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1.
Artículo en Inglés | MEDLINE | ID: mdl-33974531

RESUMEN

A slow-growing, scotochromogenic mycobacterial strain (24T) was isolated from the sputum of a Chinese male human. Phylogenetic analysis using the 16S rRNA gene assigned strain 24T to the Mycobacterium gordonae complex, which includes Mycobacterium gordonae and Mycobacterium paragordonae. The phenotypic characteristics, unique mycolic acid profile and the results of phylogenetic analysis based on hsp65 and rpoB sequences strongly supported the taxonomic status of strain 24T as a representative of a species distinct from the other members of the M. gordonae complex. The genomic G+C content of strain 24T was 65.40mol%. Genomic comparisons showed that strain 24T and M. gordonae ATCC 14470T had an average nucleotide identity (ANI) value of 81.00 % and a DNA-DNA hybridization (DDH) value of 22.80 %, while the ANI and DDH values between strain 24Tand M. paragordonae 49 061T were 80.98 and 22.80 %, respectively. In terms of phylogenetic, phenotypic and chemotaxonomic features, strain 24T is distinguishable from its closest phylogenetic relatives and represents a novel species of the genus Mycobacterium, therefore the name Mycobacterium vicinigordonae sp. nov. is proposed. The type strain is 24T (=CMCC 93559T=DSM 105979T).


Asunto(s)
Mycobacterium/clasificación , Filogenia , Esputo/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , China , ADN Bacteriano/genética , Ácidos Grasos/química , Genes Bacterianos , Humanos , Masculino , Mycobacterium/aislamiento & purificación , Infecciones por Mycobacterium/microbiología , Ácidos Micólicos/análisis , Hibridación de Ácido Nucleico , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
2.
J Environ Sci (China) ; 104: 415-429, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33985744

RESUMEN

Once contaminate the drinking water source, antibiotic resistance genes (ARGs) will propagate in drinking water systems and pose a serious risk to human health. Therefore, the drinking water treatment processes (DWTPs) are critical to manage the risks posed by ARGs. This study summarizes the prevalence of ARGs in raw water sources and treated drinking water worldwide. In addition, the removal efficiency of ARGs and related mechanisms by different DWTPs are reviewed. Abiotic and biotic factors that affect ARGs elimination are also discussed. The data on presence of ARGs in drinking water help come to the conclusion that ARGs pollution is prevalent and deserves a high priority. Generally, DWTPs indeed achieve ARGs removal, but some biological treatment processes such as biological activated carbon filtration may promote antibiotic resistance due to the enrichment of ARGs in the biofilm. The finding that disinfection and membrane filtration are superior to other DWTPs adds weight to the advice that DWTPs should adopt multiple disinfection barriers, as well as keep sufficient chlorine residuals to inhibit re-growth of ARGs during subsequent distribution. Mechanistically, DWTPs obtain direct and inderect ARGs reduction through DNA damage and interception of host bacterias of ARGs. Thus, escaping of intracellular ARGs to extracellular environment, induced by DWTPs, should be advoided. This review provides the theoretical support for developping efficient reduction technologies of ARGs. Future study should focus on ARGs controlling in terms of transmissibility or persistence through DWTPs due to their biological related nature and ubiquitous presence of biofilm in the treatment unit.


Asunto(s)
Agua Potable , Purificación del Agua , Antibacterianos/análisis , Agua Potable/análisis , Farmacorresistencia Microbiana/genética , Genes Bacterianos , Humanos
3.
Microbiome ; 9(1): 108, 2021 05 14.
Artículo en Inglés | MEDLINE | ID: mdl-33990222

RESUMEN

BACKGROUND: Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively. RESULTS: High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition. CONCLUSIONS: Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.


Asunto(s)
Metagenoma , Microbiología del Suelo , Antibacterianos , Ecosistema , Genes Bacterianos , Pradera , Humanos , ARN Ribosómico 16S/genética , Suelo , Clima Tropical , Tundra
4.
Nat Commun ; 12(1): 2653, 2021 05 11.
Artículo en Inglés | MEDLINE | ID: mdl-33976161

RESUMEN

Plasmid persistence in bacterial populations is strongly influenced by the fitness effects associated with plasmid carriage. However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. In this study, we determined the fitness effects of the major antibiotic resistance plasmid pOXA-48_K8 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. Our results show that although pOXA-48_K8 produced an overall reduction in bacterial fitness, it produced small effects in most bacterial hosts, and even beneficial effects in several isolates. Moreover, genomic results showed a link between pOXA-48_K8 fitness effects and bacterial phylogeny, helping to explain plasmid epidemiology. Incorporating our fitness results into a simple population dynamics model revealed a new set of conditions for plasmid stability in bacterial communities, with plasmid persistence increasing with bacterial diversity and becoming less dependent on conjugation. These results help to explain the high prevalence of plasmids in the greatly diverse natural microbial communities.


