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

Despite numerous studies on Escherichia coli (E. coli) from sheep, there have been few reports on the characterization of E. coli isolates from various organs of individual sheep until now. The present study conducted molecular typing, antibiotics resistance, biofilm formation, and virulence genes on E. coli isolated from 57 freshly slaughtered apparently healthy sheep carcasses, gallbladders, fecal samples, and mesenteric lymph nodes (MLNs). The results demonstrated that the detection rate of R1 LPS core type in E. coli isolated from fecal samples (70.83%) was higher than that from other organs, but the detection rate of antibiotic resistance genes was lower (P < 0.05). The predominant phylogenetic group of E. coli isolated from the carcasses was group B1 (93.33%), and the detection rate of multidrug-resistance phenotype (80%) and the resistance rate of E. coli was higher than that from other organs (P < 0.05). Interestingly, the intensity of biofilm formation of E. coli isolated from MLNs was higher than that from other organs (P < 0.05). However, except for ibeB, the detection rates of virulence genes did not differ in E.coli isolated from different organs. In conclusion, differences were noted in these parameters of E. coli isolated from different organs of individual sheep. Therefore, the data may contain considerable mistakes concerning the actual situation in the host if we only analyze the data of E. coli isolated from feces or carcasses.

• Klíčová slova
• Escherichia coli, Antibiotics resistance, Biofilm formation, Different organs, Individual sheep, Molecular typing,
• MeSH
• antibakteriální látky * farmakologie   MeSH
• bakteriální léková rezistence genetika   MeSH
• biofilmy * růst a vývoj   účinky léků   MeSH
• Escherichia coli * genetika   účinky léků   izolace a purifikace   klasifikace   fyziologie   MeSH
• faktory virulence * genetika   MeSH
• feces mikrobiologie   MeSH
• fylogeneze MeSH
• infekce vyvolané Escherichia coli mikrobiologie   veterinární   MeSH
• molekulární typizace MeSH
• nemoci ovcí mikrobiologie   MeSH
• ovce MeSH
• virulence genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antibakteriální látky * MeSH
• faktory virulence * MeSH

Fosfomycin-resistant FosA8-producing Enterobacterales are uncommon strains with extremely low incidence in Europe, based on only three reports in the literature. We detected FosA8-producing Escherichia coli ST131 in clinical isolates from two patients admitted in February 2023 to a rehabilitation unit in Italy. The occurrence of rare fosA-like genes in the high-risk clone ST131 is of clinical relevance. The dissemination of FosA-producing E. coli, although still at low levels, should be continuously monitored.

• Klíčová slova
• E. coli ST131, FosA8, Fosfomycin, Fosfomycin resistance,,
• MeSH
• antibakteriální látky * farmakologie   terapeutické užití   MeSH
• bakteriální léková rezistence MeSH
• beta-laktamasy genetika   metabolismus   MeSH
• Escherichia coli * izolace a purifikace   genetika   účinky léků   MeSH
• fosfomycin farmakologie   terapeutické užití   MeSH
• infekce vyvolané Escherichia coli * mikrobiologie   epidemiologie   MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• multilokusová sekvenční typizace MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• kazuistiky MeSH
• Geografické názvy
• Itálie epidemiologie   MeSH
• Názvy látek
• antibakteriální látky * MeSH
• beta-laktamasy MeSH
• fosfomycin MeSH

Inulin, an increasingly studied dietary fiber, alters intestinal microbiota. The aim of this study was to assess whether inulin decreases intestinal colonization by multidrug resistant E. coli and to investigate its potential mechanisms of action. Mice with amoxicillin-induced intestinal dysbiosis mice were inoculated with extended spectrum beta-lactamase producing E. coli (ESBL-E. coli). The combination of inulin and pantoprazole (IP) significantly reduced ESBL-E. coli fecal titers, whereas pantoprazole alone did not and inulin had a delayed and limited effect. Fecal microbiome was assessed using shotgun metagenomic sequencing and qPCR. The efficacy of IP was predicted by increased abundance of 74 taxa, including two species of Adlercreutzia. Preventive treatments with A. caecimuris or A. muris also reduced ESBL-E. coli fecal titers. Fecal microbiota of mice effectively treated by IP was enriched in genes involved in inulin catabolism, production of propionate and expression of beta-lactamases. They also had increased beta-lactamase activity and decreased amoxicillin concentration. These results suggest that IP act through production of propionate and degradation of amoxicillin by the microbiota. The combination of pantoprazole and inulin is a potential treatment of intestinal colonization by multidrug-resistant E. coli. The ability of prebiotics to promote propionate and/or beta-lactamase producing bacteria may be used as a screening tool to identify potential treatments of intestinal colonization by multidrug resistant Enterobacterales.

