Multiple antibiotic resistance and DNA methylation in Enterobacteriaceae isolates from different environments

Antimicrobial resistance in the wild: Insights from epigenetics

Spreading of bacterial and fungal strains that are resistant to antimicrobials poses a serious threat to the well-being of humans, animals, and plants. Antimicrobial resistance has been mainly investigated in clinical settings. However, throughout their evolutionary history microorganisms in the wild have encountered antimicrobial substances, forcing them to evolve strategies to combat antimicrobial action. It is well known that many of these strategies are based on genetic mechanisms, but these do not fully explain important aspects of the antimicrobial response such as the rapid development of resistance, reversible phenotypes, and hetero-resistance. Consequently, attention has turned toward epigenetic pathways that may offer additional insights into antimicrobial mechanisms. The aim of this review is to explore the epigenetic mechanisms that confer antimicrobial resistance, focusing on those that might be relevant for resistance in the wild. First, we examine the presence of antimicrobials in natural settings. Then we describe the documented epigenetic mechanisms in bacteria and fungi associated with antimicrobial resistance and discuss innovative epigenetic editing techniques to establish causality in this context. Finally, we discuss the relevance of these epigenetic mechanisms on the evolutionary dynamics of antimicrobial resistance in the wild, emphasizing the critical role of priming in the adaptation process. We underscore the necessity of incorporating non-genetic mechanisms into our understanding of antimicrobial resistance evolution. These mechanisms offer invaluable insights into the dynamics of antimicrobial adaptation within natural ecosystems.

Fungal Bioremediation of the β-Lactam Antibiotic Ampicillin under Laccase-Induced Conditions

Due to widespread overuse, pharmaceutical compounds, such as antibiotics, are becoming increasingly prevalent in greater concentrations in aquatic ecosystems. In this study, we investigated the capacity of the white-rot fungus, Coriolopsis gallica (a high-laccase-producing fungus), to biodegrade ampicillin under different cultivation conditions. The biodegradation of the antibiotic was confirmed using high-performance liquid chromatography, and its antibacterial activity was evaluated using the bacterial growth inhibition agar well diffusion method, with Escherichia coli as an ampicillin-sensitive test strain. C. gallica successfully eliminated ampicillin (50 mg L-1) after 6 days of incubation in a liquid medium. The best results were achieved with a 9-day-old fungal culture, which treated a high concentration (500 mg L-1) of ampicillin within 3 days. This higher antibiotic removal rate was concomitant with the maximum laccase production in the culture supernatant. Meanwhile, four consecutive doses of 500 mg L-1 of ampicillin were removed by the same fungal culture within 24 days. After that, the fungus failed to remove the antibiotic. The measurement of the ligninolytic enzyme activity showed that C. gallica laccase might participate in the bioremediation of ampicillin.

N6-methyloxyadenine-mediated detoxification and ferroptosis confer a trade-off between multi-fungicide resistance and fitness

Multi-fungicide resistance (MFR) is a serious environmental problem, which results in the excessive use of fungicides. Fitness penalty, as a common phenomenon in MFR, can partially counteract the issue of resistance due to the weakened vigor of MFR pathogens. Their underlying mechanism and relationship remain unexplained. By Oxford Nanopore Technologies sequencing and dot blot, we found that N6-methyloxyadenine (6mA) modification, the dominate epigenetic marker in Phytophthora capsici, was significantly altered after MFR emerged. Among the differently methylated genes, PcGSTZ1 could efficiently detoxify SYP-14288, a novel uncoupler, through complexing the fungicide with glutathione and induce MFR. Interestingly, PcGSTZ1 overexpression was induced by elevated 6mA levels and chromatin accessibility to its genomic loci. Moreover, the overexpression led to reactive oxygen species burst and ferroptosis in SYP-14288-resistant mutants, which enhanced the resistance and induced fitness penalty in P. capsici through triggering low energy shock adaptive response. Furthermore, this study revealed that the 6mA-PcGSTZ1-ferroptosis axis could mediate intergenerational resistance memory transmission and enabled adaptive advantage to P. capsici. In conclusion, the findings provide new insights into the biological role of 6mA as well as the mechanisms underlying the trade-off between MFR and fitness. These could also benefit disease control through the blockade of the epigenetic axis to resensitize resistant isolates.IMPORTANCEN6-methyloxyadenine (6mA) modification on DNA is correlated with tolerance under different stress in prokaryotes. However, the role of 6mA in eukaryotes remains poorly understood. Our current study reveals that DNA adenine methyltransferase 1 (DAMT1)-mediated 6mA modification at the upstream region of GST zeta 1 (GSTZ1) is elevated in the resistant strain. This elevation promotes the detoxification uncoupler and induces multifungicide resistance (MFR). Moreover, the overexpression led to reactive oxygen species burst and ferroptosis in SYP-14288-resistant mutants, which enhanced the resistance and induced fitness penalty in Phytophthora capsici through triggering low energy shock adaptive response. Furthermore, this study revealed that the 6mA-PcGSTZ1-ferroptosis axis could mediate intergenerational resistance memory transmission and enabled adaptive advantage to P. capsici. Overall, our findings uncover an innovative mechanism underlying 6mA modification in regulating PcGSTZ1 transcription and the ferroptosis pathway in P. capsici.

