Virulence, attachment and invasion of Caco-2 cells by multidrug-resistant bacteria isolated from wild animals

Dynamics of mono and dual-species biofilms of Escherichia coli and Salmonella Typhimurium: Interspatial interactions and novel inhibition strategies

Multi-species biofilms in the food industry present significant global health risks, contributing to frequent outbreaks, diseases, and fatalities. This study aimed to characterize the mono- and dual-species biofilms formed by invasive food isolates Escherichia coli EMC17 and Salmonella typhimurium SMC25, focusing on microbial load variations, interspecies interactions, and the exploration of a combinatorial inhibition strategy for biofilm disruption. The highest biofilm density was observed in dual-species cultures at equal inoculum after 96 h, as confirmed by Crystal Violet assay and exopolysaccharide (EPS) production (72 μg/ml). Dual-species biofilms showed total bacterial counts of 7.29 log10 CFU/cm2 for E. coli EMC17 and 5.95 log10 CFU/cm2 for S. Typhimurium SMC25, with both strains exhibiting strong multidrug resistance (MDR), as indicated by MAR indices of 0.46 and 0.38, respectively. Epifluorescence and confocal laser microscopy revealed synergistic interactions during dual-species biofilm development, further supported by principal component analysis, which highlighted distinct growth patterns between mono- and dual-species biofilms. Specifically, mono-species biofilms of E. coli EMC17 had a biovolume of 56.70 ± 1.36 μm3/μm2 at 96 h, whereas dual-species biofilms reached 62.61 ± 1.38 μm3/μm2. Additionally, dual-species biofilm-associated cells exhibited significantly enhanced adhesion (16.40 %) and invasion (2.07 %) potential compared to the mono-species biofilms. Furthermore, a combinatorial inhibition strategy using quercetin and citric acid demonstrated synergistic activity against the MDR strains, with fractional inhibitory concentration index (FIC) of <0.5. These findings offer new insights into the dynamics of dual-species biofilms, emphasizing the potential of phytochemical-citric acid combinations as promising alternatives to traditional antibiotics in biofilm management.

A Pan-European study of the bacterial plastisphere diversity along river-to-sea continuums

Microplastics provide a persistent substrate that can facilitate microbial transport across ecosystems. Since most marine plastic debris originates from land and reaches the ocean through rivers, the potential dispersal of freshwater bacteria into the sea represents a significant concern. To address this question, we explored the plastisphere on microplastic debris (MPs) and on pristine microplastics (pMPs) as well as the bacteria living in surrounding waters, along the river-sea continuum in nine major European rivers sampled during the 7 months of the Tara Microplastics mission. In both marine and riverine waters, we found a clear niche partitioning among MPs and pMPs plastispheres when compared to the bacteria living in the surrounding waters. Across this large dataset, we found that bacterial community structure varied along the river salinity gradient, with plastisphere communities exhibiting almost complete segregation between freshwater and marine ecosystems. We also described for the first time a virulent human pathogenic bacterium (Shewanella putrefaciens), capable of infecting human intestinal epithelial cells, detected exclusively on MPs in riverine environments. Our findings indicate that salinity is the main driver of plastisphere communities along the river-to-sea continuum, helping to mitigate the risk of pathogens transfer between freshwater and marine systems.

Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences

The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.

Exploring the exoproteome of the parasitic nematode Anisakis simplex (s. s.) and its impact on the human host - an in vitro cross-talk proteomic approach

Introduction

Anisakis simplex sensu stricto (s. s.) is one of the most widespread parasitic nematodes of marine organisms, with humans as accidental hosts. While many studies have explored nematode biology and host interactions, the role of extracellular vesicles (EVs) as signaling molecules in parasitic nematodes is less understood.

