Pathogenic Escherichia coli

Impacts of F18+Escherichia coli on Intestinal Health of Nursery Pigs and Dietary Interventions

This review focused on the impact of F18+E. coli on pig production and explored nutritional interventions to mitigate its deleterious effects. F18+E. coli is a primary cause of PWD in nursery pigs, resulting in substantial economic losses through diminished feed efficiency, morbidity, and mortality. In summary, the F18+E. coli induces intestinal inflammation with elevated IL6 (60%), IL8 (43%), and TNF-α (28%), disrupting the microbiota and resulting in 14% villus height reduction. Besides the mortality, the compromised intestinal health results in a 20% G:F decrease and a 10% ADFI reduction, ultimately culminating in a 28% ADG decrease. Among nutritional interventions to counter F18+E. coli impacts, zinc glycinate lowered TNF-α (26%) and protein carbonyl (45%) in jejunal mucosa, resulting in a 39% ADG increase. Lactic acid bacteria reduced TNF-α (36%), increasing 51% ADG, whereas Bacillus spp. reduced IL6 (27%), increasing BW (12%). Lactobacillus postbiotic increased BW (14%) and the diversity of beneficial bacteria. Phytobiotics reduced TNF-α (23%) and IL6 (21%), enhancing feed efficiency (37%). Additional interventions, including low crude protein formulation, antibacterial minerals, prebiotics, and organic acids, can be effectively used to combat F18+E. coli infection. These findings collectively underscore a range of effective strategies for managing the challenges posed by F18+E. coli in pig production.

Antimicrobial potential of unstressed and heat stressed Allium sativum

Garlic (Allium sativum) is generally known to be of medicinal value, possessing potentials that include antimicrobial activity, but are often consumed in foods after subjection to cooking heat. The antimicrobial potential of heat stressed garlic may become decreased or lost when cooked, making its medicinal benefit unavailable to consumers. The potential of uncooked and cooked extracts from garlic imported to Jamaica, to inhibit the growth of eight microbes of clinical significance was investigated. Aqueous extracts of fresh garlic of 15 g/100 ml (fw), and dried and pulverized garlic cloves of 12.5 g/100 ml, 25 g/100 ml, 50 g/100 ml, and 100 g/100 ml (dw), were tested for inhibition of microbial growth. Extracts were tested uncooked, and cooked by boiling for 5, 10, and 15 min respectively. Of all the microbes studied, C. albicans incurred the largest zone of inhibition (57.7 ± 0.6 mm at the 100 g/100 ml of the dried extract, F(3, 8) = 51.778, p < 0.001, ω2 = 0.93). Cooking of garlic extracts resulted in statistically significant decreases in zones of inhibition of microbes, as evident in the linear regression and one-way ANOVA analyses, and/or complete loss of microbial inhibition. C. albicans was the most inhibited microbe, followed by E. coli, and Salmonella sp., respectively. The use of uncooked garlic may be the best route for obtaining the greatest antimicrobial potential of garlic against susceptible bacteria and fungi because cooking heat stress resulted in the decrease and complete loss of the antimicrobial potentials of the garlic.

Mge-cluster: a reference-free approach for typing bacterial plasmids

Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. However, high-resolution population-wide analysis of plasmids has only become accessible recently with the advent of scalable long-read sequencing technology. Current typing methods for the classification of plasmids remain limited in their scope which motivated us to develop a computationally efficient approach to simultaneously recognize novel types and classify plasmids into previously identified groups. Here, we introduce mge-cluster that can easily handle thousands of input sequences which are compressed using a unitig representation in a de Bruijn graph. Our approach offers a faster runtime than existing algorithms, with moderate memory usage, and enables an intuitive visualization, classification and clustering scheme that users can explore interactively within a single framework. Mge-cluster platform for plasmid analysis can be easily distributed and replicated, enabling a consistent labelling of plasmids across past, present, and future sequence collections. We underscore the advantages of our approach by analysing a population-wide plasmid data set obtained from the opportunistic pathogen Escherichia coli, studying the prevalence of the colistin resistance gene mcr-1.1 within the plasmid population, and describing an instance of resistance plasmid transmission within a hospital environment.

Biofilm-forming antimicrobial-resistant pathogenic Escherichia coli: A one health challenge in Northeast India

This study aimed to investigate the prevalence of Shiga toxin-producing Escherichia coli (STEC), Enteropathogenic E. coli (EPEC), and Enterotoxigenic E. coli (ETEC) in common food animals (cattle, goats, and pigs) reared by tribal communities and smallholder farmers in Northeast India. The isolates were characterized for the presence of virulence genes, extended-spectrum beta-lactamases (ESBL) production, antimicrobial resistance, and biofilm production, and the results were statistically interpreted. In pathotyping 141 E. coli isolates, 10 (7.09%, 95% CI: 3.45%-12.66%) were identified as STEC, 2 (1.42%, 95% CI: 0.17%-5.03%) as atypical-EPEC, and 1 (0.71%, 95% CI: 0.02%-3.89%) as typical-EPEC. None of the isolates were classified as ETEC. Additionally, using the phenotypic combination disc method (ceftazidime with and without clavulanic acid), six isolates (46.1%, 95% CI: 19.22%-74.87%) were determined to be ESBL producers. Among the STEC/EPEC strains, eleven (84.6%, 95% CI: 54.55%-98.08%) and one (7.7%, 95% CI: 0.19%-36.03%) strains were capable of producing strong or moderate biofilms, respectively. PFGE analysis revealed indistinguishable patterns for certain isolates, suggesting clonal relationships. These findings highlight the potential role of food animals reared by tribal communities and smallholder farmers as reservoirs of virulent biofilm-forming E. coli pathotypes, with implications for food contamination and zoonotic infections. Therefore, monitoring these pathogens in food animals is crucial for optimizing public health through one health strategy.

Bacteria in cancer initiation, promotion and progression

Cancer cells originate from a series of acquired genetic mutations that can drive their uncontrolled cell proliferation and immune evasion. Environmental factors, including the microorganisms that colonize the human body, can shift the metabolism, growth pattern and function of neoplastic cells and shape the tumour microenvironment. Dysbiosis of the gut microbiome is now recognized as a hallmark of cancer by the scientific community. However, only a few microorganisms have been identified that directly initiate tumorigenesis or skew the immune system to generate a tumour-permissive milieu. Over the past two decades, research on the human microbiome and its functionalities within and across individuals has revealed microbiota-focused strategies for health and disease. Here, we review the evolving understanding of the mechanisms by which the microbiota acts in cancer initiation, promotion and progression. We explore the roles of bacteria in gastrointestinal tract malignancies and cancers of the lung, breast and prostate. Finally, we discuss the promises and limitations of targeting or harnessing bacteria in personalized cancer prevention, diagnostics and treatment.

Enteroaggregative Escherichia coli induced activation of epidermal growth factor receptor contributes to IL-8 secretion by cultured human intestinal epithelial cells

Enteroaggregative Escherichia coli (EAEC) has been identified as a new enteropathogen that causes acute and chronic diarrhea in children and travelers. One defining aspect of EAEC-pathogenesis is the induction of an inflammatory response in intestinal epithelium. In this study, we have found that EAEC-induced EGFR activation in human small intestinal and colonic epithelial was attenuated in the presence of a specific inhibitor of EGFR (Tyrphostin AG1478). Further, the aggregative stacked-brick type of adherence of this organism to both the cell lines and this pathogen-induced cytoskeletal rearrangement of these cells was also reduced in the presence of Tyrphostin AG1478. Moreover, EAEC-induced activation of downstream effectors (ERK-1/2, PI3K and Akt) of EGFR mediated cell signaling pathways were found to be suppressed in the presence of EGFR inhibitor. A decrease in IL-8 response in EAEC infected both the cell types were also noted in the presence of specific inhibitors of these downstream effectors, transcription factors and Tyrphostin AG1478. We propose that EAEC-induced activation of EGFR is quintessential for stacked-brick adherence of EAEC to human intestinal epithelial cells, their cytoskeletal rearrangements and stimulation of ERK-1/2 and PI3K/Akt mediated signal transduction pathways, resulting in the activation of NF-κB, AP-1, STAT-3 and finally IL-8 secretion by these cells.

Precision metagenomics sequencing for food safety: hybrid assembly of Shiga toxin-producing Escherichia coli in enriched agricultural water

Culture-independent metagenomic sequencing of enriched agricultural water could expedite the detection and virulotyping of Shiga toxin-producing Escherichia coli (STEC). We previously determined the limits of a complete, closed metagenome-assembled genome (MAG) assembly and of a complete, fragmented MAG assembly for O157:H7 in enriched agricultural water using long reads (Oxford Nanopore Technologies, Oxford), which were 107 and 105 CFU/ml, respectively. However, the nanopore assemblies did not have enough accuracy to be used in Single Nucleotide Polymorphism (SNP) phylogenies and cannot be used for the precise identification of an outbreak STEC strain. The present study aimed to determine the limits of detection and assembly for STECs in enriched agricultural water by Illumina MiSeq sequencing technology alone, followed by establishing the limit of hybrid assembly with nanopore long-read sequencing using three different hybrid assemblers (SPAdes, Unicycler, and OPERA-MS). We also aimed to generate a genome with enough accuracy to be used in a SNP phylogeny. The classification of MiSeq and nanopore sequencing identified the same highly abundant species. Using the totality of the MiSeq output and a precision metagenomics approach in which the E. coli reads are binned before assembly, the limit of detection and assembly of STECs by MiSeq were determined to be 105 and 107 CFU/ml, respectively. While a complete, closed MAG could not be generated at any concentration, a complete, fragmented MAG was produced using the SPAdes assembler with an STEC concentration of at least 107 CFU/ml. At this concentration, hybrid assembled contigs aligned to the nanopore-assembled genome could be accurately placed in a neighbor-joining tree. The MiSeq limit of detection and assembly was less sensitive than nanopore sequencing, which was likely due to factors including the small starting material (50 vs. 1 μg) and the dilution of the library loaded on the cartridge. This pilot study demonstrates that MiSeq sequencing requires higher coverage in precision metagenomic samples; however, with sufficient concentration, STECs can be characterized and phylogeny can be accurately determined.

