Between November 2013 and June 2014, 56 cases of bacteremia (15 deaths) associated with the use of Total Parenteral Nutrition (TPN) and/or calcium gluconate (CG) were reported in four Brazilian states. We analyzed 73 bacterial isolates from four states: 45 from blood, 25 from TPN and three from CG, originally identified as Acinetobacter baumannii, Rhizobium radiobacter, Pantoea sp. or Enterobacteriaceae using molecular methods. The first two bacterial species were confirmed while the third group of species could not be identified using standard identification protocols. These isolates were subsequently identified by Multi-Locus Sequence Analysis as Phytobacter diazotrophicus, a species related to strains from similar outbreaks in the United States in the 1970’s. Within each species, TPN and blood isolates proved to be clonal, whereas the R. radiobacter isolates retrieved from CG were found to be unrelated. This is the first report of a three-species outbreak caused by TPN contaminated with A. baumannii, R. radiobacter and P. diazotrophicus. The concomitant presence of clonal A. baumannii and P. diazotrophicus isolates in several TPN and blood samples, as well as the case of one patient, where all three different species were isolated simultaneously, suggest that the outbreak may be ascribed to a discrete contamination of TPN. In addition, this study highlights the clinical relevance of P. diazotrophicus, which has been involved in outbreaks in the past, but was often misidentified as P. agglomerans.

Although many clinically significant strains belonging to the family Enterobacteriaceae fall into a restricted number of genera and species, there is still a substantial number of isolates that elude this classification and for which proper identification remains challenging. With the current improvements in the field of genomics, it is not only possible to generate high-quality data to accurately identify individual nosocomial isolates at the species level and understand their pathogenic potential but also to analyse retrospectively the genome sequence databases to identify past recurrences of a specific organism, particularly those originally published under an incorrect or outdated taxonomy. We propose a general use of this approach to classify further clinically relevant taxa, i.e., Phytobacter spp., that have so far gone unrecognised due to unsatisfactory identification procedures in clinical diagnostics. Here, we present a genomics and literature-based approach to establish the importance of the genus Phytobacter as a clinically relevant member of the Enterobacteriaceae family.

We investigated the molecular mechanisms underlying azole resistance in seven Candida tropicalis isolates that caused candidemia and candiduria in Paraná, Brazil (2016–2022). Biofilm production, antifungal susceptibility testing, multilocus sequence typing, amplification and sequencing of ERG11, and quantification of ERG11, MDR1, and CDR1 expression levels were performed. Notably, five isolates (71.4%) were from urine samples and two (28.6%) were from blood samples. All strains were biofilm producers, with levels ranging from moderate to strong. The minimum inhibitory concentration (MIC) values ranged from 8–>64 mg/L for fluconazole and 0.25–1 mg/L for voriconazole. All isolates had mutations in ERG11; Y132F and Y257N were predominant (71.4%), followed by Y132F and S154F (14.3%) and Y257H (14.3%). No differences in ERG11 expression were found between the susceptible and resistant groups, but MDR1 and CDR1 were more highly expressed in the susceptible isolates. All the isolates contained previously unassigned diploid sequence types. The emergence of C. tropicalis azole resistance has been previously described in Brazil; however, the presence of resistant isolates in urine highlights the need for surveillance resistant strains in both urinary and invasive contexts. In our study mutations in ERG11 were the main resistance mechanism identified in C. tropicalis.

The excessive use of antibiotics in animal production has contributed to the global spread of antimicrobial resistance (AMR), posing a significant public health threat. To evaluate the antimicrobial susceptibility profiles and detect resistance genes in bacterial isolates from chicken, pork, and fish meat samples collected in the State of Paraná, Brazil, between 2017 and 2023. Meat samples (n = 418) were tested for Escherichia coli and Salmonella spp., while Klebsiella spp. (n = 265) and Pseudomonas spp. (n = 262) were included from 2019 onward. Bacterial isolation followed ISO 17604:2015 standards with MALDI‐TOF identification. Susceptibility testing was performed using the Kirby‐Bauer disk diffusion method. Detection of resistance genes (bla_TEM, bla_SHV, bla_CTX‐M, bla_KPC, bla_NDM, bla_OXA‐48, bla_VIM, bla_SPM, and mcr‐1) was conducted by real‐time PCR. Multidrug resistance (MDR) was widespread, particularly in Salmonella spp . and Pseudomonas spp ., followed by Klebsiella spp . and E. coli . Extended‐spectrum β‐lactamase (ESBL) genes were frequent in E. coli and Klebsiella spp ., while plasmid‐mediated colistin resistance ( mcr‐1 ) and carbapenemase ( bla KPC) were also identified. Resistance to third‐generation cephalosporins and ampicillin was especially high. Sampling across years and animal species may not fully reflect farm‐level resistance. The absence of molecular typing limited the ability to track clonal spread of resistant strains. Widespread AMR in foodborne bacteria was observed, with resistance levels often exceeding those reported in European monitoring. These findings underscore the need for strengthened surveillance and coordinated actions across animal and human health sectors.