Materials and methods

Therefore, the proteins present in the EVs of A. simplex (s. s.) (Anis-EVs) were identified. In addition, a cross-talk proteomic approach was used to identify differentially regulated proteins (DRPs) in the proteome of the human intestinal epithelial cell line (Caco-2) co-cultured with L3 larvae of A. simplex (s. s.) or directly exposed to two concentrations (low or high) of Anis-EVs. In addition, DRPs were identified in the proteome of A. simplex (s. s.) larvae affected by co-culture with Caco-2. To achieve this goal, the shotgun proteomics method based on isobaric mass labeling (via tandem mass tags; TMT) was used with a combination of nano high-performance liquid chromatography (nLC) coupled with an LTQ-Orbitrap Elite mass spectrometer. In addition, ELISA assays were used to demonstrate if Caco-2 respond to A. simplex (s. s.) larvae and Anis-EVs with significant changes in selected cytokines secretion.

Results

The results of this study indicate the anti-inflammatory character of Anis-EVs in relation to Caco-2. At the same time, direct treatment with Anis-EVs resulted in more significant changes in the Caco-2 proteome than co-culture with L3 larvae.

Discussion

The results obtained should lead to a better understanding of the molecular mechanisms underlying the development of A. simplex (s. s.) infection in humans and will complement the existing knowledge on the role of EVs in host-parasite communication.

Genus Shewanella: A Potential Intestinal Colonizer Associated With Post-Operative Surgical Site Infections in Coastal Regions

Background: This study aims to elucidate the clinical characteristics of Shewanella-related surgical site infections (SSIs) and assess the risk of mortality in patients by establishing a predictive model. Patients and Methods: A retrospective analysis of medical history and laboratory data of Shewanella-related SSI patients over the past decade was conducted via the electronic medical record (EMR) system. A predictive model for mortality risk in Shewanella-related SSI patients was established using plasma interleukin-6 (IL-6) levels combined with the Howell-PIRO scoring system. Results: Over the past 10 years, 45 strains of Shewanella were isolated from specimens such as bile, drainage fluid, and whole blood in patients with digestive tract SSIs. Among them, 21 of 45 (46.67%) patients underwent malignant tumor resection of the digestive system, 14 of 45 (31.11%) underwent endoscopic retrograde cholangiopancreatography (ERCP) common bile duct exploration or the stone removal, and seven of 45 (15.56%) were trauma repair patients with fractures and abdominal injuries. Among the 45 Shewanella-related SSI patients, 10 died within 30 days of infection, six cases involved infections with more than two other types of bacteria. The combined use of IL-6 and Howell-PIRO scores for mortality risk assessment yielded an receiver operating characteristic (ROC) curve with an area under the curve (AUC) of 0.9350, a positive predictive value of 92.71%, a negative predictive value of 94.58%, a diagnostic sensitivity of 95.35%, and a diagnostic specificity of 92.14%-all higher than the model using IL-6 or Howell-PIRO scores alone. Conclusions: We found that residents in coastal areas faced an increased risk of Shewanella-related SSI. Moreover, the higher the number of concurrent microbial infections occurring alongside Shewanella-related SSI, the greater the mortality rate among patients. The combined application of plasma IL-6 levels and the Howell-PIRO scoring system is beneficial for assessing patient mortality risk and guiding timely and proactive clinical interventions.

Bergenin Alleviates Ulcerative Colitis By Decreasing Gut Commensal Bacteroides vulgatus-Mediated Elevated Branched-Chain Amino Acids

Ulcerative colitis is closely associated with the dysregulation of gut microbiota. There is growing evidence that natural products may improve ulcerative colitis by regulating the gut microbiota. In this research, we demonstrated that bergenin, a naturally occurring isocoumarin, significantly ameliorates colitis symptoms in dextran sulfate sodium (DSS)-induced mice. Transcriptomic analysis and Caco-2 cell assays revealed that bergenin could ameliorate ulcerative colitis by inhibiting TLR4 and regulating NF-κB and mTOR phosphorylation. 16S rRNA sequencing and metabolomics analyses revealed that bergenin could improve gut microbiota dysbiosis by decreasing branched-chain amino acid (BCAA) levels. BCAA intervention mediated the mTOR/p70S6K signaling pathway to exacerbate the symptoms of ulcerative colitis in mice. Notably, bergenin greatly decreased the symbiotic bacteria Bacteroides vulgatus (B. vulgatus), and the gavage of B. vulgatus increased BCAA concentrations and aggravated the symptoms of ulcerative colitis in mice. Our findings suggest that gut microbiota-mediated BCAA metabolism plays a vital role in the protective effect of bergenin on ulcerative colitis, providing novel insights for ulcerative colitis prevention through manipulation of the gut microbiota.

