Detection of Multiple Resistances, Biofilm Formation and Conjugative Transfer of Bacillus cereus from Contaminated Soils

Regulation of quorum sensing for the manipulation of conjugative transfer of antibiotic resistance genes in wastewater treatment system

The emergence and transmission of antibiotic resistance genes (ARGs) through plasmid-mediated conjugation has become a significant worldwide public health threat. Biofilms are widely recognized as the primary reservoirs for ARGs, providing favorable conditions for horizontal gene transfer. Quorum sensing (QS) plays a critical role in bacterial biofilm formation, which further influences the spread of bacterial resistance. In this study, we examined the effects of vanillin, a QS inhibitor (QSI), at subinhibitory concentrations (sub-MICs) ranging from 0 - 0.1 g/L, on the transfer of ARGs between Escherichia coli and Pseudomonas aeruginosa. Our findings indicated that vanillin at sub-MICs inhibited the conjugative transfer frequency of the RP4 plasmid. This inhibition was supported by the downregulation of plasmid transfer genes. The suppression of conjugation can mainly be attributed to the inhibition of biofilm formation, the synthesis of extracellular polymeric substances (EPS), and the secretion of virulence factors, all of which are regulated by the bacterial QS system. On the other hand, the levels of ROS and cell membrane permeability were not primary explanations for this phenomenon. Furthermore, vanillin also reduced the conjugative transfer frequency of ARGs in wastewater effluent, providing a potential approach to alleviate bacterial resistance in water environments. These findings underscore the regulatory role of QSI in controlling ARGs transfer and have significant implications for manipulating the dissemination of bacterial resistance in the environment.

Impact of biochar on persistence and diffusion of antibiotic resistance genes in sediment from an aquaculture pond

Aquaculture sediments are a purported sizable pool of antibiotic resistance genes (ARGs). However, the pathways for transmission of ARGs from sediments to animals and humans remain unclear. We conducted an ARG survey in sediments from a bullfrog production facility located in Guangdong, China, and simulated zebrafish breeding systems were constructed, with or without biochar addition in sediments, to explore the effects of biochar on ARGs and their precursors of the sediment and zebrafish gut. After 60 days, 6 subtypes of ARGs and intI1 were detected, with sediments harboring more ARGs than zebrafish gut. The addition of biochar reduced the abundance of ARGs in the sediment and zebrafish gut, as well as suppressed the horizontal transmission of ARGs from sediment to zebrafish gut. Network analysis and partial least squares path modeling revealed that ARG enrichment was mainly affected by bacterial groups dominated by Nitrospirae, Gemmatimonades, Chloroflexi, and Cyanobacteria and intI1. Our findings provide insights into the transmission of ARGs from sediment to animals and highlight the efficacy of biochar amendments to aquaculture sediments to reduce the transmission of ARGs.

Paradigm shift in antibiotic-resistome of petroleum hydrocarbon contaminated soil

The increasing prevalence of antibiotic-resistant microorganisms in both clinical and environmental samples is of great concern for public health. In the present study, environmental samples from seven different sites, heavily contaminated with petroleum hydrocarbons has been examined for the antimicrobial resistome through metagenomic approach. The soil samples were found to be contaminated with high concentration of total petroleum hydrocarbons (average 45 g/kg), polyaromatic hydrocarbons (average ∑16PAH = 280 mg/kg), and heavy metals, which shapes the microbial community and their function. Proteobacteria was found to be predominant phylum in the contaminated habitat with the highest diversity (55.91%) followed by Actinobacteria (9.86%). Although the taxonomical abundance of the non-contaminated sample was not significantly different from contaminated samples, the functional abundance of genes related to antibiotic resistance was found to be higher up to 2 fold in contaminated samples. The comparative metagenomic analysis revealed a higher abundance of different antibiotic resistance genes, especially genes for fluoroquinolones was found to be higher up to 10 fold in contaminated samples. Moreover, the study has shown a significant difference in total functional diversity and abundance, mainly genes for aromatic compound metabolism and genes for phages, mobile genetic elements. These higher abundances of well recognized antibiotic resistance genes, multidrug efflux pumps, and integrons, suggest that the petroleum hydrocarbon contaminated sites can act as reservoirs for development of antibiotic resistance genes (ARGs). From this study, a significant link between the presence of petroleum hydrocarbon and the development of antibiotic resistance in the microbiome of contaminated habitat has been established.

