Genomic Analysis of Strains Isolated in the Years 2007-2022 with a Report on the Identification of the First Non-Toxigenic Gene-Bearing Strain in Poland.

Infections caused by non-toxigenic have been reported every year in Poland since 2004, with the ST8 biovar gravis strains being most commonly isolated. This study analyzed thirty strains isolated between 2017 and 2022 and six previously isolated strains. All the strains were characterized using classic methods in terms of species, biovar level, and diphtheria toxin production, as well as by means of whole genome sequencing.

The Mechanisms Involved in the Fluoroquinolone Resistance of Strains Isolated from Humans in Poland, 2018-2019: The Prediction of Antimicrobial Genes by In Silico Whole-Genome Sequencing.

Salmonellosis remains the second most common zoonosis in Europe. Resistance to fluoroquinolones (FQs) in has been increasing worldwide, with WHO considering FQ-resistant spp. as high-priority pathogens.

Prevalence of Plasmid-Mediated Quinolone Resistance (PMQRs) Determinants and Whole Genome Sequence Screening of PMQR-Producing Isolated from Men Undergoing a Transrectal Prostate Biopsy.

Unlabelled: Fluoroquinolones (FQs) are recommended as prophylaxis for men undergoing transrectal prostate biopsy (TRUS-Bx). Recent studies suggest a significant share of FQ-resistant rectal flora in post-TRUST-Bx infections.

Methods: 435 isolates from 621 patients attending 12 urological departments in Poland were screened by PCR for PMQR genes.

Epidemiological and microbiological investigation of a large increase in vibriosis, northern Europe, 2018.

BackgroundVibriosis cases in Northern European countries and countries bordering the Baltic Sea increased during heatwaves in 2014 and 2018.AimWe describe the epidemiology of vibriosis and the genetic diversity of spp. isolates from Norway, Sweden, Denmark, Finland, Poland and Estonia in 2018, a year with an exceptionally warm summer.

NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology.

Background: Next Generation Sequencing (NGS) techniques dominate today's landscape of genetics and genomics research. Though Illumina still dominates worldwide sequencing, Oxford Nanopore is one of the leading technologies currently being used by biologists, medics and geneticists across various applications. Oxford Nanopore is automated and relatively simple for conducting experiments, but generates gigabytes of raw data, to be processed by often ambiguous set of alternative bioinformatics command-line tools, and genomics frameworks which require a knowledge of bioinformatics to run.

The molecular mechanisms of fluoroquinolone resistance found in rectal swab isolates of Enterobacterales from men undergoing a transrectal prostate biopsy: the rationale for targeted prophylaxis.

Background: Transrectal ultrasound-guided prostate biopsy (TRUS-Bx) is considered an essential urological procedure for the histological diagnosis of prostate cancer. It is, however, considered a "contaminated" procedure which may lead to infectious complications. Recent studies suggest a significant share of fluoroquinolone-resistant rectal flora in post-biopsy infections.

Antimicrobial Resistance and Whole-Genome Characterisation of High-Level Ciprofloxacin-Resistant Enterica Serovar Kentucky ST 198 Strains Isolated from Human in Poland.

Background: Kentucky belongs to zoonotic serotypes that demonstrate that the high antimicrobial resistance and multidrug resistance (including fluoroquinolones) is an emerging problem. To the best of our knowledge, clinical Kentucky strains isolated in Poland remain undescribed.

Methods: Eighteen clinical Kentucky strains collected in the years 2018-2019 in Poland were investigated.

[Molecular diagnosis of COVID-19 – present experiences].

Severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2), a new highly emerging and pathogenic for human RNA virus, is responsible for the present COVID-19 pandemic. Molecular diagnostic methods, including real-time reverse transcription-PCR (RT-PCR) assay are the recommended methods for the identification and laboratory confirmation of COVID-19 cases. RT-PCR allows for detection the RNA of the virus in clinical specimens from patients suspected of COVID-19 with high specificity and sensitivity.

