Abundant rifampin resistance genes and significant correlations of antibiotic resistance genes and plasmids in various environments revealed by metagenomic analysis

Metagenomic Comparison of Antibiotic Resistance Genes Associated with Liquid and Dewatered Biosolids

Municipal biosolids (MBs) that are land-applied in North America are known to possess an active microbial population that can include human pathogens. Activated sludge is a hotspot for the accumulation of antibiotics and has been shown to be a selective environment for microorganisms that contain antibiotic resistance genes (ARGs); however, the prevalence of ARGs in MBs is not well characterized. In this study, we enriched the plasmid metagenome from raw sewage sludge and two CP2 MBs, a mesophilic anaerobic digestate and a dewatered digestate, to evaluate the presence of ARGs in mobile genetic elements. The CP2-class biosolids are similar to Class B biosolids in the United States. The CP2 biosolids must meet a microbiological cut off of 2 × 10 colony-forming units (CFU) per dry gram or 100 mL of biosolids. The enriched plasmid DNA was sequenced (Illumina MiSeq). Sequence matching against databases, including the Comprehensive Antibiotic Resistance Database (CARD), MG-RAST, and INTEGRALL, identified potential genes of interest related to ARGs and their ability to transfer. The presence and abundance of different ARGs varied between treatments with heterogeneity observed among the same sample types. The MBs plasmid-enriched metagenomes contained ARGs associated with resistance to a variety of antibiotics, including β-lactams, rifampicin, quinolone, and tetracycline as well as the detection of extended spectrum β-lactamase genes. Cultured bacteria from CP2 MBs possessed antibiotic resistances consistent with the MBs metagenome data including multiantibiotic-resistant isolates. The results from this study provide a better understanding of the ARG and MGE profile of the plasmid-enriched metagenome of CP2 MBs.

Metagenomic profiles of antibiotic resistance genes in paddy soils from South China

Overuse and arbitrary discarding of antibiotics have expanded antibiotic resistance reservoirs, from gut, waste water and activated sludge, to soil, freshwater and even the ocean. Based on the structured Antibiotic Resistance Genes Database and next generation sequencing, metagenomic analysis was used for the first time to detect and quantify antibiotic resistance genes (ARGs) in paddy soils from South China. A total of 16 types of ARGs were identified, corresponding to 110 ARG subtypes. The abundances and distribution pattern of ARGs in paddy soil were distinctively different from those in activated sludge and pristine deep ocean sediment, but close to those of sediment from human-impacted estuaries. Multidrug resistance genes were the most dominant type (38-47.5%) in all samples, and the ARGs detected encompassed the three major resistance mechanisms, among which extrusion by efflux pumps was predominant. Redundancy analysis (RDA) showed that pH was significantly correlated with the distribution of ARG subtypes (P < 0.05). Our results provided a broad spectrum profile of ARGs in paddy soil, indicating that ARGs are widespread in paddy soils of South China.

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

The risk associated with antibiotic resistance disseminating from animal and human feces is an urgent public issue. In the present study, we sought to establish a pipeline for annotating antibiotic resistance genes (ARGs) based on metagenomic assembly to investigate ARGs and their co-occurrence with associated genetic elements. Genetic elements found on the assembled genomic fragments include mobile genetic elements (MGEs) and metal resistance genes (MRGs). We then explored the hosts of these resistance genes and the shared resistome of pig, chicken and human fecal samples. High levels of tetracycline, multidrug, erythromycin, and aminoglycoside resistance genes were discovered in these fecal samples. In particular, significantly high level of ARGs (7762 ×/Gb) was detected in adult chicken feces, indicating higher ARG contamination level than other fecal samples. Many ARGs arrangements (e.g., macA-macB and tetA-tetR) were discovered shared by chicken, pig and human feces. In addition, MGEs such as the aadA5-dfrA17-carrying class 1 integron were identified on an assembled scaffold of chicken feces, and are carried by human pathogens. Differential coverage binning analysis revealed significant ARG enrichment in adult chicken feces. A draft genome, annotated as multidrug resistant Escherichia coli, was retrieved from chicken feces metagenomes and was determined to carry diverse ARGs (multidrug, acriflavine, and macrolide). The present study demonstrates the determination of ARG hosts and the shared resistome from metagenomic data sets and successfully establishes the relationship between ARGs, hosts, and environments. This ARG annotation pipeline based on metagenomic assembly will help to bridge the knowledge gaps regarding ARG-associated genes and ARG hosts with metagenomic data sets. Moreover, this pipeline will facilitate the evaluation of environmental risks in the genetic context of ARGs.