Topology and function of translocated EspZ

EspZ and Tir are essential virulence effectors of enteropathogenic Escherichia coli (EPEC). EspZ, the second translocated effector, has been suggested to antagonize host cell death induced by the first translocated effector, Tir (translocated intimin receptor). Another characteristic of EspZ is its localization to host mitochondria. However, studies that explored the mitochondrial localization of EspZ have examined the ectopically expressed effector and not the more physiologically relevant translocated effector. Here, we confirmed the membrane topology of translocated EspZ at infection sites and the involvement of Tir in confining its localization to these sites. Unlike the ectopically expressed EspZ, the translocated EspZ did not colocalize with mitochondrial markers. Moreover, no correlation has been found between the capacity of ectopically expressed EspZ to target mitochondria and the ability of translocated EspZ to protect against cell death. Translocated EspZ may have to some extent diminished F-actin pedestal formation induced by Tir but has a marked effect on protecting against host cell death and on promoting host colonization by the bacteria. Taken together, our results suggest that EspZ plays an essential role in facilitating bacterial colonization, likely by antagonizing cell death mediated by Tir at the onset of bacterial infection. This activity of EspZ, which occurs by targeting host membrane components at infection sites, and not mitochondria, may contribute to successful bacterial colonization of the infected intestine. IMPORTANCE EPEC is an important human pathogen that causes acute infantile diarrhea. EspZ is an essential virulence effector protein translocated from the bacterium into the host cells. Detailed knowledge of its mechanisms of action is, therefore, critical for better understanding the EPEC disease. We show that Tir, the first translocated effector, confines the localization of EspZ, the second translocated effector, to infection sites. This activity is important for antagonizing the pro-cell death activity conferred by Tir. Moreover, we show that translocated EspZ leads to effective bacterial colonization of the host. Hence, our data suggest that translocated EspZ is essential because it confers host cell survival to allow bacterial colonization at an early stage of bacterial infection. It performs these activities by targeting host membrane components at infection sites. Identifying these targets is critical for elucidating the molecular mechanism underlying the EspZ activity and the EPEC disease.

Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers

Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well new intergenic (orphan) TSS, not associated with known genes. Previously, it was hypothesized that many such signals represent noise or pervasive transcription, not associated with a biological function. Here, a modified Cappable-seq protocol allows determining the primary transcriptome of the enterohemorrhagic E. coli O157:H7 EDL933 (EHEC). We used four different growth media, both in exponential and stationary growth phase, replicated each thrice. This yielded 19,975 EHEC canonical and non-canonical TSS, which reproducibly occurring in three biological replicates. This questions the hypothesis of experimental noise or pervasive transcription. Accordingly, conserved promoter motifs were found upstream indicating proper TSSs. More than 50% of 5,567 canonical and between 32% and 47% of 10,355 non-canonical TSS were differentially expressed in different media and growth phases, providing evidence for a potential biological function also of non-canonical TSS. Thus, reproducible and environmentally regulated expression suggests that a substantial number of the non-canonical TSSs may be of unknown function rather than being the result of noise or pervasive transcription.

Frequencies of mobilized colistin resistance (mcr-1, 2) genes in clinically isolated Escherichia coli; a cross sectional study

OBJECTIVE

Escherichia coli (E. coli) is an opportunistic bacterium, which is globally recognized for its high prevalence and antimicrobial resistance (AMR). The presence of colistin-resistant representative mcr- 1, 2 genes in multi-drug resistant (MDR) clinically isolated E. coli is the main goal of this survey. After biochemically and molecular confirmation tests, susceptibility testing, biofilm formation, and minimum inhibitory concentration to colistin were performed on 100 E. coli isolates. Subsequently, taking advantage of uniplex-PCR, the presence of some responsible genes (mcr- 1, mcr- 2) to colistin-resistant phenotypes in mentioned bacterium was assessed.

RESULTS

Disc diffusion methods indicated that the highest resistance rate was against ampicillin (80.0%), and trimethoprim/sulfamethoxazole (63%). Among the E. coli isolates, 72 (72.0%) was determined as MDR, respectively. Moreover, 47 (47%) strains were determined as extreme beta-lactamase (ESBL) phenotypes. Among 41 slime-producing E. coli strains, 7 (17.07%), 14 (34.14%), and 20 (48.78%) strains exhibited high, moderate, and weak levels of biofilm formation, respectively. Fifty-nine (81.94%), and 1(100%) of MDR isolates were assessed as colistin resistant (MIC > 2) and susceptible (MIC ≤ 2) as well. In 26(36.11%) of colistin-resistant isolates and 1(1.38%) of colistin, susceptible isolate mcr-1 gene was found. There is no mcr- 2 gene was detected in isolates.

CONCLUSION

The diversity of high antibiotic-resistant rates could be avoided by developing appropriate healthcare policies and community awareness. Alarming resistance rates were observed in colistin and ampicillin, which should be taken into account in therapy guidelines.

Uropathogenic Escherichia coli (UPEC)-Associated Urinary Tract Infections: The Molecular Basis for Challenges to Effective Treatment

Urinary tract infections (UTIs) are among the most common bacterial infections, especially among women and older adults, leading to a significant global healthcare cost burden. Uropathogenic Escherichia coli (UPEC) are the most common cause and accounts for the majority of community-acquired UTIs. Infection by UPEC can cause discomfort, polyuria, and fever. More serious clinical consequences can result in urosepsis, kidney damage, and death. UPEC is a highly adaptive pathogen which presents significant treatment challenges rooted in a complex interplay of molecular factors that allow UPEC to evade host defences, persist within the urinary tract, and resist antibiotic therapy. This review discusses these factors, which include the key genes responsible for adhesion, toxin production, and iron acquisition. Additionally, it addresses antibiotic resistance mechanisms, including chromosomal gene mutations, antibiotic deactivating enzymes, drug efflux, and the role of mobile genetic elements in their dissemination. Furthermore, we provide a forward-looking analysis of emerging alternative therapies, such as phage therapy, nano-formulations, and interventions based on nanomaterials, as well as vaccines and strategies for immunomodulation. This review underscores the continued need for research into the molecular basis of pathogenesis and antimicrobial resistance in the treatment of UPEC, as well as the need for clinically guided treatment of UTIs, particularly in light of the rapid spread of multidrug resistance.

Characterization and comparative analysis of the Escherichia marmotae M-12 isolate from bank vole (Myodes glareolus)

The Escherichia marmotae is a bacterium of the Enterobacterales order, which was first isolated from the Himalayan marmot (Marmota himalayana). Recently E. marmotae has been shown to cause severe infections in humans. Wild animals were suggested to be a natural reservoir of this bacterium. The present study describes the first case of E. marmotae isolation from an apparently healthy wild bank vole (Myodes glareolus). Phenotype, as well as genotype-based techniques, were applied to characterize E. marmotae M-12 isolate. E. marmotae M-12 had the capsule-positive phenotype, high adhesion to human erythrocytes and HEp-2 cells as well as a low invasion into HEp-2 cells. E. marmotae M-12 was avirulent in mice. The phylogenomic analyses of E. marmotae showed dispersed phylogenetic structure among isolates of different origins. Virulome analysis of M-12 isolate revealed the presence of the following factors: siderophores, heme uptake systems, capsule synthesis, curli and type I fimbriae, flagella proteins, OmpA porin, etc. Comparative virulome analysis among available E. marmotae genomes revealed the presence of capsule K1 genes mostly in pathogenic isolates and OmpA porin presence among all strains. We assume that the K1 capsule and OmpA porin play a key role in the virulence of E. marmotae. Pathogenesis of the latter might be similar to extraintestinal pathogenic E. coli.

Antimicrobial resistance- and pathogen patterns in the fecal microbiota of sows and their offspring in German commercial pig farms

Reducing antibiotic use is one of the biggest challenges in pig farming, as antibiotics have been used for years to control typical problems such as newborn or post-weaning diarrhea. The pressure a one health approach has created on animal production regarding antimicrobial resistance is an opportunity to find other strategies against enterobacterial pathogens in suckling and weaned piglets. A farm-specific approach could have a good success due to the individual farm structures in Germany and other countries. In this study, non-metric multidimensional scaling, hierarchical clustering, and latent class analysis were used to determine the impact of antibiotic use on antibiotic resistance patterns and pathogen prevalence in 20 German pig farms. This may help to develop individualized health strategies. 802 fresh fecal samples were collected from sows and piglets from 20 piglet production and rearing farms at different production times (sows antepartum and postpartum, suckling piglets, weaned piglets). In addition, the use of antibiotics was recorded. DNA extracts were subjected to quantitative real-time qPCR with primers specific for antibiotic resistance genes (int1, sul1-3, dfrA1, mcr-1, blaCTX-M), and virulence factors of relevant bacteria (C. difficile, C. perfringens, Salmonella, Escherichia/Shigella/Hafnia, E. coli). Linear and logistic regression models were used to analyze the relationship between different antibiotics and the major genes contributing to the clustering of observations for the different animal groups. Clustering revealed different farm clusters for sows, suckling piglets, and weaned piglets, with the most remarkable diversity in antibiotic use among weaned piglets. Amoxicillin, lincomycin, and enrofloxacin were identified as the most probable cause of increased odds of the presence of relevant antibiotic resistance genes (mcr1, dfrA1, blaCTX-M). Still, direct effects of a specific antibiotic on its associated resistance gene were rare. Enrofloxacin and florfenicol favored the occurrence of C. difficile in sows. The E. coli fimbriae genes were less affected by antibiotic use in sows and piglets, but the F4 fimbriae gene could be associated with the integrase 1 gene in piglets. The results confirm that multidrug-resistant enterobacteria are widespread in German pig farms and give awareness of the impact of current antibiotic use while searching for alternative health strategies.

