Pathogenic Escherichia coli

Microbiota-derived succinate promotes enterohaemorrhagic Escherichia coli virulence via lysine succinylation

Succinate upregulates enterohaemorrhagic Escherichia coli (EHEC) virulence. Lysine succinylation, a post-translational modification, regulates cellular function in eukaryotes but is less characterized in bacteria. We hypothesized that lysine succinylation regulates EHEC virulence. Here we used SILAC-based proteomics and characterized the EHEC succinylome to show that the transcription factor, PurR, is succinylated at K24 and K55. Succinylation of PurR inhibited its ability to directly bind DNA and repress expression of a major virulence factor, the Type 3 Secretion System (T3SS), thus increasing T3SS expression. Deletion of purR, or K24E or K55E mutation, increased EHEC adherence to cells and colonization of infant rabbits. Using mice treated with streptomycin to deplete succinate, or colonized with succinate-producing Prevotella copri to increase succinate levels, we showed that microbiota-derived succinate increased succinylation of PurR to promote virulence of Citrobacter rodentium, a model for EHEC, in mice. Lastly, we identified CitC as the succinyltransferase required for PurR modification.

Antimicrobial activity of immobilized mycocins in sodium alginate on fecal coliforms

Wickerhamomyces anomalus is a yeast-producing mycocins and has antimicrobial action. Escherichia coli is the predominant bacterium of the coliforms group; its presence in water indicates fecal contamination, being used as an indicator of microbiological analyses. The immobilization of cells and substances demonstrates great potential for biotechnological applications. This work aimed to assess the activity of free and immobilized mycocins, obtained from W. anomalus, against E. coli strains and fecal coliforms. The mycocins were immobilized in different concentrations of sodium alginate and calcium chloride and tested to verify the antimicrobial activity against the E. coli strain and fecal coliforms present in water samples. The mycocins were able to inhibit all strains used in broth microdilution. Considering the problem of multidrug-resistant antibiotic strains and the need for new alternatives to improve the quality of water and sewage effluents, these results demonstrate a possible application as an alternative to an antimicrobial agent.

Emergent Escherichia coli of the highly virulent B2-ST1193 clone producing KPC-2 carbapenemase in ready-to-eat vegetables

OBJECTIVES

Critical priority carbapenem-resistant pathogens constitute a worldwide public health problem. Escherichia coli (E. coli) ST1193 is an emerging high-risk clone that demonstrates prolonged gut persistence, and association with community-onset urinary and bloodstream infections. The purpose of this study is to report microbiological and genomic data on the emergence of KPC-2-producing E. coli ST1193 in ready-to-eat (RTE) vegetables.

METHODS

RTE vegetables were purchased from markets in southeastern Brazil. Epiphytic and endophytic Gram-negative bacteria displaying resistance to broad-spectrum beta-lactams were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Whole-genome sequence was conducted using the Illumina NextSeq platform. Antimicrobial susceptibility, conjugation, and acid tolerance assays were performed. Virulence behaviour was evaluated using the Galleria mellonella (G. mellonella) infection model.

RESULTS

Epiphytic KPC-2-producing E. coli belonging to pandemic ST1193 was identified in RTE arugula. Genomic analysis predicted clinically relevant genes conferring resistance to β-lactams, fluoroquinolones, hazardous heavy metals, pesticides, disinfectants, and chlorine sanitizer. The blaKPC-2 gene was carried by a conjugative IncF plasmid. Acid tolerance of E. coli KPC-2/ST1193 during exposure to pH 2.0 was confirmed, being associated with gadWX and ibaG pH tolerance genes, supporting survival to stomach acid prior to reaching the small intestine, and potential for a dietary mode of host colonization. Virulent behaviour was supported by wide virulome of the highly virulent phylogroup B2, whereas single nucleotide polymorphisms of core genes (cgSNP)-based phylogenomics revealed clonal relationship with healthcare-associated lineages circulating in the United States, China, Mexico, France, and Brazil.

CONCLUSIONS

We report the occurrence of KPC-2-producing E. coli of the highly virulent B2-ST1193 clone in RTE vegetables, highlighting a possible route of dissemination of the World Health Organization (WHO) priority pathogens to humans. © 2024 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.

Water quality and diarrhoeagenic Escherichia coli detection in surface Pampean aquatic systems

Many surface water systems are impacted by point source pollution from sewage discharges and industrial wastes, as well as diffuse pollution from agriculture and livestock farming, inducing a potential biohazard to human, animal, and environmental health. This study aimed to determine the presence of diarrhoeagenic Escherichia coli (DEC) pathotypes and their antibiotic resistance, as well as the bacteriological, physical, and chemical water quality conditions in two Pampean peri-urban rivers (Rojas and Salado rivers, Buenos Aires, Argentina) used for recreation. Additionally, we explored the impact of the surrounding land use on the water quality. In the Rojas (R) and Salado (S) rivers, wastewater discharges from treatment plants increased nutrient content and coliform abundances at specific sampling sites (R2 and S3) and downstream (R3 and S4, respectively). Coliform abundances correlated with ammoniacal nitrogen concentrations, both exceeding recreational use guidelines. Out of 36 samples positive for DEC virulence factors, 11 DEC strains were isolated (5 enteroaggregative, 3 enteropathogenic, 1 shigatoxigenic-stx1/stx2, 1 shigatoxigenic-stx2, 1 hybrid enteroaggregative-enterotoxigenic). Six strains were resistant to one or more antibiotics. Our results suggest that differences in E. coli pathotypes between the two rivers and the water quality of each sampling site are linked to the surrounding land use, evidencing both diffuse and point source pollution.

Binding of small molecules at the P-stalk site of ricin A subunit trigger conformational changes that extend into the active site

Ricin is a category B agent for bioterrorism, and Shiga toxins are the primary virulence factors of Shiga toxin (Stx) producing Escherichia coli. Ricin and Stxs bind the ribosomal P-stalk proteins to depurinate the sarcin/ricin loop on the eukaryotic ribosome and inhibit translation. Both toxins are prime targets for therapeutic intervention because no effective therapy exists for ricin intoxication or Shiga toxin producing Escherichia coli infection. Binding of ricin toxin A subunit (RTA) to the ribosomal P-stalk stimulates depurination of the sarcin/ricin loop by an unknown mechanism. We previously identified compounds that bind the P-stalk pocket of RTA and inhibit catalytic activity. Here we characterize a second-generation lead compound, which binds the P-stalk pocket of RTA with over 30-fold improved affinity relative to the original compound and inhibits the cytotoxicity of ricin holotoxin in Vero cells with no apparent cellular toxicity by itself. This compound also shows protection against Stx2A1. X-ray crystal structure of RTA-inhibitor complexes suggests that the orientation of the carboxylic acid influences the inhibitor contacts at the P-stalk site of RTA and contributes to inhibitor potency. The structural changes triggered at the P-stalk site of RTA were validated by solution NMR-based chemical shift perturbation analysis. A key finding by NMR is that binding-induced conformational changes extend beyond the P-stalk site to residues in the active site cleft of RTA. Collectively, these results provide valuable new insight into the conformational flexibility in the C-terminal domain of RTA and its potential role in mediating the remarkable catalytic activity of ricin.

Association of iron-acquisition-related genes and milk lactoferrin concentration with the growth of Escherichia coli and Klebsiella pneumoniae in milk of dairy cows

Although the iron-acquisition systems of Escherichia coli and Klebsiella pneumoniae are known to be important for pathogenicity, the interaction between the antimicrobial potential of lactoferrin (LF) and bacterial pathogenesis via iron uptake systems in bovine mastitis is still unknown. This study aimed to evaluate the effects of the LF concentration in milk and the bacterial iron-acquisition system on bacterial growth in unpasteurized raw milk from cows. Twenty-four strains of E. coli and 20 strains of K. pneumoniae, including mastitis-derived and environmentally derived strains, were used. The growth potential of these strains was tested by incubation with unpasteurized raw whole milk and cell-free skim milk from a total of 30 quarters. The LF concentration in milk and somatic cell counts (SCCs) were measured as host factors, whereas ferric citrate, siderophores, ferrous iron, and heme iron acquisition-related genes were detected as pathogen-related factors. For E. coli, strains with fecA grew better in milk, whereas host factors, including LF levels and the SCC in milk, did not affect bacterial growth in milk. In K. pneumoniae, the presence of fecA was also related to its ability to grow in milk. LF levels and SCCs in milk were significantly and negatively correlated with bacterial counts at 6 h in the milk growth experiment. These results suggested that the ferric-citrate-uptake systems of E. coli and K. pneumoniae may strongly contribute to their proliferation in mammary glands in dairy cows, whereas a high LF concentration in milk may successfully inhibit the growth of K. pneumoniae.

