A comparative genomics approach for identifying genetic factors in Escherichia coli isolates associated with bovine diseases

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Abstract

Aims

E. coli are ubiquitously present bacterial pathogens that cause septicaemia, diarrhoea and other clinical illness in farm animals. Many pathogen factors can be associated with disease conditions. Currently, studies inferring E. coli genetic factors associated with infection in bovines are limited. Hence, the present study envisaged to determine the pathogen genetic factors associated with bovine disease conditions.

Method and Results

The comparative genomic analysis involved genome sequence data of 135 diseased and 145 healthy bovine origin E. coli strains. Phylogroups A and C, as well as pathotypes ExPEC and EPEC, were found to have a strong connection with bovine disease strains. STEC strains, including EHEC, seem to play a less important role in bovine disease. Sequence types (STs) predominant among strains from diarrhoeal origin were ST 301 (CC 165) and ST 342. Correlation of core genome phylogeny with accessory gene-based clustering, phylogroups and pathotypes indicated lineage-specific virulence factors mostly associated with disease conditions.

Conclusions

Comparative genomic analysis was applied to infer genetic factors significant in bovine disease origin E. coli strains. Isolates from bovine disease origin were enriched for the phylogroups A and C, and for the pathotypes ExPEC and EPEC. However, there was minimal evidence of STEC involvement. The study also indicated predominant genetic lineages and virulence genes (pap, sfa and afa) associated with disease origin strains.

Significance and impact of study

The study revealed significant pathotypes, phylogroups, serotypes and sequence types associated with bovine disease conditions. These identified genetic factors can be applied for disease diagnosis, implementing vaccines and therapeutic measures. In addition, E. coli isolates from the bovine species revealed a complex pattern of disease epidemiology.

Rapid phylogenetic analysis using open reading frame content patterns acquired by Oxford nanopore sequencing

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Abstract

Aims

Phylogenetic analysis based on core genome single nucleotide polymorphisms (cgSNPs) using whole-genome sequencing (WGS) is increasingly used in epidemiological investigations of bacteria. The approach, however, is both resource intensive and time-consuming. Oxford Nanopore Technologies (ONT) sequencing is capable of real-time data analysis but the high error rate hampers its application in cgSNP-based phylogenetic analysis. Here, we developed a cgSNP-independent phylogenetic analysis method using ONT read assemblies by focusing on open reading frame (ORF) content patterns.

Methods and Results

WGS data of 66 Enterobacter hormaechei strains acquired by both ONT and Illumina sequencing and 162 strains obtained from NCBI database were converted to binary sequences based on the presence or absence of ORFs using BLASTn. Phylogenetic trees calculated from binary sequences (ORF trees) were compared with cgSNP trees derived from Illumina sequences. Clusters of closely related strains in the cgSNP trees formed comparable clusters in the ORF trees built with binary sequences, and the tree topologies between them were similar based on Fowlkes–Mallows index.

Conclusions

The ORF-based phylogenetic analysis using ONT sequencing may be useful in epidemiological investigations and offer advantages over the cgSNP-based approach.

Significance and Impact of the study

Conversion of assembled WGS data to binary sequences based on the presence or absence of ORFs circumvents read error concerns with ONT sequencing. Since ONT sequencing generates data in real time and does not require major investment, this ORF-based phylogenetic analysis method has the potential to enable phylogenetic and epidemiological analysis at the point of care.

Transfer of Phi6 bacteriophage between human skin and surfaces common to consumer‐facing environments

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Abstract

Aims

This study aimed to determine the extent of Phi6 (Φ6) transfer between skin and surfaces relevant to consumer-facing environments based on inoculum matrix, surface type and contact time.

Methods and Results

Φ6 transfer rates were determined from skin-to-fomite and fomite-to-skin influenced by inoculum matrix (artificial saliva and tripartite), surface type (aluminium, plastic, stainless steel, touchscreen, vinyl and wood) and contact time (5 and 10 s). Significant differences in estimated means were observed based on surface type (both transfer directions), inoculum matrix (skin-to-fomite) and contact time (both transfer directions). During a sequential transfer experiment from fomite-to-skin, the maximum number of consecutive transfer events observed was 3.33 ± 1.19, 2.33 ± 1.20 and 1.67 ± 1.21 for plastic, touchscreen and vinyl, respectively.

Conclusions

Contact time significantly impacted Φ6 transfer rates, which may be attributed to skin absorption dynamics. Surface type should be considered for assessing Φ6 transfer rates.

