Virulence and antibiotic-resistance genes in Enterococcus faecalis associated with streptococcosis disease in fish

Metagenomic insights into the inhibitory effect of phytochemical supplementation on antibiotic resistance genes and virulence factors in the rumen of transition dairy cows

Antimicrobial resistance (AMR) is a major global health concern, with the rumen microbiota of dairy cows serving as an important reservoir for antibiotic resistance genes (ARGs) and virulence factors (VFs). This study explores the impact of dietary phytochemical supplementation on the rumen resistome and virulome of transition dairy cows using metagenomic sequencing. Naringin supplementation reduced the abundance of ARGs by up to 9.0 % and VFs by up to 7.2 % during the transition period, as indicated by metagenomic analysis (P < 0.05). Clinically high-risk ARGs, including those conferring resistance to beta-lactams (mecA), tetracyclines (tetM, tetO), and aminoglycosides (rmtF), were notably downregulated (P < 0.05). Virulence factors associated with adherence, secretion systems, and toxins were also significantly decreased (P < 0.05). Naringin altered the microbial community structure, particularly reducing the abundance of Proteobacteria, a key phylum harboring ARGs and VFs. Despite inducing increased ARG-VF network complexity, naringin supplementation promoted a less pathogenic microbiome with reduced resistance potential. These findings demonstrate the potential of naringin as a natural dietary strategy to mitigate AMR by reducing the risk of ARG and VF dissemination into the environment, while supporting rumen microbiota stability in transition dairy cows.

Antibiotic erythromycin in fish: Pharmacokinetics, effects, and health risks

Erythromycin is a macrolide antibiotic commonly utilized in veterinary medicine and aquaculture. It functions by binding to the 50S subunit of 70S ribosomes, inhibiting protein synthesis and effectively treating numerous bacterial diseases. Due to the extensive use of erythromycin, it has been detected in various aquatic systems in recent years. Multiple studies have reported the occurrence of erythromycin resistance and its adverse effects on diverse aquatic organisms. Consequently, potential environmental health risks associated with erythromycin have garnered increasing attention. As an integral component of aquatic ecosystems, fish have been the subject of numerous reports regarding the bioaccumulation and adverse effects of erythromycin; however, these data have not been collated and interpreted. This report provides a comprehensive overview of the environmental fate of erythromycin, detection methods, pharmacokinetics, and impacts on fish. In addition to the therapeutic benefits against pathogens, acute or chronic exposure of fish to erythromycin at concentrations ranging from μg/L to mg/L disrupts the primary defense, antioxidant, and xenobiotic metabolism systems, leading to oxidative stress, cellular structural damage, and metabolic disorders, manifesting as cytotoxicity, organ toxicity, neurotoxicity, developmental toxicity, and reproductive toxicity. However, further in-depth studies are warranted to evaluate the therapeutic efficacy at relatively high levels, particularly when considering pathogens with developed resistance to erythromycin, as well as the long-term effects of erythromycin exposure at environmentally relevant concentrations in fish, thereby better assessing the health risks posed by erythromycin to fish and their consumers humans.

Significant changes in gut microbiota and SCFAs among patients with newly diagnosed acute myeloid leukemia

The purpose of this study was to identify whether the gut microbiota and metabolites of newly diagnosed acute myeloid leukemia (AML) patients displayed specific characteristic alterations and whether these changes could be used as potential biomarkers for predicting the disease. Notably, the gut microbiota and metabolites of AML patients exhibited significant structural and quantitative alterations at the time of their initial diagnosis. Beneficial bacteria, including Faecalibacterium, Collinsella, Lacticaseibacillus, and Roseburia, as well as butyric acid and acetic acid, were found to be considerably reduced in newly diagnosed AML patients. In contrast, Enterococcus and Lactobacillus, especially Enterococcus, were significantly enriched. Further investigation indicated that Enterococcus could serve as a potential intestinal marker, showing a strong negative correlation with the levels of acetic and butyric acid. Importantly, assays aimed at identifying AML demonstrated that Enterococcus, butyric acid, and acetatic acid exhibited excellent predictive effectiveness. Colonizing Enterococcus from patients were isolated for pathogen investigation, which revealed that these bacteria possess several strong virulence factors and multiple drug-resistance gene characteristics. Therefore, we speculate that the increase of Enterococcus may contribute to the development and progression of AML.

Comparative genomic and antimicrobial resistance profiles of Salmonella strains isolated from pork and human sources in Sichuan, China

Introduction

Salmonella detection in retail pork is increasing, yet studies on its antimicrobial resistance (AMR) profiles and genomic characteristics remain limited. Moreover, it is still unclear whether certain Salmonella sequence types (STs) are consistently or rarely associated with pork as a transmission source. Sichuan province, the largest pork-production region in China, provides a critical setting to investigate these dynamics.

Methods

In this study, 213 Salmonella strains isolated from pork and human sources (2019-2021) underwent phenotypic AMR testing and whole-genome sequencing (WGS).

Results

Resistance profiling revealed a higher prevalence of AMR in the pork-derived strains, particularly in veterinary-associated antibiotics. We identified STs not observed in pork in this study, such as ST23 (S. Oranienburg) and the poultry-commonly associated ST32 (S. Infantis), suggesting potential non-pork transmission routes for these Salmonella STs. To quantify sequence type diversity within each sample source, we introduced the sequencing type index (ST index = number of different STs/ total isolates). The ST index was 32% (49/153) for human-derived isolates and 20% (12/60) for pork-derived isolates. PERMANOVA analysis revealed significant differences in the structural composition of sequence types between human- and pork-derived isolates (p = 0.001), indicating that pork may harbor specific Salmonella STs more frequently.