• Klíčová slova
• Escherichia coli, Inulin, intestinal colonization, microbiome, multi-drug resistance, prebiotics, resistome,
• MeSH
• amoxicilin * farmakologie   MeSH
• antibakteriální látky farmakologie   MeSH
• beta-laktamasy metabolismus   genetika   MeSH
• dysbióza mikrobiologie   farmakoterapie   MeSH
• Escherichia coli * účinky léků   genetika   MeSH
• feces * mikrobiologie   MeSH
• infekce vyvolané Escherichia coli farmakoterapie   mikrobiologie   MeSH
• inulin * farmakologie   metabolismus   MeSH
• mnohočetná bakteriální léková rezistence * MeSH
• myši MeSH
• pantoprazol * farmakologie   MeSH
• prebiotika aplikace a dávkování   MeSH
• střevní mikroflóra * účinky léků   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• amoxicilin * MeSH
• antibakteriální látky MeSH
• beta-laktamasy MeSH
• inulin * MeSH
• pantoprazol * MeSH
• prebiotika MeSH

Wildlife are implicated in the dissemination of antimicrobial resistance, but their roles as hosts for Escherichia coli that pose a threat to human and animal health is limited. Gulls (family Laridae) in particular, are known to carry diverse lineages of multiple-antibiotic resistant E. coli, including extra-intestinal pathogenic E. coli (ExPEC). Whole genome sequencing of 431 E. coli isolates from 69 healthy Australian silver gulls (Chroicocephalus novaehollandiae) sampled during the 2019 breeding season, and without antibiotic selection, was undertaken to assess carriage in an urban wildlife population. Phylogenetic analysis and genotyping resolved 123 sequence types (STs) representing most phylogroups, and identified diverse ExPEC, including an expansive phylogroup B2 cluster comprising 103 isolates (24 %; 31 STs). Analysis of the mobilome identified: i) widespread carriage of the Yersinia High Pathogenicity Island (HPI), a key ExPEC virulence determinant; ii) broad distribution of two novel phage elements, each carrying sitABCD and iii) carriage of the transmissible locus of stress tolerance (tLST), an element linked to sanitation resistance. Of the 169 HPI carrying isolates, 49 (48 %) represented diverse B2 isolates hosting FII-64 ColV-like plasmids that lacked iutABC and sitABC operons typical of ColV plasmids, but carried the serine protease autotransporter gene, sha. Diverse E. coli also carried archetypal ColV plasmids (52 isolates; 12 %). Clusters of closely related E. coli (<50 SNVs) from ST58, ST457 and ST746, sourced from healthy gulls, humans, and companion animals, were frequently identified. In summary, anthropogenically impacted gulls host an expansive E. coli population, including: i) putative ExPEC that carry ColV virulence gene cargo (101 isolates; 23.4 %) and HPI (169 isolates; 39 %); ii) atypical enteropathogenic E. coli (EPEC) (17 isolates; 3.9 %), and iii) E. coli that carry the tLST (20 isolates; 4.6 %). Gulls play an important role in the evolution and transmission of E. coli that impact human health.

• Klíčová slova
• AMR, Bacteria, Epidemiology, Escherichia coli, Genome sequencing, Virulence,
• MeSH
• antibakteriální látky MeSH
• Charadriiformes * MeSH
• divoká zvířata MeSH
• Escherichia coli genetika   MeSH
• extraintestinální patogenní Escherichia coli * genetika   MeSH
• faktory virulence genetika   MeSH
• fylogeneze MeSH
• infekce vyvolané Escherichia coli * veterinární   epidemiologie   MeSH
• lidé MeSH
• mikrobiota * MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Austrálie MeSH
• Názvy látek
• antibakteriální látky MeSH
• faktory virulence MeSH

Extraintestinal pathogenic Escherichia coli (ExPEC) sequence type (ST) 38 is one of the top 10 human pandemic lineages. Although a major cause of urinary tract and blood stream infections, ST38 has been poorly characterized from a global phylogenomic perspective. A comprehensive genome-scale analysis of 925 ST38 isolate genomes identified two broad ancestral clades and linkage of discrete ST38 clusters with specific bla CTX-M variants. In addition, the clades and clusters carry important virulence genes, with diverse but poorly characterized plasmids. Numerous putative interhost and environment transmission events were identified here by the presence of ST38 clones (defined as isolates with ≤35 SNPs) within humans, companion animals, food sources, urban birds, wildlife, and the environment. A small cluster of international ST38 clones from diverse sources, likely representing progenitors of a hospital outbreak that occurred in Brisbane, Australia, in 2017, was also identified. Our study emphasizes the importance of characterizing isolate genomes derived from nonhuman sources and geographical locations, without any selection bias.

