UNLABELLED: Listeria monocytogenes presents a significant concern for the food industry due to its ability to persist in the food processing environment. One of the factors contributing to its persistence is decreased sensitivity to disinfectants. Our objective was to assess the diversity of L. monocytogenes sensitivity to food industry disinfectants by testing the response of 1,671 L. monocytogenes isolates to quaternary ammonium compounds (QACs) and 414 isolates to peracetic acid (PAA) using broth microdilution and growth curve analysis assays, respectively, and to categorize the isolates into sensitive and tolerant. A high phenotype-genotype concordance (95%) regarding tolerance to QACs was obtained by screening the genomes for the presence of QAC tolerance-associated genes bcrABC, emrE, emrC, and qacH. Based on this high concordance, we assessed the QAC genes' dissemination among publicly available L. monocytogenes genomes (n = 39,196). Overall, QAC genes were found in 23% and 28% of the L. monocytogenes collection in this study and in the global data set, respectively. bcrABC and qacH were the most prevalent genes, with bcrABC being the most detected QAC gene in the USA, while qacH dominated in Europe. No significant differences (P > 0.05) in the PAA tolerance were detected among isolates belonging to different lineages, serogroups, clonal complexes, or isolation sources, highlighting limited variation in the L. monocytogenes sensitivity to this disinfectant. The present work represents the largest testing of L. monocytogenes sensitivity to important food industry disinfectants at the phenotypic and genomic level, revealing diversity in the tolerance to QACs while all isolates showed similar sensitivity to PAA. IMPORTANCE: Contamination of Listeria monocytogenes within food processing environments is of great concern to the food industry due to challenges in eradicating the isolates once they become established and persistent in the environment. Genetic markers associated with increased tolerance to certain disinfectants have been identified, which alongside other biotic and abiotic factors can favor the persistence of L. monocytogenes in the food production environment. By employing a comprehensive large-scale phenotypic testing and genomic analysis, this study significantly enhances the understanding of the L. monocytogenes tolerance to quaternary ammonium compounds (QACs) and the genetic determinants associated with the increased tolerance. We provide a global overview of the QAC genes prevalence among public L. monocytogenes sequences and their distribution among clonal complexes, isolation sources, and geographical locations. Additionally, our comprehensive screening of the peracetic acid (PAA) sensitivity shows that this disinfectant can be used in the food industry as the lack of variation in sensitivity indicates reliable effect and no apparent possibility for the emergence of tolerance.

• Klíčová slova
• Listeria monocytogenes, disinfectants, food industry, peracetic acid, quaternary ammonium compounds,
• MeSH
• bakteriální léková rezistence genetika   MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• dezinficiencia * farmakologie   MeSH
• fenotyp MeSH
• genom bakteriální MeSH
• genomika MeSH
• kvartérní amoniové sloučeniny * farmakologie   MeSH
• kyselina peroctová * farmakologie   MeSH
• Listeria monocytogenes * účinky léků   genetika   MeSH
• mikrobiální testy citlivosti MeSH
• potravinářská mikrobiologie MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bakteriální proteiny MeSH
• dezinficiencia * MeSH
• kvartérní amoniové sloučeniny * MeSH
• kyselina peroctová * MeSH

This report describes mutations in genes responsible for cell deformities in haemophili under beta-lactam pressure in vitro. Light and transmission electron microscopy confirmed a hypothesis regarding changes in the shape of haemophili that had become more filamentous in the presence of ampicillin (2 mg/L) and cefuroxime (8 mg/L) after 30 days of serial passage. Short-axis size increased by 28% (from 0.767 to 1.06 µm) and long-axis length increased by 54% (from 1 to 2.175 µm). Additionally, whole-genome sequencing analysis (Illumina platform, software PROKKA) revealed a variety of mutations in genes responsible for cell morphology in isolates examined in this study: ftsI (A1576 → C; G1154 → C; T986 → C; G1684 → C), mreB (C476 → T), mreC (A5 → G), mrdA (A1148 → G; C179 → T; G1613 → T), mrdB (T668 → G), mltC (C1016 → T) and rodA (T668 → G). The results of this study indicate that shifts in bacterial shape could play a role in the adaptation of haemophili to a new niche created by beta-lactams as a strategy of antibiotic therapy survival.