Clinical burden of invasive Escherichia coli disease among older adult patients treated in hospitals in the United States

BACKGROUND

Invasive extraintestinal pathogenic Escherichia coli disease (IED) can lead to severe outcomes, particularly among older adults. However, the clinical burden of IED in the U.S. has not been well characterized.

METHODS

IED encounters among patients ≥ 60 years old were identified using the PINC AI™ Healthcare Database (10/01/2015-03/31/2020) by either a positive E. coli culture in blood or another normally sterile body site and ≥ 1 sign of systemic inflammatory response syndrome or signs of sepsis, or a positive E. coli culture in urine with urinary tract infection and signs of sepsis. Medical resource utilization, clinical outcomes, and E. coli isolate characteristics were descriptively reported during the first IED encounter and during the following year (observation period).

RESULTS

Overall, 19,773 patients with IED were included (mean age: 76.8 years; 67.4% female; 78.5% with signs of sepsis). Most encounters involved community-onset IED (94.3%) and required hospitalization (96.5%; mean duration: 6.9 days), with 32.4% of patients being admitted to the intensive care unit (mean duration: 3.7 days). Most E. coli isolates were resistant to ≥ 1 antibiotic category (61.7%) and 34.4% were resistant to ≥ 3 antibiotic categories. Following their first IED encounter, 34.8% of patients were transferred to a skilled nursing/intermediate care facility, whereas 6.8% had died. During the observation period, 36.8% of patients were rehospitalized, 2.4% had IED recurrence, and in-hospital death increased to 10.9%.

CONCLUSIONS

IED is associated with substantial clinical burden at first encounter with considerable long-term consequences. Findings demonstrate the need for increased IED awareness and highlight potential benefits of prevention.

Baicalin Weakens the Porcine ExPEC-Induced Inflammatory Response in 3D4/21 Cells by Inhibiting the Expression of NF-κB/MAPK Signaling Pathways and Reducing NLRP3 Inflammasome Activation

Porcine extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of death in pigs and has led to considerable economic losses for the pig industry. Porcine ExPEC infections often cause systemic inflammatory responses in pigs, characterized by meningitis, arthritis, pneumonia, and septicemia. Baicalin has been reported to possess potent anti-inflammatory activity, but its function in porcine ExPEC remains unknown. The aim of this study was to explore the protective effect and mechanism of baicalin against the porcine ExPEC-induced inflammatory responses in 3D4/21 cells. After treatment with baicalin, the effects on cell damage, the level of pro-inflammatory cytokines, the expression of nuclear factor-κB (NF-κB)/mitogen-activated protein kinase (MAPK) signaling pathways, and the activation of NOD-like receptor protein 3 (NLRP3) inflammasomes were examined. Our results show that baicalin significantly reduced the damage to 3D4/21 cells infected with porcine ExPEC PCN033. Further study showed that baicalin significantly reduced the transcription and expression of pro-inflammatory cytokines such as interleukin-1β (IL-1β), interleukin-6 (IL-6), and interleukin-8 (IL-8). Furthermore, baicalin inhibited the phosphorylation of proteins such as P65, nuclear factor κB inhibitor α (IκBα), extracellular regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and P38 and reduced the expression levels of proteins such as NLRP3, apoptosis-associated speck-like protein containing a CARD (ASC), and caspase-1. These results reveal that baicalin reduced the damage to 3D4/21 cells by inhibiting the expression of NF-κB/MAPK signaling pathways and blocking NLRP3 inflammasome activation in 3D4/21 cells infected with porcine ExPEC. Taken together, these results suggest that baicalin may have potential as a medicine for the treatment of porcine ExPEC-infected pigs by regulating inflammatory responses. This study provides a novel potential pharmaco-therapeutic approach to preventing porcine ExPEC infection.

TRAF6 signaling in dendritic cells plays protective role against infectious colitis by limiting C. rodentium infection through the induction of Th1 and Th17 responses

Tumor necrosis factor receptor-associated factor 6 (TRAF6) plays a pivotal role in the induction of inflammatory responses not only in innate immune cells but also in non-immune cells, leading to the activation of adaptive immunity. Signal transduction mediated by TRAF6, along with its upstream molecule MyD88 in intestinal epithelial cells (IECs) is crucial for the maintenance of mucosal homeostasis following inflammatory insult. The IEC-specific TRAF6-deficient (TRAF6ΔIEC) and MyD88-deficient (MyD88ΔIEC) mice exhibit increased susceptibility to DSS-induced colitis, emphasizing the critical role of this pathway. Moreover, MyD88 also plays a protective role in Citrobacter rodentium (C. rodentium) infection-induced colitis. However, its pathological role of TRAF6 in infectious colitis remains unclear. To investigate the site-specific roles of TRAF6 in response to enteric bacterial pathogens, we infected TRAF6ΔIEC and dendritic cell (DC)-specific TRAF6-deficient (TRAF6ΔDC) mice with C. rodentium and found that the pathology of infectious colitis was exacerbated with significantly decreased survival rates in TRAF6ΔDC mice, but not in TRAF6ΔIEC mice, compared to those in control mice. TRAF6ΔDC mice showed increased bacterial burdens, marked disruption of epithelial and mucosal structures with increased infiltration of neutrophils and macrophages, and elevated cytokine levels in the colon at the late stages of infection. The frequencies of IFN-γ producing Th1 cells and IL-17A producing Th17 cells in the colonic lamina propria were significantly reduced in TRAF6ΔDC mice. Finally, we demonstrated that TRAF6-deficient DCs failed to produce IL-12 and IL-23 in response to C. rodentium stimulation, and to induce both Th1 and Th17 cells in vitro. Thus, TRAF6 signaling in DCs, but not in IECs, protects against colitis induced by C. rodentium infection by producing IL-12 and IL-23 that induce Th1 and Th17 responses in the gut.

A Decade-Long Evaluation of Neonatal Septicaemic Escherichia coli: Clonal Lineages, Genomes, and New Delhi Metallo-Beta-Lactamase Variants

Longitudinal studies of extraintestinal pathogenic Escherichia coli (ExPEC) and epidemic clones of E. coli in association with New Delhi metallo-β-lactamase (blaNDM) in septicaemic neonates are rare. This study captured the diversity of 80 E. coli isolates collected from septicaemic neonates in terms of antibiotic susceptibility, resistome, phylogroups, sequence types (ST), virulome, plasmids, and integron types over a decade (2009 to 2019). Most of the isolates were multidrug-resistant and, 44% of them were carbapenem-resistant, primarily due to blaNDM. NDM-1 was the sole NDM-variant present in conjugative IncFIA/FIB/FII replicons until 2013, and it was subsequently replaced by other variants, such as NDM-5/-7 found in IncX3/FII. A core genome analysis for blaNDM+ve isolates showed the heterogeneity of the isolates. Fifty percent of the infections were caused by isolates of phylogroups B2 (34%), D (11.25%), and F (4%), whereas the other half were caused by phylogroups A (25%), B1 (11.25%), and C (14%). The isolates were further distributed in approximately 20 clonal complexes (STC), including five epidemic clones (ST131, ST167, ST410, ST648, and ST405). ST167 and ST131 (subclade H30Rx) were dominant, with most of the ST167 being blaNDM+ve and blaCTX-M-15+ve. In contrast, the majority of ST131 isolates were blaNDM-ve but blaCTX-M-15+ve, and they possessed more virulence determinants than did ST167. A single nucleotide polymorphism (SNP)-based comparative genome analysis of epidemic clones ST167 and ST131 in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of antibiotic-resistant epidemic clones causing sepsis calls for a modification of the recommended antibiotics with which to treat neonatal sepsis. IMPORTANCE Multidrug-resistant and virulent ExPEC causing sepsis in neonates is a challenge to neonatal health. The presence of enzymes, such as carbapenemases (blaNDM) that hydrolyze most β-lactam antibiotic compounds, result in difficulties when treating neonates. The characterization of ExPECs collected over 10 years showed that 44% of ExPECs were carbapenem-resistant, possessing transmissible blaNDM genes. The isolates belonged to different phylogroups that are considered to be either commensals or virulent. The isolates were distributed in around 20 clonal complexes (STC), including two predominant epidemic clones (ST131 and ST167). ST167 possessed few virulence determinants but was blaNDM+ve. In contrast, ST131 harbored several virulence determinants but was blaNDM-ve. A comparison of the genomes of these epidemic clones in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of epidemic clones in a vulnerable population with contrasting characteristics and the presence of resistance genes call for strict vigilance.

Antimicrobial Efficacy of Cinnamon Essential Oil against Avian Pathogenic Escherichia coli from Poultry

Colibacillosis, caused by E. coli, is responsible for economic losses in the poultry industry due to mortality, decreased production, and the cost of antibiotic treatments. Prevention of colibacillosis is based on improved biosecurity measures and the use of the vaccine performed with O78 E. coli strains, which is responsible for most cases of colibacillosis. Recently, there has been increased interest in other infection control methods, such as the use of natural compounds. The aim of this study was to evaluate the antimicrobial efficacy of cinnamon essential oil (CEO) against E. coli strains isolated from poultry. The MIC50 and MIC90 of CEO were determined by testing 117 strains belonging to serogroups O78, O2, O128, O139, isolated from laying hens (91 strains), broilers (10 strains), and turkeys (16 strains). The bacterial strains were tested at cell densities of 108 and 106 CFU/mL. At the cell density of 108 CFU/mL, MIC50 and MIC90 were 0.4 and 0.5 µL/mL for most of the tested strains, while they corresponded to 0.5 µL/mL for all strains isolated from broilers and for strains belonging to serogroup O139. At the cell density of 106 CFU/mL, MIC50 and MIC90 were 0.3 and 0.4 µL/mL, regardless of bird species of origin and for strains belonging to serogroups O78 and O2. In addition, a concentration of 0.04 µL/mL of CEO corresponded both to MIC50 and MIC90 for strains belonging to serogroups O139 and O128. Based on these results, cinnamon essential oil showed an effective antibacterial activity against E. coli strains from poultry and could find field application for the prevention of colibacillosis.

