Simultaneous estimation of parameters governing the vertical and horizontal transfer of antibiotic resistance genes

Masks As a New Hotspot for Antibiotic Resistance Gene Spread: Reveal the Contribution of Atmospheric Pollutants and Potential Risks

The consumption of disposable surgical masks (DSMs) considerably increased during the coronavirus pandemic in 2019. Herein, we explored the spread of antibiotic resistance genes (ARGs) and the potential risks of antibiotic resistant bacteria (ARB) on DSMs. At environmentally relevant concentrations, the conjugate transfer frequency (CTF) of ARGs increased by 1.34-2.37 folds by 20 μg/m3 of atmospheric water-soluble inorganic ions (WSIIs), and it increased by 2.62-2.86 folds by 80 ng/m3 of polycyclic aromatic hydrocarbons (PAHs). Total suspended particulates (TSP) further promoted the CTF in combination with WSIIs or PAHs. Under WSII and PAH exposure, gene expression levels related to oxidative stress, cell membrane, and the adenosine triphosphate (ATP) were upregulated. WSIIs predominantly induced cellular contact, while PAHs triggered ATP formation and membrane damage. Molecular dynamics simulations showed that WSIIs and PAHs reduced membrane lipid fluidity and increased membrane permeability through interactions with the phosphatidylcholine bilayer. DSM filtering performance decreased, and the CTF of ARGs increased with the wearing time. The gut simulator test showed that ARB disrupted the human gut microbial community and increased total ARG abundance but did not change the ARG abundance carried by ARB themselves. A mathematical model showed that long-term WSII and PAH exposure accelerated ARG dissemination in DSMs.

Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment

The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.

Performance of sewage sludge treatment for the removal of antibiotic resistance genes: Status and prospects

Wastewater treatment plants (WWTPs) receive wastewater containing antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), which are predominant contributors to environmental pollution in water and soil. Of these sources, sludge is a more significant contributor than effluent. Knowing how sludge treatment affects the fate of ARGs is vital for managing the risk of these genes in both human and natural environments. This review therefore discusses the sources and transmission of ARGs in the environment and highlights the risks of ARGs in sludge. The effects of co-existing constituents (heavy metals, microplastics, etc.) on sludge and ARGs during treatment are collated to highlight the difficulty of treating sludge with complex constituents in ARGs. The effects of various sludge treatment methods on the abundances of ARGs in sludge and in soil from land application of treated sludge are discussed, pointing out that the choice of sludge treatment method should take into account various potential factors, such as soil and soil biology in subsequent land application. This review offers significant insights and explores the abundances of ARGs throughout the process of sludge treatment and disposal. Unintentional addition of antibiotic residues, heavy metals, microplastics and organic matter in sludge could significantly increase the abundance and reduce the removal efficiency of ARGs during treatment, which undoubtedly adds a barrier to the removal of ARGs from sludge treatment. The complexity of the sludge composition and the diversities of ARGs have led to the fact that no effective sludge treatment method has so far been able to completely eliminate the ecological risk of ARGs. In order to reduce risks resulting by transmission of ARGs, technical and management measures need to be implemented.

Interference with Bacterial Conjugation and Natural Alternatives to Antibiotics: Bridging a Gap

Horizontal gene transfer (HGT) in food matrices has been investigated under conditions that favor gene exchange. However, the major challenge lies in determining the specific conditions pertaining to the adapted microbial pairs associated with the food matrix. HGT is primarily responsible for enhancing the microbial repertoire for the evolution and spread of antimicrobial resistance and is a major target for controlling pathogens of public health concern in food ecosystems. In this study, we investigated Salmonella Heidelberg (SH) and Escherichia coli (EC) regarding gene exchange under conditions mimicking the industrial environment, with the coproducts whey (SL) and chicken juice (CJ). The S. Heidelberg strain was characterized by antibiotic susceptibility standards and PCR to detect the bla_TEM gene. A concentration of 0.39 mg/mL was determined to evaluate the anti-conjugation activity of nanostructured lipid nanocarriers (NLCs) of essential oils to mitigate β-lactam resistance gene transfer. The results showed that the addition of these coproducts promoted an increase of more than 3.5 (whey) and 2.5 (chicken juice) orders of magnitude in the conjugation process (p < 0.01), and NLCs of sage essential oil significantly reduced the conjugation frequency (CF) by 74.90, 90.6, and 124.4 times when compared to the transfers in the absence of coproducts and the presence of SL and CJ, respectively. For NLCs from olibanum essential oil, the decrease was 4.46-fold for conjugations without inhibitors and 3.12- and 11.3-fold in the presence of SL and CJ. NLCs associated with sage and olibanum essential oils effectively control the transfer of antibiotic resistance genes and are a promising alternative for use at industrial levels.

