Subsistence and complexity of antimicrobial resistance on a community-wide level

Biofilm enhanced the mitigations of antibiotics and resistome in sulfadiazine and trimethoprim co-contaminated soils

Reducing antibiotic levels in soil ecosystems is vital to curb the dissemination of antimicrobial resistance genes (ARGs) and mitigate global health threats. However, gaps persist in understanding how antibiotic resistome can be suppressed during antibiotic degradation. Herein, we investigate the efficacy of a biochar biofilm incorporating antibiotics-degrading bacterial strain (Arthrobacter sp. D2) to mitigate antibiotic resistome in non-manured and manure-amended soils with sulfadiazine (SDZ) and trimethoprim (TMP) contamination. Results show that biofilm enhanced SDZ degradation by 83.0% within three days and increased TMP attenuation by 55.4% over 60 days in non-manured soils. In the non-manured black soil, the relative abundance of ARGs increased initially after biofilm inoculation. However, by day 30, it decreased by 20.5% compared to the controls. Moreover, after 7 days, biofilm reduced TMP by 38.5% in manured soils and decreased the total ARG abundance by 19.0%. Thus, while SDZ degradation did not increase sulfonamide resistance genes, TMP dissipation led to a proliferation of insertion sequences and related TMP resistance genes. This study underscores the importance of antibiotic degradation in reducing related ARGs while cautioning against the potential proliferation and various ARGs transfer by resistant microorganisms.

Occurrence, removal efficiency, and emission of antibiotics in the sewage treatment plants of a low-urbanized basin in China and their impact on the receiving water

Sewage treatment plants (STPs) are primary sources of antibiotics in aquatic environments. However, limited research has been conducted on antibiotic attenuation in STPs and their downstream waters in low-urbanized areas. This study analyzed 15 antibiotics in the STP sewage and river water in the Zijiang River basin to quantify antibiotic transport and attenuation in the STPs and downstream. The results showed that 14 target antibiotics, except leucomycin, were detected in the STP sewage, dominated by amoxicillin (AMOX), ofloxacin, and roxithromycin. The total antibiotic concentration in the influent and effluent ranged from 158 to 1025 ng/L and 99.9 to 411 ng/L, respectively. The removal efficiency of total antibiotics ranged from 54.7 % to 75.7 % and was significantly correlated with total antibiotic concentration in the influent. The antibiotic emission from STPs into rivers was 78 kg/yr and 4.6 g/km2yr in the Zijiang River basin. The total antibiotic concentration downstream of the STP downstream was 23.6 to 213 ng/L and was significantly negatively correlated with the transport distance away from the STP outlets. Antibiotics may pose a high ecological risk to algae and low ecological risk to fish in the basin. The risk of AMOX and ciprofloxacin resistance for organisms in the basin was estimated to be moderate. This study established antibiotic removal and attenuation models in STPs and their downstream regions in a low-urbanized basin, which is important for simulating antibiotic transport in STPs and rivers worldwide.

Assessing the effects of aquaculture on tidal flat ecological status using multi-metrics interaction-based index of biotic integrity (Mt-IBI)

Given tidal flat special environmental conditions and the degree of pollution caused by human activities, there is an urgent need to quantitatively assess their ecological status. Bioindication has become an indispensable part of environmental quality monitoring on account of its sensitivity to environmental disturbance. Thus, this study used bio-indicators to establish a multi-metrics-based index of biotic integrity (Mt-IBI) to evaluate the ecological status of the tidal flats with/without aquaculture through metagenomic sequencing. Four core indexes that were significantly correlated to other indexes with redundancy (p < 0.05), including Escherichia, beta-lactam antibiotic resistance genes, cellulase and xyloglucanases and the keystone species with 21° in the network, were selected after the screening processes. By implementing Mt-IBI in the tidal flats, the ecological health of the sampling sites was categorized into three levels, with Mt-IBI values of 2.01-2.63 (severe level), 2.81-2.93 (moderate level) and 3.23-4.18 (mild level), respectively. Through SEM analysis, water chemical oxygen demand and antibiotics were determined to be the primary controlling factors of the ecological status of tidal flat regions influenced by aquaculture, followed by salinity and total nitrogen. It is worth noting that the alteration of microbial communities impacted ecological status through the mediation of antibiotics. It is hoped that the results of our study will provide a theoretical basis for coastal environment restoration and that the use of Mt-IBI to assess ecosystem status in different aquatic environments will be further popularized in the future.