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

A metagenomic approach and network analysis was used to investigate the wide-spectrum profiles of antibiotic resistance genes (ARGs) and their co-occurrence patterns in 50 samples from 10 typical environments. In total, 260 ARG subtypes belonging to 18 ARG types were detected with an abundance range of 5.4 × 10(-6)-2.2 × 10(-1) copy of ARG per copy of 16S-rRNA gene. The trend of the total ARG abundances in environments matched well with the levels of anthropogenic impacts on these environments. From the less impacted environments to the seriously impacted environments, the total ARG abundances increased up to three orders of magnitude, that is, from 3.2 × 10(-3) to 3.1 × 10(0) copy of ARG per copy of 16S-rRNA gene. The abundant ARGs were associated with aminoglycoside, bacitracin, β-lactam, chloramphenicol, macrolide-lincosamide-streptogramin, quinolone, sulphonamide and tetracycline, in agreement with the antibiotics extensively used in human medicine or veterinary medicine/promoters. The widespread occurrences and abundance variation trend of vancomycin resistance genes in different environments might imply the spread of vancomycin resistance genes because of the selective pressure resulting from vancomycin use. The simultaneous enrichment of 12 ARG types in adult chicken faeces suggests the coselection of multiple ARGs in this production system. Non-metric multidimensional scaling analysis revealed that samples belonging to the same environment generally possessed similar ARG compositions. Based on the co-occurrence pattern revealed by network analysis, tetM and aminoglycoside resistance protein, the hubs of the ARG network, are proposed to be indicators to quantitatively estimate the abundance of 23 other co-occurring ARG subtypes by power functions.

Influence of a non-hospital medical care facility on antimicrobial resistance in wastewater

The global widespread use of antimicrobials and accompanying increase in resistant bacterial strains is of major public health concern. Wastewater systems and wastewater treatment plants are considered a niche for antibiotic resistance genes (ARGs), with diverse microbial communities facilitating ARG transfer via mobile genetic element (MGE). In contrast to hospital sewage, wastewater from other health care facilities is still poorly investigated. At the instance of a nursing home located in south-west Germany, in the present study, shotgun metagenomics was used to investigate the impact on wastewater of samples collected up- and down-stream in different seasons. Microbial composition, ARGs and MGEs were analyzed using different annotation approaches with various databases, including Antibiotic Resistance Ontologies (ARO), integrons and plasmids. Our analysis identified seasonal differences in microbial communities and abundance of ARG and MGE between samples from different seasons. However, no obvious differences were detected between up- and downstream samples. The results suggest that, in contrast to hospitals, sewage from the nursing home does not have a major impact on ARG or MGE in wastewater, presumably due to much less intense antimicrobial usage. Possible limitations of metagenomic studies using high-throughput sequencing for detection of genes that seemingly confer antibiotic resistance are discussed.

Increased levels of antibiotic resistance in urban stream of Jiulongjiang River, China

The rapid global urbanization and other extensive anthropogenic activities exacerbated the worldwide human health risks induced by antibiotic resistance genes (ARGs). Knowledge of the origins and dissemination of ARGs is essential for understanding modern resistome, while little information is known regarding the overall resistance levels in urban river. In this study, the abundance of multi-resistant bacteria (MRB) and ARGs was investigated using culture-based method and high-throughput qPCR in water samples collected from urban stream and source of Jiulongjiang River, China, respectively. The abundance of MRB (conferring resistance to three combinations of antibiotics and vancomycin) was significantly higher in urban samples. A total of 212 ARGs were detected among all the water samples, which encoded resistance to almost all major classes of antibiotics and encompassed major resistant mechanisms. The total abundance of ARGs in urban samples (ranging from 9.72 × 10(10) to 1.03 × 10(11) copies L(-1)) was over two orders of magnitude higher than that in pristine samples (7.18 × 10(8) copies L(-1)), accompanied with distinct ARGs structures, significantly higher diversity, and enrichment of ARGs. Significant correlations between the abundance of ARGs and mobile genetic elements (MGEs) were observed, implicating the potential of horizontal transfer of ARGs. High abundance and enrichment of diverse ARGs and MGEs detected in urban river provide evidence that anthropogenic activities are responsible for the emergence and dissemination of ARGs to the urban river and management options should be taken into account for minimizing the spread of ARGs.

