The Ethiopian Third National Tuberculosis Drug Resistance Survey Incorporating Whole Genome Sequencing.

Background: Drug-resistant tuberculosis (DR-TB) is a major challenge hindering global tuberculosis control. Ethiopia conducted a third national antituberculosis (TB) drug resistance survey, and this is the first survey to report on drug resistance using whole genome sequencing (WGS) in addition to genotypic and phenotypic test results. The aim of this study was to obtain up-to-date information regarding the magnitude and pattern of drug resistance in Ethiopia.

Sustained outbreak of bla harbouring pathogens in an Italian tertiary hospital: Genomic insights into persistence and spreading.

Objectives: We investigated an outbreak of bla harbouring pathogens lasting over a year, affecting patients in an intensive care unit (ICU) in a tertiary hospital in Bergamo, Italy. To identify transmission routes of pathogens, we combined classical epidemiological investigation with the molecular identification of the mobile genetic elements (MGEs), integrons, and resistance cassettes that could have played a role in the outbreak persistence.

Methods: Short and long reads sequencing were performed.

Activity of imipenem/relebactam against KPC-producing Klebsiella pneumoniae and the possible role of Ompk36 mutation in determining resistance: an Italian retrospective analysis.

Background: Antimicrobial resistance in Enterobacterales represents a substantial threat in modern clinical practice and the collection of data on the efficacy of new molecules is of paramount importance. Our study aimed to analyse the in vitro activity of imipenem/cilastatin/relebactam (IMI/REL) against KPC-producing Klebsiella pneumoniae (KPC-Kp) and investigate the genetic determinants of resistance to this agent.

Methods: A total of 603 KPC-Kp strains, which were randomly collected during a multicentre study in northern Italy in the period 2016-2018, were analysed retrospectively.

High rate of macrolide resistance and closely genetically related complex strains identified among both cystic fibrosis and non-cystic fibrosis patients within two countries.

Unlabelled: is an emerging opportunistic pathogen affecting patients with chronic lung diseases, primarily cystic fibrosis (CF), or those under immunosuppression. Hence, investigations into the epidemiology and transmission of and accurate antibiotic susceptibility data are essential for the effective treatment of infections caused by this pathogen. This retrospective nationwide study included all clinical isolates ( = 59) from 29 patients diagnosed in the Czech Republic and Slovakia between 2018 and 2023.

Diversity, functional classification and genotyping of SHV β-lactamases in .

Interpreting the phenotypes of alleles in genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal alleles or additional plasmid-borne alleles that have extended-spectrum β-lactamase (ESBL) activity and/or β-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/a changes is not completely documented or understood.

Dual spatial host-bacterial gene expression in Mycobacterium abscessus respiratory infections.

Co-localization of spatial transcriptome information of host and pathogen can revolutionize our understanding of microbial pathogenesis. Here, we aimed to demonstrate that customized bacterial probes can be successfully used to identify host-pathogen interactions in formalin-fixed-paraffin-embedded (FFPE) tissues by probe-based spatial transcriptomics technology. We analyzed the spatial gene expression of bacterial transcripts with the host transcriptomic profile in murine lung tissue chronically infected with Mycobacterium abscessus embedded in agar beads.

Nanopore-based targeted sequencing test for direct tuberculosis identification, genotyping, and detection of drug resistance mutations: a side-by-side comparison of targeted next-generation sequencing technologies.

Unlabelled: We investigated the performance of the targeted next-generation sequencing (tNGS)-based Oxford Nanopore Diagnostics AmPORE TB assay, recently approved by the World Health Organization (WHO) as tuberculosis (TB) diagnostic test for the detection of drug resistance on respiratory specimens. A total of 104 DNA samples from Xpert MTB/RIF-positive TB sputum specimens were tested using the AmPORE TB kit, with the GenoScreen Deeplex Myc-TB as a comparative tNGS assay. For AmPORE TB, DNA samples were divided into five sequencing runs on the MinION device.

Transcriptomic responses to antibiotic exposure in .

Transcriptional responses in bacteria following antibiotic exposure offer insights into antibiotic mechanism of action, bacterial responses, and characterization of antimicrobial resistance. We aimed to define the transcriptional antibiotic response (TAR) in (Mtb) isolates for clinically relevant drugs by pooling and analyzing Mtb microarray and RNA-seq data sets. We generated 99 antibiotic transcription profiles across 17 antibiotics, with 76% of profiles generated using 3-24 hours of antibiotic exposure and 49% within one doubling of the WHO antibiotic critical concentration.

Acute kidney injury and acute kidney disease in high-dose cisplatin-treated head and neck cancer.

Background: In locally advanced head and neck squamous cell carcinoma (LA-SCCHN) at least 200mg/m (standard dose 300 mg/m) of cisplatin concomitant with radiotherapy represents the standard of care, both in postoperative and conservative settings. Nevertheless, high dose administration every 3 weeks is often replaced with low dose weekly cisplatin to avoid toxicities like kidney injury, though often failing to reach the therapeutic dose. Our aim was to investigate the incidence of renal impairment in the real-life setting, integrating high dose cisplatin with adequate supportive therapy, and to explore both Acute Kidney Injury (AKI) and Acute Kidney Disease (AKD), a recently described clinical renal syndrome that encompasses functional alterations of the kidney lasting fewer than 3 months.