Asunto(s)
Bacterias/genética , Transferencia de Gen Horizontal , Genes Bacterianos/genética , Variación Genética , Genoma Bacteriano/genética , Plásmidos/genética , Algoritmos , Antibacterianos/farmacología , Bacterias/clasificación , Farmacorresistencia Bacteriana Múltiple/genética , Enterobacteriaceae/clasificación , Enterobacteriaceae/genética , Microbioma Gastrointestinal/genética , Humanos , Microbiota/genética , Filogenia , Especificidad de la Especie
5.
Nat Commun ; 12(1): 2949, 2021 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-34011959

RESUMEN

The antibiotic trimethoprim (TMP) is used to treat a variety of Escherichia coli infections, but its efficacy is limited by the rapid emergence of TMP-resistant bacteria. Previous laboratory evolution experiments have identified resistance-conferring mutations in the gene encoding the TMP target, bacterial dihydrofolate reductase (DHFR), in particular mutation L28R. Here, we show that 4'-desmethyltrimethoprim (4'-DTMP) inhibits both DHFR and its L28R variant, and selects against the emergence of TMP-resistant bacteria that carry the L28R mutation in laboratory experiments. Furthermore, antibiotic-sensitive E. coli populations acquire antibiotic resistance at a substantially slower rate when grown in the presence of 4'-DTMP than in the presence of TMP. We find that 4'-DTMP impedes evolution of resistance by selecting against resistant genotypes with the L28R mutation and diverting genetic trajectories to other resistance-conferring DHFR mutations with catalytic deficiencies. Our results demonstrate how a detailed characterization of resistance-conferring mutations in a target enzyme can help identify potential drugs against antibiotic-resistant bacteria, which may ultimately increase long-term efficacy of antimicrobial therapies by modulating evolutionary trajectories that lead to resistance.


Asunto(s)
Infecciones por Escherichia coli/tratamiento farmacológico , Infecciones por Escherichia coli/microbiología , Resistencia al Trimetoprim/genética , Trimetoprim/análogos & derivados , Sustitución de Aminoácidos , Antibacterianos/química , Antibacterianos/farmacología , Cristalografía por Rayos X , Evolución Molecular Dirigida , Diseño de Fármacos , Escherichia coli/efectos de los fármacos , Escherichia coli/enzimología , Escherichia coli/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Antagonistas del Ácido Fólico/química , Antagonistas del Ácido Fólico/farmacología , Genes Bacterianos , Genotipo , Humanos , Modelos Moleculares , Mutación , Tetrahidrofolato Deshidrogenasa/química , Tetrahidrofolato Deshidrogenasa/genética , Trimetoprim/química , Trimetoprim/farmacología
6.
Huan Jing Ke Xue ; 42(6): 2937-2945, 2021 Jun 08.
Artículo en Chino | MEDLINE | ID: mdl-34032093

RESUMEN

Research on the distribution of antibiotic resistance genes (ARGs) in urban sewage treatment systems is extensive, but there is still insufficient research on their abundance in industrial wastewater recycling systems. In this study, a printing and dyeing wastewater (PDWW) recycling system was constructed, and 16S rDNA and high-throughput sequencing technology was used to analyze the microbial communities and ARG abundance during the treatment process. A total of 52 ARGs in nine categories were detected, of which the relative abundance of ß-lactam resistance genes was the highest. During the treatment cycle, the concentration of aromatic pollutants increased with an increase in the number of cycles, while the abundance of ß-lactam resistance genes increased first, decreased, and then increased (reaching 61.85% on the 100th day). At the same time, the abundance of Firmicutes, Actinobacteria, and Cyanobacteria related ARGs decreased significantly (by 84.66%, 64.38%, and 85.15%, respectively). More than 21 kinds of ARGs were significantly affected by the enrichment by the aromatic pollutants. Among them, 6 kinds of ARGs were significantly positively correlated with changes in the concentrations of the aromatic pollutants (P<0.01), while 6 were significantly negatively correlate (P<0.01). These results show that the abundance of ARGs was affected by the microbial communities and the aromatic pollutants, which increased at first, decreased, and then increased during the PPDW recycling process. This study reveals the effects of the enrichment of aromatic contaminants and changes in microbial communities on ARGs during PPDW recycling, and provides theoretical guidance for the recycling of PDWW to reduce environmental pollution associated with ARGs.