Discussion

These findings highlight the role of pork as a reservoir for certain Salmonella STs, while also implying potential non-pork transmission pathways. The ST index represents a novel metric for assessing Salmonella diversity across different sample sources, offering a better understanding of genetic variation and transmission dynamics.

Aquatic Invertebrate Antimicrobial Peptides in the Fight Against Aquaculture Pathogens

The intensification of aquaculture has escalated disease outbreaks and overuse of antibiotics, driving the global antimicrobial resistance (AMR) crisis. Antimicrobial peptides (AMPs) provide a promising alternative due to their rapid, broad-spectrum activity, low AMR risk, and additional bioactivities, including immunomodulatory, anticancer, and antifouling properties. AMPs derived from aquatic invertebrates, particularly marine-derived, are well-suited for aquaculture, offering enhanced stability in high-salinity environments. This study compiles and analyzes data from AMP databases and over 200 scientific sources, identifying approximately 350 AMPs derived from aquatic invertebrates, mostly cationic and α-helical, across 65 protein families. While in vitro assays highlight their potential, limited in vivo studies hinder practical application. These AMPs could serve as feed additives, therapeutic agents, or in genetic engineering approaches like CRISPR/Cas9-mediated transgenesis to enhance resilience of farmed species. Despite challenges such as stability, ecological impacts, and regulatory hurdles, advancements in peptidomimetics and genetic engineering hold significant promise. Future research should emphasize refining AMP enhancement techniques, expanding their diversity and bioactivity profiles, and prioritizing comprehensive in vivo evaluations. Harnessing the potential of AMPs represents a significant step forward on the path to aquaculture sustainability, reducing antibiotic dependency, and combating AMR, ultimately safeguarding public health and ecosystem resilience.

Liposome encapsulating pine bark extract in Nile tilapia: Targeting interrelated immune and antioxidant defense to combat coinfection with Aeromonas hydrophila and Enterococcus faecalis

Application of smart delivery systems for encapsulation of natural ingredients provides novel avenues and is being frequently developed. Thus, we aimed to highlight the effects of cyclosome liposomal pine bark extract (CL-PBE) on Nile tilapia growth, immunomodulation, antioxidant capacity and resistance against coinfection with Aeromonas hydrophila and Enterococcus faecalis and their associated virulence genes. The experiment was conducted on four fish groups receiving a control diet (control) along with three baseline meals supplemented with 200, 400 and 600 mg/kg diet of CL-PBE (CL-PBE 200, 400 and 600, respectively). At the end of the 12-weeks feeding trial, the tilapias were intraperitoneally challenged with virulent A. hydrophila strain and five days later, E. faecalis challenge was carried out. The results revealed that tilapias fed diets fortified with CL-PBE displayed significantly enhanced growth rate and feed conversion ratio in a dose-dependent manner. Moreover, we demonstrated that CL-PBE had potent antioxidant property presented by modulation of several markers of oxidative stress; substantial reductions in reactive oxygen species, hydrogen peroxide and malondialdehyde levels, an elevation in total antioxidant capacity and boosting glutathione peroxidase (GSH-Px), catalase (CAT) and superoxide dismutase (SOD) activities in fish serum and muscle tissues. This was also correlated with augmenting the expression of CAT, SOD, GSH-Px, Nrf2 and caspase-1 genes alongside reducing those of COX-2, HSP70 and iNOS genes in response to CL-PBE. Our data demonstrated that CL-PBE fortification counteracted the overly pronounced inflammatory response-mediated induction of IL-1β, TNF-α, MHCII and TLR2 genes at the transcriptional levels post coinfection together with promotion in MUC2 and IL-10 genes expression. Notably, our findings displayed optimal well-functioning fish immune system post dietary supplementation of CL-PBE for the protection against coinfection with A. hydrophila and E. faecalis. This was evident from the decline of their counts and hence encompassing the capacity to reduce cumulative mortality percentage in conjunction with interference with their virulence via the significant downregulatory effects of CL-PBE on E. faecalis esp and gelE and A. hydrophila act and fla virulence genes. Taken together, our study strongly suggested dietary inclusion of CL-PBE for Nile tilapias with superior growth performance and significant economic benefits coupled with potent stimulatory effects on antioxidant capacity and immune response expediting our detailed understanding of how coinfection with A. hydrophila and E. faecalis was controlled.

Genomics of Staphylococcus aureus and Enterococcus faecalis isolated from the ocular surface of dry eye disease sufferers

