Antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) constitute a serious threat to public health, and climate change has been predicted to affect the increase in bacterial pathogens harboring ARGs and VFGs. However, studies on bacterial pathogens and their ARGs and VFGs in permafrost region have received limited attention. In this study, a metagenomic approach was applied to a comprehensive survey to detect potential ARGs, VFGs, and pathogenic antibiotic resistant bacteria (PARB) carrying both ARGs and VFGs in the active layer and permafrost. Overall, 70 unique ARGs against 18 antimicrobial drug classes and 599 VFGs classified as 38 virulence factors were detected in the Arctic permafrost region. Eight genes with mobile genetic elements (MGEs) carrying ARGs were identified; most MGEs were classified as phages. In the metagenome-assembled genomes, the presence of 15 PARB was confirmed. The soil profile showed that the transcripts per million (TPM) values of ARGs and VFGs in the sub-soil horizon were significantly lower than those in the top soil horizon. Based on the TPM value of each gene, major ARGs, VFGs, and these genes in PARB from the Arctic permafrost region were identified and their distribution was confirmed. The major host bacteria for ARGs and VFGs and PARB were identified. A comparison of the percentage identity distribution of ARGs and VFGs to reference databases indicated that ARGs and VFGs in the Arctic soils differ from previously identified genes. Our results may help understand the characteristics and distribution of ARGs, VFGs, and these genes in PARB in the Arctic permafrost region. This findings suggest that the Arctic permafrost region may serve as potential reservoirs for ARGs, VFGs, and PARB. These genes could pose a new threat to human health if they are released by permafrost thawing owing to global warming and propagate to other regions.

Antibiotic resistance genes (ARGs) and virulence factors (VFs) are critical threats to human health. Their abundance in aquatic ecosystems is maintained and enhanced via selection driven by environmental xenobiotics. However, their activity and expression in these environments under xenobiotic stress remains unknown. Here ARG and VF expression profiles were examined in aquatic microcosms under ciprofloxacin, glyphosate and sertraline hydrochloride treatment. Ciprofloxacin increased total expression of ARGs, particularly multidrug resistance genes. Total expression of ARGs and VFs decreased significantly under glyphosate and sertraline treatments. However, in opportunistic human pathogens, these agents increased expression of both ARGs and VFs. Xenobiotic pollutants, such as the compounds we tested here, have the potential to disrupt microbial ecology, promote resistance, and increase risk to human health. This study systematically evaluated the effects of environmental xenobiotics on transcription of ARGs and VFs, both of which have direct relevance to human health. Transcription of such genes has been overlooked in previous studies.

The abuse or misuse of antibiotics is directly linked to the emergence of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs) in the environment. Most fish farms located on Jeju Island operate a flow-through system that pumps in seawater for fish farming and discharges it back to the ocean. To investigate the amount of ARGs that these fish farm effluents discharge into the marine environment, we conducted a metagenomic-based resistome analysis. We observed higher levels of ARGs in fish farm effluents than in seawater at beach and residential areas. A greater proportion of ARGs was found on plasmid rather than on chromosomal DNA, especially for sulfonamide and phenicol classes. The distribution of ARGs did not differ between summer and winter, but the microbial community did. In addition, fish farm samples contained significantly more opportunistic pathogens (i.e., Vibrio, Photobacterium, Aliivibrio, and Tenacibaculum) and virulence factors than non-fish farm samples. Vibrio was the most frequently identified host of ARGs and virulence factors. The presence of Vibrio in the coastal area has been increasing owing to the recent rise in the temperature of seawater. This study suggests the need for actions to treat or monitor ARGs in the coastal areas where fish farms operating a flow-through system are located.

Whether virulent human pathogenic coronaviruses (SARS-CoV, MERS-CoV, SARS-CoV-2) are effectively transmitted by aerosols remains contentious. Transmission modes of the novel coronavirus have become a hot topic of research with the importance of airborne transmission controversial due to the many factors that can influence virus transmission. Airborne transmission is an accepted potential route for the spread of some viral infections (measles, chickenpox); however, aerosol features and infectious inoculum vary from one respiratory virus to another. Infectious virus-laden aerosols can be produced by natural human respiratory activities, and their features are vital determinants for virus carriage and transmission. Physicochemical characteristics of infectious respiratory aerosols can influence the efficiency of virus transmission by droplets. This critical review identifies studies reporting instances of infected patients producing airborne human pathogenic coronaviruses, and evidence for the role of physical/chemical characteristics of human-generated droplets in altering embedded viruses’ viability. We also review studies evaluating these viruses in the air, field studies and available evidence about seasonality patterns. Ultimately the literature suggests that a proportion of virulent human coronaviruses can plausibly be transmitted via the air, even though this might vary in different conditions. Evidence exists for respirable-sized airborne droplet nuclei containing viral RNA, although this does not necessarily imply that the virus is transmittable, capable of replicating in a recipient host, or that inoculum is sufficient to initiate infection. However, evidence suggests that coronaviruses can survive in simulated droplet nuclei for a significant time (>24 h). Nevertheless, laboratory nebulized virus-laden aerosols might not accurately model the complexity of human carrier aerosols in studying airborne viral transport. In summary, there is disagreement on whether wild coronaviruses can be transmitted via an airborne path and display seasonal patterns. Further studies are therefore required to provide supporting evidence for the role of airborne transmission and assumed mechanisms underlying seasonality.