Asunto(s)
Antibacterianos , Aguas Residuales , Antibacterianos/farmacología , Colorantes , Farmacorresistencia Microbiana/genética , Genes Bacterianos/genética , Impresión Tridimensional
7.
Huan Jing Ke Xue ; 42(6): 2975-2980, 2021 Jun 08.
Artículo en Chino | MEDLINE | ID: mdl-34032097

RESUMEN

Soil is the primary interface of Earth's critical zone and plays an important role in food security and sustaining environmental balance. Antibiotic resistance genes (ARGs) pose significant threat to human health and ecosystems, with croplands being intensively affected via planting patterns and the application of fertilizers. The transmission of ARGs in croplands remains largely unknown. Using high throughput quantitative Polymerase Chain Reaction (HT-qPCR) techniques, we investigated the occurrence and diversity of ARGs and their association with heavy metals in different croplands in China. A total of 187 ARGs were identified, ranging from 89 to 159 in agricultural soils. The abundance of ARGs ranged from 6.47×109 to 1.41×1010 copies·g-1 with multidrug resistance genes being the most abundant. Heavy metals including As, Co, Cr, Mo, Ni, and Pb were correlated with ARGs using the R package 'evnfit'. Furthermore, redundancy analysis (RDA) revealed that the heavy metals explained 59.3% of the variability of ARGs in the different croplands, indicating that heavy metals might exert an important influence on the composition and transmission of ARGs. Croplands soils act as a vital reservoir and reaction media for ARGs. Different crop cultivation coupled with selection pressure of heavy metals from fertilizers could have potential impacts on the prevalence, diversity, and distribution of ARGs.


Asunto(s)
Antibacterianos , Microbiología del Suelo , Antibacterianos/farmacología , China , Productos Agrícolas/genética , Farmacorresistencia Microbiana/genética , Ecosistema , Genes Bacterianos/genética , Humanos , Estiércol , Suelo
8.
Huan Jing Ke Xue ; 42(6): 2981-2991, 2021 Jun 08.
Artículo en Chino | MEDLINE | ID: mdl-34032098

RESUMEN

Livestock breeding intensively uses veterinary antibiotics in concentrated feeding operations to improve growth and control disease. Consequently, livestock and poultry manure is an important repository of antibiotics and antibiotic resistance genes (ARGs). To understanding the distribution of antibiotics and ARGs in manure and surrounding soils of cattle farms in Ningxia, cattle manure from five breeding periods (lactation, calving, growing, pre-fattening, and post-fattening periods) and comparative soil samples were collected from the largest beef-breeding area in Ningxia. The compositions of ARGs in the samples were analyzed by UPLC-MS/MS and HT-qPCR. The results showed that:① Tetracycline, quinolone, and sulfonamide were the dominant antibiotics in cattle manure. The content of antibiotics in the manure varied greatly between different breeding periods. High amounts of antibiotics were detected during the pre-fattening and lactation periods, and the lowest amounts were detected during the calving period. ② Quinolone and tetracycline were the dominant antibiotics in the soils, and the detection rate and content of quinolone were highest. The cattle farms did not affect the distribution of antibiotics in the surrounding soils. The content of quinolone and tetracycline in the soils with cattle manure application were significantly higher than control and surrounding soils. ③ We detected 79-142 ARGs in cattle manure, with aminoglycosides the most common form. The number and relative abundance of ARGs were highest during the growing period and lowest during the calving period. The dominant ARGs were tetQ, ermF, and tetO-01 across all the breeding periods. ④ There were 35-79 ARGs in the tested soils, and multidrug and aminoglycoside ARGs were dominant. The cattle farms did not affect the number and relative abundance of ARGs in the surrounding soils; however, manure application significantly affected the number and relative abundance of ARGs. ⑤ Sulfonamide and chloramphenicol ARGs are at risk of mobilization and horizontal transport. A correlation analysis showed that the relative abundances of aminoglycoside and tetracycline in cattle manure were significantly positively correlated with their contents. ⑥ Aminoglycoside, sulfonamide, chloramphenicol, and mobile genetic elements (MGEs) in manure were significantly or extremely significantly positively correlated with aminoglycosides and sulfonamides in the soils, whereas macrolides were negatively correlated with vancomycin. These results provide baseline data to inform controls on the variety and dosages of feed and veterinary drugs in cattle farms and the application of organic fertilizers in agriculture.