Shewanella putrefaciens, a rare human pathogen: A review from a clinical perspective

Shewanella putrefaciens is a gramnegative, facultatively anaerobic, rod shaped bacterium. It belongs to the class of the Gammaproteobacteria and was first described in 1931. S. putrefaciens is part of the marine microflora and especially present in moderate and warm climates. The bacterium is a rare oppurtonistic human pathogen associated mainly with intra-abdominal as well as skin and soft tissue infections. However, it has also been reported in association with more severe diseases such as pneumonia, intracerebral and ocular infections and endocarditis. In these cases the clinical courses are often associated with underlying, predisposing diseases and risk factors. For successful treatment of S. putrefaciens, a combination of appropriate local therapy, e.g. surgical treatment or drainage, and antibiotic therapy should be performed. Since multiple resistances to antibiotics are described, the results of the antimicrobial susceptibility testing must be considered for effective therapy as well. Furthermore, a main challenge in clinical practice is the accurate microbiological identification, and especially the correct differentiation between S. putrefaciens and S. algae. Under certain circumstances, Shewanella-infections can have severe, sometimes even fatal consequences. Therefore, we decided to present the current state of knowledge as well as further aspects with regard to future diagnostics, therapy and research.

Shewanella infection in humans: Epidemiology, clinical features and pathogenicity

The genus Shewanella consists of Gram-negative proteobacteria that are ubiquitously distributed in environment. As the members of this genus have rapidly increased within the past decade, several species have become emerging pathogens worldwide, attracting the attention of the medical community. These species are also associated with severe community- and hospital-acquired infections. Patients infected with Shewanella spp. had experiences of occupational or recreational exposure; meanwhile, the process of infection is complex and the pathogenicity is influenced by a variety of factors. Here, an exhaustive internet-based literature search was carried out in PUBMED using terms “Achromobacter putrefaciens,” “Pseudomonas putrefaciens,” “Alteromonas putrefaciens” and “Shewanella” to search literatures published between 1978 and June 2022. We provided a comprehensive review on the epidemiology, clinical features and pathogenicity of Shewanella, which will contribute a better understanding of its clinical aetiology, and facilitate the timely diagnosis and effective treatment of Shewanella infection for clinicians and public health professionals.

Potential Pathogenicity of Aeromonas spp. Recovered in River Water, Soil, and Vegetation from a Natural Recreational Area

The genus Aeromonas is widely distributed in aquatic environments and is recognized as a potential human pathogen. Some Aeromonas species are able to cause a wide spectrum of diseases, mainly gastroenteritis, skin and soft-tissue infections, bacteremia, and sepsis. Currently, untreated river water is used for irrigation and recreational purposes. In this study, the Aeromonas spp. present in a river recreational environment was investigated by quantifying its presence in water, soil, and vegetation using three techniques: qPCR, plate counting in selective ADA medium, and Most Probable Number, in parallel. The presence of clones in the three types of samples was elucidated through genotyping with the ERIC-PCR technique, whereas the identification of the isolated Aeromonas was carried out by sequencing the rpoD gene. Finally, the pathogenic potential of some of the strains was explored by studying the presence and expression of virulence genes characteristic of the genus, their antimicrobial susceptibility profile, as well as the quantification of their cell damage and intracellular survival in an in vitro macrophages infection model. The results showed the presence of Aeromonas in all samples with the three quantification methods, with Aeromonas popoffii being the most prevalent species. The presence of strains with the same genotype (ERIC-PCR) was also confirmed in different samples. Some of the strains showed a high level of cell damage and intracellular bacterial survival, as well as the presence of various virulence factors. Furthermore, these strains showed resistance to some of the antibiotics tested and used therapeutically in both humans and animals. These results indicate that the presence of Aeromonas in this environment may represent a biosanitary risk that could be a public health problem.