Molecular and Genomic Analysis of the Virulence Factors and Potential Transmission of Hybrid Enteropathogenic and Enterotoxigenic Escherichia coli (EPEC/ETEC) Strains Isolated in South Korea

Hybrid strains Escherichia coli acquires genetic characteristics from multiple pathotypes and is speculated to be more virulent; however, understanding their pathogenicity is elusive. Here, we performed genome-based characterization of the hybrid of enteropathogenic (EPEC) and enterotoxigenic E. coli (ETEC), the strains that cause diarrhea and mortality in children. The virulence genes in the strains isolated from different sources in the South Korea were identified, and their phylogenetic positions were analyzed. The EPEC/ETEC hybrid strains harbored eae and est encoding E. coli attaching and effacing lesions and heat-stable enterotoxins of EPEC and ETEC, respectively. Genome-wide phylogeny revealed that all hybrids (n = 6) were closely related to EPEC strains, implying the potential acquisition of ETEC virulence genes during ETEC/EPEC hybrid emergence. The hybrids represented diverse serotypes (O153:H19 (n = 3), O49:H10 (n = 2), and O71:H19 (n = 1)) and sequence types (ST546, n = 4; ST785, n = 2). Furthermore, heat-stable toxin-encoding plasmids possessing estA and various other virulence genes and transporters, including nleH2, hlyA, hlyB, hlyC, hlyD, espC, espP, phage endopeptidase Rz, and phage holin, were identified. These findings provide insights into understanding the pathogenicity of EPEC/ETEC hybrid strains and may aid in comparative studies, virulence characterization, and understanding evolutionary biology.

Commensal Escherichia coli Strains of Bovine Origin Competitively Mitigated Escherichia coli O157:H7 in a Gnotobiotic Murine Intestinal Colonization Model with or without Physiological Stress

Cattle are a primary reservoir of enterohemorrhagic Escherichia coli (EHEC) O157:H7. Currently, there are no effective methods of eliminating this important zoonotic pathogen from cattle, and colonization resistance in relation to EHEC O157:H7 in cattle is poorly understood. We developed a gnotobiotic EHEC O157:H7 murine model to examine aspects of the cattle pathogen-microbiota interaction, and to investigate competitive suppression of EHEC O157:H7 by 18 phylogenetically distinct commensal E. coli strains of bovine origin. As stress has been suggested to influence enteric colonization by EHEC O157:H7 in cattle, corticosterone administration (±) to incite a physiological stress response was included as an experimental variable. Colonization of the intestinal tract (IT) of mice by the bovine EHEC O157:H7 strain, FRIK-2001, mimicked characteristics of bovine IT colonization. In this regard, FRIK-2001 successfully colonized the IT and temporally incited minimal impacts on the host relative to other EHEC O157:H7 strains, including on the renal metabolome. The presence of the commensal E. coli strains decreased EHEC O157:H7 densities in the cecum, proximal colon, and distal colon. Moreover, histopathologic changes and inflammation markers were reduced in the distal colon of mice inoculated with commensal E. coli strains (both propagated separately and communally). Although stress induction affected the behavior of mice, it did not influence EHEC O157:H7 densities or disease. These findings support the use of a gnotobiotic murine model of enteric bovine EHEC O157:H7 colonization to better understand pathogen-host-microbiota interactions toward the development of effective on-farm mitigations for EHEC O157:H7 in cattle, including the identification of bacteria capable of competitively colonizing the IT.

Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-Producing Escherichia coli in Presence of Commensal E. coli

The characterization of Shiga toxin-producing Escherichia coli (STEC) is necessary to assess their pathogenic potential, but isolation of the strain from complex matrices such as milk remains challenging. In previous work, we have shown the potential of long-read metagenomics to characterize eae-positive STEC from artificially contaminated raw milk without isolating the strain. The presence of multiple E. coli strains in the sample was shown to potentially hinder the correct characterization of the STEC strain. Here, we aimed at determining the STEC:commensal ratio that would prevent the characterization of the STEC. We artificially contaminated pasteurized milk with different ratios of an eae-positive STEC and a commensal E. coli and applied the method previously developed. Results showed that the STEC strain growth was better than the commensal E. coli after enrichment in acriflavine-supplemented BPW. The STEC was successfully characterized in all samples with at least 10 times more STEC post-enrichment compared to the commensal E. coli. However, the presence of equivalent proportions of STEC and commensal E. coli prevented the full characterization of the STEC strain. This study confirms the potential of long-read metagenomics for STEC characterization in an isolation-free manner while refining its limit regarding the presence of background E. coli strains.

Pneumatically Driven Microfluidic Platform and Fully Automated Particle Concentration System for the Capture and Enrichment of Pathogens

In this study, we developed a pneumatically driven microfluidic platform (PDMFP) operated by a fully automated particle concentration system (FAPCS) for the pretreatment of micro- and nano-sized materials. The proposed PDMFP comprises a 3D network with a curved fluidic chamber and channel, five on/off pneumatic valves for blocking fluid flow, and a sieve valve for sequential trapping of microbeads and target particles. Using this setup, concentrated targets are automatically released into an outlet port. The FAPCS mainly comprises solenoid valves, glass reservoirs, a regulator, pressure sensor, main printed circuit board, and liquid crystal display touch panel. All pneumatic valves in the microfluidic platform as well as the working fluids in the glass reservoirs are controlled using FAPCS. The flow rate of the working fluids is measured to demonstrate the sequential programed operation of the proposed pretreatment process using FAPCS. In our study, we successfully achieved rapid and efficient enrichment using PDMFP-FAPCS with fluorescence-labeled Escherichia coli. With pretreatment-10 min for the microbead concentration and 25 min for target binding-almost all the target bacteria could be captured. A total of 526 Gram-negative bacteria were attached to 82 beads, whereas Gram-positive bacteria were attached to only 2 of the 100 beads. Finally, we evaluated the PDMFP-FAPCS for SARS-CoV-2 receptor-binding domain (RBD)-based outer membrane vesicles (OMVs) (RBD-OMVs). Specific probes involved in PDMFP-FAPCS successfully isolated RBD-OMVs. Thus, PDMFP-FAPCS exhibits excellent enrichment of particles, including microbes and nanovesicles, and is an effective pretreatment platform for disease diagnosis and investigation.

Synergistic Antibacterial Effects of Amoxicillin and Gold Nanoparticles: A Therapeutic Option to Combat Antibiotic Resistance

Compacted Au@16-mph-16/DNA-AMOX (NSi) nanosystems were prepared from amoxicillin (AMOX) and precursor Au@16-mph-16 gold nanoparticles (Ni) using a Deoxyribonucleic acid (DNA) biopolymer as a glue. The synthesized nanocarrier was tested on different bacterial strains of Escherichia coli, Staphylococcus aureus, and Streptococcus pneumoniae to evaluate its effectiveness as an antibiotic as well as its internalization. Synthesis of the nanosystems required previous structural and thermodynamic studies using circular dichroism (CD) and UV-visible techniques to guarantee optimal complex formation and maximal DNA compaction, characteristics which facilitate the correct uptake of the nanocarrier. Two nanocomplexes with different compositions and structures, denoted NS1 and NS2, were prepared, the first involving external Au@16-mph-16 binding and the second partial intercalation. The Ni and NSi nanosystems obtained were characterized via transmission electron microscopy (TEM), zeta potential, and dynamic light scattering (DLS) techniques to measure their charge, aggregation state and hydrodynamic size, and to verify their presence inside the bacteria. From these studies, it was concluded that the zeta potential values for gold nanoparticles, NS1, and NS2 nanosystems were 67.8, -36.7, and -45.1 mV. Moreover, the particle size distribution of the Au@16-mph-16 gold nanoparticles and NS2 nanoformulation was found to be 2.6 nm and 69.0 nm, respectively. However, for NS1 nanoformulation, a bimodal size distribution of 44 nm (95.5%) and 205 nm (4.5%) was found. Minimal inhibitory concentration (MIC) values were determined for the bacteria studied using a microdilution plates assay. The effect on Escherichia coli bacteria was notable, with MIC values of 17 µM for both the NS1 and NS2 nanosystems. The Staphylococcus aureus chart shows a greater inhibition effect of NS2 and NP2 in non-diluted wells, and clearly reveals a great effect on Streptococcus pneumoniae, reaching MIC values of 0.53 µM in more diluted wells. These results are in good agreement with TEM internalization studies of bacteria that reveal significant internalization and damage in Streptococcus pneumoniae. In all the treatments carried out, the antibiotic capacity of gold nanosystems as enhancers of amoxicillin was demonstrated, causing both the precursors and the nanosystems to act very quickly, and thus favoring microbial death with a small amount of antibiotic. Therefore, these gold nanosystems may constitute an effective therapy to combat resistance to antibiotics, in addition to avoiding the secondary effects derived from the administration of high doses of antibiotics.