Molecular Mechanism of Chloramphenicol and Thiamphenicol Resistance Mediated by a Novel Oxidase, CmO, in Sphingomonadaceae

Antibiotic resistance mediated by bacterial enzyme inactivation plays a crucial role in the degradation of antibiotics in the environment. Chloramphenicol (CAP) resistance by enzymatic inactivation comprises nitro reduction, amide bond hydrolysis, and acetylation modification. However, the molecular mechanism of enzymatic oxidation of CAP remains unknown. Here, a novel oxidase gene, cmO, was identified and confirmed biochemically. The encoded CmO oxidase could catalyze the oxidation at the C-1' and C-3' positions of CAP and thiamphenicol (TAP) in Sphingobium sp. strain CAP-1. CmO is highly conserved in members of the family Sphingomonadaceae and shares the highest amino acid similarity of 41.05% with the biochemically identified glucose methanol choline (GMC) oxidoreductases. Molecular docking and site-directed mutagenesis analyses demonstrated that CAP was anchored inside the protein pocket of CmO with the hydrogen bonding of key residues glycine (G) 99, asparagine (N) 518, methionine (M) 474, and tyrosine (Y) 380. CAP sensitivity tests demonstrated that the acetyltransferase and CmO could enable a higher level of resistance to CAP than the amide bond-hydrolyzing esterase and nitroreductase. This study provides a better theoretical basis and a novel diagnostic gene for understanding and assessing the fate and resistance risk of CAP and TAP in the environment. IMPORTANCE Rising levels of antibiotic resistance are undermining ecological and human health as a result of the indiscriminate usage of antibiotics. Various resistance mechanisms have been characterized-for example, genes encoding proteins that degrade antibiotics-and yet, this requires further exploration. In this study, we report a novel gene encoding an oxidase involved in the inactivation of typical amphenicol antibiotics (chloramphenicol and thiamphenicol), and the molecular mechanism is elucidated. The findings provide novel data with which to understand the capabilities of bacteria to tackle antibiotic stress, as well as the complex function of enzymes in the contexts of antibiotic resistance development and antibiotic removal. The reported gene can be further employed as an indicator to monitor amphenicol's fate in the environment, thus benefiting risk assessment in this era of antibiotic resistance.

Natural detoxification of antibiotics in the environment: A one health perspective

The extended concept of one health integrates biological, geological, and chemical (bio-geo-chemical) components. Anthropogenic antibiotics are constantly and increasingly released into the soil and water environments. The fate of these drugs in the thin Earth space ("critical zone") where the biosphere is placed determines the effect of antimicrobial agents on the microbiosphere, which can potentially alter the composition of the ecosystem and lead to the selection of antibiotic-resistant microorganisms including animal and human pathogens. However, soil and water environments are highly heterogeneous in their local composition; thus the permanence and activity of antibiotics. This is a case of "molecular ecology": antibiotic molecules are adsorbed and eventually inactivated by interacting with biotic and abiotic molecules that are present at different concentrations in different places. There are poorly explored aspects of the pharmacodynamics (PD, biological action) and pharmacokinetics (PK, rates of decay) of antibiotics in water and soil environments. In this review, we explore the various biotic and abiotic factors contributing to antibiotic detoxification in the environment. These factors range from spontaneous degradation to the detoxifying effects produced by clay minerals (forming geochemical platforms with degradative reactions influenced by light, metals, or pH), charcoal, natural organic matter (including cellulose and chitin), biodegradation by bacterial populations and complex bacterial consortia (including "bacterial subsistence"; in other words, microbes taking antibiotics as nutrients), by planktonic microalgae, fungi, plant removal and degradation, or sequestration by living and dead cells (necrobiome detoxification). Many of these processes occur in particulated material where bacteria from various origins (microbiota coalescence) might also attach (microbiotic particles), thereby determining the antibiotic environmental PK/PD and influencing the local selection of antibiotic resistant bacteria. The exploration of this complex field requires a multidisciplinary effort in developing the molecular ecology of antibiotics, but could result in a much more precise determination of the one health hazards of antibiotic production and release.

3D-Printed Dip Slides Miniaturize Bacterial Identification and Antibiotic Susceptibility Tests Allowing Direct Mastitis Sample Analysis

The early detection of antimicrobial resistance remains an essential step in the selection and optimization of antibiotic treatments. Phenotypic antibiotic susceptibility testing including the measurement of minimum inhibitory concentration (MIC) remains critical for surveillance and diagnostic testing. Limitations to current testing methods include bulky labware and laborious methods. Furthermore, the requirement of a single strain of bacteria to be isolated from samples prior to antibiotic susceptibility testing delays results. The mixture of bacteria present in a sample may also have an altered resistance profile to the individual strains, and so measuring the susceptibility of the mixtures of organisms found in some samples may be desirable. To enable simultaneous MIC and bacterial species detection in a simple and rapid miniaturized format, a 3D-printed frame was designed for a multi-sample millifluidic dip-slide device that combines panels of identification culture media with a range of antibiotics (Ampicillin, Amoxicillin, Amikacin, Ceftazidime, Cefotaxime, Ofloxacin, Oxytetracycline, Streptomycin, Gentamycin and Imipenem) diluted in Muëller-Hinton Agar. Our proof-of-concept evaluation confirmed that the direct detection of more than one bacterium parallel to measuring MIC in samples is possible, which is validated using reference strains E. coli ATCC 25922, Klebsiella pneumoniae ATCC 13883, Pseudomonas aeruginosa ATCC 10145, and Staphylococcus aureus ATCC 12600 and with mastitis milk samples collected from Reading University Farm. When mixtures were tested, a MIC value was obtained that reflected the most resistant organism present (i.e., highest MIC), suggesting it may be possible to estimate a minimum effective antibiotic concentration for mixtures directly from samples containing multiple pathogens. We conclude that this simple miniaturized approach to the rapid simultaneous identification and antibiotic susceptibility testing may be suitable for directly testing agricultural samples, which is achieved through shrinking conventional tests into a simple "dip-and-incubate" device that can be 3D printed anywhere.

