Dariusz Wasyl

Multidrug-resistant Salmonella enterica subsp. enterica serovar Infantis clone, harbouring the pESI megaplasmid, first described in Israel in 2014, is consistently reported in poultry and humans worldwide. This study aimed to investigate the genomic epidemiology of S. Infantis collected by nine European Public Health Institutions from samples of different origins (human, food and animal sources) and understand the evolutionary dynamics of pESI-like in Europe. The resolved pESI-like sequences have also been compared with complete publicly available pESI-like sequences from other countries, in a One Health context. The circulation of a S. Infantis clone in Europe carrying the mosaic megaplasmid pESI-like has been associated with resistance to sulphonamides (sul), tetracycline (tet), streptomycin and spectinomycin (aadA1). In recent years, bla _CTX-M-1-positive pESI-like plasmids have been increasingly detected in the extended-spectrum beta-lactamase-producing S. Infantis clone. Using a combined short- and long-read sequencing approach, two main types of pESI variants have been identified, differing in the accessory gene content, including the bla _CTX-M variant, indicating a certain stability of pESI variants detected in different geographical regions and sources over time (2011-2021). Moreover, the differences were related to the acquisition of resistance, virulence or fitness-enhancing genes that would potentially benefit the Salmonella host.

Introduction: The Shewanella genus is widely distributed in aquatic environments and occurs in different niches with a wide range of temperatures and salinities. It includes a novel species, S. oncorhynchi , described as recently as 2022, causing lens atrophy, inappetence and growth retardation in rainbow trout ( Oncorhynchus mykiss , Walbaum 1792). Shewanella oncorhynchi also occurs in common carp ( Cyprinus carpio L.), but its potential pathogenicity in this species is unclear. Material and Methods: In this study, the pathogenicity of three well-characterised S. oncorhynchi strains was assessed in vivo in experimental infection of common carp and in vitro by estimation of their cytotoxicity to an epithelioma papulosum cyprini cell line. The strains’ characterisation involved whole-genome sequencing to identify possible virulence genes. Results: Our study proved the pathogenicity of S. oncorhynchi to common carp and the bacterium’s cytotoxicity to epithelioma papulosum cyprini cells. Swollen abdomens, lens opacity, areas of discoloration and skin lesions were recorded in infected common carp. However, the ability to cause disease symptoms and mortality depended on the strain. Conclusion: The study showed the potential roles of the quorum-sensing system, type IV pili, fimbriae, stress survival, iron metabolism and secretion system genes in the virulence of S. oncorhynchi . Of these, the vscC2, vscN2, vscR2, vscS2 and vscU2 type III secretion system genes potentially and probably enhance the bacterium’s ability to cause lesions in common carp.

(1) Background: Understanding the distribution of Salmonella serovars in food, animals, and their environments is crucial for identifying infection sources and monitoring pathogen prevalence in the food chain. This study analysed Salmonella serovars in Poland from 2016 to 2020, focusing on their epidemiological significance. (2) Methods: Isolation of Salmonella was carried out following PN-EN ISO 6579 standards, and serotyping was performed using the White–Kauffmann–Le Minor scheme. A total of 7104 isolates were collected from food-producing animals, their environments, food of animal origin, feedingstuffs, and fertilisers. (3) Results: A total of 175 serovars were identified, with S. Enteritidis (n = 2905; 40.9%), S. Infantis (n = 1167; 16.4%), and S. Typhimurium (n = 360; 5.1%) being the most prevalent. Species-specific patterns were observed: S. Enteritidis dominated in chickens, ducks, and cattle; S. Kentucky in turkeys; S. Typhimurium in geese; and monophasic S. Typhimurium in pigs. S. Enteritidis and S. Infantis were most frequent in food of animal origin, especially broiler meat. In feedingstuffs, S. Agona was predominant, while fertilisers mostly contained S. Derby and S. Infantis. (4) Conclusions: The study highlights the source-dependent variety of Salmonella serovars and the importance of serotyping in tracing infection routes and preventing the spread of pathogens. Identifying the most common serovars supports the development of targeted preventive measures, including improved biosecurity, hygiene, and management practices to enhance food safety.

