The interruption of bacteriological surveillance due to the COVID-19 pandemic brought serious consequences, such as the collapse of health systems and the possible increase in antimicrobial resistance. Therefore, it is necessary to know the rate of resistance and its associated mechanisms in bacteria causing hospital infections during the pandemic. The aim of this work was to show the phenotypic and molecular characteristics of antimicrobial resistance in ESKAPE bacteria in a Mexican tertiary care hospital in the second and third years of the pandemic. For this purpose, during 2021 and 2022, two hundred unduplicated strains of the ESKAPE group (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii) were collected from various clinical sources and categorized by resistance according to the CLSI. An analysis of variance (ANOVA) complemented by the Tukey test was performed to search for changes in antimicrobial susceptibility profiles during the study period. Finally, the mechanisms of resistance involved in carbapenem resistance were analyzed, and the search for efflux pumps and high-risk sequence types in A. baumannii was performed by multilocus analysis (MLST). The results showed no changes in K. pneumoniae resistance during the period analyzed. Decreases in quinolone resistance were identified in E. coli (p = 0.039) and P. aeruginosa (p = 0.03). Interestingly, A. baumannii showed increases in resistance to penicillins (p = 0.004), aminoglycosides (p < 0.001, p = 0.027), carbapenems (p = 0.027), and folate inhibitors (p = 0.001). Several genes involved in carbapenem resistance were identified (bla_NDM, bla_VIM, bla_OXA, bla_KPC, bla_OXA-40, and bla_OXA-48) with a predominance of bla_OXA-40 and the adeABCRS efflux pump in A. baumannii. Finally, MLST analysis revealed the presence of globally distributed sequence types (ST369 and ST758) related to hospital outbreaks in other parts of the world. The results presented demonstrate that the ESKAPE group has played an important role during the COVID-19 pandemic as nosocomial antibiotic-resistant pathogens and in particular A. baumannii MDR as a potential reservoir of resistance genes. The implications of the increases in antimicrobial resistance in pathogens of the ESKAPE group and mainly in A. baumannii during the COVID-19 pandemic are analyzed and discussed.

Background. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is a predisposing factor for the development of healthcare-associated infections, of which ventilator-associated pneumonia (VAP) is one. Hypothesis. VAP is caused by ESKAPE bacteria and other pathogens not detected by microbiological culture. Aim. To elucidate the bacterial pathogens of severe coronavirus disease 2019 (COVID-19) and VAP patients by massive sequencing and to predict their degree of relationship with the age and sex of the patients. Methods. Analysis of ribosomal libraries of the V3–V4 hypervariable region obtained by Illumina sequencing of bronchoalveolar lavages from COVID-19 and VAP (first wave) patients from Hospital Juárez de México. Results. Acinetobacter and Pseudomonas were the main bacterial genera in the bronchoalveolar lavages (BALs) analysed. Other members of the ESKAPE group, such as Enterococcus and Klebsiella , were also identified. Taxonomic composition per patient showed that non-ESKAPE genera were present with significant relative abundances, such as Prevotella , Stenotrophomas, Enterococcus , Mycoplasma , Serratia and Corynebacterium . Kruskal–Wallis analysis proved that VAP acquisition is an adverse event that is not influenced by the sex and age of COVID-19 patients. Discussion. Metagenomic findings in COVID-19/VAP patients highlight the importance of implementing comprehensive microbiological diagnostics by including alternative tools for the detection of the causal agents of healthcare-associated infections (HAIs). Conclusions. Timely identification of bacteria ‘not sought’ in diagnostic bacteriology laboratories will allow specific and targeted treatments. Implications for the restricted diagnosis of VAP causative agents in COVID-19 patients and the presence of pathogens not detected by classical microbiology are analysed and discussed.