Development of protective egg yolk immunoglobulins (IgY) targeting CfaB, LTB, and EtpA recombinant proteins of Enterotoxigenic Escherichia coli (ETEC) for inhibiting toxin activity and bacterial adherence

Enterotoxigenic Escherichia coli (ETEC) stands as a prevalent bacterial cause of global diarrheal incidents. ETEC's primary virulence factors encompass the B subunit of the Heat Labile Enterotoxin, along with the adhesion factors CfaB and EtpA. In this study, we isolated IgY antibodies against the three virulence factors individually, in pairs, and as triple cocktails. The in vitro efficacy of these IgY antibodies was examined, focusing on inhibiting heat-labile enterotoxin (LT) toxin cytotoxicity and impeding ETEC adherence to HT29 cells. Assessing the impact of IgY-treated bacteria on intestinal epithelial cells utilized the standard ileal loop method. Results demonstrated that the anti-LTB IgY antibody at 125 µg/ml and IgY antibodies from double and tertiary cocktails at 200 µg/ml effectively inhibited LT toxin attachment to the Y1 cell line. Pre-incubation of HT29 intestinal cells with specific IgYs reduced bacterial attachment by 59.7%. In the ileal loop test, toxin neutralization with specific IgYs curtailed the toxin's function in the intestine, leading to a 74.8% reduction in fluid accumulation compared to control loops. These findings suggest that egg yolk immunoglobulins against recombinant proteins LTB, CfaB, and EtpA, either individually or in combination, hold promise as prophylactic antibodies to impede the functioning of ETEC bacteria.

Insulin receptor tyrosine kinase substrate in health and disease (Review)

Insulin receptor (IR) tyrosine kinase substrate (IRTKS) was first identified >20 years ago as a tyrosine‑phosphorylated IR substrate and subsequently characterized as a protein containing an inverse‑Bin‑amphiphysin‑Rvs domain. Subsequent research has shown that IRTKS functions as a scaffold protein with multiple domains, which results in diverse functions in a variety of cell activities. For example, IRTKS plays roles in regulating the formation of membrane protrusions; triggering pathogen‑driven actin assembly; modulating insulin signaling, antiviral immunity and embryonic development; and promoting tumor occurrence and progression. It is also a candidate forensic biomarker of hypothermia. Nevertheless, a systematic summary of the biological functions of IRTKS and its underlying molecular mechanism is lacking. Therefore, the present review provides a comprehensive summary of the latest advancements in IRTKS research, thereby establishing a framework for understanding the contribution of IRTKS to diverse cell processes.

Genetic Determinants of Carbapenem and Fluoroquinolone Resistance in Escherichia coli Isolates of Clinical Origin

BACKGROUND

Antimicrobial resistance has emerged as a global public health challenge, leading to higher mortality rates from infections that were once treatable with antibiotics. In this study, we assessed the susceptibility of Escherichia coli strains isolated from clinical samples to carbapenems and fluoroquinolones and screened for genetic determinants mediating resistance.

MATERIALS AND METHODS

This retrospective study included 46 E. coli isolates retrieved from the stock culture collection at the Molecular Biology and Biotechnology Department of the Nigerian Institute of Medical Research. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disc diffusion method, and molecular techniques were employed to detect genetic determinants of antimicrobial resistance.

RESULTS

The E. coli isolates exhibited high resistance to fluoroquinolones, with 72% resistant to ciprofloxacin and 52% to levofloxacin. Resistance to carbapenems was relatively low, with 4% resistant to imipenem and 11% to meropenem. The prevalence of the genetic determinants gyrA, gyrB, and parC, which mediate fluoroquinolone resistance, was 26%, 24%, and 15%, respectively. blaOXA-48 and blaNDM, which mediate carbapenem resistance, were detected in only two isolates. Some isolates harbored plasmids ranging from 5 kb to 16 kb; however, no plasmid-mediated genetic determinants conferring fluoroquinolone resistance were identified.

CONCLUSION

This study revealed a high level of resistance to fluoroquinolones, emphasizing the need for judicious use of antibiotics, particularly those with low resistance rates. Continuous surveillance is essential to monitor emerging trends in resistance among bacterial pathogens.

Risk of Invasive Escherichia coli (E. coli) Disease After Elective Urologic Procedures Among Older Adults in the United States

INTRODUCTION

Little is known about the risk of invasive E. coli disease (IED) after elective urologic procedures. We estimated the risk of IED after selected urologic procedures in patients with or without antibiotic prophylaxis, and in controls with no urologic or other surgical procedures.

METHODS

The Komodo Research Database (01/01/2021-06/30/2023) was used to identify patients ≥ 60 years old with selected urological procedures (index: first urologic procedure date) and randomly selected controls without surgical procedures (index: random date). Patients with urologic procedures were classified into two cohorts based on whether or not they received antibiotic prophylaxis within 14 days prior to and on index date. Entropy balancing adjusted for differences between groups in selected patient characteristics over 6 months pre-index (baseline). IED rates within 30 days post-index were assessed based on recorded diagnosis of E. coli sepsis (ICD-10-CM: A41.51); odds ratios (OR) were estimated using weighted logistic regression. Sensitivity analyses within 90 days and using broader claims-based algorithm for IED were performed.

RESULTS

Overall, 141,418 patients had urologic procedures with antibiotic prophylaxis, 200,062 had them without antibiotic prophylaxis, and 424,254 had no procedures. Within 30 days post-index, IED rates were 0.48% and 0.72% among patients with or without antibiotic prophylaxis, respectively, vs. 0.02% among those without any procedures. Among patients with urologic procedures,  > 70% of IED events occurred within 30 days. Patients who had urologic procedures without prophylaxis had a higher risk of developing IED than those with prophylaxis (OR = 1.50, 95% confidence interval [CI: 1.37-1.65]), while patients without any procedures had a lower risk than those with urologic procedures and prophylaxis (OR = 0.04, 95% CI [0.03-0.05]). Similar results were obtained in sensitivity analyses.

CONCLUSIONS

Urologic procedures were associated with an increased IED risk even with antibiotic prophylaxis. Results suggest an unmet need for additional preventative measures to reduce the burden of IED after urologic procedures.

The Role of Quorum Sensing in Phage Lifecycle Decision: A Switch Between Lytic and Lysogenic Pathways

Phages, the most abundant and diverse lifeforms on Earth, require strict parasitism for survival. During infection, temperate phages integrate both intracellular and extracellular host information to decide between lysis and lysogeny for replication. While various environmental and physiological factors influence the lysis-lysogeny decision, recent insights into phage-bacterium interactions reveal phages' ability to communicate with and influence bacteria, leveraging the host's quorum sensing system or small molecular signals. This article provides a succinct overview of current research advancements in this field, enhancing our understanding of phage-host dynamics and providing insights into bacteria's multicellular behavior in antiviral defense.

When E. coli strikes: a necropsy analysis of a juvenile giraffe's fatal infection

BACKGROUND

As bacterial infections pose a major health risk to captive populations, disease prevention and management play a crucial role in the ex situ conservation of giraffes (Giraffa camelopardalis). This study describes the case of a giraffe that developed septicemia after an umbilical cord infection caused by Escherichia coli. To our knowledge, pathological changes in diseased giraffes caused by E. coli, which is an opportunistic pathogenic organism, have not been reported. This is the first report presenting an analysis of necropsies and subsequent microbiological investigations.

CASE PRESENTATION

The baby giraffe's mother died shortly after birth, so it had to be fed milk powder. The giraffe was healthy at first but developed symptoms like depression, loss of appetite, and lameness at 8 days old. At 14 days of age, the juvenile giraffe showed astasia and gradually died, with a disease course of 7 days. Postmortem examination revealed opisthotonus and navel swelling. Serofibrinous arthritis, serofibrinous necrotizing inflammation of periarticular soft tissue, serous omphalitis, and severe adventitia hemorrhage of the umbilical artery were observed. Severe serofibrinous pericarditis, pleuritis, and peritonitis were also observed. The interstitium of the pulmonary lobule widened because it was filled with a pale yellow translucent gelatinous exudate. Histopathologically, the calf had diffuse serous interstitial pneumonia, serous necrotizing umbilical arteritis, degenerative hepatitis with mild fibrosis, degenerative nephritis, hemorrhagic lymphadenitis, necrotizing enteritis, and necrotizing thyroiditis. Blue-stained clumps of bacteria of varying sizes and neutrophil infiltration were scattered or diffused in the interstitial connective tissue and edematous serosa of all tissues and organs, as well as in small vessels and lymphatic vessels, which were filled with many neutrophils (lymphatic spread). Single gram-negative Escherichia coli were cultured from all tissues of the animal. Polymerase chain reaction results of 16S rRNA of the isolated Escherichia coli had 99.79% homology to KJB03889.1.

CONCLUSIONS

The gross, histopathologic, microscopic, and polymerase chain reaction sequencing features reported in a juvenile giraffe were consistent with colibacillosis, which is a rare disease of giraffes. The gross, histopathologic, microscopic, and polymerase chain reaction sequencing features reported in a juvenile giraffe. This case serves as a paradigmatic illustration of a giraffe suffering from neglect and inadequate treatment, leading to severe consequences. In instances of giraffe Escherichia coli septicemia, it is imperative to thoroughly assess for underlying diseases, particularly in the absence of obvious predisposing factors. The rise of multidrug resistant organisms has constrained the efficacy of empirical antibiotic treatment, highlighting the importance of promptly conducting culture and sensitivity testing and employing antibiotic therapy guided by susceptibility results.