• Klíčová slova
• EAEC, One Health, ST38, bla CTX-M, drug resistance, enteroaggregative E. coli, genomic surveillance, phylogenomics, β-lactamase genes,
• MeSH
• Escherichia coli genetika   MeSH
• extraintestinální patogenní Escherichia coli * MeSH
• fylogeneze MeSH
• infekce vyvolané Escherichia coli * epidemiologie   MeSH
• lidé MeSH
• plazmidy MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

The fos operon encoding short-chain fructooligosaccharide (scFOS) utilization enables bacteria of the family Enterobacteriaceae to grow and be sustained in environments where they would struggle to survive. Despite several cases of the detection of the fos operon in isolates of avian and equine origins, its global distribution in bacterial genomes remains unknown. The presence of the plasmid-harbored fos operon among resistant bacteria may promote the spread of antibiotic resistance. A collection of 11,538 antimicrobial-resistant Enterobacteriaceae isolates from various sources was screened for the fosT gene encoding the scFOS transporter. Out of 307 fosT-positive isolates, 80% of them originated from sources not previously linked to fosT (humans, wastewater, and animals). The chromosomally harbored fos operon was detected in 163/237 isolates subjected to whole-genome sequencing. In the remaining 74 isolates, the operon was carried by plasmids. Further analyses focusing on the isolates with a plasmid-harbored fos operon showed that the operon was linked to various incompatibility (Inc) groups, including the IncHI1, IncF-type, IncK2, IncI1, and IncY families. Long-read sequencing of representative plasmids showed the colocalization of fos genes with antibiotic resistance genes (ARGs) in IncHI1 (containing a multidrug resistance region), IncK2 (blaTEM-1A), IncI1 [sul2 and tet(A)], and IncY [aadA5, dfrA17, sul2, and tet(A)] plasmids, while IncF-type plasmids had no ARGs but coharbored virulence-associated genes. Despite the differences in the locations and structures of the fos operons, all isolates except one were proven to utilize scFOSs. In this study, we show that the fos operon and its spread are not strictly bound to one group of plasmids, and therefore, it should not be overlooked. IMPORTANCE It was believed that members of the family Enterobacteriaceae are unable to grow under conditions with short-chain fructooligosaccharides as the only source of carbon. Nevertheless, the first Escherichia coli isolate from chicken intestine was able to utilize these sugars owing to the chromosomally harbored fos operon. Studies on E. coli isolates from horses discovered the horizontal transfer of the fos operon on IncHI1 plasmids along with genes for antibiotic resistance. The first plasmid detected was pEQ1, originating from the feces of a hospitalized horse in the Czech Republic. Follow-up studies also revealed the dissemination of the IncHI1 plasmid-harbored fos operon in the Netherlands, Germany, Denmark, and France among healthy horses. Despite several cases of detection of the fos operon, its global distribution in bacterial genomes remains unknown. The fos operon possibly plays a role in the adaptation of plasmids among resistant bacteria and therefore may promote the spread of antibiotic resistance.

• Klíčová slova
• Escherichia coli, MinION, scFOS, sequencing,
• MeSH
• antibakteriální látky * farmakologie   MeSH
• antibiotická rezistence MeSH
• beta-laktamasy genetika   MeSH
• Enterobacteriaceae MeSH
• Escherichia coli MeSH
• infekce vyvolané Escherichia coli * mikrobiologie   MeSH
• koně MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• operon MeSH
• plazmidy genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antibakteriální látky * MeSH
• beta-laktamasy MeSH
• fructooligosaccharide MeSH Prohlížeč

A complex epidemiological situation marked the health system at the time of the establishment of the Czechoslovak Republic. Reducing the number of infectious diseases was an essential task of the State Administration of Health. It required new legislation and various steps directed at reducing infectious diseases. Serious infectious diseases, such as scarlet fever, diphtheria, typhoid, dysentery, smallpox, and malaria, were among the most significant health problems in Czechoslovakia. In 1920, Act No. 412 Coll. regarding compulsory smallpox vaccination was issued, as well as government Regulation No. 298, which describes vaccination obligations and stipulated proper isolation of patients with infectious diseases. Other steps that led to improvements included establishing the National Institute of Health and mobile disinfectant units. Conclusion: The systematic development of new legislation contributed to the new Republic's proficiency at the task and the gradual reduction in the number of infectious diseases.