Multidrug antibiotic resistance in hospital wastewater as a reflection of antibiotic prescription and infection cases

Antimicrobial resistance (AMR) is an escalating issue that can render illnesses more difficult to treat if effective antibiotics become resistant. Many studies have explored antibiotic resistance in bacteria (ARB) in wastewater, comparing results with clinical data to ascertain the public health risk. However, few investigations have linked the prevalence of ARB in hospital wastewater (HWW) with these outcomes. This study aimed to bridge this gap by assessing the prevalence of ARB in HWW and its receiving waters. Among the 144 isolates examined, 24 were obtained from each of the six sites (untreated wastewater, aeration tank, sedimentation tank, effluent after disinfection, upstream canal, and downstream canal). A significant portion (87.5 %) belonged to the Enterobacteriaceae family, with Klebsiella pneumoniae as the predominant species (47.9 %). The antimicrobial sensitivity testing (AST) showed that 57.6 % of the isolates were resistant to amoxicillin/clavulanic acid (AMX), the most prevalent antibiotic used within the studied hospital. The total resistance rate before and after treatment was 27.7 % and 28.0 %, respectively, with an overall multi-drug resistance (MDR) rate of 33.3 %. The multiple antibiotic resistance index (MARI) range varied between 0.0 and 0.9. The outpatient ward's three-day mean bacterial infection cases showed a significant association (Spearman's rho = 0.98) with the MARI in the sedimentation tank. Moreover, a strong correlation (Spearman's rho = 0.88) was found between hospital effluent's MARI and the seven-day mean inpatient ward case. These findings indicate that applying wastewater-based epidemiology (WBE) to hospital wastewater could provide valuable insights into understanding ARB contamination across human domains and water cycles. Future studies, including more comprehensive collection data on symptomatic patients and asymptomatic carriers, will be crucial in fully unravelling the complexities between human health and environmental impacts related to AMR.

Antimicrobial resistance in southeast Asian water environments: A systematic review of current evidence and future research directions

Antimicrobial resistance has been a serious and complex issue for over a decade. Although research on antimicrobial resistance (AMR) has mainly focused on clinical and animal samples as essential for treatment, the AMR situation in aquatic environments may vary and have complicated patterns according to geographical area. Therefore, this study aimed to examine recent literature on the current situation and identify gaps in the AMR research on freshwater, seawater, and wastewater in Southeast Asia. The PubMed, Scopus, and ScienceDirect databases were searched for relevant publications published from January 2013 to June 2023 that focused on antimicrobial resistance bacteria (ARB) and antimicrobial resistance genes (ARGs) among water sources. Based on the inclusion criteria, the final screening included 41 studies, with acceptable agreement assessed using Cohen's inter-examiner kappa equal to 0.866. This review found that 23 out of 41 included studies investigated ARGs and ARB reservoirs in freshwater rather than in seawater and wastewater, and it frequently found that Escherichia coli was a predominant indicator in AMR detection conducted by both phenotypic and genotypic methods. Different ARGs, such as blaTEM, sul1, and tetA genes, were found to be at a high prevalence in wastewater, freshwater, and seawater. Existing evidence highlights the importance of wastewater management and constant water monitoring in preventing AMR dissemination and strengthening effective mitigation strategies. This review may be beneficial for updating current evidence and providing a framework for spreading ARB and ARGs, particularly region-specific water sources. Future AMR research should include samples from various water systems, such as drinking water or seawater, to generate contextually appropriate results. Robust evidence regarding standard detection methods is required for prospective-era work to raise practical policies and alerts for developing microbial source tracking and identifying sources of contamination-specific indicators in aquatic environment markers.