Hospital wastewater (HWW) is a major source of microbiological contamination, often released into the municipal sewage system without prior treatment. This HWW may contain pathogens with antimicrobial resistance, posing risks to public health. The aim of this work was to assess the risks associated with the seasonal release of ESKAPE bacteria resistant to β-lactam antibiotics and the release of carbapenems and cephalosporins through HWW of Hospital Juárez de México. The 12-month seasonal variation in β-lactam-resistant bacterial populations was assessed in the HWW of five discharge points. Resistant isolates were identified by mass spectrometry (MALDI-TOF) coupled with PCR assays to search for antimicrobial resistance genes, while β-lactamic antibiotics were detected using high-performance liquid chromatography (HPLC). Finally, a double-entry Vester matrix was constructed to classify the problems of HWW according to their degree of causality. Seasonal differences in bacterial loads were observed, with higher levels in warmer months. A wide variety of resistant pathogens were identified, including ESKAPE bacteria, as well as emerging bacteria carrying β-lactamase-encoding genes. The release of meropenem was detected most commonly, followed by cefepime and ceftazidime. The Vester matrix allowed the identification of critical clinical and environmental scenarios where two discharge points contribute significantly to the spread of microbiological contamination. This study highlights the importance of proper management of HWW and the need for stricter regulations to reduce the risks associated with the release of resistant pathogens with health impacts.

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.

In Mexico, hospital wastewater (HWW) is a source of chemical and microbiological contamination, and it is released into the municipal sewage system without prior treatment. This water may contain pathogenic bacteria and antimicrobial resistance genes, which represent a risk to Public Health and the environment. So far, there are no studies that analyse this problem comprehensively, relating bacterial population structures, chemical contaminants, and seasonality. The aim of this work was to seasonally characterise the bacterial communities of HWW, including clinically relevant bacteria and resistance genes in Hospital Juárez de México (HJM), and to evaluate the impact of physicochemical factors on their composition. A one-year observational, cross-sectional study was conducted at five HWW discharge points of HJM. Fourteen physicochemical parameters were determined by using standard methodologies, and statistical differences between discharges and seasons were evaluated. Bacterial communities were analysed by targeted amplicon sequencing of the V3-V4 region of the 16S rRNA gene. In addition, the presence of eight antimicrobial resistance genes of local epidemiological importance was assessed. Data were analysed using alpha and beta diversity indices, principal component analysis, and multivariate statistical tests. HWW showed high taxonomic diversity, with Proteobacteria, Firmicutes, and Bacteroidetes standing out. Clinically relevant bacteria were identified in 73.3% of the analyses, with Enterobacter and Escherichia-Shigella predominating. Total and dissolved solids, temperature, nitrate, and pH significantly influenced the bacterial composition of HWW. Seven out of the eight genes evaluated were identified, with bla_KPC, bla_OXA-40, and mcr-1 being the most frequent, showing significant seasonal differences. This study underlines the microbiological and chemical complexity of HWW, highlighting the impact of clinically relevant bacteria and antimicrobial resistance genes on Public Health. The findings emphasise the need to implement hospital waste management programmes and ideally specific treatment plants to minimise the associated risks and protect the environment and human health.

Advances in the knowledge of the pathogenesis of SARS-CoV-2 allowed the survival of COVID-19 patients in intensive care units. However, due to the clinical characteristics of severe patients, they resulted in the appearance of colonization events. Therefore, we speculate that strains of Candida spp. isolated from COVID-19 patients have virulent genetic and phenotypic backgrounds involved in clinical worsening of patients. The aim of this work was to virutype Candida spp. strains isolated from colonized COVID-19 patients, analyze their genomic diversity, and establish clonal dispersion in care areas. The virulent potential of Candida spp. strains isolated from colonized COVID-19 patients was determined through adhesion tests and the search for genes involved with adherence and invasion. Clonal association was done by analysis of intergenic spacer regions. Six species of Candida were involved as colonizing pathogens in COVID-19 patients. The genotype analysis revealed the presence of adherent and invasive backgrounds. The distribution of clones was identified in the COVID-19 care areas, where C. albicans was the predominant species. Evidence shows that Candida spp. have the necessary genetic tools to be able colonize the lungs, and could be a possible causal agent of coinfections in COVID-19 patients. The detection of dispersion of opportunistic pathogens can be unnoticed by classical epidemiology. Epidemiological surveillance against opportunistic fungal pathogens in COVID-19 patients is an immediate need, since the findings presented demonstrate the potential virulence of Candida spp.