Characterization of the flanking region of the Shiga toxin operon in Stx2a bacteriophages reveals a diversity of the NanS-p sialate O-acetylesterase gene

Shiga toxin-producing E. coli (STEC) are diarrheagenic strains that can cause bloody diarrhea and hemolytic-uremic syndrome. Their main virulence factor, the Shiga toxin (Stx), is encoded by phages integrated into the bacterial chromosome. Stx phages are widely diverse and carry many genes with limited or unknown function. As the toxin subtype Stx2a is associated with highly pathogenic strains, this study was mainly focused on the characterization of the stx flanking region of Stx2a phages. Of particular interest was a sialate O-acetylesterase (NanS-p), which has been described previously to be encoded downstream stx in some phage genomes and may confer a growth advantage for STEC. Complete DNA sequences of Stx2a phages and prophages were retrieved from the GenBank database, and the genomic regions from anti-terminator Q to holin S genes were bioinformatically analyzed. Predicted NanSp sequences from phages encoding other Stx subtypes were also studied. Additionally, expression of nanS-p was quantified by qPCR in strains selected from our laboratory collection. The analysis of Stx2a phage genomes showed that all carried the Q, stx2a, nanS-p and S genes, but with allele diversity and other sequence differences. In particular, sequence differences were detected in each of the three domains of NanS-p esterases encoded by Stx2a phages and other Stx phages; however, nanS-p was not identified in the Stx2e, Stx2f and Stx2g phages analyzed. The expression of nanS-p increased in most stx2a-positive strains under phage inducing conditions, as was previously shown for stx2a. As the present work showed diversity at the Q-S region among Stx phages, and particularly in the encoded NanS-p enzyme, future studies will be necessary to evaluate if NanS-p variants differ in their activity and to assess the impact of the absence of nanS-p in certain Stx phages.

Evaluation of Covalent Organic Frameworks for the low-cost, rapid detection of Shiga Toxin-producing Escherichia coli in ready-to-eat salads

BACKGROUND

Ready-to-eat products, such as leafy greens, must be carefully controlled as they are directly consumed without any treatment to reduce the presence of potential pathogens. Food industries, especially those that process products with short shelf-life, demand rapid detection of foodborne pathogens such as Shiga Toxin-producing Escherichia coli (STEC). In this sense, molecular methods can fulfill both requirements of turnaround time and consumer safety. The most popular rapid methods are those based on real-time PCR (qPCR) however, vegetables contain inhibitory compounds that may inhibit the amplification reaction thus, there is a need for novel sample preparation protocols.

RESULTS

In the current study, a low-cost sample treatment based on sequential filtration steps was developed. This protocol was combined with covalent organic frameworks (COFs), and compared against a chelating resin, to evaluate their performance by multiplex qPCR targeting the major virulence genes of STEC, namely stx1, stx2, and eae, along with the rfbE for the specific identification of serogroup O157 due to its particularly high incidence, and an Internal Amplification Control to assess reaction inhibition. The optimized sample treatment effectively removed vegetable qPCR inhibitory compounds, and it was possible to detect STEC in spiked ready-to-eat salad samples in one working day, roughly 5 h, with an LOD₅₀ of 8.7 CFU/25 g with high diagnostic sensitivity and specificity. The method was also assessed in samples with cold-stressed bacteria with good results, further demonstrating its applicability.

SIGNIFICANCE

It was demonstrated for the first time that COFs are suitable for DNA extraction and purification. In addition to this, due to the tunable nature of these materials, it is envisioned that future modifications in terms of pore size or combination with magnetic materials, will allow to further improve their performance. In addition to this, the rapid and low-cost sample treatment protocol developed demonstrated suitable for the rapid screening of STEC vegetable samples.

Bacterial toxins and heart function: heat-labile Escherichia coli enterotoxin B promotes changes in cardiac function with possible relevance for sudden cardiac death

Bacterial toxins can cause cardiomyopathy, though it is not its most common cause. Some bacterial toxins can form pores in the membrane of cardiomyocytes, while others can bind to membrane receptors. Enterotoxigenic E. coli can secrete enterotoxins, including heat-resistant (ST) or labile (LT) enterotoxins. LT is an AB5-type toxin that can bind to specific cell receptors and disrupt essential host functions, causing several common conditions, such as certain diarrhea. The pentameric B subunit of LT, without A subunit (LTB), binds specifically to certain plasma membrane ganglioside receptors, found in lipid rafts of cardiomyocytes. Isolated guinea pig hearts and cardiomyocytes were exposed to different concentrations of purified LTB. In isolated hearts, mechanical and electrical alternans and an increment of heart rate variability, with an IC50 of ~0.2 μg/ml LTB, were observed. In isolated cardiomyocytes, LTB promoted significant decreases in the amplitude and the duration of action potentials. Na+ currents were inhibited whereas L-type Ca2+ currents were augmented at their peak and their fast inactivation was promoted. Delayed rectifier K+ currents decreased. Measurements of basal Ca2+ or Ca2+ release events in cells exposed to LTB suggest that LTB impairs Ca2+ homeostasis. Impaired calcium homeostasis is linked to sudden cardiac death. The results are consistent with the recent view that the B subunit is not merely a carrier of the A subunit, having a role explaining sudden cardiac death in children (SIDS) infected with enterotoxigenic E. coli, explaining several epidemiological findings that establish a strong relationship between SIDS and ETEC E. coli.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-023-01100-6.

Economic burden of invasive Escherichia coli disease among older adult patients treated in hospitals in the United States

BACKGROUND: Although invasive Escherichia coli disease (IED) can lead to severe clinical outcomes, little is known about the associated medical resource use and cost burden of IED in US hospitals. OBJECTIVE: To comprehensively describe medical resource use and costs associated with IED during the initial IED event and over the subsequent 12 months. METHODS: Patients aged 60 years or older with 1 or more IED encounters were identified from the PINC AI Healthcare US hospital database (October 1, 2015, to March 31, 2020). The index encounter was defined as the first encounter with a positive E coli culture in a normally sterile site (group 1 IED) or positive E coli culture in urine with signs of sepsis (group 2 IED). Encounters with a positive culture from other bacteria or fungal pathogens were excluded. Outcomes were descriptively reported between admission and discharge for the index encounter and more than 1 - year post-index discharge. Medical resource use and costs included inpatient admissions and outpatient hospital services; costs were reported from a hospital's perspective (ie, charged amount) in 2021 USD. RESULTS: A total of 19,773 patients were identified (group 1 IED = 51.8%; group 2 IED = 48.2%). Mean age was 76.8 years, 67.4% were female, and 82.1% were White. Most index encounters were community-onset (94.3%) and led to hospitalization (96.5%) (mean inpatient days = 6.9 days). During the 1 - year post-index, 36.8% of patients had 1 or more all-cause hospitalizations. Mean [median] total all-cause hospital costs (as captured through the PINC AI Healthcare database) amounted to $16,760 [$11,340] during the index encounter and $10,942 [$804] during the 1 - year post-index; these costs were higher in the presence of sepsis and multidrug resistance and among hospital-onset IED. CONCLUSIONS: IED is associated with a substantial medical resource use and economic burden both during the initial encounter and over the following year in older adults. This highlights the critical need and potential benefits of preventive measures that may reduce the incidence of IED and associated economic burden. DISCLOSURES: This study was funded by Janssen Global Services, LLC. Dr Hernandez-Pastor is an employee of Janssen Pharmaceutica NV. Dr Geurtsen is an employee of Janssen Vaccines & Prevention BV. Dr Baugh is an employee of Janssen Research & Development, LLC. Dr El Khoury is an employee of Janssen Global Services, LLC. Dr Kalu and Dr Krishnarajah are employees of Janssen Scientific Affairs, LLC. Dr Gauthier-Loiselle, Ms Bungay, and Mr Cloutier are employees of Analysis Group, Inc., a consulting company that provided paid consulting services to Janssen Global Services, LLC. Dr Saade received consultation and speaker fees from Janssen.

Biosensing Systems Based on Graphene Oxide Fluorescence Quenching Effect

Graphene oxide (GO) is a versatile material obtained by the strong oxidation of graphite. Among its peculiar properties, there is the outstanding ability to significantly alter the fluorescence of many common fluorophores and dyes. This property has been exploited in the design of novel switch-ON and switch-OFF fluorescence biosensing platforms for the detection of a plethora of biomolecules, especially pathological biomarkers and environmental contaminants. Currently, novel advanced strategies are being developed for therapeutic, diagnostic and theranostic approaches to widespread pathologies caused by viral or bacterial agents, as well as to cancer. This work illustrates an overview of the most recent applications of GO-based sensing systems relying on its fluorescence quenching effect.

A chimeric protein-based vaccine elicits a strong IgG antibody response and confers partial protection against Shiga toxin-producing Escherichia coli in mice

Background

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen that causes gastrointestinal infections, ranging from acute diarrhea and dysentery to life-threatening diseases such as Hemolytic Uremic Syndrome. Currently, a vaccine to prevent STEC infection is an unmet medical need.

Results

We developed a chimeric protein-based vaccine targeting seven virulence factors of STEC, including the Stx2B subunit, Tir, Intimin, EspA, Cah, OmpT, and AggA proteins. Immunization of mice with this vaccine candidate elicited significant humoral and cellular immune responses against STEC. High levels of specific IgG antibodies were found in the serum and feces of immunized mice. However, specific IgA antibodies were not detected in either serum or feces. Furthermore, a significantly higher percentage of antigen-specific CD4+ T cells producing IFN-γ, IL-4, and IL-17 was observed in the spleens of immunized mice. Notably, the immunized mice showed decreased shedding of STEC O157:H7 and STEC O91:H21 strains and were protected against weight loss during experimental infection. Additionally, infection with the STEC O91:H21 strain resulted in kidney damage in control unimmunized mice; however, the extent of damage was slightly lower in immunized mice. Our findings suggest that IgG antibodies induced by this vaccine candidate may have a role in inhibiting bacterial adhesion and complement-mediated killing.