Significance and Impact of the Study

Although the persistence of Φ6 on fomites has been characterized, limited data are available regarding the transfer of Φ6 among skin and fomites. Determining Φ6 transfer rates for surfaces in consumer-facing environments based on these factors is needed to better inform future virus transmission mitigation strategies.

Ultrasound‐assisted encapsulation of curcumin and fisetin into Saccharomyces cerevisiae cells: a multistage batch process protocol

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Ultrasound-assisted encapsulation of curcumin and fisetin into Saccharomyces cerevisiae cells: a multistage batch process protocol

Significance and Impact of the Study: To the best of our knowledge, this is the first report investigating an ultrasound-assisted batch encapsulation of lipophilic bioactive molecules into Saccharomyces cerevisiae cells. Although ultrasound is a mild, nonthermal, and straightforward cell permeabilization process, few works have investigated it for encapsulation purposes. This study presents a new perspective on the application of ultrasound technology to develop a more economical and eco-friendly process for the food industry, creating a rational way to internalize lipophilic molecules into yeasts via successive stages of encapsulation.


Abstract

Some of the challenges of yeast encapsulation protocols are low phytochemical internalization rates and limited intracellular compartments of yeasts. This study uses an ultrasound-assisted batch encapsulation (UABE) protocol to optimize the encapsulation of curcumin and fisetin by recovering nonencapsulated biomaterial and further incorporating it into nonloaded yeasts in three encapsulation stages (1ES, 2ES and 3ES). The effect of selected acoustic energies (166·7 and 333·3 W l−1) on the encapsulation efficiency (EE), yield (EY) and antioxidant activity retention were evaluated, and then, compared with a control process (without ultrasound treatment). Compared to the control, enhanced EEs were achieved for both curcumin (10·9% control to 58·5% UABE) and fisetin (18·6% control to 76·6% UABE) after 3ES and the use of 333·3 W l−1. Similarly, the yeast maximum loading capacity was improved from 6·6 to 13·4 mg g−1 for curcumin and from 11·1 to 26·4 mg g−1 for fisetin after UABE protocol. The antioxidant activity of produced biocapsules was positively correlated with the bioactive-loaded content of yeasts when ultrasound treatment was applied. Overall, results from this study provide valuable information regarding UABE processes, and moreover, bring new and creative perspectives for ultrasound technology in the food industry.

Molecular mechanisms and clonal lineages of colistin‐resistant bacteria across the African continent: a scoping review

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Molecular mechanisms and clonal lineages of colistin-resistant bacteria across the African continent: a scoping review

Significance and Impact of the Study: Increasing usage of antimicrobial compounds in human and veterinary medicine has contributed to the global emergence and transmission of antimicrobial-resistant bacteria, representing a major concern for human and animal health. According to many international and governmental organizations, the impact of antimicrobial resistance will be particularly significant in low-income regions across Africa, Asia, and Latin America. Accordingly, the development and implementation of multidisciplinary (i.e. One Health) evidence-based control programs and strategies are critical. Colistin is a ‘last-resort’ antimicrobial treatment for multidrug-resistant Gram-negative infections including pneumonia from Enterobacterales; however, high rates of colistin resistance have been reported globally, including Africa. A more profound understanding of the molecular mechanisms underlying colistin resistance is required for the development of effective surveillance programs and innovative therapies against multidrug-resistant bacteria.


Abstract

Colistin (also known as polymyxin E), a polymyxin antibiotic discovered in the late 1940s, has recently reemerged as a last-line treatment option for multidrug-resistant infections. However, in recent years, colistin-resistant pathogenic bacteria have been increasingly reported worldwide. Accordingly, the presented review was undertaken to identify, integrate and synthesize current information regarding the detection and transmission of colistin-resistant bacteria across the African continent, in addition to elucidating their molecular mechanisms of resistance. PubMed, Google Scholar and Science Direct were employed for study identification, screening and extraction. Overall, based on the developed literature review protocol and associated inclusion/exclusion criteria, 80 studies published between 2000 and 2021 were included comprising varying bacterial species and hosts. Numerous mechanisms of colistin resistance were reported, including chromosomal mutation(s) and transferable plasmid-mediated colistin resistance (encoded by mcr genes). Perhaps unexpectedly, mcr-variants have exhibited rapid emergence and spread across most African regions. The genetic variant mcr-1 is predominant in humans, animals and the natural environment, and is primarily carried by IncHI2- type plasmid. The highest number of studies reporting the dissemination of colistin-resistant Gram-negative bacteria were conducted in the North African region.