The combinational effects between sulfonamides and metals on nematode Caenorhabditis elegans

As emerging pollutants, antibiotic sulfonamides are continuously emitted into the environment and encounter those already-existing contaminants, e.g., heavy metals, which may cause toxicity interactions in polluted habitats. So far, the sulfonamide mixture effects and the combinational effects between sulfonamides and metals have been seldom studied. In this study, lifespan, lethality (24 and 120 h), locomotion behavior and growth (96 h) of Caenorhabditis elegans were measured after exposure to mixtures containing sulfonamides (sulfadiazine, sulfapyridine, sulfamethoxazole and sulfamethazine as representatives) and/or metals (cadmium, copper, lead and zinc as representatives) at environmental concentrations. Results showed that sulfonamides did not cause acute (24 h) lethality at chosen concentrations, but they decreased the lifespan in a concentration dependent fashion. Moreover, sulfonamide mixtures caused synergisms at higher concentrations but antagonisms at lower concentrations on the subacute (120 h) lethal effects. The toxicity interactions of sulfonamide mixtures were addition action on body bending frequency, and antagonism on reversal movement and body length. In sulfonamide and metal mixtures, the toxicity interactions were different in acute and subacute lethal results, indicating the influence of the exposure time. According to the comparison among effects of mixtures containing sulfonamides and/or metals, subacute lethality of sulfonamides was enhanced by metals based on the synergistic mixture effects, while their inhibitions on the growth and behavior were weakened by metals based on the antagonistic mixture effects. Our findings highlighted studies on combinational effects between emerging and common contaminants for more accurate environmental risk evaluation, and also urged further mechanism studies.

Insights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes

In recent years a major worldwide problem has arisen with regard to infectious diseases caused by resistant bacteria. Resistant pathogens are related to high mortality and also to enormous healthcare costs. In this field, cultured microorganisms have been commonly focused in attempts to isolate antibiotic resistance genes or to identify antimicrobial compounds. Although this strategy has been successful in many cases, most of the microbial diversity and related antimicrobial molecules have been completely lost. As an alternative, metagenomics has been used as a reliable approach to reveal the prospective reservoir of antimicrobial compounds and antibiotic resistance genes in the uncultured microbial community that inhabits a number of environments. In this context, this review will focus on resistance genes as well as on novel antibiotics revealed by a metagenomics approach from the soil environment. Biotechnology prospects are also discussed, opening new frontiers for antibiotic development.

Contamination of water resources by pathogenic bacteria

Water-borne pathogen contamination in water resources and related diseases are a major water quality concern throughout the world. Increasing interest in controlling water-borne pathogens in water resources evidenced by a large number of recent publications clearly attests to the need for studies that synthesize knowledge from multiple fields covering comparative aspects of pathogen contamination, and unify them in a single place in order to present and address the problem as a whole. Providing a broader perceptive of pathogen contamination in freshwater (rivers, lakes, reservoirs, groundwater) and saline water (estuaries and coastal waters) resources, this review paper attempts to develop the first comprehensive single source of existing information on pathogen contamination in multiple types of water resources. In addition, a comprehensive discussion describes the challenges associated with using indicator organisms. Potential impacts of water resources development on pathogen contamination as well as challenges that lie ahead for addressing pathogen contamination are also discussed.

Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants

This study applied Illumina high-throughput sequencing to explore the microbial communities and functions in anaerobic digestion sludge (ADS) from two wastewater treatment plants based on a metagenomic view. Taxonomic analysis using SILVA SSU database indicated that Proteobacteria (9.52-13.50 %), Bacteroidetes (7.18 %-10.65 %) and Firmicutes (7.53 %-9.46 %) were the most abundant phyla in the ADS. Differences of microbial communities between the two types of ADS were identified. Genera of Methanosaeta and Methanosarcina were the major methanogens. Functional analysis by SEED subsystems showed that the basic metabolic functions of metagenomes in the four ADS samples had no significant difference among them, but they were different from other microbial communities from activated sludge, human faeces, ocean and soil. Abundances of genes in methanogenesis pathway were also quantified using a methanogenesis genes database extracted from KEGG. Results showed that acetotrophic was the major methanogenic pathway in the anaerobic sludge digestion.