Ocular surface inflammatory disorders, such as dry eye, are becoming increasingly prevalent. Developing new treatment strategies targeting harmful bacteria could provide significant therapeutic benefits. The purpose of this study was to characterize the common ocular pathogen Staphylococcus aureus and the rarer endophthalmitis-associated species Enterococcus faecalis isolated from the ocular surface of dry eye disease patients in Norway. Together the 7 isolates (5 S. aureus and 2 E. faecalis) comprise the complete set of members of each species isolated in our previous study of the ocular microbiome of 61 dry eye sufferers. We aimed to investigate the pathogenic potential of these isolates in relation to ocular surface health. To this end, we used whole genome sequencing, multiplex PCR directed at virulence genes and antibiotic susceptibility tests encompassing clinically relevant agents. The E. faecalis isolates showed resistance to only gentamicin. S. aureus isolates displayed susceptibility to most of the tested antibiotics, except for two isolates which showed resistance to trimethoprim/sulfamethoxazole and three isolates which were resistant to ampicillin. Susceptibilities included sensitivity to several first-line antibiotics for treatment of ocular infections by these species. Thus, treatment options would be available if required. However, spontaneous resistance development to gentamicin and rifampicin occurred in some S. aureus which could be a cause for concern. Whole genome sequencing of the isolates showed genome sizes ranging from 2.74 to 2.83 Mbp for S. aureus and 2.86 Mbp for E. faecalis, which is typical for these species. Multilocus sequence typing and phylogenetic comparisons with previously published genomes, did not suggest the presence of eye-specific clusters for either species. Genomic analysis indicated a high probability of pathogenicity among all isolates included in the study. Resistome analysis revealed the presence of the beta-lactamase blaZ gene in all S. aureus isolates and the dfrG gene in two of them; while E. faecalis isolates carried the lsa(A) gene which confers intrinsic resistance to lincosamides and streptogramin A in this species. Screening for virulence factors revealed the presence of various pathogenicity associated genes in both S. aureus and E. faecalis isolates. These included genes coding for toxin production and factors associated with evading the host immune system. Some of the identified genes (tst, hylA & hylB) are suggested to be linked to the pathophysiology of dry eye disease. Lastly, the presence of specific S. aureus virulence genes was confirmed through multiplex PCR analysis.

Assessment of prevalence, antibiotic resistance, and virulence profiles of biofilm-forming Enterococcus faecalis isolated from raw seafood in Bangladesh

Enterococcus faecalis are often resistant to different classes of antibiotics, harbor virulence determinants, and produce biofilm. The presence of E. faecalis in raw seafood exhibits serious public health significance. This study aimed to identify antibiotic resistance patterns and virulence factors in biofilm-forming E. faecalis strains extracted from seafood in Bangladesh. A total of 150 samples of raw seafood, comprising 50 shrimps, 25 crabs, and 75 fish, were collected and subjected to culturing, biochemical, and PCR assays to detect E. faecalis. The biofilm-forming abilities of the isolates were determined by Congo Red agar (CRA) plate and Crystal Violet Micro-titer Plate (CVMP) tests. Antibiotic resistance profiles were evaluated using the disk diffusion method. Virulence genes of the isolates were detected by PCR assay. The occurrence of E. faecalis was 29.3 % (44/150), which was higher in crabs and fish (36 %) than in shrimps (16 %). In CRA and CVMP tests, biofilm-forming abilities were observed in 88.64 % of the isolates, whereas 11 (25 %) and 28 (63.6 %) were strong- and intermediate-biofilm formers, respectively. All the isolates contained at least two virulence genes, including pil and ace (97.7 %), sprE (95.5 %), gelE (90.9 %), fsrB (79.6 %), agg (70.5 %), fsrA (68.2 %), and fsrC (61.4 %). All the isolates were phenotypically resistant to penicillin, followed by ampicillin and rifampicin (86.4 %), erythromycin (13.7 %), and tetracycline, vancomycin, norfloxacin, and linezolid (2.3 %). Resistant gene bla TEM was found in 61.4 % of the isolates. Moreover, the study found that E. faecalis strains with strong biofilm-forming capabilities had significantly higher levels of virulence genes and antibiotic resistance (p < 0.05) compared to those with intermediate and/or no biofilm-forming abilities. To the best of our knowledge, this research represents the first instance in Bangladesh of assessing antibiotic resistance and identifying virulence genes in biofilm-forming E. faecalis strains isolated from seafood samples. Our study revealed that seafood is a carrier of antibiotic-resistant, virulent, and biofilm-forming E. faecalis, demonstrating a potential public health threat.

Whole genome sequencing (WGS) analysis of antimicrobial resistance (AMR) milk and dairy-derived pathogens from Anand, Gujarat, India

This study aimed to evaluate the antimicrobial resistance (AMR) patterns and genomic characteristics of Enterococcus faecalis, Enterococcus faecium, and Staphylococcus aureus strains isolated from dairy products, including buttermilk, curd, ice cream, and sweets, in the Anand region of Gujarat, India. A total of 205 isolates were analysed, with the highest contamination levels found in buttermilk and curd. The bacterial isolates were identified using biochemical tests and advanced Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) mass spectrometry. Antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer disk diffusion method, following CLSI guidelines, focusing on common antibiotics used for treating dairy-related bacterial infections. Resistance profiles were analysed using WHONET software.s The findings revealed significant multidrug resistance (MDR), particularly among E. faecium and E. faecalis, with over 95 % resistance to key antibiotics, including linezolid, ciprofloxacin, cefpodoxime, and carbapenems. Many strains were classified as MDR, XDR, and PDR. Staphylococcus aureus also exhibited substantial resistance to penicillin and enrofloxacin. whole-genome sequencing (WGS) and phylogenetic analysis to identify AMR determinants and conduct nucleotide sequence alignment. The study identified several antibiotic resistance genes, including LiaF, which regulates the expression of LiaR and LiaS genes. WGS revealed that genes such as GdpD, MprF, and PgsA encode intrinsic resistance determinants, contributing to antibiotic resistance. Additional AMR mechanisms were identified, including ABC transporter efflux pumps and the regulation of resistance genes by LiaR and LiaS. Phylogenetic analysis indicates a close relationship between Enterococcus faecium 640 1352.18624 and Enterococcus durans FB129-CNAB-4 883162.3.

