Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms

Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data

Metagenomics has emerged as a central technique for studying the structure and function of microbial communities. Often the functional analysis is restricted to classification into broad functional categories. However, important phenotypic differences, such as resistance to antibiotics, are often the result of just one or a few point mutations in otherwise identical sequences. Bioinformatic methods for metagenomic analysis have generally been poor at accounting for this fact, resulting in a somewhat limited picture of important aspects of microbial communities. Here, we address this problem by providing a software tool called Mumame, which can distinguish between wildtype and mutated sequences in shotgun metagenomic data and quantify their relative abundances. We demonstrate the utility of the tool by quantifying antibiotic resistance mutations in several publicly available metagenomic data sets. We also identified that sequencing depth is a key factor to detect rare mutations. Therefore, much larger numbers of sequences may be required for reliable detection of mutations than for most other applications of shotgun metagenomics. Mumame is freely available online (http://microbiology.se/software/mumame).

A conceptual framework for the environmental surveillance of antibiotics and antibiotic resistance

Environmental surveillance of antibiotics and antibiotic resistance could contribute toward the protection of human, animal and ecosystem health. However, justification for the choice of markers and sampling sites that informs about different risk scenarios is often lacking. Here, we define five fundamentally different objectives for surveillance of antibiotics and antibiotic resistance in the environment. The first objective is (1) to address the risk of transmission of already antibiotic-resistant bacteria to humans via environmental routes. The second is (2) to address the risk for accelerating the evolution of antibiotic resistance in pathogens through pollution with selective agents and bacteria of human or animal origin. The third objective is (3) to address the risks antibiotics pose for aquatic and terrestrial ecosystem health, including the effects on ecosystem functions and services. The two final objectives overlap with those of traditional clinical surveillance, namely, to identify (4) the population-level resistance prevalence and (5) population-level antibiotic use. The latter two environmental surveillance objectives have particular potential in countries where traditional clinical surveillance data and antibiotic consumption data are scarce or absent. For each objective, the levels of evidence provided by different phenotypic and genotypic microbial surveillance markers, as well as antibiotic residues, are discussed and evaluated on a conceptual level. Furthermore, sites where monitoring would be particularly informative are identified. The proposed framework could be one of the starting points for guiding environmental monitoring and surveillance of antibiotics and antibiotic resistance on various spatiotemporal scales, as well as for harmonizing such activities with existing human and animal surveillance systems.

Metagenomic characterization of antibiotic resistance genes in Antarctic soils

Antibiotic resistance genes (ARGs) are considered environmental pollutants. Comprehensive characterization of the ARGs in pristine environments is essential towards understanding the evolution of antibiotic resistance. Here, we analyzed ARGs in soil samples collected from relatively pristine Antarctica using metagenomic approaches. We identified 79 subtypes related to 12 antibiotic classes in Antarctic soils, in which ARGs related to multidrug and polypeptide were dominant. The characteristics of ARGs in Antarctic soils were significantly different from those in active sludge, chicken feces and swine feces, in terms of composition, abundance and potential transferability. ARG subtypes (e.g., bacA, ceoB, dfrE, mdtB, amrB, and acrB) were more abundant than others in Antarctic soils. Approximately 60% of the ARGs conferred antibiotic resistance via an efflux mechanism, and a low fraction of ARGs (∼16%) might be present on plasmids. Culturable bacterial consortiums isolated from Antarctic soils were consistently susceptible to most of the tested antibiotics frequently used in clinical therapies. The amrB and ceoB carried by culturable species did not express the resistance to aminoglycoside and fluoroquinolone at the levels of clinical concern. Our results suggest that the wide use of antibiotics may have contributed to developing higher antibiotic resistance and mobility.

Human health risk assessment of antibiotic resistance associated with antibiotic residues in the environment: A review

The extensive use of antibiotics leading to the rapid spread of antibiotic resistance poses high health risks to humans, but to date there is still lack of a quantitative model to properly assess the risks. Concerns over the health risk of antibiotic residues in the environment are mainly (1) the potential hazard of ingested antibiotic residues in the environment altering the human microbiome and promoting emergence and selection for bacteria resistance inhabiting the human body, and (2) the potential hazard of creating a selection pressure on environmental microbiome and leading to reservoirs of antibiotic resistance in the environment. We provide a holistic view of health risk assessment of antibiotic resistance associated with antibiotic residues in the environment in contrast with that of the antibiotic resistant bacteria and discuss the main knowledge gaps and the future research that should be prioritized to achieve the quantitative risk assessment. We examined and summarized the available data and information on the four core elements of antibiotic resistance associated with antibiotic residues in the environment: hazard identification, exposure assessment, dose-response assessment, and risk characterization. The data required to characterize the risks of antibiotic residues in the environment is severely limited. The main future research needs have been identified to enable better assessments of antibiotic resistance associated with antibiotic residues in the environment: (1) establishment of a standardized monitoring guide of antibiotic residues and antibiotic resistance in the environment, (2) derivation of the relationship between antibiotic levels and pathogenic antibiotic-resistance development in different settings, and (3) establishment of the dose-response relationship between pathogenic antibiotic resistant bacteria and various infection diseases. After identification of key risk determinant parameters, we propose a conceptual framework of human health risk assessments of antibiotic residues in the environment. CAPSULE: A holistic view of human health risk assessment of antibiotic residues in the environment was provided.

Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments

Discharge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. However, it is unclear whether increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments is due to on-site selection pressure by residual antibiotics, or is simply a result of fecal contamination with resistant bacteria. Here we analyze relative resistance gene abundance and accompanying extent of fecal pollution in publicly available metagenomic data, using crAssphage sequences as a marker of human fecal contamination (crAssphage is a bacteriophage that is exceptionally abundant in, and specific to, human feces). We find that the presence of resistance genes can largely be explained by fecal pollution, with no clear signs of selection in the environment, with the exception of environments polluted by very high levels of antibiotics from manufacturing, where selection is evident. Our results demonstrate the necessity to take into account fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance.

Increased abundance of antibiotic resistance genes in the environment may be due to selection pressure by residual antibiotics, or to contamination with resistant bacteria from human faeces. Here, Karkman et al. analyze metagenomic data and find evidence supporting the second scenario in most cases.

A Comprehensive Screening of Escherichia coli Isolates from Scandinavia's Largest Sewage Treatment Plant Indicates No Selection for Antibiotic Resistance

There is concern that sewage treatment plants (STPs) serve as hotspots for emergence and selection of antibiotic resistant bacteria. However, field studies investigating resistance selection by comparing bacterial populations in influents and effluents have produced variable and sometimes contradictive results. Also, large taxonomic changes between influents and effluents make interpretation of studies measuring relative gene abundances ambiguous. The aim here was to investigate whether within-species selection occurs by conducting a comprehensive screening of Escherichia coli isolated from composite influent and effluent samples collected at Scandinavia's largest STP, accompanied by analyses of antibiotics residues. In total, 4028 isolates, collected on eight occasions during 18 months, were screened for resistance to seven antibiotics. Although differences in proportions of resistant E. coli between influent and effluent samples were detected for a few antibiotics on two occasions, aggregated data over time showed no such differences for any of the investigated antibiotics. Neither was there any enrichment of multiresistant or extended-spectrum beta-lactamase-producing isolates through the treatment process. Despite some antibiotics were detected at or close to concentrations predicted to provide some selective pressure, field observations of resistance profiles in E. coli do not provide support for systematic selection in the investigated STP.

Prevalence of Multidrug-Resistant Escherichia coli Isolated from Drinking Water Sources

The control of infectious diseases is badly endangered by the rise in the number of microorganisms that are resistant to antimicrobial agents. This is because infections caused by resistant microorganisms often fail to respond to conventional treatment, resulting in prolonged illness and greater risk of death. Antimicrobial-resistant bacteria are also present in various water sources. This study therefore sought to document the microbiological quality and antibiograms of bacterial isolates (E. coli strains) from six different water sources in order to determine their safety for human consumption and to provide updated antibiotic data for pragmatic treatment of patients. Bacteria isolation and identification was done using API and conventional methods. Antibiotic susceptibility testing was conducted using the Kirby-Bauer method. Results obtained indicated that all the water sources tested were of poor quality. Bacteria isolated included E. coli, Enterobacter spp., Klebsiella spp., Salmonella typhi, Streptococcus spp., Proteus vulgaris, Vibrio cholera, Shigella spp., Pseudomonas aeruginosa, and Enterococcus faecalis. The prevalence of multidrug-resistant E. coli was 49.48%. E. coli isolates showed high resistance patterns to the tested antibiotics. They were most resistant to penicillin (32.99%), cefuroxime (28.87%), erythromycin (23.71%), and tetracycline (21.45%). In contrast, they were susceptible to nitrofurantoin (93.8%), cefotaxime and amikacin (91.75%), gentamicin (90.7%), nalidixic acid (89.65%), ciprofloxacin (74.2%), chloramphenicol (69.07%), pipemidic acid (65.97%), and cefuroxime (52.58%). Sixty-three percent (63%) of the multidrug-resistant E. coli strains recorded a multiple antibiotic resistance (MAR) index value >0.2. The susceptible antibiotics, especially the nitrofurantoin, are hence recommended in the practical treatment of waterborne bacterial diseases.