Conclusion

This study provides evidence that IgG responses are involved in the host defense against STEC. However, our results do not rule out that other classes of antibodies also participate in the protection against this pathogen. Additional work is needed to improve the protection conferred by our vaccine candidate and to elucidate the relevant immune responses that lead to complete protection against this pathogen.

Genomic and functional portrait of multidrug-resistant, hydrogen sulfide (H2S)-producing variants of Escherichia coli

Atypical Escherichia coli forms exhibit unusual characteristics compared to typical strains. The H2S-producing variants of some atypical E. coli strains cause a wide range of illnesses in humans and animals. However, there are sparse reports on such strains worldwide. We performed whole-genome sequencing (WGS) and detailed characterization of four H2S-producing E. coli variants from poultry and human clinical sources in Dhaka, Bangladesh. All four isolates were confirmed as E. coli using biochemical tests and genomic analysis, and were multidrug-resistant (MDR). WGS analysis including an additional Chinese strain, revealed diverse STs among the five H2S-producing E. coli genomes, with clonal complex ST10 being detected in 2 out of 5 genomes. The predominant phylogroup detected was group A (n = 4/5). The blaTEM1B (n = 5/5) was the most predominant extended-spectrum beta-lactamase (ESBL) gene, followed by different alleles of blaCTX-M (blaCTX-M -55,-65,-123; n = 3/5). Multiple plasmid replicons were detected, with IncX being the most common. One E. coli strain was classified as enteropathogenic E. coli. The genomes of all five isolates harbored five primary and four secondary function genes related to H2S production. These findings suggest the potential of these isolates to cause disease and spread antibiotic resistance. Therefore, such atypical E. coli forms should be included in differential diagnosis to understand the pathogenicity, antimicrobial resistance and evolution of H2S-producing E. coli.

Updates on the Virulence Factors Produced by Multidrug-Resistant Enterobacterales and Strategies to Control Their Infections

The Enterobacterales order is a massive group of Gram-negative bacteria comprised of pathogenic and nonpathogenic members, including beneficial commensal gut microbiota. The pathogenic members produce several pathogenic or virulence factors that enhance their pathogenic properties and increase the severity of the infection. The members of Enterobacterales can also develop resistance against the common antimicrobial agents, a phenomenon called antimicrobial resistance (AMR). Many pathogenic Enterobacterales members are known to possess antimicrobial resistance. This review discusses the virulence factors, pathogenicity, and infections caused by multidrug-resistant Enterobacterales, especially E. coli and some other bacterial species sharing similarities with the Enterobacterales members. We also discuss both conventional and modern approaches used to combat the infections caused by them. Understanding the virulence factors produced by the pathogenic bacteria will help develop novel strategies and methods to treat infections caused by them.

Alternate Antimicrobial Therapies and Their Companion Tests

New antimicrobial approaches are essential to counter antimicrobial resistance. The drug development pipeline is exhausted with the emergence of resistance, resulting in unsuccessful trials. The lack of an effective drug developed from the conventional drug portfolio has mandated the introspection into the list of potentially effective unconventional alternate antimicrobial molecules. Alternate therapies with clinically explicable forms include monoclonal antibodies, antimicrobial peptides, aptamers, and phages. Clinical diagnostics optimize the drug delivery. In the era of diagnostic-based applications, it is logical to draw diagnostic-based treatment for infectious diseases. Selection criteria of alternate therapeutics in infectious diseases include detection, monitoring of response, and resistance mechanism identification. Integrating these diagnostic applications is disruptive to the traditional therapeutic development. The challenges and mitigation methods need to be noted. Applying the goals of clinical pharmacokinetics that include enhancing efficacy and decreasing toxicity of drug therapy, this review analyses the strong correlation of alternate antimicrobial therapeutics in infectious diseases. The relationship between drug concentration and the resulting effect defined by the pharmacodynamic parameters are also analyzed. This review analyzes the perspectives of aligning diagnostic initiatives with the use of alternate therapeutics, with a particular focus on companion diagnostic applications in infectious diseases.

Mitogen-Activated Protein Kinases (MAPKs) and Enteric Bacterial Pathogens: A Complex Interplay

Diverse extracellular and intracellular cues activate mammalian mitogen-activated protein kinases (MAPKs). Canonically, the activation starts at cell surface receptors and continues via intracellular MAPK components, acting in the host cell nucleus as activators of transcriptional programs to regulate various cellular activities, including proinflammatory responses against bacterial pathogens. For instance, binding host pattern recognition receptors (PRRs) on the surface of intestinal epithelial cells to bacterial pathogen external components trigger the MAPK/NF-κB signaling cascade, eliciting cytokine production. This results in an innate immune response that can eliminate the bacterial pathogen. However, enteric bacterial pathogens evolved sophisticated mechanisms that interfere with such a response by delivering virulent proteins, termed effectors, and toxins into the host cells. These proteins act in numerous ways to inactivate or activate critical components of the MAPK signaling cascades and innate immunity. The consequence of such activities could lead to successful bacterial colonization, dissemination, and pathogenicity. This article will review enteric bacterial pathogens' strategies to modulate MAPKs and host responses. It will also discuss findings attempting to develop anti-microbial treatments by targeting MAPKs.

zol & 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 (MGEs), 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 or homologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of protein-encoding ortholog groups for individual genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of statistics for each inferred ortholog group. These programs are showcased through application to: (i) longitudinal tracking of a virus in metagenomes, (ii) discovering novel population-genetic insights of two common BGCs in a fungal species, and (iii) uncovering large-scale evolutionary trends of a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.

Bacteriophages for the Targeted Control of Foodborne Pathogens

Foodborne illness is exacerbated by novel and emerging pathotypes, persistent contamination, antimicrobial resistance, an ever-changing environment, and the complexity of food production systems. Sporadic and outbreak events of common foodborne pathogens like Shiga toxigenic E. coli (STEC), Salmonella, Campylobacter, and Listeria monocytogenes are increasingly identified. Methods of controlling human infections linked with food products are essential to improve food safety and public health and to avoid economic losses associated with contaminated food product recalls and litigations. Bacteriophages (phages) are an attractive additional weapon in the ongoing search for preventative measures to improve food safety and public health. However, like all other antimicrobial interventions that are being employed in food production systems, phages are not a panacea to all food safety challenges. Therefore, while phage-based biocontrol can be promising in combating foodborne pathogens, their antibacterial spectrum is generally narrower than most antibiotics. The emergence of phage-insensitive single-cell variants and the formulation of effective cocktails are some of the challenges faced by phage-based biocontrol methods. This review examines phage-based applications at critical control points in food production systems with an emphasis on when and where they can be successfully applied at production and processing levels. Shortcomings associated with phage-based control measures are outlined together with strategies that can be applied to improve phage utility for current and future applications in food safety.

Self-Assembly, In Vitro Gene Transfection, and Antimicrobial Activity of Biodegradable Cationic Bolaamphiphiles

Bolaamphiphiles or bolaforms have drawn particular interest in drug and gene delivery, and studies of bolaforms have been growing continuously. Bolaforms, due to their unique structure, exhibit specific self-assembly behavior in water. The present work aims to develop biodegradable cationic bolaforms with a better gene transfection ability. In this work, a novel cationic bolaform (Bola-1) with head groups bearing hydroxyl (OH) functionality was designed and synthesized to investigate self-assembly and gene transfection efficiency. The self-assembly behavior of Bola-1 in water was compared with that of the hydrochloride salt (Bola-2) of its precursor molecule to investigate the effect of the -OH functionality on their solution properties. Several techniques, including surface tension, electrical conductivity, fluorescence probe, calorimetry, dynamic light scattering, and atomic force microscopy, were employed for the physicochemical characterization of Bola-1 and Bola-2. Despite the presence of polar urea groups in the spacer chain, both bolaforms were found to form spherical or elongated micelles above a relatively low critical aggregation concentration (CAC). The presence of the OH group was found to significantly affect the CAC value. The results of calorimetric measurements suggested a thermodynamically favorable aggregate formation in salt-free water. Despite stronger binding efficiency with calf thymus DNA, in vitro gene transfection studies performed using adherent cell Hek 293 suggested that both Bola-1 and Bola-2 have gene transfection efficiency comparable to that of turbofectamine standard. Both bolaforms were found to exhibit significant in vitro cytotoxicity at higher concentrations. Also, the bolaforms showed beneficial antibacterial activity at higher concentrations.

Nano-sized warriors: zinc chromium vanadate nanoparticles as a dual solution for eradicating waterborne enterobacteriaceae and fighting cancer

The revolution of biomedical applications has opened new avenues for nanotechnology. Zinc Chromium vanadate nanoparticles (VCrZnO4 NPs) have emerged as an up-and-coming candidate, with their exceptional physical and chemical properties setting them apart. In this study, a one-pot solvothermal method was employed to synthesize VCrZnO4 NPs, followed by a comprehensive structural and morphological analysis using a variety of techniques, including X-Ray diffraction, scanning electron microscopy, high-resolution transmission electron microscopy, Energy-dispersive X-ray, and X-ray photoelectron spectroscopy. These techniques confirmed the crystallinity of the NPs. The VCrZnO4 NPs were tested for their antibacterial activity against primary contaminants such as Enterobacteriaceae, including Shigella flexneri, Salmonella cholerasis, and Escherichia coli, commonly found in hospital settings, using the broth dilution technique. The results indicated a stronger antibacterial activity of VCrZnO4 NPs against Shigella and Salmonella than E. coli. Electron microscopy showed that the NPs caused severe damage to the bacterial cell wall and membrane, leading to cell death. In addition, the study evaluated the anticancer activities of the metal complexes in vitro using colorectal cancer cells (HCT-116) and cervical cancer cells (HELA), along with non-cancer cells and human embryonic kidney cells (HEK-293). A vanadium complex demonstrated efficient anticancer effects with half-inhibitory concentrations (IC₅₀) of 38.50+3.50 g/mL for HCT-116 cells and 42.25+4.15 g/mL for HELA cells. This study highlights the potential of Zinc Chromium vanadate nanoparticles as promising candidates for antibacterial and anticancer applications. Various advanced characterization techniques were used to analyze the properties of nanomaterials, which may help develop more effective and safer antibacterial and anticancer agents in the future.

