Impact of the COVID-19 pandemic on the distribution and resistance of multidrug-resistant genes in Minas Gerais, Brazil: challenges and implications

Background: Following the COVID-19 pandemic, a significant rise in multidrug-resistant pathogens such as Acinetobacter, Enterobacter, Escherichia, Klebsiella, Providencia, Pseudomonas and Serratia spp. was observed in Minas Gerais, Brazil. Diagnostic disparities and antimicrobial overuse for COVID-19-associated pneumonia likely contributed to resistance gene spread. Methods: This retrospective, cross-sectional, descriptive study analysed 13,012 Gram-negative bacterial isolates collected from hospitals across Minas Gerais between 2016 and 2022. Samples, including urine, tracheal secretion, blood and surgical wound exudate, were referred to the state public health laboratory (LACEN-MG) based on resistance patterns detected via antibiograms. Genotypic analysis involved PCR screening for resistance genes (blaKPC, blaOXA, blaNDM, blaSPM, blaVIM, blaIMP), categorized by pandemic period (pre-, during and post-COVID-19). The presence of at least one gene indicated multidrug resistance. Results: Among isolates, 70.8% were fermenting bacilli, mainly Klebsiella spp. (73.8%), 29.2% were non-fermenting, mostly Acinetobacter spp. (62.1%) and Pseudomonas spp. (37.9%). Post-pandemic resistance increased significantly (p<0.05). blaKPC declined in relative frequency (66.3% pre-pandemic to 44.4% post-pandemic) but absolute numbers rose (n=2,906). blaOXA and blaNDM increased to 41.1% and 13.5%, respectively, with blaNDM increasing over sixfold. Mcr-1 appeared exclusively post-pandemic in four isolates. blaSPM, blaVIM and blaIMP remained rare; blaIMP was detected only post-pandemic (0.24%, n=16). Conclusions: Post-pandemic, resistance gene profiles diversified, with expansion of blaOXA, blaNDM and emergence of mcr-1. Strengthened molecular surveillance, equitable diagnostic access and antimicrobial stewardship are urgently needed in Brazil.