Advantages of long- and short-reads sequencing for the hybrid investigation of the genome.

Introduction: In the fight to limit the global spread of antibiotic resistance, computational challenges associated with sequencing technology can impact the accuracy of downstream analysis, including drug resistance identification, transmission, and genome resolution. About 10% of (MTB) genome is constituted by the PE/PPE family, a GC-rich repetitive genome region. Although sequencing using short read technology is widely used, it is well recognized its limit in the PE/PPE regions due to the unambiguously mapping process onto the reference genome.

The Impact of a Mediterranean-like Diet with Controlled Protein Intake on the Onco-Nephrological Scenario: Time for a New Perspective.

Chronic kidney disease (CKD) represents a frequent comorbidity in cancer patients, especially for patients affected by urological cancers. Unfortunately, impaired kidney function may limit the choice of adequate oncological treatments for their potential nephrotoxicity or due to contraindications in case of a low glomerular filtration rate. For these patients, tailored nephrological and nutritional management is mandatory.

The impact of near-infrared autofluorescence on postoperative hypoparathyroidism during total thyroidectomy: a case-control study.

Purpose: Near-infrared autofluorescence is a new technology in thyroid surgery to better localize and preserve parathyroid glands. The purpose of this study is to assess if the adoption of NIR-AF can improve in short-, medium-, and long-term post-operative calcium and PTH levels compared to conventional "naked eye" surgery in patients undergoing TT for benign or malignant conditions.

Methods: 134 patients undergone total thyroidectomy between January 2020 and June 2022; 67 were treated with conventional thyroidectomy, the other 67 underwent surgery adopting an autofluorescence detecting device.

Renal Function Outcomes in Metastatic Non-Small-Cell Lung Carcinoma Patients Treated with Chemotherapy or Immune Checkpoint Inhibitors: An Unexpected Scenario.

Immune checkpoint inhibitors (ICIs) and platinum-based chemotherapy (CT) are effective therapeutic agents for the palliative treatment of metastatic non-small-cell lung cancer (NSCLC); the aim of our study was to investigate the acute and chronic renal toxicities in this setting. We collected data on 292 patients who received cisplatin (35%), carboplatin-based regimens (25%), or ICI monotherapy (40%). The primary and secondary outcomes were compared to the acute kidney injury (AKI) rate and the mean estimated GFR (eGFR) decay between groups, respectively, over a mean follow-up duration of 15 weeks.

Detection of NDM-1/5 and OXA-48 co-producing extensively drug-resistant hypervirulent Klebsiella pneumoniae in Northern Italy.

Objectives: Using a hybrid long-read sequencing approach, we aimed to fully characterise four extensively-drug resistant (XDR) hypervirulent Klebsiella pneumoniae isolates, one of which represented the first strain isolated in Italy co-expressing NDM-1/5 and OXA-48 carbapenemases.

Methods: Whole-genome sequencing was performed using Illumina and Oxford Nanopore Technology platforms. An assembly pipeline was used to recover the structures both of the chromosome and plasmids.

The Role of Vascular Lesions in Diabetes Across a Spectrum of Clinical Kidney Disease.

Introduction: The clinical-histologic correlation in diabetic nephropathy is not completely known.

Methods: We analyzed nephrectomy specimens from 90 patients with diabetes and diverse degrees of proteinuria and glomerular filtration rate (GFR).

Results: Thirty-six (40%) subjects had normoalbuminuria, 33 (37%) microalbuminuria, and 21 (23%) non-nephrotic proteinuria.

Unexpected Outcomes of Renal Function after Radical Nephrectomy: Histology Relevance along with Clinical Aspects.

Acute kidney injury (AKI) and chronic kidney disease (CKD) are common events after radical nephrectomy (RN). In this study we aimed to predict AKI and CKD after RN relying on specific histological aspects. We collected data from a cohort of 144 patients who underwent radical nephrectomy.

Preliminary Study on Pasta Samples Characterized in Antioxidant Compounds and Their Biological Activity on Kidney Cells.

Pasta is one of the basic foods of the Mediterranean diet and for this reason it was chosen for this study to evaluate its antioxidant properties. Three types of pasta were selected: buckwheat, rye and egg pasta. Qualitative-quantitative characterization analyses were carried out by HPLC-DAD to identify antioxidant compounds.

Renal function outcomes in patients with muscle-invasive bladder cancer treated with neoadjuvant pembrolizumab and radical cystectomy in the PURE-01 study.

The use of pembrolizumab has been largely accepted in several advanced types of cancers. PURE 01 study (NCT02736266) enrolled consecutively 143 patients with muscle-invasive bladder cancer who received 3 cycles of pembrolizumab 200 mg every 3 weeks before planned radical cystectomy (RC). Clinical, pathological and laboratory data were collected to investigate the relationship between renal function, immunotherapy and cancer-related outcomes.

Renal histology across the stages of chronic kidney disease.

Background: The chronic kidney disease (CKD) classification represents a simple tool to evaluate kidney disease. However, it is not based on kidney histology and this might limit the correlation between renal function and histological damage. The aim of this study was to examine the presence and magnitude of the discordance between CKD classification and kidney histology.