Risk Factors and Associated Outcomes of Virulence Genes eae, entB, and pipD Carriage in Escherichia coli, Klebsiella pneumoniae, and Salmonella spp. From HIV-1 and HIV-Negative Gastroenteritis Patients in the Dschang Regional Hospital Annex

Background Enterobacteriaceae is one of the main families of gram-negative bacilli responsible for serious infections in humans. The severity of infection by these bacteria is a product of many factors, including virulence properties and antimicrobial resistance. This severity may be further intensified if there is an association between these factors and a depressed immune system, such as in HIV patients. This study aimed to determine the distribution of representative virulence genes among key Enterobacteriaceae isolates from HIV-1 and non-HIV gastroenteritis patients and the relationship between carrying these virulence genes and antimicrobial susceptibility, seropositive status, and severity of symptoms associated with Enterobacteriaceae infections in Dschang Regional Hospital Annex. Methodology A total of 200 gastroenteritis patients (100 HIV-1 and 100 non-HIV patients) were selected and evaluated for symptoms associated with gastroenteritis. Stool samples were obtained and cultured, from which Escherichia coli, Klebsiella pneumoniae, and Salmonella spp. isolates were obtained. Antibiotic susceptibility tests were performed on the isolates by agar disc diffusion using commonly used antibiotics. These isolates were tested for the possession of virulence genes by polymerase chain reaction (PCR); eae for E. coli, entB for K. pneumoniae, and pipD for Salmonella spp. Correlation tests and risk assessments were performed between the presence of virulence genes, antibiotic resistance, and specific symptoms. Results The isolates obtained from HIV-positive and HIV-negative patients were, respectively, 61 against 62 for E. coli, 10 against 21 for K. pneumoniae, and 11 against 15 for Salmonella spp.These organisms showed the highest resistance to amoxicillin and clavulanic acid, while the least resistance was observed against ofloxacin, gentamicin, and amikacin in both groups of patients. The virulence genes showed a generally higher occurrence in isolates from HIV-negative patients than HIV-positive patients, with the eae gene 5/61 (8.20%) against 12/62 (19.35%), the entB gene 4/10 (40.00%) against 14/21 (66.66%), and the pipD gene 5/11 (45.45%) against 7/15 (46.46%) in HIV-positive and negative patients, respectively. There was a significant correlation between eae gene carriage and resistance against imipenem (p = 0.047), gentamycin (p = 0.047), and doxycycline (p = 0.029); entB gene carriage and resistance toward levofloxacin (p = 0.017) in K. pneumoniae; and pipD gene carriage and resistance against levofloxacin (p = 0.039), imipenem (p = 0.041), and doxycycline (p = 0.042). The carriage of the virulence genes was seen to be a stronger risk only for the resistance of K. pneumoniae to ceftriaxone (odds ratio (OR) = 2.286) and gentamycin (OR = 3.000), and Salmonella spp. against imipenem (OR = 2.750) and doxycycline (OR = 2.118). The development of severe symptoms correlated significantly with virulence gene carriage in isolates, mainly in HIV-positive patients with eae (p = 0.017) and pipD (p = 0.025), with a strong risk association with the pipD gene (OR = 2.665). Conclusions Antibiotic resistance was associated with virulence gene carriage, indicating that virulence and antibiotic resistance can associate their effects and contribute to poor outcomes in the treatment of bacterial diseases in HIV patients. The possession of virulence genes increased the severity of symptoms associated with gastroenteritis in HIV-positive patients.

Orally delivered single-domain antibodies against gastrointestinal pathogens

Single-domain antibodies (sdAbs) are exceptionally stable fragments derived from the antigen-binding domains of immunoglobulins. They can withstand extreme pH, high temperature, and proteolysis, making them suitable for controlling gastrointestinal (GI) infections in humans and animals. sdAbs may function in their native soluble form, although different derived protein formats and the use of delivery vehicles can be useful for improved oral delivery. We discuss selected examples of the use of orally delivered sdAbs for protecting humans and animals against GI infections caused by pathogenic bacteria, viruses, and parasites. We finally provide perspectives on how sdAbs may be applied industrially and what challenges should be overcome for orally delivered sdAbs to reach the market.

Shiga Toxin-Producing Escherichia coli (STEC) Associated with Calf Mortality in Uruguay

In Uruguay, the mortality of dairy calves due to infectious diseases is high. Escherichia coli is a natural inhabitant of the intestinal microbiota, but can cause several infections. The aim of the work was to characterize E. coli isolates from intestinal and extraintestinal origin of dead newborn calves. Using PCR, virulence gene characteristics of pathogenic E. coli were searched. The pathogenic E. coli were molecularly characterized and the phylogroup, serogroup and the Stx subtype were determined. Antibiotic susceptibility was determined using the Kirby-Bauer disk diffusion method and plasmid-mediated quinolone resistance (PMQR) genes with PCR. Finally, clonal relationships were inferred using PFGE. Gene characteristics of the Shiga toxin-producing E. coli (STEC), Enteropathogenic E. coli (EPEC) and Necrotoxigenic E. coli (NTEC) were identified. The prevalence of the iucD, afa8E, f17, papC, stx1, eae and ehxA genes was high and no f5, f41, saa, sfaDE, cdtIV, lt, sta or stx2 were detected. The prevalence of STEC gene stx1 in the dead calves stood out and was higher compared with previous studies conducted in live calves, and STEC LEE+ (Enterohemorrhagic E. coli (EHEC)) isolates with stx1/eae/ehxA genotypes were more frequently identified in the intestinal than in the extraintestinal environment. E. coli isolates were assigned to phylogroups A, B1, D and E, and some belonged to the O111 serogroup. stx1a and stx1c subtypes were determined in STEC. A high prevalence of multi-resistance among STEC and qnrB genes was determined. The PFGE showed a high diversity of pathogenic strains with similar genetic profiles. It can be speculated that EHEC (stx1/eae/ehxA) could play an important role in mortality. The afa8E, f17G1 and papC genes could also have a role in calf mortality. Multidrug resistance defies disease treatment and increases the risk of death, while the potential transmissibility of genes to other species constitutes a threat to public health.

Virulence of Shigatoxigenic and Enteropathogenic Escherichia coli O80:H2 in Galleria mellonella Larvae: Comparison of the Roles of the pS88 Plasmids and STX2d Phage

The invasiveness properties of Shigatoxigenic and enteropathogenic Escherichia coli (STEC and EPEC) O80:H2 in humans and calves are encoded by genes located on a pS88-like ColV conjugative plasmid. The main objectives of this study in larvae of the Galleria mellonella moth were therefore to compare the virulence of eight bovine STEC and EPEC O80:H2, of two E. coli pS88 plasmid transconjugant and STX2d phage transductant K12 DH10B, of four E. coli O80:non-H2, and of the laboratory E. coli K12 DH10B strains. Thirty larvae per strain were inoculated in the last proleg with 10 μL of tenfold dilutions of each bacterial culture corresponding to 10 to 10⁶ colony-forming units (CFUs). The larvae were kept at 37 °C and their mortality rate was followed daily for four days. The main results were that: (i) not only the STEC and EPEC O80:H2, but also different E. coli O80:non-H2 were lethal for the larvae at high concentrations (from 10⁴ to 10⁶ CFU) with some variation according to the strain; (ii) the Stx2d toxin and partially the pS88 plasmid were responsible for the lethality caused by the E. coli O80:H2; (iii) the virulence factors of E. coli O80:non-H2 were not identified. The general conclusions are that, although the Galleria mellonella larvae represent a useful first-line model to study the virulence of bacterial pathogens, they are more limited in identifying their actual virulence properties.

Production of Reactive Oxygen (ROS) and Nitrogen (RNS) Species in Macrophages J774A.1 Activated by the Interaction between Two Escherichia coli Pathotypes and Two Probiotic Commercial Strains

Probiotics play an important role against infectious pathogens, such as Escherichia coli (E. coli), mainly through the production of antimicrobial compounds and their immunomodulatory effect. This protection can be detected both on the live probiotic microorganisms and in their inactive forms (paraprobiotics). Probiotics may affect different cells involved in immunity, such as macrophages. Macrophages are activated through contact with microorganisms or their products (lipopolysaccharides, endotoxins or cell walls). The aim of this work was the evaluation of the effect of two probiotic bacteria (Escherichia coli Nissle 1917 and Bifidobacterium animalis subsp. lactis HN019 on macrophage cell line J774A.1 when challenged with two pathogenic strains of E. coli. Macrophage activation was revealed through the detection of reactive oxygen (ROS) and nitrogen (RNS) species by flow cytometry. The effect varied depending on the kind of probiotic preparation (immunobiotic, paraprobiotic or postbiotic) and on the strain of E. coli (enterohemorrhagic or enteropathogenic). A clear immunomodulatory effect was observed in all cases. A higher production of ROS compared with RNS was also observed.