Augmented dissemination of antibiotic resistance elicited by non-antibiotic factors

The emergence and rapid spread of antibiotic resistance seriously compromise the clinical efficacy of current antibiotic therapies, representing a serious public health threat worldwide. Generally, drug-susceptible bacteria can acquire antibiotic resistance through genetic mutation or gene transfer, among which horizontal gene transfer (HGT) plays a dominant role. It is widely acknowledged that the sub-inhibitory concentrations of antibiotics are the key drivers in promoting the transmission of antibiotic resistance. However, accumulating evidence in recent years has shown that in addition to antibiotics, non-antibiotics can also accelerate the horizontal transfer of antibiotic resistance genes (ARGs). Nevertheless, the roles and potential mechanisms of non-antibiotic factors in the transmission of ARGs remain largely underestimated. In this review, we depict the four pathways of HGT and their differences, including conjugation, transformation, transduction and vesiduction. We summarize non-antibiotic factors accounting for the enhanced horizontal transfer of ARGs and their underlying molecular mechanisms. Finally, we discuss the limitations and implications of current studies.

Co-Existence of Oxazolidinone Resistance Genes cfr(D) and optrA on Two Streptococcus parasuis Isolates from Swine

This study was performed to investigate the presence and characteristics of the oxazolidinone resistance genes optrA and cfr(D) in Streptococcus parasuis. In total, 36 Streptococcus isolates (30 Streptococcus suis isolates, 6 Streptococcus parasuis isolates) were collected from pig farms in China in 2020-2021, using PCR to determine the presence of optrA and cfr. Then, 2 of the 36 Streptococcus isolates were further processed as follows. Whole-genome sequencing and de novo assembly were employed to analyze the genetic environment of the optrA and cfr(D) genes. Conjugation and inverse PCR were employed to verify the transferability of optrA and cfr(D). The optrA and cfr(D) genes were identified in two S. parasuis strains named SS17 and SS20, respectively. The optrA of the two isolates was located on chromosomes invariably associated with the araC gene and Tn554, which carry the resistance genes erm(A) and ant(9). The two plasmids that carry cfr(D), pSS17 (7550 bp) and pSS20-1 (7550 bp) have 100% nucleotide sequence identity. The cfr(D) was flanked by GMP synthase and IS1202. The findings of this study extend the current knowledge of the genetic background of optrA and cfr(D) and indicate that Tn554 and IS1202 may play an important role in the transmission of optrA and cfr(D), respectively.

Response of Antibiotic Resistance Genes and Related Microorganisms to Arsenic during Vermicomposting of Cow Dung

Antibiotic resistance pollution in livestock manure is a persistent issue that has drawn public attention. Vermicomposting is an ecofriendly biological process that can render livestock manure harmless and resourceful. However, little is known about the impact of vermicomposting on antibiotic resistance in livestock manure under stress caused by potentially toxic arsenic levels. Herein, lab-scale vermicomposting was performed to comprehensively evaluate the shift in antibiotic resistance genes (ARGs) and related microorganisms in fresh earthworm casts as well as vermicompost product health (i.e., nutrient availability and enzyme activity) when they were fed on arsenic-contaminated cow manure. The results showed that the earthworms' interaction with cow dung led to a significant reduction in ARG concentrations, especially for tetracycline ARGs (tet-ARGs), β-lactam ARGs (bla-ARGs), and quinolone ARGs (qnr-ARGs). However, arsenic significantly enhanced ARG accumulation in earthworm casts in a dose-dependent manner. Moreover, vermicomposting increased the percentage of Bacteroidota in the converted products. Furthermore, arsenic exposure at low concentrations promoted the proliferation of Proteobacteria, whereas high concentrations had little effect on Proteobacteria. Our study provides valuable insight into the changes in the antibiotic resistome and related microorganisms during vermicomposting of arsenic-amended cow manure, and it is crucial to explain the environmental impact of earthworms and improve our understanding of the reciprocal benefits of soil invertebrates.

Bacteriophages: Underestimated vehicles of antibiotic resistance genes in the soil

Bacteriophages (phages), the most abundant biological entities on Earth, have a significant effect on the composition and dynamics of microbial communities, biogeochemical cycles of global ecosystems, and bacterial evolution. A variety of antibiotic resistance genes (ARGs) have been identified in phage genomes in different soil samples. Phages can mediate the transfer of ARGs between bacteria via transduction. Recent studies have suggested that anthropogenic activities promote phage-mediated horizontal gene transfer events. Therefore, the role of phages in the dissemination of ARGs, which are a potential threat to human health, may be underestimated. However, the contribution of phages to the transfer of ARGs is still poorly understood. Considering the growing and wide concerns of antibiotic resistance, phages should be considered a research focus in the mobile resistome. This review aimed to provide an overview of phages as vehicles of ARGs in soil. Here, we summarized the current knowledge on the diversity and abundance of ARGs in soilborne phages and analyzed the contribution of phages to the horizontal transfer of ARGs. Finally, research deficiencies and future perspectives were discussed. This study provides a reference for preventing and controlling ARG pollution in agricultural systems.