The effects of kelp powder and fucoidan on the intestinal digestive capacity, immune response, and bacterial community structure composition of large yellow croakers (Larimichthys crocea)

Feed terrestrial components can induce intestinal stress in fish, affecting their overall health and growth. Recent studies suggest that seaweed products may improve fish intestinal health. In this experiment, three types of feed were prepared: a basic diet (C group), a diet with 0.2 % fucoidan (F group), and a diet with 3 % kelp powder (K group). These diets were fed to large yellow croaker (Larimichthys crocea) over an 8-week period. Each feed was randomly assigned to three seawater cages (4.0 m × 4.0 m × 5.0 m) containing 700 fish per cage. The study assessed changes in growth and intestinal health, including intestinal tissue morphology, digestive enzyme activities, expression of immune-related genes, and bacterial community structure. Results showed that incorporating seaweed products into the diet improved the growth and quality traits of large yellow croakers and significantly enhanced their intestinal digestive capacity (P < 0.05). Specifically, the 0.2 % fucoidan diet significantly increased the intestinal villus length and the activities of digestive enzymes such as trypsin, lipase, and α-amylase (P < 0.05). The 3 % kelp powder diet significantly enhanced the intestinal crypt depth and the activities of trypsin and lipase (P < 0.05). Both seaweed additives significantly enhanced intestinal health by mitigating inflammatory factors. Notably, the control group's biomarkers indicated a high presence of potential pathogenic bacteria, such as Streptococcus, Pseudomonas, Enterococcus, Herbaspirillum, Neisseria, Haemophilus, and Stenotrophomonas. After the addition of seaweed additives, these bacteria were no longer the indicator bacteria, while the abundance of beneficial bacteria like Ligilactobacillus and Lactobacillus increased. Significant reductions in the expression of inflammatory factors (e.g., il-6, tnf-α, ifn-γ in the fucoidan group and il-8 in the kelp powder group) further supported these findings. Our findings suggested that both seaweed additives helped balance intestinal microbial communities and reduce bacterial antigen load. Considering the effects, costs, manufacturing, and nutrition, adding 3 % kelp powder to the feed of large yellow croaker might be preferable. This study substantiated the beneficial effects of seaweed on the aquaculture of large yellow croaker, particularly in improving intestinal health. These findings advocated for its wider and more scientifically validated use in fish farming practices.

Prevalence of opportunistic pathogens and anti-microbial resistance in urban aquaculture ponds

Bacterial antimicrobial resistance (AMR) has emerged as a significant concern worldwide. The microbial community profile and potential AMR level in aquaculture ponds are often undervalued and attract less attention than other aquatic environments. We used amplicon and metagenomic shotgun sequencing to study microbial communities and AMR in six freshwater polyculture ponds in rural and urban areas of Bangladesh. Amplicon sequencing revealed different community structures between rural and urban ponds, with urban ponds having a higher bacterial diversity and opportunistic pathogens including Streptococcus, Staphylococcus, and Corynebacterium. Despite proteobacterial dominance, Firmicutes was the most interactive in the community network, especially in the urban ponds. Metagenomes showed that drug resistance was the most common type of AMR found, while metal resistance was only observed in urban ponds. AMR and metal resistance genes were found mainly in beta and gamma-proteobacteria in urban ponds, while AMR was found primarily in alpha-proteobacteria in rural ponds. We identified potential pathogens with a high profile of AMR and metal resistance in urban aquaculture ponds. As these ponds provide a significant source of protein for humans, our results raise significant concerns for the environmental sustainability of this food source and the dissemination of AMR into the food chain.

Genomic Insights of a Methicillin-Resistant Biofilm-Producing Staphylococcus aureus Strain Isolated From Food Handlers

Methicillin-resistant Staphylococcus aureus (MRSA) is an important zoonotic pathogen associated with a wide range of infections in humans and animals. Thus, the emergence of MRSA clones poses an important threat to human and animal health. This study is aimed at elucidating the genomics insights of a strong biofilm-producing and multidrug-resistant (MDR) S. aureus MTR_BAU_H1 strain through whole-genome sequencing (WGS). The S. aureus MTR_BAU_H1 strain was isolated from food handlers' hand swabs in Bangladesh and phenotypically assessed for antimicrobial susceptibility and biofilm production assays. The isolate was further undergone to high throughput WGS and analysed using different bioinformatics tools to elucidate the genetic diversity, molecular epidemiology, sequence type (ST), antimicrobial resistance, and virulence gene distribution. Phenotypic analyses revealed that the S. aureus MTR_BAU_H1 strain is a strong biofilm-former and carries both antimicrobial resistance (e.g., methicillin resistance; mecA, beta-lactam resistance; blaZ and tetracycline resistance; tetC) and virulence (e.g., sea, tsst, and PVL) genes. The genome of the S. aureus MTR_BAU_H1 belonged to ST1930 that possessed three plasmid replicons (e.g., rep16, rep7c, and rep19), seven prophages, and two clustered regularly interspaced short palindromic repeat (CRISPR) arrays of varying sizes. Phylogenetic analysis showed a close evolutionary relationship between the MTR_BAU_H1 genome and other MRSA clones of diverse hosts and demographics. The MTR_BAU_H1 genome harbours 42 antimicrobial resistance genes (ARGs), 128 virulence genes, and 273 SEED subsystems coding for the metabolism of amino acids, carbohydrates, proteins, cofactors, vitamins, minerals, and lipids. This is the first-ever WGS-based study of a strong biofilm-producing and MDR S. aureus strain isolated from human hand swabs in Bangladesh that unveils new information on the resistomes (ARGs and correlated mechanisms) and virulence potentials that might be linked to staphylococcal pathogenesis in both humans and animals.