Bordetella trematum is a rare member of the genus Bordetella, primarily associated with human wound infections rather than respiratory diseases. The bacterium has been isolated from various clinical specimens, including ear inflammatory discharge, diabetic ulcers, and chronic wounds. The study aimed to characterize the genomes and antimicrobial resistance (AMR) profiles of B. trematum obtained from the fecal samples of asymptomatic highland eyelash pit vipers (Bothriechis schlegelii). The identification was conducted using MALDI-TOF mass spectrometry and biochemical tests. AMR was assessed using the microbroth dilution method, while whole-genome sequencing was performed on the Illumina NextSeq platform. The isolates displayed characteristic B. trematum biochemical features and demonstrated a resistance to cefotaxime, ciprofloxacin, and trimethoprim, while one also exhibited a resistance to ceftazidime. The whole-genome sequencing and comparison with limited public data revealed a high diversity within B. trematum, reaching >48,000 single nucleotide polymorphisms (SNPs), with 64 SNP differentiating tested snake isolates and thus, being considered epidemiologically unrelated. This is the first report of B. trematum isolated from an animal source in Europe. The findings provide valuable insights into this rare bacterium’s phenotypic and genomic characteristics, addressing an important knowledge gap in its ecology and AMR profile.

Since 2014, the long‐term decreasing trend in human salmonellosis, caused mainly by the consumption of Salmonella ‐contaminated poultry products, has stagnated in the European Union (EU). As Poland has been the leading poultry meat producer in the EU since 2014, we analysed whole genome sequences of 275 Salmonella ( S .) Enteritidis strains from the poultry food production chain ( n = 216) and humans ( n = 59) (2008–2019) to shed light on the genetic content and relatedness of the S . Enteritidis population in Poland. Most (99.3%) of the strains belonged to ST11. Overall, 5.8% of strains possessed at least one antimicrobial resistance gene (ARG), the most common being qnrB19 ( n = 9). Mutations in quinolone resistance‐determining regions (QRDRs) were observed in 46.9% of strains, and the most common mutation was gyrA (S83Y; n = 95). In 95.6% of strains, at least one plasmid replicon was detected, with the highest prevalence of IncFII(S)_1 ( n = 263) and IncFIB(S)_1 ( n = 262). The composition of Salmonella pathogenicity islands (SPIs) was uniform among 96.7% of strains carrying CS54, SPI‐1‐SPI‐3, SPI‐5, SPI‐6, SPI‐9, SPI‐12 and SPI‐14. Core genome multilocus sequence typing (cgMLST) analysis revealed no apparent clustering based on source or year of isolation. None of the genetic determinants studied here seemed to trigger changes in Salmonella epidemiology. However, other factors, such as improvements in reporting and control, could influence infection trends and are, therefore, worth further elucidation.

Salmonella Mbandaka is one of the most globally widespread serovars, occurring in many sources and included among twenty serovars that contribute to human salmonellosis in Europe. In Poland, it has been noted in non-human sources since 1996, being found firstly in feeds and later in waterfowl and chicken. Over the years, it gained epidemiological importance, being isolated from a wide range of animal species, including livestock. Generally, it is characterized by sensitivity to most antimicrobials and the ability to form biofilms. The occurrence of cephalosporin-resistant Salmonella in non-human sources is an extremely rare phenomenon in Poland. In this report, we characterized the full genome of the ESBL-producing S. Mbandaka strain isolated from a broiler farm environment (boot swab sample) in Poland in 2022. The isolate was serotyped as S. Mbandaka according to the White–Kaufmann–Le Minor scheme. Antimicrobial susceptibility testing performed with the microbroth dilution method showed its resistance to ampicillin, cefotaxime, ceftazidime, ciprofloxacin, and nalidixic acid. The whole-genome sequence was reconstructed using short and long reads and assembled into the complete chromosome and three plasmids: IncI1 pST113 (89,439 bp), Col(pHAD28) (2699 bp), and Col440 (2495 bp). The strain belonged to sequence type ST413. Plasmid analysis showed bla_CTX-M-8 mobilization on IncI1(alpha) surrounded with insertion sequences. The analyzed genome content draws attention to the possibility of the horizontal spread of the resistance genes. To the best of our knowledge, this is the first report of bla_CTX-M-8-positive Salmonella in Poland.

Contaminations with cephalosporin-resistant Escherichia coli across the food chain may pose a significant threat to public health because those antimicrobials are critically important in human medicine. The impact of the presented data is especially significant concerning Poland’s role as one of the leading food producers in the EU. This work aimed to characterize the genomic contents of cephalosporin-resistant Escherichia coli (n = 36) isolated from retail meat to expand the official AMR monitoring reported by EFSA. The ESBL mechanism was predominant (via bla_CTX-M-1 and bla_SHV-12), with the AmpC-type represented by the bla_CMY-2 variant. The strains harbored multiple resistance genes, mainly conferring resistance to aminoglycosides, sulfonamides, trimethoprim, tetracyclines. In some isolates, virulence factors—including intimin (eae) and its receptor (tir) were detected, indicating significant pathogenic potential. Resistance genes showed a link with IncI1 and IncB/O/K/Z plasmids. Cephalosporinases were particularly linked to ISEc9/ISEc1 (bla_CTX-M-1 and bla_CMY-2). The association of virulence with mobile elements was less common—mostly with IncF plasmids. The analysis of E. coli isolated from retail meat indicates accumulation of ARGs and their association with various mobile genetic elements, thus increasing the potential for the transmission of resistance across the food chain.