Aeromonas allosaccharophila Strain AE59-TE2 Is Highly Antagonistic towards Multidrug-Resistant Human Pathogens, What Does Its Genome Tell Us?

Multidrug-resistant bacteria are of critical importance and a problem for human health and food preservation; the discovery of new antimicrobial substances to control their proliferation is part of the solution. This work reports on 57 antagonistic Aeromonas strains, of which 38 strains were antagonistic towards problematic human pathogens. The genome of the most antagonistic strain was sequenced and identified as Aeromonas allosaccharophila. Its genome was fully annotated and mined for genes that might explain that activity. Strain AE59-TE was antagonistic toward clinically relevant gram-negative and gram-positive multidrug-resistant bacteria, including Klebsiella pneumoniae KPC, Escherichia coli ESBL, Salmonella typhimurium, and Staphylococcus aureus MRSA. Strain AE59-TE2 was identified by multilocus sequence analysis. Genome mining identified four genes homologous to the bacteriocin, zoocin A from Streptococcus equi and a gene 98% similar to cvpA linked to colicin V production. A. allosaccharophila strain AE59-TE2 produced antimicrobial activity against a broad range of bacteria, including important gram-negative bacteria, not typically targeted by bacteriocins. Herewere described novel zoocin genes that are promising for industrial applications in the food and health sectors. Interesting and important antagonistic activity is described combined with the first detailed genomic analysis of the species Aeromonas allosaccharophila.

An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity

The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). Since aeromonads were first associated with human disease, gastroenteritis, bacteremia, and wound infections have dominated. The literature shows that the pathogenic potential of Aeromonas is considered multifactorial and the presence of several virulence factors allows these bacteria to adhere, invade, and destroy the host cells, overcoming the immune host response. Based on current information about the ecology, epidemiology, and pathogenicity of the genus Aeromonas, we should assume that the infections these bacteria produce will remain a great health problem in the future. The ubiquitous distribution of these bacteria and the increasing elderly population, to whom these bacteria are an opportunistic pathogen, will facilitate this problem. In addition, using data from outbreak studies, it has been recognized that in cases of diarrhea, the infective dose of Aeromonas is relatively low. These poorly known bacteria should therefore be considered similarly as enteropathogens like Salmonella and Campylobacter.

Comparative transcriptomics and histopathological analysis of crucian carp infection by atypical Aeromonas salmonicida

Aeromonas salmonicida is a ubiquitous fish pathogen known to cause furunculosis. With the emergence of new subtypes and the expansion of the host range, it has threatened the health of a variety of marine and freshwater fish, particularly the non-salmonids, manifesting differently from the classical furunculosis. Although there have been reports of infection by atypical strains on the crucian carp, the pathogenesis and tissue pathology remain unclear. In this study, transcriptomics and histopathology were used to analyze the immune response and lesions of crucian carp infected with A. salmonicida. Comparative analysis showed 6579 differentially expressed genes (DEGs) (3428 down-regulated and 3151 up-regulated) were identified on day 5 post-infection (5 dpi). Further annotation and analysis revealed that the DEGs were enriched in enzyme regulator activity, response to oxidative stress, iron ion homeostasis and other functions, and mitogen-activated protein kinase (MAPK), nuclear factor-κB (NF-κB), toll-like receptor (TLR), and nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) etc., and immune-related signaling pathways. Meanwhile, the four C-type lysozyme genes found in all DEGs were significantly up-regulated after infection. In addition, there was severe bleeding on the body of the infected fish. Also, the intestine, liver, spleen, and kidney showed varying degrees of inflammatory damage, especially the goblet cell hyperplasia of intestinal mucosa epithelium and degeneration and necrosis of renal tubular epithelium cells. Additionally, with the increase in pathogen concentration, the cumulative mortality increased, the severity of lesions in the hindgut and head-kidney tissues increased. The relative expression levels of four immune-related genes (TNF-α, IL-1β, IL-11, C-lysozyme) were also significantly upregulated, compared with the control (P < 0.05). In conclusion, this study provides a scientific basis for further study on the immune response, pathological diagnosis, and prevention of crucian carp infection caused by atypical A. salmonicida.