• Klíčová slova
• Beta-lactams, Haemophili, Whole-genome sequencing,
• MeSH
• ampicilin farmakologie   MeSH
• antibakteriální látky * farmakologie   MeSH
• beta-laktamy * farmakologie   MeSH
• cefuroxim farmakologie   MeSH
• genom bakteriální * MeSH
• Haemophilus influenzae * genetika   účinky léků   MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• mutace MeSH
• sekvenování celého genomu * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• ampicilin MeSH
• antibakteriální látky * MeSH
• beta-laktamy * MeSH
• cefuroxim MeSH

The yeast Magnusiomyces capitatus is an opportunistic human pathogen causing rare yet severe infections, especially in patients with hematological malignancies. Here, we report the 20.2 megabase genome sequence of an environmental strain of this species as well as the genome sequences of eight additional isolates from human and animal sources providing an insight into intraspecies variation. The distribution of single-nucleotide variants is indicative of genetic recombination events, supporting evidence for sexual reproduction in this heterothallic yeast. Using RNAseq-aided annotation, we identified genes for 6518 proteins including several expanded families such as kexin proteases and Hsp70 molecular chaperones. Several of these families are potentially associated with the ability of M. capitatus to infect and colonize humans. For the purpose of comparative analysis, we also determined the genome sequence of a closely related yeast, Magnusiomyces ingens. The genome sequences of M. capitatus and M. ingens exhibit many distinct features and represent a basis for further comparative and functional studies.

• Klíčová slova
• Comparative genome analysis, Magnusiomyces, Pathogenicity, Sexual reproduction, Yeast,
• MeSH
• anotace sekvence MeSH
• antifungální látky farmakologie   MeSH
• faktory virulence MeSH
• fenotyp MeSH
• fylogeneze MeSH
• genom fungální * MeSH
• genomika * metody   MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• multigenová rodina MeSH
• mykózy mikrobiologie   MeSH
• oportunní infekce mikrobiologie   MeSH
• rekombinace genetická MeSH
• Saccharomycetales klasifikace   genetika   růst a vývoj   patogenita   MeSH
• výpočetní biologie metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antifungální látky MeSH
• faktory virulence MeSH

BACKGROUND: Morganella spp are opportunistic pathogens involved in various infections. Intrinsic resistance to multiple antibiotics (including colistin) combined with the emergence of carbapenemase producers reduces the number of active antimicrobials. The aim of this study was to characterise genetic features related to the spread of carbapenem-resistant Morganella spp. METHODS: This comparative genomic study included extensively drug-resistant Morganella spp isolates collected between Jan 1, 2013, and March 1, 2021, by the French National Reference Center (NRC; n=68) and European antimicrobial resistance reference centres in seven European countries (n=104), as well as one isolate from Canada, two reference strains from the Pasteur Institute collection (Paris, France), and two colistin-susceptible isolates from Bicêtre Hospital (Kremlin-Bicêtre, France). The isolates were characterised by whole-genome sequencing, antimicrobial susceptibility testing, and biochemical tests. Complete genomes from GenBank (n=103) were also included for genomic analysis, including phylogeny and determination of core genomes and resistomes. Genetic distance between different species or subspecies was performed using average nucleotide identity (ANI). Intrinsic resistance mechanisms to polymyxins were investigated by combining genetic analysis with mass spectrometry on lipid A. FINDINGS: Distance analysis by ANI of 275 isolates identified three groups: Morganella psychrotolerans, Morganella morganii subspecies sibonii, and M morganii subspecies morganii, and a core genome maximum likelihood phylogenetic tree showed that the M morganii isolates can be separated into four subpopulations. On the basis of these findings and of phenotypic divergences between isolates, we propose a modified taxonomy for the Morganella genus including four species, Morganella psychrotolerans, Morganella sibonii, Morganella morganii, and a new species represented by a unique environmental isolate. We propose that M morganii include two subspecies: M morganii subspecies morganii (the most prevalent) and M morganii subspecies intermedius. This modified taxonomy was supported by a difference in intrinsic resistance to tetracycline and conservation of metabolic pathways such as trehalose assimilation, both only present in M sibonii. Carbapenemase producers were mostly identified among five high-risk clones of M morganii subspecies morganii. The most prevalent carbapenemase corresponded to NDM-1, followed by KPC-2, and OXA-48. A cefepime-zidebactam combination was the most potent antimicrobial against the 172 extensively drug-resistant Morganella spp isolates in our collection from different European countries, which includes metallo-β-lactamase producers. Lipid A analysis showed that the intrinsic resistance to colistin was associated with the presence of L-ARA4N on lipid A. INTERPRETATION: This global characterisation of, to our knowledge, the widest collection of extensively drug-resistant Morganella spp highlights the need to clarify the taxonomy and decipher intrinsic resistance mechanisms, and paves the way for further genomic comparisons. FUNDING: None.