• Klíčová slova
• First Czechoslovak Republic, infectious diseases, medical facilities, laws and government regulations,
• MeSH
• 1. světová válka MeSH
• akademie a ústavy MeSH
• břišní tyfus * prevence a kontrola   MeSH
• lidé MeSH
• pravé neštovice * prevence a kontrola   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Salmonella spp. is a common zoonotic pathogen, causing gastrointestinal infections in people. Pigs and pig meat are a major source of infection. Although farm biosecurity is believed to be important for controlling Salmonella transmission, robust evidence is lacking on which measures are most effective. This study enrolled 250 pig farms across nine European countries. From each farm, 20 pooled faecal samples (or similar information) were collected and analysed for Salmonella presence. Based on the proportion of positive results, farms were categorised as at higher or lower Salmonella risk, and associations with variables from a comprehensive questionnaire investigated. Multivariable analysis indicated that farms were less likely to be in the higher-risk category if they had '<400 sows'; used rodent baits close to pig enclosures; isolated stay-behind (sick) pigs; did not answer that the hygiene lock/ anteroom was easy to clean; did not have a full perimeter fence; did apply downtime of at least 3 days between farrowing batches; and had fully slatted flooring in all fattener buildings. A principal components analysis assessed the sources of variation between farms, and correlation between variables. The study results suggest simple control measures that could be prioritised on European pig farms to control Salmonella.

• Klíčová slova
• Salmonella, biosecurity, effectiveness, pig, risk factor,
• MeSH
• biologická bezpečnost MeSH
• chov zvířat metody   MeSH
• farmy MeSH
• nemoci prasat * epidemiologie   prevence a kontrola   MeSH
• prasata MeSH
• Salmonella MeSH
• salmonelová infekce u zvířat * epidemiologie   prevence a kontrola   MeSH
• zvířata MeSH
• Check Tag
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Evropa epidemiologie   MeSH

Salmonella infections are still considered a persistent problem in veterinary medicine. Vaccination is one of the tools for decreasing the burden of many pathogens on animals. However, the efficiency of available commercial or experimental vaccines against non-typhoid Salmonella strains is not yet sufficient. We followed the path of an inactivated vaccine that is safe and well accepted, but whose presented antigen spectrum is limited. We improved this issue by using diverse cultivation conditions mimicking bacterial protein expression during the natural infection process. The cultivation process was set up to simulate the host environment to enhance the expression of SPI-1 (Salmonella pathogenicity island) proteins, SPI-2 proteins, siderophore-related proteins, and flagellar proteins. Three different cultivation media were used and subsequent cultures were mixed together, inactivated, and used for the immunization of post-weaned piglets. A mixture of recombinant Salmonella proteins was also used as a recombinant vaccine for comparison. The clinical symptoms during the subsequent experimental infection, antibody response, and organ bacterial loads were examined. One day after the infection, we observed an increased rectal temperature in the group of unvaccinated animals and the animals vaccinated with the recombinant vaccine. The increase in the temperature of the pigs vaccinated with the inactivated Salmonella mixture was significantly lower. In the same group, we also found lower bacterial loads in the ileum content and the colon wall. The IgG response to several Salmonella antigens was enhanced in this group, but it did not reach the titers of the group vaccinated with the recombinant vaccine. To summarize, the pigs vaccinated with an inactivated mixture of Salmonella cultures mimicking protein expression changes during the natural infection exhibited less serious clinical symptoms and lower bacterial load in the body after the experimental infection compared to the unvaccinated pigs and the pigs vaccinated with a mixture of recombinant Salmonella proteins.

• Klíčová slova
• Post-weaned piglets, Salmonella Typhimurium, Vaccine, Virulence proteins,
• MeSH
• antigeny bakteriální genetika   MeSH
• atenuované vakcíny MeSH
• inaktivované vakcíny MeSH
• nemoci prasat * mikrobiologie   MeSH
• prasata MeSH
• protilátky bakteriální MeSH
• Salmonella typhimurium MeSH
• salmonelová infekce u zvířat * mikrobiologie   MeSH
• salmonelové vakcíny * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antigeny bakteriální MeSH
• atenuované vakcíny MeSH
• inaktivované vakcíny MeSH
• protilátky bakteriální MeSH
• salmonelové vakcíny * MeSH