Antibody response to lipopolysaccharides and recombinant proteins of Shiga toxin (STX)-producing Escherichia coli (STEC) in children with haemolytic uraemic syndrome in Poland.

Typical haemolytic uraemic syndrome (STEC-HUS), caused by Shiga toxin (Stx)-producing Escherichia coli (STEC), is a serious, life-threating disease that mainly affects children. Bacteriological and genetic tests are commonly used in the routine laboratory diagnosis of STEC-HUS; however, serological methods have emerged as useful and reliable diagnostic tools, especially when bacterial isolation fails. In this study, we present the results of the serological investigation of 72 paediatric patients suspected for HUS, hospitalized during 2011-2019 at the Department of Pediatrics and Nephrology of Children's Hospitals in Poland.

Characterization of a bacteriophage, vB_Eco4M-7, that effectively infects many Escherichia coli O157 strains.

The characterization of a recently isolated bacteriophage, vB_Eco4M-7, which effectively infects many, though not all, Escherichia coli O157 strains, is presented. The genome of this phage comprises double-stranded DNA, 68,084 bp in length, with a GC content of 46.2%.

MLST-based genetic relatedness of Campylobacter jejuni isolated from chickens and humans in Poland.

Campylobacter jejuni infection is one of the most frequently reported foodborne bacterial diseases worldwide. The main transmission route of these microorganisms to humans is consumption of contaminated food, especially of chicken origin. The aim of this study was to analyze the genetic relatedness of C.

Genetic diversity of Francisella tularensis in Poland with comments on MLVA genotyping and a proposition of a novel rapid v4-genotyping.

We investigated the genotypes of Francisella tularensis (F. tularensis) strains isolated in Poland during the period 1953-2013 and studied their genetic relationship to F. tularensis strains isolated in other countries using MLVA.

Clinical outcomes for cystic fibrosis patients with Pseudomonas aeruginosa cross-infections.

Introduction: Pseudomonas aeruginosa cross-infections are related to increased morbidity and mortality in cystic fibrosis (CF).

Objectives: The aim of the study was to evaluate the incidence of cross-infections with P. aeruginosa in children with CF.

-SVR Based Genetic Diversity of Multiresistant Isolated From Chickens and Humans.

is one of the most common causes of human foodborne bacterial infections worldwide. The objective of this study was to assess the molecular diversity, using sequencing, of 602 isolated from chicken food chain, i.e.

Draft genome sequence of an Escherichia coli ST410 isolate co-harbouring bla, bla, bla, aac(3)-IIa and aac(6')-Ib-cr genes with gyrA and parC mutations isolated from a paediatric patient in Poland.

Objectives: Escherichia coli is one of the major causative agents of nosocomial infections. Here we report the first draft genome sequence of an E. coli strain (no.

Emergence of Enterobacteriaceae co-producing CTX-M-15, ArmA and PMQR in Poland.

Background: Plasmid-mediated extended-spectrum β-lactamases (ESBLs), 16S rRNA methylases and quinolone resistance mechanisms (PMQRs) are well-known agents conferring resistance to more than 1 antimicrobial in its group. The accumulation of these agents poses, therefore, a serious risk to public health.

Objectives: The objective of this study was to investigate the presence of common ß-lactamases and 16S rRNA methylases in Qnr-producing Enterobacteriaceae and their genetic relatedness.

Antimicrobial Resistance and Virulence-Associated Traits of Isolated From Poultry Food Chain and Humans With Diarrhea.

The objective of this study was to test the prevalence of virulence-associated markers and antimicrobial resistance in 624 isolated from poultry food chain, i. e., chicken feces ( = 160), poultry carcasses ( = 157), poultry meat ( = 152) and from humans ( = 155).

Ciprofloxacin and nalidixic acid resistance of Salmonella spp. isolated from retail food in Poland.