• MeSH
• antibakteriální látky * farmakologie   MeSH
• bakteriální proteiny * genetika   metabolismus   MeSH
• beta-laktamasy * genetika   metabolismus   MeSH
• enterobakteriální infekce * mikrobiologie   epidemiologie   MeSH
• fylogeneze * MeSH
• genom bakteriální * genetika   MeSH
• genomika MeSH
• karbapenemy farmakologie   MeSH
• kolistin farmakologie   MeSH
• lidé MeSH
• mikrobiální testy citlivosti * MeSH
• mnohočetná bakteriální léková rezistence genetika   MeSH
• Morganella * genetika   MeSH
• sekvenování celého genomu MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH
• Geografické názvy
• Evropa epidemiologie   MeSH
• Názvy látek
• antibakteriální látky * MeSH
• bakteriální proteiny * MeSH
• beta-laktamasy * MeSH
• carbapenemase MeSH Prohlížeč
• karbapenemy MeSH
• kolistin MeSH

OBJECTIVES: The aim of this study was to analyse the DNA sequences of three teicoplanin-resistant Staphylococcus epidermidis isolates collected from patients not previously treated with glycopeptide antibiotics. METHODS: The minimum inhibitory concentrations (MICs) of 12 antibiotics, including teicoplanin and vancomycin, were determined by the broth microdilution method. Genomic DNA was isolated, was sequenced by HiSeqX paired-end sequencing and was assembled into draft genome sequences using MyPro pipeline. RESULTS: Analysis of the draft genome sequences demonstrated that the teicoplanin-resistant S. epidermidis isolates belonged to multilocus sequence typing (MLST) sequence types ST5 and ST87 and encoded multiple antimicrobial resistance genes, including the methicillin resistance gene mecA. CONCLUSIONS: This report highlights the risk of dissemination of S. epidermidis strains resistant to a wide range of clinically important antibiotics.

• Klíčová slova
• Staphylococcus epidermidis, Teicoplanin resistance, Whole-genome sequencing,
• MeSH
• antibakteriální látky farmakologie   MeSH
• bakteriální léková rezistence * MeSH
• genom bakteriální * MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• multilokusová sekvenční typizace MeSH
• sekvenování celého genomu MeSH
• stafylokokové infekce mikrobiologie   MeSH
• Staphylococcus epidermidis klasifikace   účinky léků   MeSH
• techniky typizace bakterií MeSH
• teikoplanin farmakologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antibakteriální látky MeSH
• teikoplanin MeSH

UNLABELLED: The paper presents the study of a set of isolates of Streptococcus pneumoniae, which comprised two heterogeneous subpopulations, one of which was susceptible and the other resistant to optochin. The aim of the study was to compare the results of serotyping, multilocus sequence typing (MLST), ribosomal multilocus sequence typing (rMLST), and variation analysis of these subpopulations and to investigate the genetic probable causes of optochin resistance. The strains studied were cultured from samples taken from patients with invasive pneumococcal disease in the Czech Republic in 2019 and 2020. A total of 10 studied pairs of isolates were subject to serotyping and whole-genome sequencing (WGS). None of the typing methods (serotyping, MLST, or rMLST) applied to pairs of optochin-susceptible and optochin-resistant isolates revealed differences in serotype, sequence type, or ribosomal sequence type. The WGS data analysis identified point mutations in ATP (adenosine triphosphate) synthase genes in 8 of the 10 optochin-resistant isolates. In seven optochin-resistant isolates, the mutation was found in the atpC gene and in one isolate in the atpA gene. One of the mutations in the atpC gene has not yet been published in the literature; it is a mutation at position 143T > C with an amino acid change of Val48Ala. In 8 out of the 10 optochin-resistant isolates, the possible genetic basis for resistance was identified, involving point mutations in the atpA and atpC genes. In the remaining two isolates, no clear genetic explanation for the optochin resistance in S. pneumoniae was found, based on current knowledge. IMPORTANCE: Globally, among the most fundamental tests used for the identification of Streptococcus pneumoniae isolates is determining susceptibility to optochin. In the last 2 decades, optochin-resistant strains have been frequently reported in the literature, which can lead to the misidentification of S. pneumoniae. This study compares whole-genome sequencing data of optochin-susceptible and optochin-resistant subpopulations of S. pneumoniae isolates and investigates the genetic probable causes of resistance in the genomes of optochin-resistant subpopulations.