The Therapeutic Potential of Gut-Microbiota-Derived Metabolite 4-Phenylbutyric Acid in Escherichia coli-Induced Colitis

Pathogenic Escherichia coli (E. coli) is a widely distributed pathogen that can cause varying degrees of zoonotic diseases, and infected animals often experience intestinal inflammation accompanied by diarrhea and dysbiosis. Previously, for the first time, we isolated Escherichia coli primarily of type B2 from a large-scale dairy farm in Yunnan, China. The 16s rRNA sequencing showed significant differences in the gut microbiota of calves infected with B2 E. coli, with higher abundance of harmful bacteria and lower abundance of beneficial bacteria compared with healthy calves. The metabolomics indicated that the concentrations of oxoadipic acid, 16-oxopalmitate, oerillyl alcohol, palmitoleic acid, and 4-phenylbutyrate (4-PBA) were significantly higher in the healthy group than in the infected group. The mouse model was established to assess the regulatory effect of 4-PBA on E. coli-induced colitis. Both oral administration of 4-PBA and fecal microbiota transplantation (FMT) had strong resistance to E. coli infection, improved survival rate and body weight, reduced intestinal tissue damage, decreased the levels of pro-inflammatory cytokines (TNF-α, IL-6, and IL-1β), and restrained TLR4/MyD88/NF-κB pathway. Our study demonstrated that 4-PBA could relieve E. coli-induced colitis by improving gut microbiota structure and inhibiting the expression of pro-inflammatory cytokines through the TLR4/MyD88/NF-κB pathway. The present finding reveals the therapeutic potential of the gut-microbiota-derived metabolite 4-PBA for the treatment of colitis caused by E. coli.

Lineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli

BACKGROUND

The opportunistic bacterium Escherichia coli can invade normally sterile sites in the human body, potentially leading to life-threatening organ dysfunction and even death. However, our understanding of the evolutionary processes that shape its genetic diversity in this sterile environment remains limited. Here, we aim to quantify the frequency and characteristics of homologous recombination in E. coli from bloodstream infections.

RESULTS

Analysis of 557 short-read genome sequences revealed that the propensity to exchange DNA by homologous recombination varies within a distinct population (bloodstream) at narrow geographic (Dartmouth Hitchcock Medical Center, New Hampshire, USA) and temporal (years 2016 - 2022) scope. We identified the four largest monophyletic sequence clusters in the core genome phylogeny that are represented by prominent sequence types (ST): BAPS1 (mainly ST95), BAPS4 (mainly ST73), BAPS10 (mainly ST131), BAPS14 (mainly ST58). We show that the four dominant clusters vary in different characteristics of recombination: number of single nucleotide polymorphisms due to recombination, number of recombination blocks, cumulative bases in recombination blocks, ratio of probabilities that a given site was altered through recombination and mutation (r/m), and ratio of rates at which recombination and mutation occurred (ρ/θ). Each sequence cluster contains a unique set of antimicrobial resistance (AMR) and virulence genes that have experienced recombination. Common among the four sequence clusters were the recombined virulence genes with functions associated with the Curli secretion channel (csgG) and ferric enterobactin transport (entEF, fepEG). We did not identify any one recombined AMR gene that was present in all four sequence clusters. However, AMR genes mdtABC, baeSR, emrKY and tolC had experienced recombination in sequence clusters BAPS4, BAPS10, and BAPS14. These differences lie in part on the contributions of vertically inherited ancestral recombination and contemporary branch-specific recombination, with some genomes having relatively higher proportions of recombined DNA.

CONCLUSIONS

Our results highlight the variation in the propensity to exchange DNA via homologous recombination within a distinct population at narrow geographic and temporal ranges. Understanding the sources of the genetic variation in invasive E. coli will help inform the implementation of effective strategies to reduce the burden of disease and AMR.

The Results of Intestinal Villi of Laying Hens Exposed With Avian Pathogenic Escherichia coli (APEC) After Giving Citric Acid and Dextrose

The condition known as colibacillosis is still very common in Indonesia, which means that laying hens affected by it are unable to achieve their peak egg production phase. Instead, their egg production is delayed and more susceptible to infection by other diseases. The goal of this study is to determine if the mixture of citric acid and dextrose can inhibit the growth of Avian Pathogenic Escherichia coli (APEC) bacteria in laying hens, ultimately leading to the control of colibacillosis cases in Indonesia. A total of 240 laying hen heads in all were split up into 6 treatments, each with 40 replications.The group received the following treatments: T0 is a treatment for laying hens free of APEC infection and they are given no drink that contains any mixture of citric acid and dextrose. T0 (-) is a treatment for laying hens free of APEC infection but a drink mixture of citric acid and dextrose is administered at a dose of 1 g/2.5 L of drinking water. T0 (+) is a treatment for laying hens infected with APEC up to 2 mL/head orally (3 × 108 CFU/mL) and given a drink without the mixture of citric acid and dextrose. T1 is a treatment for laying hens infected with APEC up 2 mL/head orally (3 × 108 CFU/mL) and given a mixture of citric acid and dextrose at a dose of 1 g/1.25 L of drinking water. T2 is a treatment for laying hens infected with APEC up to 2 mL/head orally (3 × 108 CFU/mL) and given a mixture of citric acid and dextrose at a dose of 1 g/2.5 L of drinking water. T3 is a treatment for laying hens infected with APEC up to 2 mL/head orally (3 × 108 CFU/mL) and given a mixture of citric acid and dextrose at a dose of 1 g/3.75 L of drinking water. The results of this study stated that the mixture of citric acid and dextrose showed a significant decrease in the appearance of the intestinal villi of laying hens, because the results were actually less good compared to the treatment infected with APEC. It is suspected that the dose given may still be excessive in concentration. This can be seen from the dose with the highest concentration range (T1) to the lowest (T3) which showed an image of intestinal villi that had a tendency to improve. Therefore, further research and studies are needed regarding the use of a mixture of citric acid and dextrose in laying hens infected with APEC with a lower dose.

The Antimicrobial Peptide D-CONGA-Q7 Eradicates Drug-Resistant E. coli by Disrupting Bacterial Cell Membranes

Escherichia coli (E. coli) is a zoonotic bacterium widespread in the environment, highly transmissible, and responsible for significant economic losses and millions of cases of illness annually. The rise of multidrug-resistant (MDR) strains has rendered last-line antibiotics such as polymyxin and meropenem ineffective, making the development of new antibiotics urgent. Although D-CONGA-Q7 has broad-spectrum bactericidal activity, its underlying mechanism remains poorly understood. In this study, we used in vitro and in vivo experiments to demonstrate that D-CONGA-Q7 effectively kills both antibiotic-sensitive and multidrug-resistant strains of E. coli. D-CONGA-Q7 disrupts the cell membranes of Gram-negative bacteria, and the treatment of E. coli strain LN175 with D-CONGA-Q7 resulted in a significant up-regulation of the Mlac gene, suggesting that D-CONGA-Q7 may interact with phospholipids in the cell membrane. Furthermore, in treating K88-induced bacterial enteritis in the small intestine, D-CONGA-Q7 significantly reduced intestinal inflammation. In conclusion, this study provides a novel approach to combat drug-resistant E. coli.

Quinolone Resistance Genes qnr, aac(6')-Ib-cr, oqxAB, and qepA in Environmental Escherichia coli: Insights into Their Genetic Contexts from Comparative Genomics

Previous studies have reported the occurrence of transferable quinolone resistance determinants in environmental Escherichia coli. However, little is known about their vectors and genetic contexts. To gain insights into these genetic characteristics, we analyzed the complete genomes of 53 environmental E. coli isolates containing one or more transferable quinolone resistance determinants, including 20 sequenced in this study and 33 sourced from RefSeq. The studied genomes carried the following transferable quinolone resistance determinants alone or in combination: aac(6')-Ib-cr, oqxAB, qepA1, qnrA1, qnrB4, qnrB7, qnrB19, qnrD1, qnrS1, and qnrS2, with qnrS1 being predominant. These resistance genes were detected on plasmids of diverse replicon types; however, aac(6')-Ib-cr, qnrS1, and qnrS2 were also detected on the chromosome. The genetic contexts surrounding these genes included not only those found in clinical isolates but also novel contexts, such as qnrD1 embedded within a composite transposon-like structure bounded by Tn3-derived inverted-repeat miniature elements (TIMEs). This study provides deep insights into mobile genetic elements associated with transferable quinolone resistance determinants, highlighting the importance of genomic surveillance of antimicrobial-resistant bacteria in the environment.