Asunto(s)
Estiércol , Suelo , Animales , Antibacterianos/farmacología , Bovinos , Cromatografía Liquida , Farmacorresistencia Microbiana , Granjas , Genes Bacterianos/genética , Microbiología del Suelo , Espectrometría de Masas en Tándem
9.
Huan Jing Ke Xue ; 42(6): 2992-2999, 2021 Jun 08.
Artículo en Chino | MEDLINE | ID: mdl-34032099

RESUMEN

To investigate the effects of temperature and stirring on antibiotic resistance genes (ARGs) and microbial communities during the anaerobic digestion of dairy manure, mesophilic and thermophilic anaerobic digestion experiments were performed with and without stirring. Two-way analysis of variance indicated that temperature affected biogas production more strongly than stirring (η2=0.934>0.911), and thermophilic and stirring increased the total biogas yield by 13.93% and 12.63%, respectively. The effect of temperature on the removal of ARGs was also stronger than that of stirring (η2=0.992>0.920), where thermophilic conditions enhanced the reduction of ARGs and MGEs to 0.09-1.53 (logarithm), while stirring had no significant effects. When temperature was altered from mesophilic to thermophilic, the microbial communities shifted, with Firmicutes becoming the dominant phylum after thermophilic anaerobic digestion, with a relative abundance of >86%. Network analysis demonstrated that eight genera including Sedimentibacter, Sphaerochaeta, and Pseudomonas were the hosts of ARGs and MGEs, and the redundancy analysis suggested that physicochemical parameters play important roles in shaping microbial communities, especially TAN and TVFAs, which indirectly affected the ARGs by altering their host bacteria.


Asunto(s)
Estiércol , Microbiota , Anaerobiosis , Antibacterianos/farmacología , Farmacorresistencia Microbiana/genética , Genes Bacterianos/genética , Microbiota/genética , Temperatura
10.
BMC Infect Dis ; 21(1): 421, 2021 May 05.
Artículo en Inglés | MEDLINE | ID: mdl-33952197

RESUMEN

BACKGROUND: Streptococcus pneumoniae serotype 8 incidence has increased in Denmark after the introduction of pneumococcal conjugated vaccines (PCV). The mechanism behind the serotype 8 replacement is not well understood. In this study, we aimed to present epidemiological data on invasive pneumococcal disease (IPD) and molecular characterization of 96 serotype 8 clinical isolates. METHODS: IPD data from 1999 to 2019 were used to calculate the incidence and age distribution. Whole-genome sequencing (WGS) analysis was performed on 96 isolates (6.8% of the total serotype 8 IPD isolates in the period) to characterize the isolates with respect to pneumococcal lineage traits, a range of genes with potential species discrimination, presence of colonization and virulence factors, and molecular resistance pattern. RESULTS: The serotype 8 IPD incidence increased significantly (P < 0.05) for the age groups above 15 years after the introduction of PCV13, primarily affecting the elderly (65+). All isolates were phenotypically susceptible to penicillin, erythromycin and clindamycin. Molecular characterization revealed seven different MLST profiles with ST53 as the most prevalent lineage (87.5%) among the analyzed serotype 8 isolates. The genes covering the cell-surface proteins: lytA, rspB, pspA, psaA & Xisco and the pneumococcal toxin pneumolysin = ply were present in all isolates, while genes for the membrane transporter proteins: piaA/piaB/piaC; the capsular genes: cpsA (wzg) & psrP; the metallo-binding proteins zmpB & zmpC; and the neuroamidase proteins: nanA/nanB were variably present. Surprisingly, the putative transcriptional regulator gene SP2020 was not present in all isolates (98%). Susceptibility to penicillin, erythromycin and clindamycin was molecularly confirmed. CONCLUSION: The observed serotype 8 replacement was not significantly reflected with a change in the MLST profile or changes in antibiotic resistance- or virulence determinants.