• Klíčová slova
• Streptococcus pneumoniae, optochin, whole genome sequencing,
• MeSH
• antibakteriální látky * farmakologie   MeSH
• bakteriální léková rezistence * genetika   MeSH
• bakteriální proteiny genetika   MeSH
• chinin analogy a deriváty   MeSH
• genom bakteriální MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• multilokusová sekvenční typizace MeSH
• pneumokokové infekce mikrobiologie   MeSH
• sekvenování celého genomu MeSH
• sérotypizace MeSH
• Streptococcus pneumoniae * genetika   účinky léků   izolace a purifikace   klasifikace   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• antibakteriální látky * MeSH
• bakteriální proteiny MeSH
• chinin MeSH
• ethylhydrocupreine MeSH Prohlížeč

AIMS: Screening of bacterial flora for strains producing metabolites with inhibitory effects on the human pathogenic oomycete Pythium insidiosum. Separation and characterization of extracts from Pseudomonas stutzeri with anti-Pythium inhibitory activity. Search for genes with anti-Pythium effect within the genome of P. stutzeri. METHODS: A total of 88 bacterial strains were isolated from water resources in northeastern Thailand. Two screening methods were used to establish their inhibitory effects on P. insidiosum. One strain, P. stutzeri ST1302 was randomly chosen, and the extract with anti-P. insidiosum activity was fractionated and subfractionated using liquid column chromatography and purified by thin layer chromatography. The chemical structure of purified fractions was determined by Fourier transform infrared spectroscopy, nuclear magnetic resonance and mass spectrometry. Further, search for genes involved in the anti-Pythium activity (phenazine-1-carboxylic acid, 2,4-diacetylphloroglucinol, pyoluteorin and pyrrolnitrin) was undertaken in this P. stutzeri strain using primers described in the literature. RESULTS: Anti-P. insidiosum activity was detected in 16 isolates (18.2%). In P. stutzeri ST1302, a subfraction labeled PYK7 exhibited strong activity against this oomycete. It was assigned to the diketopiperazines as cyclo(D-Pro-L-Val). In the search for genes, one gene region was successfully amplified. This corresponded to pyrrolnitrin. The results suggest the possibility of using the related metabolites against P. insidiosum. This is the first report on the inhibitory effects of P. stutzeri against this oomycete. The results may contribute to the development of antimicrobial drugs/probiotics against pythiosis.

• MeSH
• diketopiperaziny farmakologie   MeSH
• genom bakteriální MeSH
• mikrobiální testy citlivosti MeSH
• Pseudomonas stutzeri chemie   genetika   izolace a purifikace   MeSH
• pyrrolnitrin farmakologie   MeSH
• pythióza farmakoterapie   mikrobiologie   MeSH
• Pythium účinky léků   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Thajsko MeSH
• Názvy látek
• diketopiperaziny MeSH
• pyrrolnitrin MeSH

BACKGROUND: Since the incidence of vancomycin-resistant enterococci (VRE) is increasing and treatment options remain limited, we aimed to investigate the epidemiology of vancomycin- and tigecycline-resistant enterococci in a university hospital using whole genome sequencing (WGS). METHODS: Between April and December 2021, 102 VRE isolates were collected from a single tertiary care hospital in the Czech Republic. Forty selected isolates underwent antimicrobial susceptibility testing and WGS (Illumina short reads and long reads with MinION in selected isolates). RESULTS: All Enterococcus faecium isolates were resistant to ampicillin, carrying the PBP5_Met485Ala, PBP5_Glu629Val, and fluoroquinolones carrying the GyrA_Ser83Ile and ParC_Ser80Ile substitutions. The vanA operon was found on pELF2-like plasmids and plasmids carrying rep17 and/or rep18b genes. The novel Tn1546 structural variants were identified in vanA-carrying isolates. The vanB operon was located on the chromosome within a Tn1549 structural variant. Linezolid resistance was detected in one isolate carrying the 23S rDNA_G2576T substitution. Twenty-two isolates were resistant to tigecycline (tet(L), tet(M) and rpsJ_del 155-166 or RpsJ_Lys57Arg). Discrepancies between phenotypic and genotypic resistance profiles were observed for daptomycin (RpoB_Ser491Phe), trimethoprim/sulfamethoxazole (dfrG gene), nitrofurantoin (NmrA_Gln48Lys substitution without the EF0404 and EF0648 genes) and tetracycline (truncated TetM). The two multilocus sequence typing (MLST) schemes identified different numbers of STs: 5 STs, with ST117 as the predominant one (n = 32, 80%), versus 10 STs, with ST138 (27.5%), ST136 (25%), and ST1067 (20%) being the most frequent, respectively. The whole genome MLST revealed clonal clustering (0-7 allele differences) among isolates of the same ST. When comparing ST117 isolates from our study with 2,204 ST117 isolates from 15 countries, only one Czech isolate clustered closely with strains from Germany and the Netherlands, differing by just 16 alleles. CONCLUSIONS: The spread of E. faecium isolates ST117 resistant to vancomycin and tigecycline was identified. The discrepancies between resistance genotypes and phenotypes highlight the importance of combining molecular and phenotypic surveillance in antimicrobial resistance monitoring.