Effects of fructooligosaccharides and Lactobacillus reuteri on the composition and metabolism of gut microbiota in students

Fructooligosaccharides (FOSs) and Lactobacillus reuteri have shown great potential in treating gastrointestinal diseases by regulating gut microbiota and metabolites. However, the synergistic effect between these two remains unclear. In this study, an in vitro fermentation model was constructed to investigate the regulatory effects of FOSs and L. reuteri on the gut microbiota of healthy student populations. After 24 hours of fecal fermentation, the results indicated that the experimental group added with FOSs had increased relative abundances of Bifidobacterium and Lactobacillus, while it exhibited lower relative abundances of Escherichia-Shigella and Bacteroides. Conversely, the groups added with L. reuteri had higher relative abundances of Bacillus and unclassified_c_Bacilli. The results of microbial metabolism revealed that the addition of FOSs produced a large amount of acetic acid, but reduced the contents of propionic acid, butyric acid, isobutyric acid, and isovaleric acid, along with reducing the production of H2, H2S and NH3. In contrast, the addition of L. reuteri had no significant effect on metabolism. Compared to the single additions, the combination of FOSs and L. reuteri had its advantages and had a more balanced microbial structure and metabolic regulation similar to the addition of FOSs alone. Additionally, correlation analysis revealed a negative correlation between gas production and Bifidobacterium, Lactobacillus, and Bacillus, and a positive correlation with Escherichia-Shigella and Bacteroides. Moreover, the formation of acetic acid was positively correlated with Bifidobacterium and negatively correlated with Escherichia-Shigella. These findings demonstrated that the combination of FOSs and L. reuteri can effectively synergistically regulate the fecal microbiome of students. This study can provide a theoretical reference for the precise development of functional foods. However, the regulatory mechanisms need further in-depth investigation.

Cross-Sectional Assessment on Carbapenem-Resistant Gram-Negative Bacteria Isolated from Patients in Moldova

Information on the molecular epidemiology and carbapenem resistance mechanisms in Gram-negative bacterial isolates in Moldova is scarce. To close this knowledge gap, carbapenem-resistant Gram-negative bacteria were collected over an 11-month period in a routine diagnostic laboratory in Moldova. Antimicrobial susceptibility was phenotypically and genotypically assessed. Phylogenetic relationships were investigated and multi-locus sequence types were provided. The assessment indicated several clusters of phylogenetically closely related carbapenem-resistant Klebsiella pneumoniae (sequence types ST101, ST395 and ST377), Acinetobacter baumannii (ST2, ST19 and ST78) and Pseudomonas aeruginosa (ST357 and ST654) isolates next to a number of less frequently observed species and sequence types. A phylogenetic relationship to characterized isolates from neighboring Ukraine could be confirmed. Identified carbapenemase genes comprised blaOXA-23, blaOXA-72 and blaGES-11 in A. baumannii, blaKPC-3, blaNDM-1 and blaOXA-48 in K. pneumoniae, as well as blaVIM-2 in Pseudomonas aeruginosa. In conclusion, the assessment suggested the spread of carbapenem-resistant Gram-negative bacteria in Moldova which were partly pre-described from neighboring Ukraine, as well as likely spill-over events, facilitating the regional spread of carbapenem-resistant clones. Several isolates with very high genomic similarity further support the hypothesis of likely regional transmission events driven by several evolutionary successful clonal lineages.

Role of E-cadherin in epithelial barrier dysfunction: implications for bacterial infection, inflammation, and disease pathogenesis

Epithelial barriers serve as critical defense lines against microbial infiltration and maintain tissue homeostasis. E-cadherin, an essential component of adherens junctions, has emerged as a pivotal molecule that secures epithelial homeostasis. Lately, its pleiotropic role beyond barrier function, including its involvement in immune responses, has become more evident. Herein, we delve into the intricate relationship between (dys)regulation of epithelial homeostasis and the versatile functionality of E-cadherin, describing complex mechanisms that underlie barrier integrity and disruption in disease pathogenesis such as bacterial infection and inflammation, among others. Clinical implications of E-cadherin perturbations in host pathophysiology are emphasized; downregulation, proteolytic phenomena, abnormal localization/signaling and aberrant immune reactions are linked with a broad spectrum of pathology beyond infectious diseases. Finally, potential therapeutic interventions that may harness E-cadherin to mitigate barrier-associated tissue damage are explored. Overall, this review highlights the crucial role of E-cadherin in systemic health, offering insights that could pave the way for strategies to reinforce/restore barrier integrity and treat related diseases.

Genome Sequencing and Assembly of Enterotoxigenic Escherichia coli E9034A: Role of LngA, CstH, and FliC in Intestinal Cell Colonization and the Release of the Proinflammatory Cytokine IL-8

Enterotoxigenic Escherichia coli (ETEC) produces two types of enterotoxins, LTs and STs, as well as several colonization factors (CFs), including CS21, CS3 fimbriae, and flagellar structures. This study investigated how these structures contribute to ETEC colonization and the immune response in HT-29 and HuTu-80 intestinal cells. ETEC strains with single, double, and triple mutations in the lngA, cstH, and fliC genes were generated and confirmed using PCR and Western blotting. The colonization of HT-29 and HuTu-80 intestinal cells by the ETEC E9034A strain, which was fully sequenced using a hybrid approach involving both Illumina and Oxford Nanopore technologies, was used to generate the mutant and recombinant proteins. The colonization and adherence of E9034A and its mutants were assessed through colony-forming unit (CFU) counts. Cytokine levels were assessed using flow cytometry and analyzed via FlowJo 7.6.1. Quantitative analysis revealed that the absence of the lngA, cstH, and fliC genes significantly (p < 0.01) reduced ETEC adherence to HT-29 and HutU-80 cells. In addition, only ETEC strains expressing the FliC protein induced IL-8 secretion. These findings suggest that LngA, CstH, and FliC in ETEC E9034A enhance adherence to intestinal cells and trigger the release of IL-8.

Targeting Enterotoxins: Advancing Vaccine Development for Enterotoxigenic Escherichia coli ETEC

Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease worldwide, particularly in children in low- and middle-income countries. Its ability to rapidly colonize the intestinal tract through diverse colonization factors and toxins underpins its significant public health impact. Despite extensive research and several vaccine candidates reaching clinical trials, no licensed vaccine exists for ETEC. This review explores the temporal and spatial coordination of ETEC virulence factors, focusing on the interplay between adherence mechanisms and toxin production as critical targets for therapeutic intervention. Advancements in molecular biology and host-pathogen interaction studies have uncovered species-specific variations and cross-reactivity between human and animal strains. In particular, the heat-labile (LT) and heat-stable (ST) toxins have provided crucial insights into molecular mechanisms and intestinal disruption. Additional exotoxins, such as EAST-1 and hemolysins, further highlight the multifactorial nature of ETEC pathogenicity. Innovative vaccine strategies, including multiepitope fusion antigens (MEFAs), mRNA-based approaches, and glycoconjugates, aim to enhance broad-spectrum immunity. Novel delivery methods, like intradermal immunization, show promise in eliciting robust immune responses. Successful vaccination against ETEC will offer an effective and affordable solution with the potential to greatly reduce mortality and prevent stunting, representing a highly impactful and cost-efficient solution to a critical global health challenge.

Biochemical characterization of the Escherichia coli surfaceome: a focus on type I fimbriae and flagella

The Escherichia coli surfaceome consists mainly of the large surface organelles expressed by the organism to navigate and interact with the surrounding environment. The current study focuses on type I fimbriae and flagella. These large polymeric surface organelles are composed of hundreds to thousands of subunits, with their large size often preventing them from being studied in their native form. Recent studies are accumulating which demonstrate the glycosylation of surface proteins or virulence factors in pathogens, including E. coli. Using biochemical and glycobiological techniques, including biotin-hydrazide labeling of glycans and chemical and glycosidase treatments, we demonstrate (i) the presence of a well-defined and chemically resistant FimA oligomer in several strains of pathogenic and non-pathogenic E. coli, (ii) the major subunit of type I fimbriae, FimA, in pathogenic and laboratory strains is recognized by concanavalin A, (iii) standard methods to remove N-glycans (PNGase F) or a broad-specificity mannosidase fail to remove the glycan structure, despite the treatments resulting in altered migration in SDS-PAGE, (iv) PNGase F treatment results in a novel 32 kDa band recognized by anti-FliC antiserum. While the exact identity of the glycan(s) and their site of attachment currently elude detection by conventional glycomics/glycoproteomics, the current findings highlight a potential additional layer of complexity of the surface (glyco) proteome of the commensal or adhesive and invasive E. coli strains studied.

Lack of basic sanitation influence on the enteropathogen presence in a river of the Brazilian Legal Amazon

Water systems globally are declining in water quality, largely due to anthropogenic activities, with freshwater contamination reaching unprecedented levels. The Brazilian Legal Amazon (BLA), holding 13.56% of the world's fresh water, is affected due to the lack of basic sanitation. This study assesses the quality of the Lontra River, in southeastern BLA, by monitoring physicochemical and microbiological parameters and detecting DEC E. coli and Salmonella spp. over 16 months, following current regulations. The data were analyzed using Pearson's chi-square and Fisher's exact test (p ≤ 0.05), Kruskal-Wallis test (p ≤ 0.05), with Tukey post hoc (α = 0.05), and Spearman's correlation (p ≤ 0.05). Results showed pH levels were below the optimal range established by Brazilian water quality indices and legislation, with seasonal variations, and dissolved oxygen also below acceptable limits. Thermotolerant coliforms (TtC) exceeded thresholds, signaling microbiological contamination. DEC E. coli and Salmonella spp. were detected in 32.14% and 67.85% of samples, respectively, even in those with low TtC levels. No correlation was found between TtC and pathogen presence, suggesting that meeting minimum water quality standards does not guarantee the absence of pathogenic microorganisms. These findings reveal significant environmental and public health risks related to surface water quality in the Lontra River. Also highlight discrepancies between regulatory water quality standards and the actual conditions observed, underscoring the need for regionally adapted water monitoring and management practices to protect both environmental and public health in the BLA.