Viability and transcriptional responses of multidrug resistant E. coli to chromium stress

The viability of multidrug resistant (MDR) bacteria in environment is critical for the spread of antimicrobial resistance. In this study, two Escherichia coli strains, MDR LM13 and susceptible ATCC25922, were used to elucidate differences in their viability and transcriptional responses to hexavalent chromium (Cr(VI)) stress. The results show that the viability of LM13 was notably higher than that of ATCC25922 under 2-20 mg/L Cr(VI) exposure with bacteriostatic rates of 3.1%-57%, respectively, for LM13 and 0.9%-93.1%, respectively, for ATCC25922. The levels of reactive oxygen species and superoxide dismutase in ATCC25922 were much higher than those in LM13 under Cr(VI) exposure. Additionally, 514 and 765 differentially expressed genes were identified from the transcriptomes of the two strains (log₂|FC| > 1, p < 0.05). Among them, 134 up-regulated genes were enriched in LM13 in response to external pressure, but only 48 genes were annotated in ATCC25922. Furthermore, the expression levels of antibiotic resistance genes, insertion sequences, DNA and RNA methyltransferases, and toxin-antitoxin systems were generally higher in LM13 than in ATCC25922. This work shows that MDR LM13 has a stronger viability under Cr(VI) stress, and therefore may promote the dissemination of MDR bacteria in environment.

The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145

DNA methylation is an epigenetic modification detected in both prokaryotic and eukaryotic genomic DNAs. In bacteria, the importance of 5-methylcytosine (m5C) in gene expression has been less investigated than in eukaryotic systems. Through dot-blot analysis employing m5C antibodies against chromosomal DNA, we have previously demonstrated that m5C influences the differentiation of Streptomyces coelicolor A(3)2 M145 in solid sporulating and liquid non-sporulating complex media. Here, we mapped the methylated cytosines of the M145 strain growing in the defined Maltose Glutamate (MG) liquid medium. Sequencing of the M145 genome after bisulfite treatment (BS-sequencing) evidenced 3360 methylated cytosines and the two methylation motifs, GGCmCGG and GCCmCG, in the upstream regions of 321 genes. Besides, the role of cytosine methylation was investigated using the hypo-methylating agent 5'-aza-2'-deoxycytidine (5-aza-dC) in S. coelicolor cultures, demonstrating that m5C affects both growth and antibiotic biosynthesis. Finally, quantitative reverse-transcription polymerase-chain-reaction (RT-qPCR) analysis of genes containing the methylation motifs in the upstream regions showed that 5-aza-dC treatment influenced their transcriptional levels and those of the regulatory genes for two antibiotics. To the best of our knowledge, this is the first study that reports the cytosine methylome of S. coelicolor M145, supporting the crucial role ascribed to cytosine methylation in controlling bacterial gene expression.

Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis

Although polymerase chain reaction (PCR) amplification and sequencing of the bacterial 16S rDNA region has numerous scientific applications, it does not provide DNA methylation information. Herein, we propose a simple extension for bisulfite sequencing to investigate 5-methylcytosine residues in the bacterial 16S rDNA region from clinical isolates or flora. Multiple displacement amplification without DNA denaturation was used to preferentially pre-amplify single-stranded bacterial DNA after bisulfite conversion. Following the pre-amplification, the 16S rDNA region was analyzed using nested bisulfite PCR and sequencing, enabling the simultaneous identification of DNA methylation status and sequence data. We used this approach (termed sm16S rDNA PCR/sequencing) to identify novel methylation sites and a methyltransferase (M. MmnI) in Morganella morganii and different methylation motifs among Enterococcus faecalis strains from small volumes of clinical specimens. Further, our analysis suggested that M. MmnI may be correlated to erythromycin resistance. Thus, sm16S rDNA PCR/sequencing is a useful extension method for analyzing the DNA methylation of 16S rDNA regions in a microflora, providing additional information not provided by conventional PCR. Given the relationship between DNA methylation status and drug resistance in bacteria, we believe this technique can be effectively applied in clinical sample testing.