Linkage of antibiotic resistance genes, associated bacteria communities and metabolites in the wheat rhizosphere from chlorpyrifos-contaminated soil

Rhizosphere is a crucial site for the proliferation of antibiotic resistance genes (ARGs) in agricultural soil. Pesticide contamination is ubiquitous in soil, such as chlorpyrifos as one of the most commonly used pesticides. However, limited knowledge is reported about ARGs profiles changes and the driving mechanism of ARGs prevalence in rhizosphere soil after adding pesticide. In this study, irrespective of chlorpyrifos presence, the abundances of ARGs (tetM, tetO, tetQ, tetW, tetX, sul1 and sul2) and intI1 in rhizosphere soil of wheat were obviously higher than those in bulk soil. 20.0 mg·kg^-1 chlorpyrifos significantly increased the abundance of total ARGs and intI1 in bulk soil, respectively, at day 50 and 100, but not in rhizosphere soil. Rhizosphere influence on ARGs was far greater than chlorpyrifos. ARGs and intI1 abundances were higher at day 50 than ones at day 100. C/N ratio and NO₃^--N content, which were affected by rhizosphere and cultivation time, significantly explained the increased ARGs. Compared to bulk soil, rhizosphere shifted host bacteria of tetracycline resistance genes (TRGs), intI1 at genus level, and host bacteria of sul1, sul2 at phylum level. Rhizosphere simplified the linkage of ARGs, host bacteria and metabolites. Bacterial communities played important roles in the variation of ARGs and intI1, and the difference in the distribution of potential hosts between bulk and rhizosphere soil was related to metabolites abundance and composition. These results provide valuable information for understanding the linkage of ARGs, associated bacteria communities and metabolites in the wheat rhizosphere soil.

Fungicide-Tolerant Plant Growth-Promoting Rhizobacteria Mitigate Physiological Disruption of White Radish Caused by Fungicides Used in the Field Cultivation

Excessive use of fungicides in agriculture may result in substantial accumulation of active residues in soil, which affect crop health and yield. We investigated the response of Raphanus sativus (white radish) to fungicides in soil and potential beneficial interactions of radish plants with fungicide-tolerant plant growth-promoting rhizobacteria (PGPR). The PGPR were isolated from cabbage and mustard rhizospheres. Morphological and biochemical characteristics measured using standard methods, together with analysis of partial 16S rRNA gene sequences, revealed that fungicide-tolerant PGPR, isolates PS3 and AZ2, were closely related to Pseudomonas spp. These PGPR survived in the presence of high fungicide concentrations i.e., up to 2400 μg mL-1 carbendazim (CBZM) and 3200 μg mL-1 hexaconazole (HEXA). Bacterial isolates produced plant growth stimulants even under fungicide stress, though fungicides induced surface morphological distortion and alteration in membrane permeability of these bacteria, which was proved by a set of microscopic observations. Fungicides considerably affected the germination efficiency, growth, and physiological development of R. sativus, but these effects were relieved when inoculated with PGPR isolates. For instance, CBZM at 1500 mg kg-1 decreased whole dry biomass by 71%, whole plant length by 54%, total chlorophyll by 50%, protein content by 61%, and carotenoid production by 29%. After applying isolate AZ2 for white radish grown in CBZM (10 mg kg-1)-amended soil, it could improve plant growth and development with increased whole plant dry weight (10%), entire plant length (13%) and total chlorophyll content (18%). Similarly, isolate PS3 enhanced plant survival by relieving plant stress with declined biomarkers, i.e., proline (12%), malondialdehyde (3%), ascorbate peroxidase (6.5%), catalase (18%), and glutathione reductase (4%). Application of isolates AZ2 and PS3 could be effective for remediation of fungicide-contaminated soil and for improving the cultivation of radish plants while minimizing inputs of fungicides.