Campylobacter jejuni and other emerging Campylobacteraceae in retail beef liver – an underestimated potential source?

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Campylobacter jejuni and other emerging Campylobacteraceae in retail beef liver – an underestimated potential source?

Significance and Impact of the Study: Campylobacteraceae has been associated with both intestinal and systemic disease in humans and animals; however, their transmission routes are not entirely clear. Although some species are transmitted by the consumption of chicken or beef meat, other foods such as beef liver have been far less studied. Therefore, this study provides information on retail bovine liver as an underestimated reservoir of diverse Campylobacteraceae, such as Arcobacter butzleri, Campylobacter fetus and Campylobacter coli and its antibiotic resistance profiles. Additionally, the genetic concordance found between Campylobacter jejuni isolates from livers with clinical strains isolated previously in Chile suggests a potential zoonotic relationship.


Abstract

Bovine by-products, such as liver, could be an underestimated source of Campylobacter jejuni. Therefore, our aims were to evaluate the occurrence of C. jejuni and other Campylobacteraceae in retail beef liver and characterize their antibiotic resistance (ciprofloxacin, tetracycline, erythromycin and gentamicin) and potential genetic relationship by flagellin gene restriction fragment length polymorphism (flaA-RFLP) and multilocus sequence typing with clinical strains. Seventy-six out of 206 samples (36·9%) were positive for Campylobacter and related organisms. Arcobacter butzleri was the most frequently isolated species (21·8%), followed by C. jejuni (9·7%), C. fetus (7·8%) and C. coli (1%). The C. jejuni strains showed resistance to tetracycline (17·2%) or ciprofloxacin (6·9%), with only one strain resistant to both antibiotics. Meanwhile, 8·3% of ciprofloxacin resistance was observed in C. fetus. The other species showed no resistance. Most of the clonal complexes (CC) in which the C. jejuni genotypes were grouped (CC-21, 42, 48 and 52), coincided with genotypes of clinical strains previously reported in Chile. As such, this study provides evidence that beef liver could be an underestimated route for resistant C. jejuni to humans. Further studies should assess whether this food could play a role in the transmission of other emerging Campylobacteraceae such as those reported here.

Evaluation of antimicrobial activity of thiolated methylated N‐(4‐N,N‐dimethylaminobenzyl) chitosan as a new derivative of chitosan

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Evaluation of antimicrobial activity of thiolated methylated N-(4-N,N-dimethylaminobenzyl) chitosan as a new derivative of chitosan

Significance and Impact of the Study: Bacterial infection is a major challenge in the world. Using membrane-targeting cationic polymers make an efficient approach for fighting bacterial infection. In this study, thiolated, methylated N-(4-N,N-dimethylaminobenzyl) chitosan polymer showed efficient antimicrobial effects against Gram-positive and Gram-negative bacteria and also against yeast.


Abstract

Despite chitosan, a natural cationic polysaccharide derived from chitin, being applied as an antimicrobial agent, many studies are being performed for enhancing its capability to fight against pathogens. The aim of this study was to investigate the antibacterial effect of thiolated methylated N-(4-N,N-dimethylaminobenzyl) chitosan (TTMAC) polymer and its nanoparticles as a novel derivation of chitosan. The polymer derivative was synthetized and characterized via 1H NMR, Fourier transform infrared and the Elman test. The nanoparticles with different N/P ratios were prepared by the ionic gelation method and were characterized by dynamic light scattering and transmission electron microscopy. The cellular toxicity of polymer and nanoparticles at different concentrations were evaluated on human MCF-7 cell line. Antimicrobial assay was performed on Escherichia coli (ATCC 25922), Staphylococcus aureus (ATCC 25923) and Candida albicans (ATCC 10231) as Gram-negative, Gram-positive and yeast pathogens, respectively. The obtained results have shown the TTMAC polymer has a higher inhibition activity against microbial pathogens and also lower cellular toxicity in comparison with chitosan polymer. Furthermore, chitosan nanoparticles in comparison with TTMAC nanoparticles have lower size and highest zeta potential in different ratio and chitosan nanoparticles have more inhibitory effects against microbial pathogens. In conclusion, TTMAC derivative in polymeric form can be a promising tool against microbial pathogens.

