The horizontal transfer of antibiotic resistance genes in Gram-negative bacteria, mainly through plasmids, is one of the greatest concerns for health systems worldwide and has been a growing threat in hospitals related to healthcare-associated infections by multidrug-resistant bacteria. Here we present p henotypic and genomic characterization of a KPC-2 and MCR-1.27-producing Klebsiella pneumoniae strain isolated from a paediatric patient at an oncologic hospital in Belém, Pará State, Brazilian Amazon region. Antibiotic susceptibility test, whole genome sequencing, and in silico analysis were used to characterize the bacterial isolate (IEC48020) received in the Evandro Chagas Institute. The isolate was resistant to carbapenems, colistin, polymyxin B, and several other antimicrobials and was susceptible in vitro just to tigecycline, classified as an extensively drug-resistant phenotype. Genomic analysis revealed IEC48020 strain belonged to sequence type 11, clonal complex 258 high-risk clone and the presence of eight plasmids, two of them harbouring mcr-1.27 and bla_KPC-2 genes, and the presence of virulence-related genes encoding yersiniabactin, phospholipase D, and traT genes. The presence and dissemination of high-risk clone bacteria with high disseminating plasmids containing antibiotic resistance genes for last resource antibiotics treatment options is a threat to the healthcare system and demands efforts in surveillance and epidemiological research for better knowledge of the actual situation of antibiotic resistance in the healthcare system, especially in the Amazon region, Brazil.

Background: The global impact of the SARS-CoV-2 pandemic on antimicrobial resistance (AMR) patterns has been significant. In northern Brazil, Carbapenem-resistant Klebsiella pneumoniae (CRKP) are a major concern, with an observed shift from Klebsiella pneumoniae carbapenemase (KPC) to New Delhi metallo-β-lactamase (NDM) during the pandemic. Methods: This cross-sectional study analyzed 775 carbapenem-resistant K. pneumoniae isolates collected from 25 hospitals in the Brazilian Amazon Region (states of Pará and Acre) between 2018 and 2021. The isolates were tested for the presence of carbapenemase genes (bla_KPC, bla_NDM, bla_OXA-48, bla_IMP, bla_VIM, bla_AIM, bla_DIM, bla_GIM and bla_SIM). Results: Of the isolates analyzed, n = 653/775 (84%) were carbapenemase producers, with the most prevalent being bla_KPC n = 446/775 (57.5%) and bla_NDM n = 243/775 (31.4%). A significant increase in NDM producers was observed during the pandemic, rising from n = 1/250 (8.4%) pre-pandemic to n = 222/525 (42.3%) during the pandemic, while KPC producers declined from n = 172/250 (68.8%) to n = 274/525 (52.2%) (p < 0.001). Adult intensive care units (ICUs) were the primary source of isolates n = 357/775 (46%), with a notable increase in tracheal secretion and surveillance swab samples during the pandemic. Regression analysis confirmed a strong upward trend in the prevalence of bla_NDM (R² = 0.778). Conclusions: The shift from KPC to NDM producers in northern Brazil highlights an evolving AMR landscape, partly driven by the pandemic. Strengthened infection control measures, antimicrobial stewardship and continuous surveillance are essential to mitigate the spread of NDM-producing K. pneumoniae in settings with limited resources.

Clinical emergent bacterial pathogens are a great threat to the global health system, chiefly Gram-negative carbapenem-resistant Enterobacterales and the Klebsiella pneumoniae species complex. Here, we present the molecular and phenotypic characterization of Klebsiella quasipneumoniae subs. similipneumoniae IEC57090 strain, belonging to ST138 and showing a multidrug resistance phenotype. The bla_NDM-7 present in one of the two resistance plasmids carried by the isolate, the antibiotic resistance genes fosA, oqxAB, and acrR, and gene mutations on porins ompK36 and ompK37, both associated with cephalosporin and carbapenem resistance, were detected. Virulence factors such as the clusters of type I and III fimbria, type IV pili genes, and genes associated with the K1 capsule, siderophore production, and multiple mobile genetic elements (MGE) were predicted. The emergence of silent pathogens in clinical environments highlights the importance of active research on new threads that may compromise the last resources of antimicrobials, such as carbapenems, specifically on mobile genetic elements containing carbapenemases in emergent pathogens, which can spread these antimicrobial resistance elements. This study reinforces that molecular biology vigilance can prevent outbreaks and help to better understand antimicrobial resistance and pathogens in clinical environment dynamics.