Risk of penicillin fermentation dreg: Increase of antibiotic resistance genes after soil discharge

Penicillin fermentation dreg (PFD) is a solid waste discharged by pharmaceutical enterprises in the fermentation production process. Due to the residual antibiotic of PFD, the risk of antibiotic resistance bacteria (ARB) generation should be considered in the disposal process. High-throughput quantitative PCR (HT-qPCR) and 16S rRNA gene sequencing were performed to investigate the effect of PFD on the dynamics of antibiotic resistance genes (ARGs) and bacterial community during a lab-scale soil experiment. After the application of PFD, the bacterial number and diversity showed an obvious decrease in the initial days. The abundances of Streptomyces and Bacillus, which are the most widespread predicted source phyla of ARGs, increased remarkably from 4.42% to 2.59%-22.97% and 21.35%. The increase of ARGs was observed during the PFD application and the ARGs carried by PFD itself contributed to the initiation of soil ARGs. The results of redundancy analysis (RDA) show that the shift in bacterial community induced by variation of penicillin content is the primary driver shaping ARGs compositions.

Root colonization by heavy metal resistant Enterobacter and its influence on metal induced oxidative stress on Cajanus cajan

BACKGROUND

Heavy metal resistant bacterium Enterobacter sp. C1D was evaluated for cadmium (Cd) mediated exopolysaccharide production, biofilm formation and legume root colonization ability under Cd stress to alleviate metal induced stress.

RESULTS

The plant was sensitive to Cd (IC₅₀ 3-4 μg mL^-1 ), whereas the bacterium showed high Cd tolerance (MIC₉₉ 120 μg mL^-1 ). Confocal laser scanning microscopy of the Cajanus cajan roots showed heavy loads of green fluorescence protein labelled Enterobacter sp. C1D on the surface of plant root, specifically at the point of root hair/lateral root formation along with cortex, even under metal stress. The root colonizing ability of Enterobacter sp. C1D was not affected by the presence of Rhizobium and the bacteria could be observed after 30 days of incubation in soil. Various plant growth parameters, antioxidant metabolites and oxidative stress indicator were significantly influenced by bacterial treatment, which, overall, reduced the adverse effect of Cd.

CONCLUSION

Heavy metal tolerant bacteria may be a good choice for the development of biofertilizers and may work well with the native soil microbes such as Rhizobium under the metal polluted soil. © 2019 Society of Chemical Industry.

A Field Study Into Hong Kong's Wet Markets: Raised Questions Into the Hygienic Maintenance of Meat Contact Surfaces and the Dissemination of Microorganisms Associated With Nosocomial Infections

Millions every day purchase their raw meat in wet markets around the globe, especially in Hong Kong city, where modern and a traditional way of living is made possible. While food hygiene standards in Hong Kong have more recently focused on the safety of meat sold in these wet markets, the hygienic surface level of wooden cutting boards used for processing meats is seldom observed. This original study performed microbial community profiling, as well as isolating and identifying various strains multiple wooden cutting boards from nine wet markets located on Hong Kong Island. Our study also investigated the efficiency of scraping the surface of cutting boards as a traditional cleaning technique in Hong Kong. Results indicate that these hygienic practices are inefficient for guarantying proper surface hygiene as some most tested cutting boards were found to harbor microbial species typically associated with hospital nosocomial infections, such as Klebsiella pneumoniae. Further analysis also led to discovering the presence of antibiotic-resistant genes (ARGs) among isolated strains. Our results showcase the significance and effects of cross-contamination in Hong Kong wet markets, especially with regards to the potential spreading of clinically-relevant strains and ARGs on food processing surfaces. This study should, therefore, serve as a basis to review current hygienic practices in Hong Kong's wet market on a larger scale, thereby improving food safety and ultimately, public health.