Different species of Shewanella spp. widely inhabit freshwater and marine environments. Some of them are opportunistic fish pathogens. The application of high‐throughput sequencing enabled the characterization and taxonomic reclassification of many Shewanella spp. species. Still, some strains collected from fish need to be better recognized. The aim of the present study was to classify and determine the phylogenetic relationships of Shewanella spp. collected from fish. The complete genomes of 94 strains of Shewanella spp. from different fish species were sequenced using Illumina platform (MiSeq). The 16S rRNA gene, genomic features and whole‐genome relationships of those bacteria were comprehensively analysed in comparison to reference strains. Whole‐genome analysis showed that the tested Shewanella spp. strains were clustered into six groups similar to reference strains of S. xiamenensis, S. oneidensis, S. glacialipiscicola, S. hafniensis, S. baltica and S. oncorhynchi. Our study indicates that the whole‐genome sequence analysis enabled taxonomic classification and assessment of the diversity of the Shewanella spp. strains, as opposed to recently the gold standard method of 16S rRNA amplicon sequencing. The high genetic diversity and low similarity to the reference genome of S. oneidensis indicate that the group of strains may be a subspecies or even new species. Furthermore, we showed that the most frequent Shewanella spp. species occurring in freshwater fish in our study is the recently described species S. oncorhynchi.

Enterococci as opportunistic bacteria are important for human health. Due to the prevalence and ease of acquisition and transfer of their genes, they are an excellent indicator of environmental contamination and the spread of antimicrobial resistance. The aim of the study was to assess the prevalence of Enterococcus spp. in wild birds in Poland, determination of antimicrobial susceptibility and WGS analysis of Enterococcus (E.) faecium and E. faecalis. For this purpose, 138 samples from various species of free-living birds were tested, with 66.7% positive results. Fourteen species were detected, with E. faecalis being the most common, followed by E. casseliflavus and E. hirae. In antimicrobial susceptibility testing, 10.0% of E. faecalis and 50.0% of E. faecium showed resistance to one antimicrobial agent, in addition the MDR phenotype which was found in one E. faecium. The most common resistance phenotype included tetracycline and quinupristin/dalfopristin. The WGS analysis confirmed the significant advantage of the virulence gene diversity of E. faecalis strains over E. faecium. In addition, plasmid replicons were found in 42.0% of E. faecalis and 80.0% of E. faecium. The obtained results confirm free-living birds can be a reservoir of Enterococcus spp. with a considerable zoonotic potential.

Introduction: Factors other than PD-L1 (Programmed Death Ligand 1) are being sought as predictors for cancer immuno- or chemoimmunotherapy in ongoing studies and long-term observations. Despite high PD-L1 expression on tumor cells, some patients do not benefit from immunotherapy, while others, without the expression of this molecule, respond to immunotherapy. Attention has been paid to the composition of the gut microbiome as a potential predictive factor for immunotherapy effectiveness. Materials and Methods: Our study enrolled 47 Caucasian patients with stage IIIB or IV non-small cell lung cancer (NSCLC). They were eligible for treatment with first- or second-line immunotherapy or chemoimmunotherapy. We collected stool samples before the administration of immunotherapy. We performed next-generation sequencing (NGS) on DNA isolated from the stool sample and analyzed bacterial V3 and V4 of the 16S rRNA gene. Results: We found that bacteria from the families Barnesiellaceae, Ruminococcaceae, Tannerellaceae, and Clostridiaceae could modulate immunotherapy effectiveness. A high abundance of Bacteroidaaceae, Barnesiellaceae, and Tannerellaceae could extend progression-free survival (PFS). Moreover, the risk of death was significantly higher in patients with a high content of Ruminococcaceae family (HR = 6.3, 95% CI: 2.6 to 15.3, p < 0.0001) and in patients with a low abundance of Clostridia UCG-014 (HR = 3.8, 95% CI: 1.5 to 9.8, p = 0.005) regardless of the immunotherapy line. Conclusions: The Clostridia class in gut microbiota could affect the effectiveness of immunotherapy, as well as the length of survival of NSCLC patients who received this method of treatment.