Architectural analysis of root system and phytohormone biosynthetic genes expression in wheat (Triticum aestivum L.) inoculated with Penicillium oxalicum

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Architectural analysis of root system and phytohormone biosynthetic genes expression in wheat (Triticum aestivum L.) inoculated with Penicillium oxalicum

Significance and Impact of the Study; Although the impact of microbes on plant growth promotion and root architecture has been widely examined using bacteria, the role of fungi is much less studied. Here, we examined the effect of a potential fungal plant growth promoter Penicillium oxalicum T4 on root architecture and growth of wheat seedlings. Confocal scanning laser micrographs and scanning electron micrographs indicted profuse colonization in wheat roots and induction of root hairs, respectively. Furthermore, P. oxalicum T4 was shown to modulate the expression of host genes related to root growth and development. Overall, P. oxalicum T4 was found to hold promise as a potential microbial formulation for boosting wheat growth.


Abstract

In this study, a fungal plant growth promoter Penicillium oxalicum T4 isolated from non-rhizosphere soil of Arunachal Pradesh, India, was screened for different plant growth promoting traits in a gnotobiotic study. Though inoculation improved the overall growth of the plants, critical differences were observed in root architecture. Confocal Laser Scanning Microscope, Scanning electron microscope and the stereo microscopic study showed that inoculated wheat plants could develop profuse root hairs as compared to control. Root scanning indicated improvement in cumulative root length, root area, root volume, number of forks, links, crossings, and other parameters. A confocal scanning laser microscope indicated signs of endophytic colonization in wheat roots. Gene expression studies revealed that inoculation of T4 modulated the genes affecting root hair development. Significant differences were marked in the expression levels of TaRSL4, TaEXPB1, TaEXPB23, PIN-FORMED protein, kaurene oxidase, lipoxygenase, ACC synthase, ACC oxidase, 9-cis-epoxycarotenoid dioxygenase, and ABA 8′-hydroxylase genes. These genes contribute to early plant development and ultimately to biomass accumulation and yield. The results suggested that P. oxalicum T4 has potential for growth promotion in wheat and perhaps also in other cereals.

Synergistic effects of a functional bacterial consortium on enhancing phenanthrene biodegradation and counteracting rare earth biotoxicity in liquid and slurry systems

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Synergistic effects of a functional bacterial consortium on enhancing phenanthrene biodegradation and counteracting rare earth biotoxicity in liquid and slurry systems

Significance and Impact of the Study: This study focused on the effect of rare earth (REs) on the biodegradation of polycyclic aromatic hydrocarbons (PAHs). The RE ions Ce3+ and Y3+ inhibited Moraxella osloensis CFP312 from degrading phenanthrene without affecting its glucose utilization. This inhibition effect can be relieved through co-cultivation with Bacillus subtilis MSP117, which has high adsorption capacity for RE ions in liquid and slurry systems. MSP117 adsorbed and fixed RE ions on its cell surfaces, thereby reducing the bioavailability of RE ions. This study provides a feasible way for the bioremediation of the co-pollution of RE and organic pollutants.


Abstract

The biodegradation of polycyclic aromatic hydrocarbons (PAHs) by micro-organisms in the environment is often inhibited by coexisting metal ions. The aim of this work is to study a bacterial consortium for enhancing phenanthrene biodegradation under the inhibition effect of the rare earth (RE) ions Ce3+ and Y3+. This bacterial consortium was composed of two bacteria, namely, the RE-adsorbing Bacillus subtilis MSP117 and the phenanthrene-degrading Moraxella osloensis CFP312. Ce3+ and Y3+ at the concentration of 1·15 mmol l−1 inhibited CFP312 from degrading phenanthrene but not glucose. Using glucose as a co-substrate could promote the proliferation of CFP312 but decreased phenanthrene degradation. Adsorption experiments and electron microscopy imaging showed that CFP312 had no RE ions adsorption capacity for RE ions and that RE elements could not be observed on its cell surfaces. MSP117 could adsorb 0·14 and 0·12 mmol g−1 wet cells of Ce3+ and Y3+ in aqueous solution, respectively, thus demonstrating considerable adsorption capacity. The MSP117 cell surface immobilized part of the free RE ions and reduced their bioaccessibility, thereby alleviating their biotoxic effect on phenanthrene degradation by CFP312. In liquid and slurry systems, glucose, which was used as the co-substrate of the bacterial consortium, must be kept at a low level to avoid the catabolism repression of phenanthrene degradation by CFP312.