Metagenomic assembly provides a deep insight into the antibiotic resistome alteration induced by drinking water chlorination and its correlations with bacterial host changes

Chlorination can contribute to the enrichment of specific antibiotic resistance genes (ARGs) in drinking water, but the underlying molecular ecological mechanisms remain unknown, which may hinder the assessment and control of the resulting health risks. In this study, metagenomic assembly and Resfams annotation were used to profile the co-occurrence patterns of ARGs, mobile genetic elements (MGEs) and their bacterial hosts, as well as the correlations of potential pathogens with the antibiotic resistome, in a full-scale drinking water treatment and transportation system. Seven ARG types involved in different resistance mechanisms occurred in drinking water and chlorination enhanced the total abundance of the ARGs (p <  0.05). The ARGs encoding resistance-nodulation-cell division and ATP-binding cassette antibiotic efflux pumps predominated in all the samples and were primarily responsible for the ARG accumulation. After chlorination, the ARGs were primarily carried by predominant Sphingomonas, Polaromonas, Hyphomicrobium, Acidovorax, Pseudomonas and Fluviicola. Further, enrichment of the bacterial hosts and MGEs greatly contributed to alteration of the antibiotic resistome. Pseudomonas alcaligenes, carrying multiple ARGs, was identified as a potential pathogen in the chlorinated drinking water. These findings provide novel insights into the host-ARG relationship and the mechanism underlying the resistome alteration during drinking water chlorination.

Occurrence of antibiotic resistance genes in extracellular and intracellular DNA from sediments collected from two types of aquaculture farms

The occurrence and quantities of ARGs in extracellular and intracellular DNA (eARGs and iARGs) from sediments collected in two different types of aquaculture farms were investigated. A total of 20 ARG subtypes associated with 7 categories of commonly used antibiotics (e.g., aminoglycosides, beta-lactams, sulfonamides, tetracyclines) were identified, and some of these subtypes were not related to the antibiotics used. ARGs are mainly present in the iDNA form with the ratio of the total iARGs to eARGs being in the range of 7.9-45.5. The ratio of eARG to iARGs varies greatly with ARG subtypes, probably due to their differences in persistence as a part of eDNA. Significant correlation between int1 and ARGs was observed for both eDNA and iDNA in sediments from the aquaculture farms. Moreover, ARG pollution was more serious in bullfrog ponds than polyculture ponds due to the more frequent use of antibiotics in bullfrog rearing operations.

Biofilm research within irrigation water distribution systems: Trends, knowledge gaps, and future perspectives

Biofilms in irrigation water distribution systems (IWDSs) play an essential role in spreading pathogens, chemical pollutants, and environmental pollutants into downstream irrigated crops and thus should be considered a potential threat to food safety. Although the role of biofilms in drinking water distribution systems has been extensively studied in the last decade, the research on IWDS biofilms in this period has been limited. This review identifies research gaps in the field of IWDS biofilms, provides perspectives on experimental designs for investigating IWDS biofilms, and suggests potential strategies worth pursuing in IWDS management. The current state of the art of IWDS biofilms is discussed, and an analysis of the challenges in IWDS biofilm research is presented. Furthermore, this review proposes useful advanced technologies that allow a practical, in-depth fundamental understanding of IWDS biofilms. In a nutshell, this article provides future directions and insights into detailed experimental designs on a relatively under-reported research topic: "IWDS biofilms."

Complex pollution of antibiotic resistance genes due to beta-lactam and aminoglycoside use in aquaculture farming

The prevalence of antibiotic resistance in the modern world has raised global concerns for public health. Establishing relationships between antibiotic use and antibiotic resistance genes (ARGs) is essential to understanding the dissemination and accumulation of ARGs in a human-impacted environment. In this study, ARG profiles in the sediments from a bullfrog farm, where penicillin and amoxicillin (beta-lactams) and gentamicin (aminoglycoside) were used for prophylactic purposes, were analyzed using metagenomic approaches. Analysis of both extracellular and intracellular DNA (eDNA and iDNA) demonstrated that use of the above-mentioned antibiotics led to complex pollution of ARGs not only related to beta-lactams and aminoglycoside but also to sulfonamides, tetracyclines, and macrolides. Most of the ARGs in the sediments from the bullfrog farm were likely carried by plasmids. A significant correlation was observed between the total abundance of ARG-related plasmids and that of plasmid-carrying ARGs. Approximately 85% of the plasmids likely present in the sediment from the bullfrog farm possessed at least 3 ARG subtypes, which conferred the resistance of bacterial hosts to different antibiotic categories. Our results suggest that antibiotics could lead to complex pollution of ARGs unrelated to those administered due to the concurrence of ARGs in the plasmids.