Bacillus subtilis MZ-01 alleviates diarrhea caused by ETEC K88 by reducing inflammation and promoting intestinal health

AIMS

The purpose of this study was to investigate the effects of Bacillus subtilis supplementation on the health of weaned piglets and whether B. subtilis supplementation can reduce the damage of piglets induced by ETEC K88.

METHODS AND RESULTS

The experiment was designed with a 2 × 2 factorial arrangement, comprising the control group, B. subtilis (PRO) group, Escherichia coli K88 (ETEC) group, and B. subtilis + ETEC (PRO + ETEC) group. Regardless of the presence of ETEC, the addition of PRO increased the piglets' final body weight, average daily gain, and daily feed intake. Additionally, PRO primarily achieves a reduction in heat-stable enterotoxin (ST) levels, suppresses the expression of NF-κB, TLR4, and MyD88 mRNA in the jejunum and ileum, lowers pro-inflammatory factors in the blood and small intestine, enhances the expression of tight junction proteins in the small intestine, improves the composition of the colonic microbiota, increases colonic short-chain fatty acid contents, thereby alleviating diarrhea and mitigating bodily damage caused by ETEC K88 infection.

CONCLUSION

The addition of B. subtilis MZ-01 alleviated ETEC K88-induced piglet diarrhea by reducing ST levels, decreasing pro-inflammatory factors in the blood and intestine, and enhancing the intestinal barrier and tight junction proteins.

Epidemiological and molecular characteristics of extraintestinal pathogenic escherichia coli isolated from diseased cattle and sheep in Xinjiang, China from 2015 to 2019

Escherichia coli has become a common causative agent of infections in animals, inflicting serious economic losses on livestock production and posing a threat to public health. Escherichia coli infection is common and tends to be complex in Xinjiang, a major region of cattle and sheep breeding in China. This study aims to explore the current status and molecular characteristics of Escherichia coli infection in cattle and sheep in Xinjiang, as part of the disease prevention and control strategy. Herein we isolated Extraintestinal pathogenic Escherichia coli (ExPEC) from the liver, spleen, lung, heart, and lymph nodes of infected cattle and sheep (Xinjiang, China), and phylogenetic grouping, serotyping, and multilocus sequence typing were performed to determine epidemic and molecular characteristics. We also assessed their biofilm formation ability. A total of 132 strains of ExPEC were identified from diseased cattle and sheep, belonging to 7 phylogenetic groups. A and B1 are advantageous groups. Further, 22 serogroups were found, with O101 (26/132), O154 (14/132), and O65 (8/132) being the predominant ones. Among the seven sequence types identified by multilocus sequence typing, ST10 was the most common, followed by ST23 and ST457. Of 132, 105 (79.5%) strains were able to form biofilms: 15 strains (11.4%) were strong, 28 (21.2%) were medium, and 62 (47%) were weak biofilm producers. These findings will contribute to a better understanding of the molecular epidemiology of ExPEC in Xinjiang, China, and can be applied to the development, prevention, and disease control of future diagnostic tools and vaccine.

Microbiome characterization of patients with Crohn disease and the use of fecal microbiota transplantation: A review

Inflammatory bowel disease is a chronic inflammatory condition predominantly affecting the intestines, encompassing both ulcerative colitis and Crohn disease (CD). As one of the most common gastrointestinal disorders, CD's pathogenesis is closely linked with the intestinal microbiota. Recently, fecal microbiota transplantation (FMT) has gained attention as a potential treatment for CD, with the effective reestablishment of intestinal microecology considered a crucial mechanism of FMT therapy. This article synthesizes the findings of population-based cohort studies to enhance our understanding of gut microbial characteristics in patients with CD. It delves into the roles of "beneficial" and "pathogenic" bacteria in CD's development. This article systematically reviews and compares data on clinical response rates, remission rates, adverse events, and shifts in bacterial microbiota. Among these studies, gut microbiome analysis was conducted in only 7, and a single study examined the metabolome. Overall, FMT has demonstrated a partial restoration of typical CD-associated microbiological alterations, leading to increased α-diversity in responders and a moderate shift in patient microbiota toward the donor profile. Several factors, including donor selection, delivery route, microbial state (fresh or frozen), and recipient condition, are identified as pivotal in influencing FMT's effectiveness. Future prospective clinical studies with larger patient cohorts and improved methodologies are imperative. In addition, standardization of FMT procedures, coupled with advanced genomic techniques such as macroproteomics and culture genomics, is necessary. These advancements will further clarify the bacterial microbiota alterations that significantly contribute to FMT's therapeutic effects in CD treatment, as well as elucidate the underlying mechanisms of action.

zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters

Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements, such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of evolutionary statistics for each inferred ortholog group. Importantly, in comparison to tools for visual exploration of homologous relationships between gene clusters, zol can scale to handle thousands of gene cluster instances and produce detailed reports that are easy to digest. To showcase fai and zol, we apply them for: (i) longitudinal tracking of a virus in metagenomes, (ii) performing population genetic investigations of BGCs for a fungal species, and (iii) uncovering evolutionary trends for a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.

Human microbiota peptides: important roles in human health

Covering: 1974 to 2024Human microbiota consist of a diverse array of microorganisms, such as bacteria, Eukarya, archaea, and viruses, which populate various parts of the human body and live in a cooperatively beneficial relationship with the host. They play a crucial role in supporting the functional balance of the microbiome. The coevolutionary progression has led to the development of specialized metabolites that have the potential to substitute traditional antibiotics in combating global health challenges. Although there has been a lot of research on the human microbiota, there is a considerable lack of understanding regarding the wide range of peptides that these microbial populations produce. Particularly noteworthy are the antibiotics that are uniquely produced by the human microbiome, especially by bacteria, to protect against invasive infections. This review seeks to fill this knowledge gap by providing a thorough understanding of various peptides, along with their in-depth biological importance in terms of human disorders. Advancements in genomics and the understanding of molecular mechanisms that control the interactions between microbiota and hosts have made it easier to find peptides that come from the human microbiome. We hope that this review will serve as a basis for developing new therapeutic approaches and personalized healthcare strategies. Additionally, it emphasizes the significance of these microbiota in the field of natural product discovery and development.

In situ dressing based on a D-π-A structured aggregation-induced emission photosensitizer for healing infected wounds

Photodynamic antimicrobial therapy (aPDT) can effectively kill bacteria without promoting drug resistance. However, the phototoxicity of photosensitizers in aPDT against normal cells hinders their practical applications. In this work, we report the utilization of an aggregation-induced emission (AIE)-active photosensitizer, DTTPB, to develop antibacterial dressing for effective eradication of both Gram-positive and Gram-negative bacteria. The D-π-A structure of DTTPB facilitates efficient ROS generation in the aggregate state, addressing the limitations of a traditional photosensitizer. Notably, DTTPB demonstrates good biocompatibility towards normal cells, which minimizes its phototoxicity to normal tissues. To demonstrate its practical implications, DTTPB is combined with Carbomer 940 to create an injectable hydrogel dressing (DTTPB@gel). DTTPB@gel not only adheres to wounds but also maintains the antimicrobial properties of DTTPB, which together contributes to its enhanced wound-healing performance. Biocompatibility and toxicity assessments confirm the safety of this novel material, highlighting its potential as a practical and effective treatment for bacterial infections in wounds. The results underscore the importance of innovative antimicrobial strategies in fighting against antibiotic resistance, paving the way for safer and more effective therapeutic options.

Genomic and Drug Resistance Profile of Bovine Multidrug-Resistant Escherichia coli Isolated in Kazakhstan

While studying the prevalence and profile of antibiotic resistance among E. coli isolated from the feces of calves with signs of colibacillosis, a strain with a wide spectrum of drug resistance was isolated. Whole-genome sequencing, followed by bioinformatic processing and the annotation of genes of this strain, showed that the genome has a total length of 4,803,482 bp and contains 4986 genes, including 122 RNA genes. A total of 31% of the genes are functionally significant and represent 26 functional groups. Additionally, 55 antibiotic resistance genes were revealed. A phenotypic drug-resistance study was performed according to CASFM and CLSI guidelines, which showed that the investigated strain was resistant to eight antibacterial drugs of different classes, including colistin. This is the first report on the AMR profile of an E. coli isolate obtained from a sick calf with evidence of escherichiosis in Kazakhstan. The provided information on the genome will be valuable in studying the evolution and development of antibiotic-resistant forms of E. coli and increase our knowledge of pathogenicity. It may also be a source for future comparative studies of the virulence and drug resistance of E. coli isolates.