Stimulation of Sulfonamides Antibacterial Drugs Activity as a Result of Complexation with Ru(III): Physicochemical and Biological Study

Antibiotic resistance is a global problem, and one promising solution to overcome this issue is using metallodrugs, which are drugs containing metal ions and ligands. These complexes are superior to free ligands in various characteristics including anticancer properties and mechanism of action. The pharmacological potential of metallodrugs can be modulated by the appropriate selection of ligands and metal ions. A good example of proper coordination is the combination of sulfonamides (sulfamerazine, sulfathiazole) with a ruthenium(III) ion. This work aimed to confirm that the activity of sulfonamides antibacterial drugs is initiated and/or stimulated by their coordination to an Ru(III) ion. The study determined the structure, electrochemical profile, CT-DNA affinity, and antimicrobial as well as anticancer properties of the synthesized complexes. The results proved that Ru(III) complexes exhibited better biological properties than the free ligands.

Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants

Antibiotic subsistence in bacteria represents an alternative resistance machinery, while paradoxically, it is also a cure for environmental resistance. Antibiotic-subsisting bacteria can detoxify antibiotic-polluted environments and prevent the development of antibiotic resistance in environments. However, progress toward efficient in situ engineering of antibiotic-subsisting bacteria is hindered by the lack of mechanistic and predictive understanding of the assembly of the functioning microbiome. By top-down manipulation of wastewater microbiomes using sulfadiazine as the single limiting source, we monitored the ecological selection process that forces the wastewater microbiome to perform efficient sulfadiazine subsistence. We found that the community-level assembly selects for the same three families rising to prominence across different initial pools of microbiomes. We further analyzed the assembly patterns using a linear model. Detailed inspections of the sulfonamide metabolic gene clusters in individual genomes of isolates and assembled metagenomes reveal limited transfer potential beyond the boundaries of the Micrococcaceae lineage. Our results open up new possibilities for engineering specialist bacteria for environmental applications.

The ecology of plasmid-coded antibiotic resistance: a basic framework for experimental research and modeling

Many antibiotic resistance genes are associated with plasmids. The ecological success of these mobile genetic elements within microbial communities depends on varying mechanisms to secure their own propagation, not only on environmental selection. Among the most important are the cost of plasmids and their ability to be transferred to new hosts through mechanisms such as conjugation. These are regulated by dynamic control systems of the conjugation machinery and genetic adaptations that plasmid-host pairs can acquire in coevolution. However, in complex communities, these processes and mechanisms are subject to a variety of interactions with other bacterial species and other plasmid types. This article summarizes basic plasmid properties and ecological principles particularly important for understanding the persistence of plasmid-coded antibiotic resistance in aquatic environments. Through selected examples, it further introduces to the features of different types of simulation models such as systems of ordinary differential equations and individual-based models, which are considered to be important tools to understand these complex systems. This ecological perspective aims to improve the way we study and understand the dynamics, diversity and persistence of plasmids and associated antibiotic resistance genes.

Living with sulfonamides: a diverse range of mechanisms observed in bacteria

Sulfonamides are the oldest class of synthetic antibiotics still in use in clinical and veterinary settings. The intensive utilization of sulfonamides has been leading to the widespread contamination of the environment with these xenobiotic compounds. Consequently, in addition to pathogens and commensals, also bacteria inhabiting a wide diversity of environmental compartments have been in contact with sulfonamides for almost 90 years. This review aims at giving an overview of the effect of sulfonamides on bacterial cells, including the strategies used by bacteria to cope with these bacteriostatic agents. These include mechanisms of antibiotic resistance, co-metabolic transformation, and partial or total mineralization of sulfonamides. Possible implications of these mechanisms on the ecosystems and dissemination of antibiotic resistance are also discussed. KEY POINTS: • Sulfonamides are widespread xenobiotic pollutants; • Target alteration is the main sulfonamide resistance mechanism observed in bacteria; • Sulfonamides can be modified, degraded, or used as nutrients by some bacteria.