Novel evidence on sepsis-inducing pathogens: from laboratory to bedside

Sepsis is a life-threatening condition and a significant cause of preventable morbidity and mortality globally. Among the leading causative agents of sepsis are bacterial pathogens Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Streptococcus pyogenes, along with fungal pathogens of the Candida species. Here, we focus on evidence from human studies but also include in vitro and in vivo cellular and molecular evidence, exploring how bacterial and fungal pathogens are associated with bloodstream infection and sepsis. This review presents a narrative update on pathogen epidemiology, virulence factors, host factors of susceptibility, mechanisms of immunomodulation, current therapies, antibiotic resistance, and opportunities for diagnosis, prognosis, and therapeutics, through the perspective of bloodstream infection and sepsis. A list of curated novel host and pathogen factors, diagnostic and prognostic markers, and potential therapeutical targets to tackle sepsis from the research laboratory is presented. Further, we discuss the complex nature of sepsis depending on the sepsis-inducing pathogen and host susceptibility, the more common strains associated with severe pathology and how these aspects may impact in the management of the clinical presentation of sepsis.

Absorbance biosensors-based hybrid [Formula: see text] nanosheets for Escherichia coli detection

Detecting Escherichia coli is essential in biomedical, environmental, and food safety applications. In this paper, we have developed a simple, rapid, sensitive, and selective E. coli DNA sensor based on the novel hybrid-type [Formula: see text] and [Formula: see text] nanosheets. The sensor uses the absorbance measurement to distinguish among the DNA of E. coli, Vibrio proteolyticus, and Bacillus subtilis when implemented in conjunction with [Formula: see text]-probes. Our experiments showed that the absorbance increased when sensors detected E. coli DNA, whereas it decreased when sensors detected V. proteolyticus and B. subtilis DNA. To the best of authors' knowledge, there are no reports using the novel hybrid-[Formula: see text] and [Formula: see text] materials for differentiating three types of DNA using cost-effective and rapid absorbance measurements. In addition, the label-free E. coli DNA biosensor exhibited a linear response in the range of 0 fM to 11.65 fM with a limit of detection of 2 fM. The effect of [Formula: see text]-probes on our sensors' working performance is also investigated. Our results will facilitate further research in pathogen detection applications, which have not been fully developed yet.

Isolation and characterization of novel lytic bacteriophages that infect multi drug resistant clinical strains of Escherichia coli

The pathogenic strains of Escherichia coli (E. coli) are frequent cause of urinary tract infections including catheter-associated, soft tissue infections and sepsis. The growing antibiotic resistance in E. coli is a major health concern. Bacteriophages are specific for their bacterial host, thus providing a novel and effective alternatives. This study focuses on isolation of bacteriophages from urban sewage treatment plants. Initially 50 different bacteriophages have been isolated against non-resistant reference E. coli strain and fifty multidrug resistant clinical isolates of extraintestinal infections. Out of which only thirty-one lytic phages which gave clear plaques were further analysed for different physico-chemical aspects such as thermal inactivation, pH, effect of organic solvents and detergents. Two bacteriophages, ASEC2201 and ASEC2202, were selected for their ability to withstand temperature fluctuation from -20 to 62 °C and a pH range from 4 to 10. They also showed good survival (40-94%) in the presence of organic solvents like ethanol, acetone, DMSO and chloroform or ability to form plaques even after the treatment with detergents like SDS, CTAB and sarkosyl. Both efficiently killed reference strain and 40-44% of multidrug resistant clinical isolates of E. coli. Later ASEC2201 and ASEC2202 were subjected to morphological characterisation through transmission electron microscopy, which revealed them to be tailed phages. The genomic analysis confirmed them to be Escherichia phages which belonged to family Drexlerviridae of Caudovirales.

Ultrasensitive and Rapid Visual Detection of Escherichia coli O157:H7 Based on RAA-CRISPR/Cas12a System

Escherichia coli (E. coli) O157:H7 is a major foodborne and waterborne pathogen that can threaten human health. Due to its high toxicity at low concentrations, it is crucial to establish a time-saving and highly sensitive in situ detection method. Herein, we developed a rapid, ultrasensitive, and visualized method for detecting E. coli O157:H7 based on a combination of Recombinase-Aided Amplification (RAA) and CRISPR/Cas12a technology. The CRISPR/Cas12a-based system was pre-amplified using the RAA method, which showed high sensitivity and enabled detecting as low as ~1 CFU/mL (fluorescence method) and 1 × 10² CFU/mL (lateral flow assay) of E. coli O157:H7, which was much lower than the detection limit of the traditional real-time PCR technology (10³ CFU/mL) and ELISA (10⁴~10⁷ CFU/mL). In addition, we demonstrated that this method still has good applicability in practical samples by simulating the detection in real milk and drinking water samples. Importantly, our RAA-CRISPR/Cas12a detection system could complete the overall process (including extraction, amplification, and detection) within 55 min under optimized conditions, which is faster than most other reported sensors, which take several hours to several days. The signal readout could also be visualized by fluorescence generated with a handheld UV lamp or a naked-eye-detected lateral flow assay depending on the DNA reporters used. Because of the advantages of being fast, having high sensitivity, and not requiring sophisticated equipment, this method has a promising application prospect for in situ detection of trace amounts of pathogens.

COVID-19 and brain-heart-lung microbial fingerprints in Italian cadavers

Introduction: The fact that SARS-CoV-2, the coronavirus that caused COVID-19, can translocate within days of infection to the brain and heart and that the virus can survive for months is well established. However, studies have not investigated the crosstalk between the brain, heart, and lungs regarding microbiota that simultaneously co-inhabit these organs during COVID-19 illness and subsequent death. Given the significant overlap of cause of death from or with SARS-CoV-2, we investigated the possibility of a microbial fingerprint regarding COVID-19 death. Methods: In the current study, the 16S rRNA V4 region was amplified and sequenced from 20 COVID-19-positive and 20 non-COVID-19 cases. Nonparametric statistics were used to determine the resulting microbiota profile and its association with cadaver characteristics. When comparing non-COVID-19 infected tissues versus those infected by COVID-19, there is statistical differences (p < 0.05) between organs from the infected group only. Results: When comparing the three organs, microbial richness was significantly higher in non-COVID-19-infected tissues than infected. Unifrac distance metrics showed more variance between control and COVID-19 groups in weighted analysis than unweighted; both were statistically different. Unweighted Bray-Curtis principal coordinate analyses revealed a near distinct two-community structure: one for the control and the other for the infected group. Both unweighted and weighted Bray-Curtis showed statistical differences. Deblur analyses demonstrated Firmicutes in all organs from both groups. Discussion: Data obtained from these studies facilitated the defining of microbiome signatures in COVID-19 decedents that could be identified as taxonomic biomarkers effective for predicting the occurrence, the co-infections involved in its dysbiosis, and the evolution of the virus.

Nanobodies: the Potential Application in Bacterial Treatment and Diagnosis

An infection caused by bacteria is one of the main factors that poses a threat to human health. A recent report from the World Health Organization (WHO) has highlighted that bacteria that cause blood infections have become increasingly drug-resistant. Therefore, it is crucial to research and develop new techniques for detecting and treating these infections. Since their discovery, nanobodies have exhibited numerous outstanding biological properties. They are easy to express, modify, and have high stability, robust permeability and low immunogenicity, all of which indicate their potential as a substitute. Nanobodies have been utilized in a variety of studies on viruses and cancer. This article primarily focuses on nanobodies and introduces their characteristics and application in the diagnosis and treatment of bacterial infections.

Characterization of the Bacterial Communities in Cichorium intybus According to Cultivation and Storage Conditions

Chicory leaves (Cichorium intybus) are widely consumed due to their health benefits. They are mainly consumed raw or without adequate washing, which has led to an increase in food-borne illness. This study investigated the taxonomic composition and diversity of chicory leaves collected at different sampling times and sites. The potential pathogenic genera (Sphingomonas, Pseudomonas, Pantoea, Staphylococcus, Escherichia, and Bacillus) were identified on the chicory leaves. We also evaluated the effects of various storage conditions (enterohemorrhagic E. coli contamination, washing treatment, and temperature) on the chicory leaves' microbiota. These results provide an understanding of the microbiota in chicory and could be used to prevent food-borne illnesses.

RNA in situ hybridization of Escherichia coli in equine endometrial biopsies

Endometritis is one of the major causes of infertility in mares. Escherichia coli and β-haemolytic streptococci are among the bacterial species most frequently isolated from the equine uterus. Some bacteria such as β-hemolytic streptococci, can persist in dormant forms and cause prolonged, latent or recurrent infections. Dormant bacteria may be present despite negative bacterial cultures, and they are resistant to antimicrobial treatment due to their resting metabolic state. The purpose of this study was to study formalin-fixed paraffin-embedded equine endometrial biopsies for the presence and localization of E. coli-bacteria, with a chromogenic RNAscope^®-method for detection of E. coli-related 16S ribosomal RNA. Hematoxylin-eosin-stained endometrial biopsies were evaluated to determine the level of inflammation and degeneration. During estrus, samples were taken for endometrial culture and cytology with a double-guarded uterine swab. The samples included eight samples with moderate to severe endometrial inflammation detected in endometrial histopathology, and growth of E. coli in bacterial culture, six samples with moderate to severe endometrial inflammation but negative bacterial culture, and five samples with no endometrial pathology (grade I endometrial biopsy, negative endometrial culture and cytology) serving as controls. Positive and negative control probes were included in the RNA in situ hybridization, and results were confirmed with a fluorescence detection method (fluorescence in situ hybridization). Only unspecific signals of limited size and frequency of occurrence were detected in all samples, with random localization in the endometrium. No samples contained rod-shaped signals corresponding to bacterial findings. In conclusion, there was no evidence of bacterial invasion in the endometrium regardless of the inflammatory status of the biopsy or previous bacterial culture results. According to these findings on a small number of samples, invasion of E. coli is not a common finding in the lamina propria of mares, but these bacteria may also evade detection due to localized foci of infections, or supra-epithelial localization under the cover of biofilm. These bacteria and biofilm covering the epithelium may also be lost during formalin-fixation and processing.