Prediction of anastomotic insufficiency based on the mucosal microbiome prior to colorectal surgery: a proof-of-principle study

Anastomotic leakage (AL) is a potentially life-threatening complication following colorectal cancer (CRC) resection. In this study, we aimed to unravel longitudinal changes in microbial structure before, during, and after surgery and to determine if microbial alterations may be predictive for risk assessment between sufficient anastomotic healing (AS) and AL prior surgery. We analysed the microbiota of 134 colon mucosal biopsies with 16S rRNA V1-V2 gene sequencing. Samples were collected from three location sites before, during, and after surgery, and patients received antibiotics after the initial collection and during surgery. The microbial structure showed dynamic surgery-related changes at different time points. Overall bacterial diversity and the abundance of some genera such as Faecalibacterium or Alistipes decreased over time, while the genera Enterococcus and Escherichia_Shigella increased. The distribution of taxa between AS and AL revealed significant differences in the abundance of genera such as Prevotella, Faecalibacterium and Phocaeicola. In addition to Phocaeicola, Ruminococcus2 and Blautia showed significant differences in abundance between preoperative sample types. ROC analysis of the predictive value of these genera for AL revealed an AUC of 0.802 (p = 0.0013). In summary, microbial composition was associated with postoperative outcomes, and the abundance of certain genera may be predictive of postoperative complications.

Enrofloxacin, Effective Treatment of Pseudomonas aeruginosa and Enterococcus faecalis Infection in Oreochromis niloticus

Enrofloxacin is a broad-spectrum synthetic antimicrobial drug widely used in veterinary medicine. The present study aimed to determine the effective enrofloxacin dose for treating Pseudomonas aeruginosa and Enterococcus faecalis infection in Oreochromis niloticus. P. aeruginosa and E. faecalis isolates were verified using selective differential media and biochemically using the Vitek 2 test. Bacterial isolates were virulent for O. niloticus with LD50 equal to 2.03 × 106 and 2.22 × 107 CFU fish-1 for P. aeruginosa and E. faecalis, respectively. Infected fish suffered from decreased feed intake followed by off-food, tail erosion, darkening of the external body surface, exophthalmia, ascites, and loss of escape reflex. Internally, congested hemorrhagic hepatopancreas with engorged distended gall bladder were dominant. The posterior kidney was congested with enlarged spleen, and empty elementary tract. Pathologically, severe degenerative changes were dominant in the hepatopancreas, posterior kidney, spleen, stomach, and gills of infected fish. Antimicrobial sensitivity test indicated the high susceptibility of P. aeruginosa and E. faecalis to enrofloxacin with MIC estimated at 1 and 0.0625 µg/mL, respectively. Enrofloxacin effectively protected O. niloticus against E. faecalis and P. aeruginosa infection when used with medicated feed at doses of 10 and 20 mg kg-1 body weight.

Antimicrobial resistance and genomic investigation of Salmonella isolated from retail foods in Guizhou, China

Introduction

Salmonella is a major foodborne pathogen worldwide that causes severe morbidity and mortality. It is mainly caused by consuming contaminated food, with retail food considered the primary source.

Methods

In Guizhou, China, 102 Salmonella strains isolated from 2016 to 2021 underwent phenotypic antimicrobial resistance testing and whole-genome sequencing (WGS) to understand Salmonella diversity, including serotypes, sequencing types (STs), antimicrobial genes, virulence genes, plasmid types, multi-locus sequence types (MLST), and core genome MLST (cgMLST).

Results and discussion

S.Typhimurium was the dominant serotype, and O:4(B) was the leading serogroup. The most prevalent genotype was ST40. Phenotypic antimicrobial resistance identified 66.7% of the sampled isolates as multi-drug resistant (MDR). S.Enteritidis (n = 7), S.Typhimurium (n = 1), S.Indiana (n = 1), S.Kentucky (n = 1), S.Uganda (n = 1), all of which were MDR, were resistant to Colistin. Resistance rates varied significantly across different strains and food types, particularly meat products exhibiting higher resistance. Notably, significant increases in resistance were observed from 2016 to 2021 for the following: ≥ 1 resistant (P = 0.001), MDR (P = 0.001), ampicillin (P = 0.001), tetracycline (P < 0.001), chloramphenicol (P = 0.030), and trimethoprim/sulfamethoxazole (P = 0.003). The marked escalation in drug resistance over the recent years, coupled with the varying resistance rates among food sources, underscores the growing public health concern. Our findings highlight the need for a coordinated approach to effectively monitor and respond to Salmonella infections in Guizhou, China.

Responses of the intestinal microbiota to exposure of okadaic acid in marine medaka Oryzias melastigma

It is still limited that how the microalgal toxin okadaic acid (OA) affects the intestinal microbiota in marine fishes. In the present study, adult marine medaka Oryzias melastigma was exposed to the environmentally relevant concentration of OA (5 μg/L) for 10 days, and then recovered in fresh seawater for 10-days depuration. Analysis of taxonomic composition and diversity of the intestinal microbiota, as well as function prediction analysis and histology observation were carried out in this study. Functional prediction analysis indicated that OA potentially affected the development of colorectal cancer, protein and carbohydrate digestion and absorption functions, and development of neurodegenerative diseases like Parkinson's disease, which may be associated with changes in Proteobacteria and Firmicutes in marine medaka. Significant increases of C-reactive protein (CRP) and inducible nitric oxide synthase (iNOS) levels, as well as the changes of histology of intestinal tissue demonstrated that an intestinal inflammation was induced by OA exposure in marine medaka. This study showed that the environmental concentrations of OA could harm to the intestinal microbiota thus threatening the health of marine medaka, which hints that the chemical ecology of microalgal toxins should be paid attention to in future studies.

