceptibility rates (53% and 48%, respectively) to all antimicrobials. The main β-lactamases involved in resistance were bla_SHV, bla_CTX-M, and bla_TEM in K. pneumoniae, while the predominant carbapenemases were bla_OXA-24, bla_OXA-23 in A. baumannii, bla_NDM in K. pneumoniae, and bla_VIM in P. aeruginosa. Among Gram-positives, methicillin-resistant S. aureus accounted for 33.8% of isolates, and vancomycin resistance was higher in E. faecium (28%) than in E. faecalis (1.3%). Pulsed-field gel electrophoresis revealed endemic circulation of A. baumannii clones (Pulsotypes 1AC, 2AM), persistent for over a decade, and interhospital dissemination of S. aureus and K. pneumoniae clones. These findings underscore the epidemiological relevance of MDR ESKAPE pathogens during the COVID-19 pandemic and highlight the urgent need to optimize empirical therapy and maintain continuous genomic surveillance to enhance infection control in Mexican hospitals.

Los microorganismos son de gran interés porque colonizan todo tipo de ambiente, sin embargo, uno de los problemas al que nos enfrentamos para conocer su diversidad biológica es que no todos los microorganismos son cultivables. El desarrollo de nuevas tecnologías como la generación de vectores de clonación aunado al desarrollo de técnicas de secuenciación de alto rendimiento ha favorecido el surgimiento de una nueva herramienta llamada metagenómica, la cual nos permite estudiar genomas de comunidades enteras de microorganismos. Debido a que ningún ambiente es idéntico a otro, es importante mencionar que dependiendo del tipo de muestra a analizar será el tipo de reto al cual nos enfrentaremos al trabajar con metagenómica, en el caso específico del suelo existen diversas variantes como la contaminación del suelo con metales pesados o diversos compuestos químicos que podrían limitar los estudios. Sin embargo, pese a las limitaciones que el mismo ambiente presenta, la metagenómica ha permitido tanto el descubrimiento de nuevos genes como la caracterización de las comunidades microbianas que influyen positivamente en el desarrollo de plantas, lo cual en un futuro podría generar un gran impacto en la agricultura. En este artículo se realizó una revisión de diversas investigaciones que han empleado metagenómica, reportadas en las bases de datos de PudMed y Google Schoolar, con el objetivo de examinar los beneficios y limitaciones de las diversas metodologías empleadas en el tratamiento del ADN metagenómico de suelo y el impacto de la metagenómica en la agricultura.