Novel Cationic Bolaamphiphiles for Protein and DNA Binding, Gene Delivery, and Antimicrobial Applications

In this study, we have designed and developed a cationic bolaform C12-(2,3-dihydroxy-N, N-dimethyl-N-(2-ureidoethyl)propan-1-aminium chloride)2 (C12(DDUPAC)2) that is derived from biocompatible molecules. The bolaform C12(DDUPAC)2 has hydroxyl (OH) functionality at both the cationic head groups. The impact of head group structure on the self-assembly and effectiveness of gene transfection and antimicrobial activity was investigated and compared with that of the hydrochloride salt C12-(N, N-dimethyl-N-(2-ureidoethan-1-aminium chloride)2 (C12(DUAC)2) of its precursor molecule. The formation of spherical as well as rod-like self-assembled structures was found to occur above a relatively low critical aggregation concentration (CAC) by the bolaforms. The results of calorimetric measurements demonstrated thermodynamically favorable aggregation in water. Interaction studies of the cationic bolaforms with the calf thymus DNA revealed stronger binding of C12(DDUPAC)2 in comparison to C12(DUAC)2, which explained higher in vitro gene transfection efficiency of C12(DDUPAC)2 than C12(DUAC)2. Both bolaforms interact weakly with the bovine serum albumin protein. MTT-based in vitro cytotoxicity assay was performed and both bolaforms were found to have marginal cytotoxicity. Further, both bolaforms exhibit advantageous antibacterial activity against E. coli and potent antifungal activity against Fusarium oxysporum at high dosages.

Virulence of Bacteria Causing Mastitis in Dairy Cows: A Literature Review

Bovine mastitis, a prevalent disease in dairy farms, exerts a profound negative influence on both the health and productivity of dairy cattle, leading to substantial economic losses for the dairy industry. The disease is associated with different bacterial agents, primarily Gram-positive cocci (e.g., Staphylococcus spp., Streptococcus spp.) and Gram-negative bacilli (e.g., Escherichia coli, Klebsiella pneumoniae). These pathogens induce mastitis through diverse mechanisms, intricately linked to the virulence factors they carry. Despite previous research on the virulence factors of mastitis-causing bacteria in dairy cattle, there remains a significant gap in our comprehensive understanding of these factors. To bridge these gaps, this manuscript reviews and compiles research on the virulence factors of these pathogens, focusing on their roles in mammary tissue infection, immune evasion, adherence to mammary epithelial cells, and invasion and colonization of the mammary gland. These processes are analyzed in depth to provide a comprehensive framework to promote a deeper understanding of dairy pathogenic bacteria and their pathogenic mechanisms and to provide new insights into the control of mastitis in dairy cattle.

A novel small RNA regulates Locus of Enterocyte Effacement and site-specific colonization of enterohemorrhagic Escherichia coli O157:H7 in gut

Enterohemorrhagic Escherichia coli (EHEC) is a contagious foodborne pathogen that specifically colonizes the human large intestine, which is regulated by different environmental stimuli within the gut. Transcriptional regulation of EHEC virulence and infection has been extensively studied, while the posttranscriptional regulation of these processes by small RNAs (sRNAs) remains not fully understood. Here we present a virulence-regulating pathway in EHEC O157:H7, in which the sRNA EvrS binds to and destabilizes the mRNA of Z2269, a novel transcriptional regulator. In turn, Z2269 indirectly activates the expression of LEE (locus of enterocyte effacement) pathogenicity island through the master regulator Ler. Importantly, the expression of EvrS is modulated by environmental oxygen levels. EvrS also exhibits lower expression in the colon compared to the ileum, influencing the site-specific colonization of EHEC O157:H7 in mice. These results indicate that the oxygen status within the intestine may regulate the expression of EvrS, thereby modulating virulence factors of EHEC and contributing to successful infection in vivo. This study has broader implications for understanding sRNA functions in spatiotemporal virulence control of EHEC and may provide novel strategies to prevent EHEC infections.

Evaluation of the antibacterial activity of essential oils from oregano (Origanum vulgare) against Escherichia coli strains isolated from meat products

The objective of this study was to analyze the antimicrobial and anti-stick capacity of essential oil extracted from oregano (Origanum vulgare) in relation to various strains of Escherichia coli (Ec 41, Ec 42, Ec 44, Ec 45) isolated from meat products. Techniques such as Determination of Minimum Inhibitory Concentration were used (MIC) and Minimum Bactericidal Concentration (CBM). Furthermore, the method was used disk diffusion method to examine the interaction between O. vulgare essential oil and synthetic antibiotics. Determination of the Inhibitory Concentration was also carried out Minimum Adhesion (CIMA). The results indicated that O. vulgare oil demonstrated antimicrobial activity against the E. coli strains tested, with values of MIC ranging between 256 μg/mL and 512 μg/mL, and MBC values ranging between 256 μg/mL and 1.024 μg/mL. Regarding associations, it was observed that O. vulgare had an antagonistic effect towards certain antibiotics, mainly ampicillin, showing greater interference from the essential oil. Furthermore, the oil was effective in inhibiting the adherence of E. coli bacterial strains, demonstrating a more significant antibiofilm agent than 0.12% chlorhexidine digluconate, a commonly used antibacterial. In short, O. vulgare essential oil exhibited antimicrobial potential against E. coli strains isolated from meat products, suggesting which, upon more detailed investigations, could be used both in isolation or in combination with synthetic antibiotics to combat infections caused by this pathogen.

Exploring the antioxidant and antimicrobial properties of five indigenous Kenyan plants used in traditional medicine

Defined by the World Health Organization (WHO) as indigenous knowledge and practices used for maintaining health and treating illnesses, traditional medicine (TM) represents a rich reservoir of ancient healing practices rooted in cultural traditions and accumulated wisdom over centuries. Five indigenous Kenyan plant species traditionally used in African TM, named Afzelia quanzensis, Azadirachta indica, Gigasiphon macrosiphon, Grewia bicolor, and Lannea schweinfurthii, represent a valuable resource in healing practices, yet their chemical composition and bioactivity remain understudied. To depict a primary bio-chemical characterization of these plants, their antioxidant and antimicrobial features have been evaluated by the use of methods validated in this context. G. bicolor, and G. macrosiphon were found to have great potential as sources of bioactive metabolites, such as chlorophyll a (1456.29 µg/ g DW; 1104.33 µg/ g DW), chlorophyll b (712.48 µg/ g DW; 443.31 µg/ g DW), and carotenoids (369.71 µg/ g DW; 300 µg/ g DW) as well as phenols (31.78 mg GAE/g DW; 27.54 GAE/g DW), and exhibiting high antioxidant activity, according to TEAC, DPPH and FRAP assays. Additionally, L. schweinfurthii and G. macrosiphon demonstrated antimicrobial activity against the Gram-negative bacteria E. coli, as well as against Gram-positive ones, S. aureus and B. subtilis.

Luminescent Cu nanoclusters-encapsulated ZIF-8 as on-off-on fluorescent probe for efficient and selective quantification of E. coli

Rapid and accurate detection of Escherichia coli (E. coli) is critical for maintaining water quality, and protecting aquatic ecosystems and public health. This research focuses on the development of a Förster resonance energy transfer (FRET)-based "turn-on" fluorescent nanosensor for real time, sensitive detection of E. coli. Copper nanoclusters-encapsulated metal organic frameworks (CuNCs@ZIF-8) were sythesized as a fluorescent donor with excellent luminescence properties. Further, MnO2 nanospheres were synthesized as a receptor with good adsorption and quenching abilities. This novel nanoconjugate (CuNCs@ZIF-8@ MnO2) was employed for the construction of a sensitive, accurate, and rapid sensing platform against E. coli in water on the basis of p-benzoquinone/hydroquinone (p-BQ/HQ) redox pair formation. Fluorescence is quenched by energy transfer when MnO2 nanospheres are added to CuNCs@ZIF-8. Upon contact with E. coli, NADH-quinone reductase converts p-BQ to HQ, which reduces MnO2 to Mn2+, releasing the nanospheres and restoring fluorescence in the composite. Based on this FRET ON-OFF-ON fluorescent probe, E. coli can be detected across a broad concentration range (5 × 101 to 5 × 105 CFU/mL), with a detection limit as low as 8 CFU/mL within 50 min. The sensor's practicality was verified through the investigation of E. coli in real water samples, with recoveries in the range 94.3 to 106.5%. This approach offers an efficient method for on-site detection and quantification of E. coli in both environment and food safety domains.