Distribution of amino acid substitutions in the quinolone resistance-determining region (QRDR) of gyrA, gyrB, parC, parE and determinants of plasmid-mediated quinolone resistance (PMQR) were investigated among quinolone-resistant Salmonella spp. strains isolated from retail food in Poland in the years 2008-2013. Ten different amino acid substitutions were identified in QRDRs.

The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory - sequencing and analysis strategies.

Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like Bacillus anthracis, Francisella tularensis, Yersinia pestis, Ebola virus, MERS, Lassa virus etc.

Usefulness of in-house obtained recombinant proteins Yop of Yersinia enterocolitica as highly specific antigens in ELISA and recom-dot performed in the serodiagnosis of yersiniosis.

Introduction: Proper analysis of the human immune response is crucial in the laboratory diagnosis of many bacterial infections-The current serological diagnosis of yersiniosis often is carried out using ELISA with native antigens. However, recombinant proteins increase the specificity of the serological assays, particularly in patients with chronic, non- specific infections. The aim of the present study was to evaluate the usefulness of in-house obtained recombinant proteins Yop of Yersinia enterocolitica as highly specific antigens in ELISA and recom-dot performed in the serodiagnosis of yersiniosis.

Distribution of carbapenem resistance mechanisms in Pseudomonas aeruginosa isolates among hospitalised children in Poland: Characterisation of two novel insertion sequences disrupting the oprD gene.

This study aimed to analyse the distribution of carbapenem resistance mechanisms among Pseudomonas aeruginosa clinical isolates. Fifty-five P. aeruginosa isolates, resistant both to imipenem and meropenem, from children hospitalised in 2009-2010 were studied.

Distribution of 16S rRNA Methylases Among Different Species of Aminoglycoside-Resistant Enterobacteriaceae in a Tertiary Care Hospital in Poland.

Background: Aminoglycosides are a group of antimicrobial agents still the most commonly used in the treatment of life-threatening bacterial infections in human and animals. The emergence and spread of 16S rRNA methylases, which confer high-level resistance to the majority of clinically relevant aminoglycosides, constitute a major public health concern.

Objectives: Our goal was to evaluate the distribution of 16S rRNA methylases among different species of Enterobacteriaceae during a five month-long survey in a tertiary hospital in Warszawa, Poland.

[Use of selected recombinant proteins in serodiagnosis of infections caused by verotoxigenic Escherichia coli (VTEC) in humans].

Introduction: Verocytotoxin-producing E. coli (VTEC) are a significant cause of haemor- rhagic colitis (HC) and haemolytic uremic syndrome (HUS) in humans. Because VTEC isolates are usually present in patients' feces for only a limited period of time serodiagnosis based on the purified antigens have become the useful tool for laboratory diagnosis and monitoring of prevalence of VTEC infections.

[Whole cell protein profiling characterization of Corynebacterium diphtheriae clinical isolates collected from various infections].

Introduction: Corynebacterium diphtheriae can cause various infections such as diphtheria, wound infections, septic arthritis, bacteraemia and endocarditis. Different virulence properties of the isolates might be related to different virulence factors expressed by the isolates. The objective of this study was to explore whether whole cell protein profiling might be useful in prediction of pathogenic properties of C.

Characterisation of Yersinia Secretion Apparatus--Pathogenicity Island (Ysa-PI) of Yersinia enterocolitica 1B/O8 in Poland: an Idle Ysa is a Specific Hallmark of the Epidemic Sensu Stricto Strain.

Yersinia secretion apparatus (Ysa), the chromosomal type three secretion system (T3SS) is considered to contribute to virulence of high-pathogenicity Yersina enterocolitica biovar 1B. DNA-sequence of Ysa pathogenicity island was determined for clinical isolate DM0110 of Y enterocolitica 1B/08 with origin in Poland. We found a premature stop-codon in the regulatory gene ysrR (mutation at position 269).