“Biofilm Formationand Antibiotic Resistance Profiles of Water-borne Pathogens

Water sources (surface water, drinking water, rivers, and ponds) are significant reservoirs for transmitting antibiotic-resistant bacteria. In addition, these waters are an important public health problem because they are suitable environments for transferring antibiotic resistance genes between bacterial species. Our study aimed to assess the prevalence of Extended-spectrum beta-lactamase (ESBL) producing isolates in water samples, the susceptibility of the isolates to the specified antibiotics, the determination of biofilm ability, antibiotic resistance genes, and the molecular typing of the isolates. For this purpose, Polymerase chain reaction (PCR) and Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analyses were used. Out of 70 isolates, 15 (21%) were ESBL producing, and sent for the MALDI-TOF analysis, where Escherichia coli, Acinetobacter calcoaceticus, Enterobacter bugandensis, Acinetobacter pittii, Pseudomonas aeruginosa, Acinetobacter junii, Pseudomonas oleovorans, and Enterobacter ludwigigii were identified. Moreover, colistin resistance genes (mcr1/2/6, mcr 4, mcr 5, mcr 3/7, and mcr 8), ESBL-encoding genes(bla_SHV, bla_TEM, and bla_CTX-M) and carbapenemase genes (bla_NDM, bla_OXA-48, and bla_KPC) using molecular analysis (PCR) were confirmed. The colistin resistance gene was detected at 80% (12/15) in the isolates obtained. The distribution of these isolates according to resistance genes was found as mcr 1/2/6 4 (20%), mcr3/7 3 (13%), and mcr 5 (40%). Additionally, the isolates harbored bla_SHV(6.6%) and bla_TEM (6.6%) genes. However, bla_NDM, bla_OXA-48, bla_KPC, and bla_CTX-M genes were not detected in any isolates. According to the Congo red agar method, seven (46.6%) isolates showed negative biofilm ability, and eight (53.3%) showed moderate biofilm ability. However, the microplate method detected weak biofilm in 53.3% of the isolates.In conclusion, this study provides evidence for the existence of multidrug-resistant bacteria that co-exist with mcr and ESBL genes in water sources. These bacteria can migrate to other environments and pose increasing threats to public health.

Bacteria spatial tracking in Urban Park soils with MALDI-TOF Mass Spectrometry and Specific PCR

Urban parks constitute one of the main leisure areas, especially for the most vulnerable people in our society, children, and the elderly. Contact with soils can pose a health risk. Microbiological testing is a key aspect in determining whether they are suitable for public use. The aim of this work is to map the spatial distribution of potential dangerous Enterobacteria but also bioremediation useful (lipase producers) isolates from soils in an urban park in the area of Valencia (Spain). To this end, our team has collected 25 samples of soil and isolated 500 microorganisms, using a mobile application to collect information of the soil samples (i.e. soil features, temperature, humidity, etc.) with geolocation. A combined protocol including matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing PCR has been established to characterize the isolates. The results have been processed using spatial statistical techniques (using Kriging method), taking into account the number of isolated strains, also proving the reactivity against standard pathogenic bacterial strains (Escherichia coli, Bacillus cereus, Salmonella, Pseudomonas and Staphylococcus aureus), and have increased the number of samples (to 896 samples) by interpolating spatially each parameter with this statistical method. The combined use of methods from biology and computer science allows the quality of the soil in urban parks to be predicted in an agile way, which can generate confidence in its use by citizens.