Assessment of heat-killed E. coli expressing Chikungunya virus E2 protein as a candidate vaccine for dual protection against Chikungunya virus and E. coli

The Chikungunya virus (CHIKV) is a mosquito-borne virus with a long history of recurring epidemics transmitted through Aedes mosquitoes. The rapid spread of CHIKV has intensified the need for potent vaccines. Escherichia coli (E.coli), a vital part of human gut microbiota, is utilized in recombinant DNA technology for cloning. However, its high adaptability can lead to severe infections in humans. This study aimed to develop the candidate dual vaccine against CHIKV and E. coli. For this, we expressed the CHIKV E2 protein in the E. coli Rosetta Bl21 cells and the protein expression was confirmed by western blotting. The IgG immune response of the candidate vaccine was determined against CHIKV and E. coli by ELISA. Further, the potential of antibodies to neutralize CHIKV was evaluated via Tissue Culture Infectious Dose 50 (TCID50). We observed that cells expressing E2 protein with alum immunized mice serum showed a five-fold higher IgG immune response against CHIKV, compared to control cells. The CHIKV neutralization assay results showed a two-fold decrease in CHIKV TCID50 value after 12 hours and a three-fold reduction after 120 hours. Similarly, the vaccine formulation also elicited a significantly higher IgG immune response against E. coli. The results suggested that expressing CHIKV E2 protein in E. coli is a potential approach for generating an IgG immune response against CHIKV and E. coli both. This study proposes a faster, safer, and cost-effective recombinant protein-based vaccine development.

The pathogenicity traits of avian pathogenic Escherichia coli O25-ST131 associated with avian colibacillosis in Georgia poultry and their genotypic and phenotypic overlap with other extraintestinal pathogenic E. coli

AIMS

To characterize Escherichia coli O25 ST131 (O25-ST131) isolated from Georgia poultry-a "global high-risk" clonal strain.

METHODS AND RESULTS

Using multiplex PCR to detect target genes in 98 isolates of avian pathogenic E. coli (APEC) O25 recovered from avians diagnosed with colibacillosis (n = 87) and healthy chicks (n = 11) in Georgia, USA. Eighty-eight isolates were classified as sequence type ST131 clade b and 56% (n = 49) belong to the phylogenetic group B2. Overall, 17% were identified as uropathogenic E. coli (UPEC)-like and 94% of the isolates formed strong to moderate biofilms. The extended-spectrum β-lactamases encoding genes, blaCTX M-15 (24%), carbapenemases encoding genes, and blaOXA48 (16%) were also detected. The isolates harbored FIB (88%), FIC (28%), A/C (14%), and FIIA (6%) plasmid replicons. Interestingly, 78% of the isolates were found to be resistant to chicken serum and 92% showed capabilities for growth in human urine. The isolates showed phenotypic resistance to several antibiotics including chloramphenicol (63%), ciprofloxacin (57%), trimethoprim-sulfamethoxazole (28%), streptomycin (17%), and cefoxitin and meropenem (14%) using the national antimicrobial resistance monitoring system panel.

CONCLUSIONS

Overall, our study provides evidence of the virulence of these global "high-risk" clones in Georgia poultry with some isolates showing genotypic overlap between APEC and UPEC. Also, this clone harbored several virulence genes, antimicrobial-resistant genes, and plasmids. Interestingly, the majority of APEC O25-ST131 isolates can survive and grow in both chicken serum and human urine and warrant further investigation of their potential pathogenicity for both chickens and humans.

Genetic Determinants and Biofilm Properties Useful in Estimation of UTI Pathogenicity of the Escherichia coli Strains Isolated from Free-Living Birds

Background/Objectives: According to the One Health concept, wild birds can be indicators of ecosystem pollution and disease incidence. Escherichia coli strains are widespread worldwide, but there are still few reports on the association of human infections with a potential reservoir of highly pathogenic human strains in wild birds. Fecal E. coli with uropathogenic potential (UPEC) can be transmitted between birds and humans and may be a risk factor for urinary tract infections (UTIs). Results: The results showed that above 50% of the isolates were grouped as highly pathogenic, according to Clermont phylogroup classification. Such strains were found to be stronger biofilm producers, with a higher adherence of monocytes than low pathogenic. However, the highest cytotoxicity was observed for strains described as aquatic environmental. Convergence of the results of the analysis of monocyte activation by E. coli strains and the ability to form biofilm by individual phylogroups of the strains tested was demonstrated. Genetic determinants of the uropathogenicity of E. coli (UPEC) correlate with the evidence of strain pathogenicity during monocyte activation in in vitro assays. Methods: In this study, we assessed the virulence potential of environmental strains isolated from wild waterfowl using genetic analysis (Clermont phylogroup classification) and phenotypic methods, including analysis of the human monocyte response to biofilm formation. The estimation of the ability to form biofilms was tested using crystal violet, and the pathogenic potential of strains by monocyte activation assay including changes in morphology, adhesion and cytotoxicity. Conclusions: In conclusion, the virulence of E. coli strains isolated from free-living birds is significant, and they can be considered environmental reservoirs of pathogenic strains. According to our observations, they can be responsible for the dissemination of uropathogenic strains among humans.

Normal Gut Microbiomes in Diverse Populations: Clinical Implications

The human microbiome is a sensor and modulator of physiology and homeostasis. Remarkable tractability underpins the promise of therapeutic manipulation of the microbiome. However, the definition of a normal or healthy microbiome has been elusive. This is in part due to the underrepresentation of minority groups and major global regions in microbiome studies to date. We review studies of the microbiome in different populations and highlight a commonality among health-associated microbiome signatures along with major drivers of variation. We also provide an overview of microbiome-associated therapeutic interventions for some widespread, widely studied diseases. We discuss sources of bias and the challenges associated with defining population-specific microbiome reference bases. We propose a roadmap for defining normal microbiome references that can be used for population-customized microbiome therapeutics and diagnostics.

Effect of Matrine on growth performance, gut health, and gut microbiota in chickens infected with avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) is a major cause of avian colibacillosis. Matrine, a natural component derived from Sophora flavescens, exhibits various pharmacological effects, including anti-inflammatory and antioxidant activities. However, its role in mitigating APEC-induced intestinal damage in chickens remains insufficiently understood. This study aimed to explore the protective effects and potential mechanisms of matrine against APEC-induced intestinal damage. Chickens were administered matrine (10 or 20 mg/kg) from 6 days old for 5 days, followed by an APEC intraperitoneal injection on day 10. After 72 h of APEC infection, tissues were collected for analysis. Results indicated that pretreatment with matrine alleviated the symptoms of APEC infection in chickens, improving survival rates and promoting weight gain. Additionally, pretreatment with matrine reduced the secretion and gene expression of IL-1β, IL-6, and TNF-α in intestinal tissues, while enhancing serum SOD, GSH, and CAT activity, as well as gene expression levels in the intestine. Pretreatment with matrine reduced the levels of TLR4, MyD88, and NF-κB in intestinal tissues. Moreover, pretreatment with matrine ameliorated intestinal inflammation and pathological damage, restoring the expression of ZO-1, Occludin, and MUC2 in the intestine during APEC infection. Furthermore, pretreatment with matrine alleviated gut microbiota dysbiosis by lowering the abundance of harmful bacteria. In summary, matrine alleviated APEC-induced intestinal inflammation and damage, potentially by inhibiting NF-κB signaling pathway and reshaping the gut microbiota. These findings provide promising insights into the prevention and treatment of avian colibacillosis.

vB_EcoM-P896 coliphage isolated from duck sewage can lyse both intestinal pathogenic Escherichia coli and extraintestinal pathogenic E. coli

Pathogenic Escherichia coli strains cause diseases in both humans and animals. The limiting factors to prevent as well as control infections from pathogenic E. coli strains are their pathotypes, serotypes, and drug resistance. Herein, a bacteriophage (vB_EcoM-P896) has been isolated from duck sewage. Furthermore, aside from targeting intestinal pathogenic E. coli strains like enteropathogenic E. coli, Shiga toxin-producing E. coli, entero-invasive E. coli, and enteroaggregative E. coli, vB_EcoM-P896 can cause lysis in extraintestinal pathogenic E. coli strains such as avian pathogenic E. coli. Stability analysis revealed that vB_EcoM-P896 was stable under the following conditions: temperature, 4℃-50℃; pH, 3-11. The sequencing of the vB_EcoM-P896 genome was conducted utilizing an HiSeq system (Illumina, San Diego, CA) and subjected to de novo assembling with the aid of Spades 3.11.1. The characteristics of the DNA genome were as follows: size, 170,656 bp; GC content, 40.4%; the number of putative coding regions, 294. Transmission electron microscopy analysis of morphology and genome analysis revealed that the phage vB_EcoM-P896 belonged to the order Caudovirales and the family Myoviridae. The pan-genome analysis of vB_EcoM-P896 was divided into two levels. The first level involved the analysis of 91 strains of muscle tail phages, which were mainly divided into 5 groups. The second level involved the analysis of 24 strains of myophage with high homology. Of the 1480 gene clusters, 23 were shared core genes. Neighbor-joining phylogenetic trees were constructed using the Poisson model with MEGA6.0 based on the conserved sequences of phage proteins, the amino acid sequence of the terminase large subunit, and tail fibrin. Further analysis revealed that vB_EcoM-P896 was a typical T4-like potent phage with potential clinical applications.