Unravelling the genomic secrets of bacterial fish pathogens: a roadmap to aquaculture sustainability

In the field of aquaculture, bacterial pathogens pose significant challenges to fish health and production. Advancements in genomic technologies have revolutionized our understanding of bacterial fish pathogens and their interactions with their host species. This review explores the application of genomic approaches in the identification, classification, and characterization of bacterial fish pathogens. Through an extensive analysis of the literature, we have compiled valuable data on 79 bacterial fish pathogens spanning 13 different phyla, encompassing their whole genome sequences. By leveraging high-throughput sequencing techniques, researchers have gained valuable insights into the genomic makeup of these pathogens, enabling a deeper understanding of their virulence factors and mechanisms of host interaction. Furthermore, genomic approaches have facilitated the discovery of potential vaccine and drug targets, opening up new avenues for the development of effective interventions against fish pathogens. Additionally, the utilization of genomics in fish disease resistance and control in aquaculture has shown promising results, enabling the identification of genetic markers associated with disease resistance traits. This review highlights the significant contributions of genomics to the field of fish pathogen research and underscores its potential for improving disease management strategies and enhancing the sustainability of aquaculture practices.

Insights into antibiotic and heavy metal resistance interactions in Escherichia coli isolated from livestock manure and fertilized soil

Heavy metal and antibiotic-resistant bacteria from livestock feces are ecological and public health problems. However, the distribution and relationships of antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs), and virulence factors (VFs) and their transmission mechanisms remain unclear. Therefore, we investigated the resistance of Escherichia coli, the prevalence of its ARGs, HMRGs, and VFs, and their transmission mechanisms in livestock fresh feces (FF), composted feces (CF), and fertilized soil (FS). In total, 99.54% (n = 221) and 91.44% (n = 203) of E. coli were resistant to at least one antibiotic and one heavy metal, respectively. Additionally, 72.52% (n = 161) were multi-drug resistant (MDR), of which Cu-resistant E. coli accounted for 72.67% (117/161). More than 99.34% (88/89) of E. coli carried multidrug ARGs, VFs, and the Cu resistance genes cueO and cusABCRFS. The Cu resistance genes cueO and cusABCRFS were mainly located on chromosomes, and cueO and cusF were positively associated with HMRGs, ARGs, and VFs. The Cu resistance genes pcoABCDRS were located on the plasmid pLKYL-P02 flanked by ARGs in PF18C from FF group and on chromosomes flanked by HMRGs in SAXZ1-1 from FS group. These results improved our understanding of bacterial multidrug and heavy metal resistance in the environment.

Genomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates

Stenotrophomonas maltophilia is a rapidly evolving multidrug-resistant opportunistic pathogen that can cause serious infections in immunocompromised patients. Although phage therapy is one of promising strategies for dealing with MDR bacteria, the main challenges of phage therapeutics include accumulation of phage resistant mutations and acquisition of the phage defense systems. To systematically evaluate the impact of (pro)phages in shaping genetic and evolutionary diversity of S. maltophilia, we collected 166 S. maltophilia isolates from three hospitals in southern China to analyze its pangenome, virulence factors, prophage regions, and anit-viral immune systems. Pangenome analysis indicated that there are 1328 saturated core genes and 26961 unsaturated accessory genes in the pangenome, suggesting existence of highly variable parts of S. maltophilia genome. The presence of genes in relation to T3SS and T6SS mechanisms suggests the great potential to secrete toxins by the S. maltophilia population, which is contrary to the conventional notion of low-virulence of S. maltophilia. Additionally, we characterized the pan-immune system maps of these clinical isolates against phage infections and revealed the co-harboring of CBASS and anti-CBASS in some strains, suggesting a never-ending arms race and the co-evolutionary dynamic between bacteria and phages. Furthermore, our study predicted 310 prophage regions in S. maltophilia with high genetic diversity. Six viral defense systems were found to be located at specific position of the S. maltophilia prophage genomes, indicating potential evolution of certain site/region similar to bacterial 'defense islands' in prophage. Our study provides novel insights into the S. maltophilia pangenome in relation to phage-defense mechanisms, which extends our understanding of bacterial-phage interactions and might guide the application of phage therapy in combating S. maltophilia infections.

Resistome, mobilome, virulome analysis and phylogenomics of Enterococcus faecalis isolated from raw muscle foods of beef origin in Gauteng, South Africa

Enterococcus faecalis is a ubiquitous bacterium found in various environments, including processed beef meat, and is known for its importance in both food safety and public health. This pivotal significance stems not solely from its virulence but also from its adeptness in eliciting multidrug-resistant infections in humans. The aim of this study was to investigate the population structure, resistome, mobilome, and virulome of E. faecalis obtained from processed beef meat sources in South Africa. A total of eight genomes sequenced in this study were examined, alongside 78 publicly available, high-quality genomes of E. faecalis, with a comprehensive analysis conducted to identify antimicrobial resistance (AMR) determinants, virulence factors, and mobile genetic elements (MGE). Six distinct sequence types (STs) (ST79, ST860, ST40, ST238, ST21, and ST700) and 41 core virulence factors were found across all the genomes. The virulence factors included genes encoding adherence (ace, asa1, Ef0485, ebpA, ebpB, ebpC, srtC); exoenzyme (Ef3023, Ef0818, gelE, sprE); immunomodulation (cpsA, cpsB, cpsC, cpsD, cpsE, cpsF, cpsG, cpsH, cpsI, cpsK), and biofilm formation (bopD, fsrA, fsrB, fsrC). In addition, AMR genes were identified across all genomes, which include aminoglycoside resistance (ant(6)-Ia), trimethoprim resistance (dfrA), drug and biocide resistance (efrA and efrB), multidrug efflux pump (emeA), clindamycin quinupristin-dalfopristin, dalfopristin resistance (lsaA), and tetracycline resistance (tetM). The genomes of E. faecalis sequenced here contained a variety of MGEs, including Insertion Sequences (ISs), transposons, prophages, and plasmids, which may have facilitated genetic exchange within and between these species. The results highlight that beef meat products act as a reservoir for virulent E. faecalis strains possessing antibiotic-resistance traits. This study provides insight into the genomic characteristics, antimicrobial resistance genes, virulence factors, and genetic mobile elements associated with eight E. faecalis isolates from processed beef meat in the Gauteng province of South Africa.