Per- and Poly-fluoroalkyl substances (PFAS) are one of the major persistent environmental contaminants. Epidemiological studies have linked PFAS exposures to altered immunity and increased occurrence of infections in children. However, the mechanisms leading to immune susceptibility to bacterial infections remains unclear. To elucidate the mechanism, transcriptional alteration in the Caenorhabditis elegans model caused by a PFAS contaminated environmental water and two reconstituted PFAS solutions were evaluated using RNA-sequencing. PFAS affected the expression of several genes involved in C. elegans immune surveillance to Gram-positive bacteria (cpr-2, tag-38, spp-1, spp-5, clec-7, clec-172). The combined exposure to PFAS and Staphylococcus aureus significantly reduced C. elegans survival and increased intestinal membrane permeability. Furthermore, the growth of S. aureus in the presence of PFAS increased the expression of virulence genes, specifically, the virulence gene regulator saeR and α-hemolysin, hla, which resulted in increased hemolytic activity. The present study demonstrated that PFAS exposure not only increased C. elegans susceptibility to pathogens by reducing host immunity and increasing intestinal membrane permeability, but also increased bacteria virulence. This presents a broader implication for humans and other animals, where environmental contaminants simultaneously reduce host resilience, while, increasing microbial pathogenicity.

As zoned areas of industries, industrial parks have great impacts on the environment. Several studies have demonstrated that chemical compounds and heavy metals released from industrial parks can contaminate soil, water, and air. However, as an emerging pollutant, antimicrobial resistance genes (ARGs) in industrial parks have not yet been investigated. Here, we collected soil samples from 35 sites in an industrial park in China and applied a metagenomics strategy to profile the ARGs and virulence factors (VFs). We further compared the relative abundance of ARGs between the sites (TZ_31–35) located in a beta-lactam antimicrobial-producing factory and other sites (TZ_1–30) in this industrial park. Metagenomic sequencing and assembly generated 14, 383, 065 contigs and 17, 631, 051 open reading frames (ORFs). Taxonomy annotation revealed Proteobacteria and Actinobacteria as the most abundant phylum and class, respectively. The 32 pathogenic bacterial genera listed in the virulence factor database (VFDB) were all identified from the soil metagenomes in this industrial park. In total, 685,354 ARGs (3.89% of the ORFs) and 272,694 virulence factors (VFs) (1.55% of the ORFs) were annotated. These ARGs exhibited resistance to several critically important antimicrobials, such as rifampins, fluroquinolones, and beta-lactams. In addition, no significant difference in the relative abundance of ARGs was observed between sites TZ_31–35 and TZ_1–30, indicating that ARGs have already disseminated widely in this industrial park. The present study gave us a better understanding of the whole picture of the resistome and virulome in the soil of the industrial park and suggested that we should treat the industrial park as a whole in the surveillance and maintenance of ARGs.

Mycotoxins are increasingly considered as micropollutants in the environment. Fumonisins, as one of the most important mycotoxins, cause potential health threats to humans and animals due to their ubiquitous contamination on cereals, fruit, vegetables and other environmental samples around the world. However, the contribution of fumonisins to the interaction of fungi with plant hosts is not still fully understood. Here, we investigated the effect of fumonisin B1 (FB1) on the infection of Fusarium proliferatum on banana fruit and the underlying mechanisms from the host perspective. Our results found that FB1 treatment increased the aggressiveness of F. proliferatum on banana fruit and inhibited the defense ability of banana fruit via decreasing phenylalanine ammonia lyase (PAL), β-1,3-glucanase (GLU) and chitinase (CHI) activities. Meanwhile, FB1 accelerated cell death, indicated by higher relative conductivity, MDA content and higher transcripts of cell death-related genes. FB1 treatment resulted in higher hydrogen peroxide (H₂O₂) content possibly due to MaRBOHs induction. These consequences accelerated the ROS-dependent cell death, which subsequently result in reduction of disease resistance of banana fruit. Additionally, energy metabolism and MaDORN1s-mediated eATP signaling might involve in FB1-meidiated suppression of banana defense responses. Collectively, results of the current study indicated that FB1 contamination triggered the cell death of banana peel, subsequently instigating the invasion and growth of F. proliferatum on banana fruit. In summary, for the first time, we demonstrated a previously unidentified role of fumonisins as a potential virulence factor of F. proliferatum in modulating fruit defense response, which provides new insight on the biological roles of fumonisins.