Escherichia coli: An arduous voyage from commensal to Antibiotic-resistance

Escherichia coli (E. coli), a normal intestinal microbiota is one of the most common pathogen known for infecting urinary tract, wound, lungs, bone marrow, blood system and brain. Irrational and overuse of commercially available antibiotics is the most imperative reason behind the emergence of the life threatening infections caused due to antibiotic resistant pathogens. The World Health Organization (WHO) identified antimicrobial resistance (AMR) as one of the 10 biggest public health threats of our time. This harmless commensal can acquire a range of mobile genetic elements harbouring genes coding for virulence factors becoming highly versatile human pathogens causing severe intestinal and extra intestinal diseases. Although, E. coli has been the most widely studied micro-organism, it never ceases to astound us with its ability to open up new research avenues and reveal cutting-edge survival mechanisms in diverse environments that impact human and surrounding environment. This review aims to summarize and highlight persistent research gaps in the field, including: (i) the transfer of resistant genes among bacterial species in diverse environments, such as those associated with humans and animals; (ii) the development of resistance mechanisms against various classes of antibiotics, including quinolones, tetracyclines, etc., in addition to β-lactams; and (iii) the relationship between resistance and virulence factors for understanding how virulence factors and resistance interact to gain a better grasp of how resistance mechanisms impact an organism's capacity to spread illness and interact with the host's defences. Moreover, this review aims to offer a thorough overview, exploring the history and factors contributing to antimicrobial resistance (AMR), the different reported pathotypes, and their links to virulence in both humans and animals. It will also examine their prevalence in various contexts, including food, environmental, and clinical settings. The objective is to deliver a more informative and current analysis, highlighting the evolution from microbiota (historical context) to sophisticated diseases caused by highly successful pathogens. Developing more potent tactics to counteract antibiotic resistance in E. coli requires filling in these gaps. By bridging these gaps, we can strengthen our capacity to manage and prevent resistance, which will eventually enhance public health and patient outcomes.

Pathogenic Factors and Recent Study on the Rapid Detection of Shiga Toxin-Producing Escherichia coli (STEC)

This comprehensive review delves into the pathogenicity and detection of Shiga Toxin-Producing Escherichia coli (STEC), shedding light on its various genetic and clinical manifestations. STEC originating from E. coli acquires pathogenicity through mobility and genetic elements. The pathogenicity of STEC is explored in terms of clinical progression, complications, and key toxins such as Shiga toxin (Stx). Stx1 and Stx2 are two distinct Stx types exhibiting different toxicities, with Stx2 often associated with severe diseases. This review also delves into Subtilase cytotoxin, an additional cytotoxin produced by some STEC strains. Pathogenic mechanisms of STEC, such as attaching and effacing intestinal lesions, are discussed, with a focus on roles of genetic factors. Plasmids in STEC can confer unique pathogenicity. Hybridization with other pathogenic E. coli can create more lethal pathogens. This review covers a range of detection methods, ranging from DNA amplification to antigen detection techniques, emphasizing the need for innovative approaches to improve the sensitivity and speed of STEC diagnosis. In conclusion, understanding diverse aspects of STEC pathogenicity and exploring enhanced diagnostic methods are critical to addressing this foodborne pathogen effectively.

Seasonal Analysis of Pathogenic Escherichia coli Contamination in Vegetables, Washing Water, and Vendor Hygiene: Virulence Group Classification and Antibiotic Resistance

This study, conducted between June 2022 and March 2023 in Dhaka, examined Escherichia coli prevalence in 874 samples from vegetables, vegetable wash water, and hand swabs from vendors during summer and winter. Of the total samples, 782 (89.50%) tested positive for E. coli , with 95.52% of samples in summer and 80.87% in winter. While overall E. coli prevalence showed no significant seasonal difference, pathotype prevalence was significantly higher in summer across all sample types, except for the CVD432 gene. E. coli isolated from spring onions had the highest prevalence of E. coli O157:H7 (19.23%) and the stx1 gene (30.76%), while capsicum isolates showed the highest prevalence of stx2 (40.00%), eaeA (20.00%), ipaH (35.00%), and eltB (20.00%) genes. In winter, coriander had the highest E. coli O157:H7 (14.28%), and cucumber isolates had the highest stx1 (19.04%) gene. Isolates from tomato and capsicum recorded elevated stx2 levels (16.00%). Carrot isolates exhibited the highest eaeA prevalence (11.42%), coriander isolates had the highest ipaH occurrence (14.28%), and tomato isolates had the highest eltB levels (16.00%). A significant seasonal difference was observed in only the stx1 gene, which was higher in summer for all vegetables. Antibiotic susceptibility testing of 1206 isolates revealed widespread resistance, particularly to ampicillin and erythromycin. Significant seasonal differences in resistance were noted in vegetable samples, but not in water and hand swab samples. Multidrug resistance was highest in isolates from spring onions (56.60% in summer) and carrots (71.87% in winter), with extensively drug-resistant isolates highest in mint (2.17% in summer) and carrots (6.25% in winter).

Genome sequencing of Escherichia coli phage UFJF_EcSW4 reveals a novel lytic Kayfunavirus species

The Escherichia coli phage UFJF_EcSW4 was isolated from polluted stream water and showed clear lysis plaques on the host, measuring 0.67 ± 0.43 mm, with a titer of 9.57 ± 0.23 log PFU/ml. It demonstrated a very narrow host range, infecting only its host. Additionally, it has a short latent period of 9 min, a burst size of 49 PFU/infected cell, and stability over a wide range of pH, temperature, and free residual chlorine. The phage has a double-stranded DNA genome spanning 40,299 bp, with a GC content of 49.87% and short-direct terminal repeats (DTR) sequences of 286 bp. The UFJF_EcSW4 genome contains 55 genes, organized into functional modules with a unidirectional arrangement, regulated by 22 promoters (three from the phage and 19 from the host) and three Rho-independent terminators. Comparative analysis revealed that the UFJF_EcSW4 genome shares an average genomic similarity of 77.82% with the genome sequences of phages from the Kayfunavirus genus but does not surpass the 95% threshold necessary for species classification. Therefore, the UFJF_EcSW4 is a novel Kayfunavirus UFJF_EcSW4 species belonging to the Studiervirinae subfamily.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04172-7.

Prevalence and Zoonotic Risk of Multidrug-Resistant Escherichia coli in Bovine Subclinical Mastitis Milk: Insights Into the Virulence and Antimicrobial Resistance

The emergence of antibiotic-resistant microorganisms has made antimicrobial resistance a global issue, and milk is a potential source for the propagation of resistant bacteria causing zoonotic diseases. Subclinical mastitis (SCM) cases, often overlooked and mixed with normal milk in dairy farms, frequently involve E. coli, which can spread through contaminated milk. We conducted this study to determine the prevalence of virulence genes, antibiotic resistance genes (ARGs), antimicrobial susceptibility, and the genetic relatedness of multidrug-resistant (MDR) Shiga toxin-producing E. coli (STEC) isolated from SCM milk. SCM-positive bovine milk was subjected to E. coli detection using cultural, biochemical, and molecular methods. Further, we detected STEC virulence genes including stx1, stx2, and eaeA. STEC isolates were tested for ARGs including blaSHV, CITM, tetA, and aac(3)-IV, and underwent antimicrobial susceptibility tests. Moreover, we performed a phylogenetic analysis of the stx1 gene of MDR-STEC. SCM was detected in 47.2% of milk samples of which 50.54% were E. coli positive. About 17.20% of E. coli isolates contained STEC virulence genes, and stx2 was the most prevalent. Moreover, all STEC isolates harbored at least one of the ARGs, while about 43.75% of the isolates carried multiple ARGs. Additionally, all the STEC isolates showed multidrug resistance, and were found to be fully resistant against amoxicillin, followed by ampicillin (87.50%) and gentamycin (75%); and were mostly sensitive to aztreonam (81.25%) and meropenem (68.75%). In phylogeny analysis, the stx1 gene of isolated MDR-STEC showed close relatedness with disease-causing non-O157 and O157 strains of different sources including cattle, humans, and food.

Fecal microbiome alterations of mice following immunization with gold nanoparticle vaccines against enterohemorrhagic Escherichia coli

BACKGROUND

Enterohemorrhagic Escherichia coli (EHEC), a group of enteric pathogenic bacteria that is a major cause of human diarrheal disease, must interact with the diverse intestinal microbiome during colonization and subsequently overcome the environmental challenges to survive and cause disease. While this relationship, and how the microbiome modulates infection of EHEC, has been studied, it is less understood how the microbiome is impacted during treatment for an EHEC infection. One area that is notably lacking in knowledge is how vaccination can impact the intestinal microbiome composition, and therefore, influence vaccine efficacy. We previously developed vaccine formulations consisting of gold nanoparticles (AuNPs) conjugated to various EHEC antigens and tested them in mice models using both EHEC and its murine counterpart Citrobacter rodentium. The goal of this study was to evaluate the relationship between these EHEC vaccines and their effects on the gut microbiome.

RESULTS

We found that immunization with the vaccines or adjuvant-only control did not lead to major alterations in the composition of the fecal microbiome; however, there were measurable variations in individual mice within the same vaccine group housed in separate cages. Also, immunization with one vaccine (AuNP-EscC) prevented both a decrease in the diversity of the fecal microbiome and an increase in detectable C. rodentium following infection compared to control animals.

CONCLUSIONS

Overall, our small study argues in favor of evaluating the intestinal microbiome during vaccine development not just for EHEC, but for other enteric pathogens.