Biocide Tolerance and Impact of Sanitizer Concentrations on the Antibiotic Resistance of Bacteria Originating from Cheese

In this study, we determined and identified the bacterial diversity of different types of artisanal and industrially produced cheese. The antibiotic (erythromycin, chloramphenicol, kanamycin, ampicillin, clindamycin, streptomycin, tetracycline, and gentamicin) and biocide (peracetic acid, sodium hypochlorite, and benzalkonium chloride) resistance of clinically relevant bacteria was determined as follows: Staphylococcus aureus, Macrococcus caseolyticus, Bacillus sp., Kocuria varians, Escherichia coli, Enterococcus faecalis, Citrobacter freundii, Citrobacter pasteurii, Klebsiella oxytoca, Klebsiella michiganensis, Enterobacter sp., Enterobacter cloacae, Enterobacter sichuanensis, Raoultella ornithinolytica, Shigella flexneri, and Salmonella enterica. Also, the effect of the sub-inhibitory concentration of three biocides on antibiotic resistance was determined. The microbiota of evaluated dairy products comprise diverse and heterogeneous groups of bacteria with respect to antibiotic and disinfectant tolerance. The results indicated that resistance was common in the case of ampicillin, chloramphenicol, erythromycin, and streptomycin. Bacillus sp. SCSSZT2/3, Enterococcus faecalis SRGT/1, E. coli SAT/1, Raoultella ornithinolytica MTT/5, and S. aureus SIJ/2 showed resistance to most antibiotics. The tested bacteria showed sensitivity to peracetic acid and a different level of tolerance to benzalkonium chloride and sodium hypochlorite. The inhibition zone diameter of antibiotics against Enterococcus faecalis SZT/2, S. aureus JS11, E. coli CSKO2, and Kocuria varians GRT/10 was affected only by the sub-inhibitory concentration of peracetic acid.

Genomic Landscape of Multidrug Resistance and Virulence in Enterococcus faecalis IRMC827A from a Long-Term Patient

We report on a highly virulent, multidrug-resistant strain of Enterococcus faecalis IRMC827A that was found colonizing a long-term male patient at a tertiary hospital in Khobar, Saudi Arabia. The E. faecalis IRMC827A strain carries several antimicrobial drug resistance genes and harbours mobile genetic elements such as Tn6009, which is an integrative conjugative element that can transfer resistance genes between bacteria and ISS1N via an insertion sequence. Whole-genome-sequencing-based antimicrobial susceptibility testing on strains from faecal samples revealed that the isolate E. faecalis IRMC827A is highly resistant to a variety of antibiotics, including tetracycline, doxycycline, minocycline, dalfopristin, virginiamycin, pristinamycin, chloramphenicol, streptomycin, clindamycin, lincomycin, trimethoprim, nalidixic acid and ciprofloxacin. The isolate IRMC827A carries several virulence factors that are significantly associated with adherence, biofilm formation, sortase-assembled pili, manganese uptake, antiphagocytosis, and spreading factor of multidrug resistance. The isolate also encompasses two mutations (G2576T and G2505A) in the 23S rRNA gene associated with linezolid resistance and three more mutations (gyrA p.S83Y, gyrA p.D759N and parC p.S80I) of the antimicrobial resistance phenotype. The findings through next-generation sequencing on the resistome, mobilome and virulome of the isolate in the study highlight the significance of monitoring multidrug-resistant E. faecalis colonization and infection in hospitalized patients. As multidrug-resistant E. faecalis is a serious pathogen, it is particularly difficult to treat and can cause fatal infections. It is important to have quick and accurate diagnostic tests for multidrug-resistant E. faecalis, to track the spread of multidrug-resistant E. faecalis in healthcare settings, and to improve targeted interventions to stop its spread. Further research is necessary to develop novel antibiotics and treatment strategies for multidrug-resistant E. faecalis infections.

Antimicrobial Resistance, Biofilm Formation, and Virulence Determinants in Enterococcus faecalis Isolated from Cultured and Wild Fish