Antibiotic resistance among gram-negative bacteria is increasingly becoming a problem of global concern. Particularly problematic is the emergence of resistance to last-resort antibiotics such as carbapenems and colistin. The increasing number of reports on the plasmid-mediated colistin resistance gene mcr-1 in isolates worldwide is raising concerns for the future usefulness of this class of antibiotics. Dissemination of mcr-1 is believed to have originated mainly from animal breeding, however, the role of the environment as a transmission source is not yet fully understood. In the current study, 89 extended-spectrum β-lactamase-producing Escherichia coli isolated from 231 samples from different environmental sources in 12 villages in a rural area of Shandong, China, were screened for mcr-1. 17 (19.1%) mcr-1-positive isolates were found from different environmental sources, aggregated in 6 villages. Plasmids of three different Inc-groups carrying mcr-1 were confirmed, indicating that the widespread geographical distribution of mcr-1 in the local area is due to a number of different plasmids. Additionally, almost a third (29.4%) of the isolates carried virulence factors associated to intestinal pathogenic E. coli. These results illustrate the high complexity of the transmission patterns of mcr-1 among different environmental matrices on a local scale and the potential for the environment to facilitate dissemination and emergence of antibiotic-resistant and virulent strains of bacteria.

Phytophthora capsici, an economically devastating oomycete pathogen, causes devastating disease epidemics on a wide range of vegetable plants and pose a grave threat to global vegetables production. Heavy metals and acid pH are newly co-occurring stresses to soil micro-organisms, but what can be expected for mycelia growth and virulence and how they injure the oomycetes (especially P. capsici) remains unknown. Here, the effects of different heavy metals (Cu²⁺, Cr²⁺, and Hg²⁺) on mycelia growth and virulence were investigated at different pHs (4.0 vs. 7.0) and the plausible molecular and physiological mechanisms were analyzed. In the present study, we compared the effective inhibition of different heavy metals (Cu²⁺, Cr²⁺, and Hg²⁺) and acid pH on a previously genome sequenced P. capsici virulent strain LT1534. Both stress factors independently affected its mycelia growth and sporulation. Next, we investigated whether ROS participated in the pH-inhibited mycelial growth, finding that the ROS scavenger, catalase (CAT), significantly inhibited the acid pH-induced ROS in mycelia. Additionally, because MAPK specially transmits different stress responsive signals in environment into cells, we employed CAT and a p38-MAPK pathway inhibitor to investigate ROS and p38-MAPK roles in heavy metal-inhibited mycelia growth at different pHs (4.0 vs. 7.0), finding that they significantly inhibited growth. Furthermore, ROS and p38-MAPK influenced the heavy metal-induced TBARS content, total antioxidant capacity (TAC), and CAT activity at different pHs, and also reduced the expression of infection-related laccases (PcLAC2) and an effector-related protein (PcNLP14). We propose that acid pH stress accelerates how heavy metals inhibit mycelium growth, sporulation, and virulence change in P. capsici, and posit that ROS and p38-MAPK function to regulate the molecular and physiological mechanisms underlying this toxicity. Although these stresses induce molecular and physiological challenges to oomycetes, much remains to be known the mechanisms dedicated to resolve these environmental stresses.

In soils, the presence of clinically relevant bacteria carrying ARGs, including extended-spectrum β-lactamase- and plasmid-mediated AmpC β-lactamase-encoding genes, is an underestimated public health problem that requires more attention. For this investigation, 300 samples from agricultural and non-agricultural soils were used to obtain 41 MDR E. coli isolates, standing out the resistance to β-lactams, fluoroquinolones and colistin. Virulence genes related to diarrheagenic E. coli and extraintestinal pathogenic E. coli were detected. Several ARGs were found, highlighting the presence of at least one β-lactamase-encoding gene (blaTEM, blaCMY, blaSHV, blaOXA₋₁₋ₗᵢₖₑ, blaCTX₋M₋₂, and/or blaCTX₋M₋₁₅) in each isolate. Among the fluoroquinolone-resistant E. coli isolates, the plasmid-mediated quinolone resistance genes (qnrB and oqxA) and substitutions in the quinolone resistance-determining regions were detected. Some isolates were resistant to colistin (MICs of 4–8 mg/L) and, although no mcr-like gene was detected, substitutions in the two-component systems involving PhoP/PhoQ and PmrA/PmrB were found. Furthermore, the E. coli isolates presented plasmids and class 1 integrons, the last one detected in all isolates. The ARGs blaTEM, aadA and dfrA and the lpfA virulence-associated gene presented statistically significant differences (P < 0.05) in agricultural soils, while the blaOXA₋₁₋ₗᵢₖₑ gene presented a statistically significant difference in non-agricultural soils. Thirty-eight sequence types (STs) were identified among the isolates, spotlighting the 20 different STs that carried blaCMY and blaCTX₋M₋ₜyₚₑ genes and those commonly reported in infections worldwide. The occurrence of virulent, multidrug- and colistin-resistant E. coli isolates in soils could lead to contamination of surrounding environments and food, increasing the risk of human and animal exposure. Therefore, this study contributes to a better understanding of E. coli in soils and reinforces the importance of the One Health approach to antimicrobial resistance surveillance.