Multiwalled Carbon Nanotubes Promote Bacterial Conjugative Plasmid Transfer

Multiwalled carbon nanotubes (MWCNTs) regularly enter aquatic environments due to their ubiquity in consumer products and engineering applications. However, the effects of MWCNT pollution on the environmental microbiome are poorly understood. Here, we evaluated whether these carbon nanoparticles can elevate the spread of antimicrobial resistance by promoting bacterial plasmid transfer, which has previously been observed for copper nanomaterials with antimicrobial properties as well as for microplastics. Through a combination of experimental liquid mating assays between Pseudomonas putida donor and recipient strains with plasmid pKJK5::gfpmut3b and mathematical modeling, we here demonstrate that the presence of MWCNTs leads to increased plasmid transfer rates in a concentration-dependent manner. The percentage of transconjugants per recipient significantly increased from 0.21 ± 0.04% in absence to 0.41 ± 0.09% at 10 mg L-1 MWCNTs. Similar trends were observed when using an Escherichia coli donor hosting plasmid pB10. The identified mechanism underlying the observed dynamics was the agglomeration of MWCNTs. A significantly increased number of particles with >6 μm diameter was detected in the presence of MWCNTs, which can in turn provide novel surfaces for bacterial interactions between donor and recipient cells after colonization. Fluorescence microscopy confirmed that MWCNT agglomerates were indeed covered in biofilms that contained donor bacteria as well as elevated numbers of green fluorescent transconjugant cells containing the plasmid. Consequently, MWCNTs provide bacteria with novel surfaces for intense cell-to-cell interactions in biofilms and can promote bacterial plasmid transfer, hence potentially elevating the spread of antimicrobial resistance. IMPORTANCE In recent decades, the use of carbon nanoparticles, especially multiwalled carbon nanotubes (MWCNTs), in a variety of products and engineering applications has been growing exponentially. As a result, MWCNT pollution into environmental compartments has been increasing. We here demonstrate that the exposure to MWCNTs can affect bacterial plasmid transfer rates in aquatic environments, an important process connected to the spread of antimicrobial resistance genes in microbial communities. This is mechanistically explained by the ability of MWCNTs to form bigger agglomerates, hence providing novel surfaces for bacterial interactions. Consequently, increasing pollution with MWCNTs has the potential to elevate the ongoing spread of antimicrobial resistance, a major threat to human health in the 21st century.

Effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of antibiotic resistance genes in water environments: A review

Antibiotic resistance has created obstacles in the treatment of infectious diseases with antibiotics. The horizontal transfer of antibiotic resistance genes (ARGs) can exacerbate the dissemination of antibiotic resistance in water environments. In addition to antibiotic selective pressure, multiple non-antibiotic factors can affect the horizontal transfer of ARGs. Herein, we seek to comprehensively review the effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of ARGs in water environments, especially contaminants from human activities and water treatment processes. Four pathways have been identified to accomplish horizontal gene transfer (HGT), i.e., conjugation, transformation, transduction, and vesiduction. Changes in conjugative frequencies by non-antibiotic factors are mainly related to their concentrations, which conform to hormesis. Relevant mechanisms involve the alteration in cell membrane permeability, reactive oxygen species, SOS response, pilus, and mRNA expression of relevant genes. Transformation induced by extracellular DNA may be more vulnerable to non-antibiotic factors than other pathways. Except bacteriophage infection, the effects of non-antibiotic factors on transduction exhibit many similarities with that of conjugation. Given the secretion of membrane vesicles stimulated by non-antibiotic factors, their effects on vesiduction can be inferred. Furthermore, contaminants from human activities at sub-inhibitory or environmentally relevant concentrations usually promote HGT, resulting in further dissemination of antibiotic resistance. The horizontal transfer of ARGs is difficult to be inhibited by individual water treatment processes (e.g., chlorination, UV treatment, and photocatalysis) unless they attain sufficient intensity. Accordingly, the synergistic application containing two or more water treatment processes is recommended. Overall, we believe this review can elucidate the significance for risk assessments of contaminants from human activities and provide insights into the development of environment-friendly and cost-efficient water treatment processes to inhibit the horizontal transfer of ARGs.