Fish has always been an integral part of Bengali cuisine and economy. Fish could also be a potential reservoir of pathogens. This study aimed to inquisite the distribution of virulence, biofilm formation, and antimicrobial resistance of Enterococcus faecalis isolated from wild and cultivated fish in Bangladesh. A total of 132 koi fish (Anabas scandens) and catfish (Heteropneustes fossilis) were collected from different markets in the Mymensingh district and analyzed to detect E. faecalis. E. faecalis was detected by conventional culture and polymerase chain reaction (PCR), followed by the detection of virulence genes by PCR. Antibiotic susceptibility was determined using the disk diffusion method, and biofilm-forming ability was investigated by crystal violet microtiter plate (CVMP) methods. A total of 47 wild and 40 cultured fish samples were confirmed positive for E. faecalis by PCR. The CVMP method revealed four per cent of isolates from cultured fish as strong biofilm formers, but no strong producers were found from the wild fish. In the PCR test, 45% of the isolates from the wild and cultivated fish samples were found to be positive for at least one biofilm-producing virulence gene, where agg, ace, gelE, pil, and fsrC genes were detected in 80, 95, 100, 93, and 100% of the isolates, respectively. Many of the isolates from both types of samples were multidrug resistant (MDR) (73% in local fish and 100% in cultured fish), with 100% resistance to erythromycin, linezolid, penicillin, and rifampicin in E. faecalis from cultured fish and 73.08, 69.23, 69.23, and 76.92%, respectively, in E. faecalis from wild fish. This study shows that E. faecalis from wild fish have a higher frequency of virulence genes and biofilm-forming genes than cultivated fish. However, compared to wild fish, cultured fish were found to carry E. faecalis that was more highly multidrug resistant. Present findings suggest that both wild and cultured fish could be potential sources for MDR E. faecalis, having potential public health implications.

Resistance Profiles and Virulence Determinants in Biofilm-Forming Enterococcus faecium Isolated from Raw Seafood in Bangladesh

Pathogenic, antibiotic-resistant, and biofilm-forming bacteria can be transferred to humans through the consumption of contaminated seafood. The present study was carried out to determine antibiotic resistance profiles and virulence determinants in biofilm-forming Enterococcus faecium isolated from seafood in Bangladesh. A total of 150 seafood samples, including shrimp (n = 50), crabs (n = 25), and marine fish (n = 75), were screened using cultural, staining, biochemical, polymerase chain reaction (PCR), Congo red (CR), and disk diffusion (DD) assays. In PCR, E. faecium was detected in 27.3% (41/150; CI95% 20.8; 34.9) of samples, where marine fish (34.7%, CI95% 24.9; 45.9) had the highest prevalence (p < 0.05) compared to crabs (32%, CI95% 17.2; 51.6) and shrimp (14%, CI95% 7.0; 26.1). Thirty-two (78.1%, CI95% 63.3; 88.0) of the E. faecium isolates were determined to be biofilm formers in the CR test, where 43.9% (18/41, CI95% 29.9; 59.0) and 34.2% (14/41, CI95% 21.6; 49.5) of the isolates were strong and intermediate biofilm formers, respectively. In PCR, virulence genes, i.e., pil (100%), ace (92.7%), agg (68.3%), fsrA (65.9%), gelE (63.4%), sprE (53.7%), fsrB (51.2%), and fsrC (43.9%), were detected in E. faecium isolates. All the E. faecium isolates were phenotypically resistant to ≥3 antimicrobial categories and ≥3 antibiotics, including WHO-classified reserve antibiotics linezolid (70.7%) and fosfomycin (19.5%). Moreover, the multiple antibiotic resistance index ranged up to 0.8, showing resistance to ten antibiotics and eight antibiotic classes. In this study, the prevalence of virulence genes and antibiotic resistance was significantly greater (p < 0.05) in strong biofilm-forming E. faecium strains as compared to strains with intermediate and non-biofilm-forming abilities. As far as we know, this study, for the first time in Bangladesh, determined antibiotic resistance and detected virulence genes in biofilm-forming E. faecium isolated from seafood samples. The data from this study could play a significant role in evaluating potential health hazards linked to the ingestion of uncooked or minimally processed seafood.

Antimicrobial Resistance Profiles, Virulence Determinants, and Biofilm Formation in Enterococci Isolated from Rhesus Macaques (Macaca mulatta): A Potential Threat for Wildlife in Bangladesh?

Enterococci are commensal bacteria that inhabit the digestive tracts of animals and humans. The transmission of antibiotic-resistant genes through human-animal contact poses a potential public health risk worldwide, as zoonoses from wildlife reservoirs can occur on every continent. The purpose of this study was to detect Enterococcus spp. in rhesus macaques (Macaca mulatta) and to investigate their resistance patterns, virulence profiles, and biofilm-forming ability. Conventional screening of rectal swabs (n = 67) from macaques was followed by polymerase chain reaction (PCR). The biofilm-forming enterococci were determined using the Congo red agar plate assay. Using the disk diffusion test (DDT), antibiogram profiles were determined, followed by resistance and virulence genes identification by PCR. PCR for bacterial species confirmation revealed that 65.7% (44/67) and 22.4% (15/67) of the samples tested positive for E. faecalis and E. faecium, respectively. All the isolated enterococci were biofilm formers. In the DDT, enterococcal isolates exhibited high to moderate resistance to penicillin, rifampin, ampicillin, erythromycin, vancomycin, and linezolid. In the PCR assays, the resistance gene bla_TEM was detected in 61.4% (27/44) of E. faecalis and 60% (9/15) of E. faecium isolates. Interestingly, 88.63 % (39/44) of E. faecalis and 100% (15/15) of E. faecium isolates were phenotypically multidrug-resistant. Virulence genes (agg, fsrA, fsrB, fsrC, gelE, sprE, pil, and ace) were more frequent in E. faecalis compared to E. faecium; however, isolates of both Enterococcus spp. were found negative for the cyl gene. As far as we know, the present study has detected, for the first time in Bangladesh, the presence of virulence genes in MDR biofilm-forming enterococci isolated from rhesus macaques. The findings of this study suggest employing epidemiological surveillance along with the one-health approach to monitor these pathogens in wild animals in Bangladesh, which will aid in preventing their potential transmission to humans.