Long-term spatiotemporal variation of antimicrobial resistance genes within the Serratia marcescens population and transmission of S. marcescens revealed by public whole-genome datasets

The development of antimicrobial resistance (AMR) is accelerated by the selective pressure exerted by the widespread use of antimicrobial drugs, posing an increasing danger to public health. However, long-term spatiotemporal variation in AMR genes in microorganisms, particularly in bacterial pathogens in response to antibiotic consumption, is not fully understood. Here, we used the NCBI RefSeq database to collect 478 whole-genome sequences for Serratia marcescens ranging from 1961 up to 2019, to document global long-term AMR trends in S. marcescens populations. In total, 100 AMR gene subtypes (16 AMR gene types) were detected in the genomes of S. marcescens populations. We identified 3 core resistance genes in S. marcescens genomes, and a high diversity of AMR genes was observed in S. marcescens genomes after corresponding antibiotics were discovered and introduced into clinical practice, suggesting the adaptation of S. marcescens populations to challenges with therapeutic antibiotics. Our findings indicate spatiotemporal variation of AMR genes in S. marcescens populations in relation to antibiotic consumption and suggest the potential transmission of S. marcescens isolates harboring AMR genes among countries and between the environment and the clinic, representing a public health threat that necessitates international solidarity to overcome.

Occurrence and removal of antibiotics, antibiotic resistance genes, and bacterial communities in hospital wastewater

Hospital wastewater contains a variety of human antibiotics and pathogens, which makes the treatment of hospital wastewater essential. However, there is a lack of research on these pollutants at hospital wastewater treatment plants. In this study, the characteristics and removal of antibiotics and antibiotic resistance genes (ARGs) in the independent treatment processes of hospitals of different scales (primary hospital, H1; secondary hospital, H2; and tertiary hospital, H3) were investigated. The occurrence of antibiotics and ARGs in wastewater from three hospitals varied greatly. The first-generation cephalosporin cefradine was detected at a concentration of 2.38 μg/L in untreated wastewater from H1, while the fourth-generation cephalosporin cefepime had the highest concentration, 540.39 μg/L, at H3. Ofloxacin was detected at a frequency of 100% and had removal efficiencies of 44.2%, 51.5%, and 81.6% at H1, H2, and H3, respectively. The highest relative abundances of the β-lactam resistance gene bla_GES-1 (1.77×10^-3 copies/16S rRNA), the quinolone resistance gene qnrA (8.81×10^-6 copies/16S rRNA), and the integron intI1 (1.86×10^-4 copies/16S rRNA) were detected in the treated wastewater. The concentrations of several ARGs were increased in the treated wastewater (e.g. bla_OXA-1, bla_OXA-10, and bla_TEM-1). Several pathogenic or opportunistic bacteria (e.g. Acinetobacter, Klebsiella, Aeromonas, and Pseudomonas) were observed at high relative abundances in the treated wastewater. These results suggested the co-occurrence of antibiotics, ARGs, and antibiotic-resistant pathogens in hospital wastewater, and these factors may spread into the receiving aquatic environment.

Photocatalytic graphitic carbon nitride-chitosan composites for pathogenic biofilm control under visible light irradiation

Photocatalysis holds promise for inactivating environmental pathogens. Visible-light-responsive composites of carbon-doped graphitic carbon nitride and chitosan with high reactivity and processability were fabricated, and they can control pathogenic biofilms for environmental, food, biomedical, and building applications. The broad-spectrum biofilm inhibition and eradication of the photocatalytic composites against Staphylococcus epidermidis, Pseudomonas aeruginosa PAO1, and Escherichia coli O157: H7 under visible light irradiation were demonstrated. Extracellular polymeric substances in Escherichia coli O157: H7 biofilms were most resistant to photocatalytic oxidation, which led to reduced performance for biofilm removal. ¹O₂ produced by the composites was believed to dominate biofilm inactivation. Moreover, the composites exhibited excellent performance for inhibiting biofilm development in urine, highlighting the promise for inactivating environmental biofilms developed from multiple bacterial species. Our study provides fundamental insights into the development of new photocatalytic composites, and elucidates the mechanism of how the photocatalyst reacts with a microbiological system.