PAHs accelerate the propagation of antibiotic resistance genes in coastal water microbial community

Antibiotic resistance genes (ARGs) have been regarded as emerging contaminants and have attracted growing attention owing to their widespread presence in the environment. In addition to the well-documented selective pressure of antibiotics, ARGs have also become prevalent because of anthropogenic impacts. Coastal habitats are located between terrestrial and marine ecosystems, which are a hotspot for anthropogenic impacts. Excessive accumulation of polycyclic aromatic hydrocarbons (PAHs) has posed a serious threat to coastal habitats, but no information is available on the effect of PAHs on antibiotic resistance in the microbial community of coastal environments. In this study, the effect of two typical PAHs, naphthalene and phenanthrene, on antibiotic resistance propagation was investigated in a coastal microbial community. The results indicated that the presence of 100 mg/L of naphthalene or 10 mg/L of phenanthrene significantly enhanced the abundance of class I integrase gene (intI1), sulfanilamide resistance gene (sulI), and aminoglycosides resistance gene (aadA2) in the microbial community. Horizontal gene transfer experiment demonstrated that increased abundance of ARGs was primarily a result of conjugative transfer mediated by class I integrons. These findings provided direct evidence that coastal microbial community exposed to PAHs might have resulted in the dissemination of ARGs and implied that a more comprehensive risk assessment of PAHs to natural ecosystems and public health is necessary.

Polycyclic aromatic hydrocarbons (PAHs) enriching antibiotic resistance genes (ARGs) in the soils

The prevalence of antibiotic resistance genes (ARGs) in modern environment raises an emerging global health concern. In this study, soil samples were collected from three sites in petrochemical plant that represented different pollution levels of polycyclic aromatic hydrocarbons (PAHs). Metagenomic profiling of these soils demonstrated that ARGs in the PAHs-contaminated soils were approximately 15 times more abundant than those in the less-contaminated ones, with Proteobacterial being the preponderant phylum. Resistance profile of ARGs in the PAHs-polluted soils was characterized by the dominance of efflux pump-encoding ARGs associated with aromatic antibiotics (e.g., fluoroquinolones and acriflavine) that accounted for more than 70% of the total ARGs, which was significantly different from representative sources of ARG pollution due to wide use of antibiotics. Most of ARGs enriched in the PAHs-contaminated soils were not carried by plasmids, indicating the low possibilities of them being transferred between bacteria. Significant correlation was observed between the total abundance of ARGs and that of Proteobacteria in the soils. Proteobacteria selected by PAHs led to simultaneously enriching of ARGs carried by them in the soils. Our results suggested that PAHs could serve as one of selective stresses for greatly enriching of ARGs in the human-impacted environment.

Bacillus cereus Biofilms-Same, Only Different

Bacillus cereus displays a high diversity of lifestyles and ecological niches and include beneficial as well as pathogenic strains. These strains are widespread in the environment, are found on inert as well as on living surfaces and contaminate persistently the production lines of the food industry. Biofilms are suspected to play a key role in this ubiquitous distribution and in this persistency. Indeed, B. cereus produces a variety of biofilms which differ in their architecture and mechanism of formation, possibly reflecting an adaptation to various environments. Depending on the strain, B. cereus has the ability to grow as immersed or floating biofilms, and to secrete within the biofilm a vast array of metabolites, surfactants, bacteriocins, enzymes, and toxins, all compounds susceptible to act on the biofilm itself and/or on its environment. Within the biofilm, B. cereus exists in different physiological states and is able to generate highly resistant and adhesive spores, which themselves will increase the resistance of the bacterium to antimicrobials or to cleaning procedures. Current researches show that, despite similarities with the regulation processes and effector molecules involved in the initiation and maturation of the extensively studied Bacillus subtilis biofilm, important differences exists between the two species. The present review summarizes the up to date knowledge on biofilms produced by B. cereus and by two closely related pathogens, Bacillus thuringiensis and Bacillus anthracis. Economic issues caused by B. cereus biofilms and management strategies implemented to control these biofilms are included in this review, which also discuss the ecological and functional roles of biofilms in the lifecycle of these bacterial species and explore future developments in this important research area.