• Klíčová slova
• Daptomycin, Long-read sequencing, Plasmids, Structural variants, Whole-genome sequencing, antimicrobial resistance,
• MeSH
• antibakteriální látky * farmakologie   MeSH
• bakteriální proteiny genetika   MeSH
• Enterococcus faecium * genetika   účinky léků   izolace a purifikace   klasifikace   MeSH
• enterokoky rezistentní vůči vankomycinu * genetika   účinky léků   izolace a purifikace   MeSH
• genom bakteriální MeSH
• grampozitivní bakteriální infekce * mikrobiologie   epidemiologie   MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• mnohočetná bakteriální léková rezistence genetika   MeSH
• multilokusová sekvenční typizace MeSH
• rezistence na vankomycin genetika   MeSH
• sekvenování celého genomu MeSH
• tigecyklin * farmakologie   MeSH
• vankomycin * farmakologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika epidemiologie   MeSH
• Názvy látek
• antibakteriální látky * MeSH
• bakteriální proteiny MeSH
• tigecyklin * MeSH
• vankomycin * MeSH

Colicin FY is a plasmid encoded toxin that recognizes a yersinia-specific outer membrane protein (YiuR) as a receptor molecule. We have previously shown that the activity spectrum of colicin FY comprises strains of the genus Yersinia. In this study, we analyzed the activity of colicin FY against 110 Yersinia enterocolitica isolates differing in geographical origin and source. All isolates were characterized through analysis of 16S rRNA genes, serotyping, biotyping, restriction profiling of genomic DNA, detection of virulence markers and susceptibility to antibiotics. This confirmed the broad variability of the collection, in which all 110 Y. enterocolitica isolates, representing 77 various strains, were inhibited by colicin FY. Although isolates showed variable levels of susceptibility to colicin FY, it was not associated with any strain characteristic. The universal susceptibility of Y. enterocolitica strains to colicin FY together with the absence of activity towards strains outside the Yersinia genus suggests potential therapeutic applications for colicin FY.

• MeSH
• bakteriální léková rezistence účinky léků   MeSH
• faktory virulence genetika   metabolismus   MeSH
• genom bakteriální * MeSH
• koliciny farmakologie   MeSH
• mikrobiální testy citlivosti MeSH
• Yersinia enterocolitica genetika   izolace a purifikace   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• faktory virulence MeSH
• koliciny MeSH

A 2-year national genomic screening in the Czech Republic identified a notable prevalence of the New Delhi metallo-β-lactamase 5 (NDM-5)-producing Escherichia coli sequence type 38 (ST38) in the city of Brno. Forty-two ST38 E. coli isolates harbored the blaNDM-5 gene on the chromosome. Virulence factors confirmed the persistence of these isolates through biofilm formation. Single Nucleotide Polymorphisms (SNPs)-based phylogeny and CRISPR assay typing showed minimal genomic variations, implying a clonally driven outbreak. Results suggest that this high-risk clone may impose a nationwide problem.

• Klíčová slova
• Escherichia coli, ST38, blaNDM-5,
• MeSH
• antibakteriální látky farmakologie   MeSH
• beta-laktamasy * genetika   MeSH
• biofilmy růst a vývoj   MeSH
• epidemický výskyt choroby * MeSH
• Escherichia coli * genetika   účinky léků   izolace a purifikace   enzymologie   MeSH
• faktory virulence genetika   MeSH
• fylogeneze MeSH
• genom bakteriální MeSH
• genomika metody   MeSH
• infekce vyvolané Escherichia coli * mikrobiologie   epidemiologie   MeSH
• jednonukleotidový polymorfismus * MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika epidemiologie   MeSH
• Názvy látek
• antibakteriální látky MeSH
• beta lactamase NDM-5, E coli MeSH Prohlížeč
• beta-laktamasy * MeSH
• faktory virulence MeSH