Corynebacterium urealyticum is a non-diphtherial urease-producing clinically relevant corynebacterial, most frequently involved in urinary tract infections. Most of the C. urealyticum clinical isolates are frequently resistant to several antibiotics. We investigated the susceptibility of 40 C. urealyticum isolated in our institution during the period 2005–2017 to eight compounds representative of the main clinically relevant classes of antimicrobial agents. Antimicrobial susceptibility was determined by the Epsilometer test. Resistance genes were searched by PCR. All strains were susceptible to vancomycin whereas linezolid and rifampicin also showed good activity (MICs₉₀ = 1 and 0.4 mg/L, respectively). Almost all isolates (39/40, 97.5%) were multidrug resistant. The highest resistance rate was observed for ampicillin (100%), followed by erythromycin (95%) and levofloxacin (95%). Ampicillin resistance was associated with the presence of the blaA gene, encoding a class A β-lactamase. The two rifampicin-resistant strains showed point mutations driving amino acid replacements in conserved residues of RNA polymerase subunit β (RpoB). Tetracycline resistance was due to an efflux-mediated mechanism. Thirty-nine PFGE patterns were identified among the 40 C. urealyticum, indicating that they were not clonally related, but producing sporadic infections. These findings raise the need of maintaining surveillance strategies among this multidrug resistant pathogen.

Corynebacterium spp. are Gram-positive rods that are recognized to cause opportunistic diseases under certain predisposing clinical conditions. Some species have been described in urinary tract infections. In this report we document a new episode of urinary tract infection caused by Corynebacterium phoceense and describe the whole-genome sequencing, phenotypic characteristics and mass spectra obtained by matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Based on genome identification and DNA-to-DNA hybridization, we can assume that our strain is the second isolate of C. phoceense to be described in a urine sample. No other infectious diseases have been reported to be associated with this species.

Herein, we combined different bioinformatics tools and databases (BV-BRC, ResFinder, RAST, and KmerResistance) to perform a prediction of antimicrobial resistance (AMR) in the genomic sequences of 107 Corynebacterium striatum isolates for which trustable antimicrobial susceptibility (AST) phenotypes could be retrieved. Then, the reliabilities of the AMR predictions were evaluated by different metrics: area under the ROC curve (AUC); Major Error Rates (MERs) and Very Major Error Rates (VMERs); Matthews Correlation Coefficient (MCC); F1-Score; and Accuracy. Out of 15 genes that were reliably detected in the C. striatum isolates, only tetW yielded predictive values for tetracycline resistance that were acceptable considering Food and Drug Administration (FDA)'s criteria for quality (MER < 3.0% and VMER with a 95% C.I. ≤1.5-≤7.5%); this was accompanied by a MCC score higher than 0.9 for this gene. Noteworthy, our results indicate that other commonly used metrics (AUC, F1-score, and Accuracy) may render overoptimistic evaluations of AMR-prediction reliabilities on imbalanced datasets. Accordingly, out of 10 genes tested by PCR on additional multidrug-resistant Corynebacterium spp. isolates (n = 18), the tetW gene rendered the best agreement values with AST profiles (94.11%). Overall, our results indicate that genome-based AMR prediction can still be challenging for MDR clinical isolates of emerging Corynebacterium spp.

Severe asthma is a heterogeneous condition often resistant to conventional corticosteroid therapy, necessitating the identification of novel biomarkers and therapeutic targets. This study investigates immunological, transcriptional, and proteomic biomarkers in severe asthma patients from the Brazilian ProAR cohort. Cytokines were measured using a multiplex technology and the differential sputum cell count was performed by cytospin preparations. Sputum transcriptomics was performed by RNA-seq using Ion S5 next-generation sequencing platform. The proteomic study of sputum was performed by liquid chromatography–tandem mass spectrometry (LC-MS/MS) using Q Exactive Orbitrap technology. Compared to mild-to-moderate asthma (MMA) and treatment-controlled severe asthma (SAC), the treatment-resistant severe asthma (SAR) group exhibited increased sputum neutrophilia, eosinophilia, and elevated IL-6 and TNF levels, correlating with impaired lung function. Transcriptomic and proteomic analyses revealed a Th2-independent molecular signature characterized by downregulation of the Hippo signaling pathway and upregulation of JAK–STAT inflammatory cascades. Distinctive microRNA profiles suggest regulatory involvement in inflammatory and proliferative processes. These findings align with prior studies, reinforcing the presence of an IL-6- and TNF-high severe asthma phenotype across diverse populations. Our results highlight key inflammatory pathways that may underlie corticosteroid resistance, offering potential targets for personalized therapeutic interventions in severe asthma.

Herein, we describe the detection of a SARS-CoV-2 genome through metatranscriptome next-generation sequencing directly from the nasopharyngeal swab of a suspected case of local transmission of Covid-19, in Brazil. Depletion of human ribosomal RNA and use of an optimized in-house developed bioinformatics strategy contributed to successful detection of the virus.

A pandemia de COVID-19, causada pelo SARS-CoV-2, trouxe à tona a importância das tecnologias de sequenciamento de nova geração (NGS) tanto na descoberta do vírus quanto na determinação de novas variantes. Em 2022, a Organização Mundial da Saúde emitiu uma estratégia global de vigilância genômica para patógenos de potencial pandêmico e epidêmico. Neste sentido, este trabalho busca implementar, comparar e validar protocolos que utilizam apenas dados brutos de sequenciamento para diagnóstico e determinação de variantes do vírus. Foram utilizados dados de 15 novos sequenciamentos de SARS-CoV-2, obtidos por metodologia direcionada Ion Ampliseq (n = 10) ou por abordagem metatranscriptômica (n = 5). A montagem dessas sequências foi realizada pelas plataformas ID-seq, CoronaSPAdes, PATRIC, BV-BRC e Genome Detective. Já a anotação foi realizada pelas plataformas BV-BRC, Genome Detective, GISAID e Nextclade. Inicialmente, a plataforma BV-BRC se mostrou a mais eficiente na determinação correta das variantes, porém, sofreu perda de especificidade após atualizações. Já o Genome Detective, em sua versão atualizada, apresentou uma maior capacidade de determinar a variante do vírus. A plataforma GISAID não gerou resultados satisfatórios para as amostras avaliadas, enquanto o Nextclade foi capaz de apontar a variante na maioria das nossas amostras, mostrando-se como uma plataforma confiável. Amostras sequenciadas pela metodologia Ion Ampliseq apresentaram valores mais uniformes e mais próximos das referências, em comparação à abordagem metatranscriptômica, evidenciando que o tipo de sequenciamento direcionado influencia a montagem e anotação.