Asunto(s)
Farmacorresistencia Microbiana/genética , Infecciones Neumocócicas/epidemiología , Infecciones Neumocócicas/microbiología , Streptococcus pneumoniae/efectos de los fármacos , Streptococcus pneumoniae/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Niño , Preescolar , Dinamarca/epidemiología , Farmacorresistencia Microbiana/efectos de los fármacos , Genes Bacterianos , Humanos , Incidencia , Lactante , Proteínas de Transporte de Membrana/genética , Persona de Mediana Edad , Tipificación de Secuencias Multilocus , Vacunas Neumococicas/farmacología , Serogrupo , Streptococcus pneumoniae/clasificación , Streptococcus pneumoniae/aislamiento & purificación , Vacunación , Vacunas Conjugadas/farmacología , Factores de Virulencia/genética , Adulto Joven
11.
Sci Total Environ ; 773: 145643, 2021 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-33940744

RESUMEN

Antibiotic resistance genes (ARGs) and microplastics in the environment are of great public concern due to their potential risk to human health. Microplastics can form distinct bacterial communities and absorb pollutants from the surrounding environment, which provide potential hosts and exert possible selection pressure of ARGs. We provide a practical evaluation of the scientific literature regarding this issue. The occurrence and transport of ARGs on microplastics in wastewater treatment plants, aquatic, terrestrial, and air environments were summarized. Selective enrichment of ARGs and antibiotic resistance bacteria on microplastics have been confirmed in different environments. Aggregates may be crucial to understand the behavior and transport of ARGs on microplastics, especially in the aquatic and terrestrial environment. Microplastics could be a carrier of ARGs between the environment and animals. Accumulation of pollutants and dense bacterial communities on microplastics provide favorable conditions for higher transfer rate and evolution of ARGs. More studies are still needed to understand the enrichment, transport, and transfer of ARGs on microplastics and provide a fundamental basis for evaluating their exposure health risk to humans.


Asunto(s)
Microplásticos , Plásticos , Animales , Antibacterianos , Farmacorresistencia Microbiana/genética , Genes Bacterianos , Humanos , Plásticos/toxicidad
12.
Sci Total Environ ; 779: 146329, 2021 Jul 20.
Artículo en Inglés | MEDLINE | ID: mdl-34030225

RESUMEN

As a by-product in the pharmaceutical industry, antibiotic fermentation residue is expected to be able to be utilized after effectively removing the antibiotics. However, evaluation of the effect of fermentation residue application on soil, especially the in situ environmental consequences considering not only the antibiotic resistance gene (ARG) abundance but also the resistome risk, has still not been sufficiently evaluated. Herein, the impact of treated erythromycin fermentation residue (EFR) on the resistome and risk score in soybean planting soil was investigated. Treated EFR application with dosages of 3750 kg (EFR250) and 7500 kg (EFR500) per hm2 soil did not increase the diversity (Shannon index, 2.84-3.38) or relative abundance (0.086-0.142 copies/16S rRNA gene) of the soil resistome compared with the Control (CK: 2.92-3.2, 0.088-0.096 copies/16S rRNA gene). Soil resistome risk scores calculated by metagenomic assembly, showing the dissemination potential of ARGs, ranged from 22.9 to 25.0, and were also not significantly different between treated EFR amended soil and the Control. Notably, the diversity of the resistome increased at the sprout stage (Mann-Whitney U test, P < 0.05) and the abundance of some ARG types (macrolide-lincosamide-streptogramin, aminoglycoside and tetracycline, etc.) shifted along the course of soybean growth (Kruskal-Wallis test, P < 0.05). Structural equation model analysis showed that the soybean growth period affected the composition of ARGs by affecting the microbial community, which was further supported by Procrustes analysis (P < 0.05) and metagenomic binning. Our findings emphasized that soil ARG abundance and resistome risk did not increase during one-time field application of treated EFR at the studied dosage. Comprehensive consideration including resistome risk and multiple influencing factors also should be given for further assessment of fermentation residue application.


Asunto(s)
Eritromicina , Suelo , Antibacterianos , Fermentación , Genes Bacterianos , ARN Ribosómico 16S , Microbiología del Suelo , Soja
13.
Sci Total Environ ; 778: 146348, 2021 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-34030387

RESUMEN

The persistence of antibiotics in the environment because of human activities, such as seafood cultivation, has attracted great attention as they can give rise to antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). In this study, we explored the inactivation and removal efficiencies of Escherichia coli SR1 and sul1 (plasmid-encoded ARGs), respectively, in their extracellular and intracellular forms (eARGs and iARGs) by three commonly used fishery oxidants, namely chlorine, bromine, and potassium permanganate (KMnO4), at the practical effective concentration range (0.5, 5, and 15 mg/L). Kinetics data were obtained using laboratory phosphate-buffered saline (PBS). Following the same fishery oxidation methods, the determined kinetics models were tested by studying the SR1 and sul1 disinfection efficiencies in (sterilized) pond water matrix. At concentrations of 5 and 15 mg/L, all three oxidants achieved sufficient cumulative integrated exposure (CT values) to completely inactivate SR1 and efficiently remove sul1 (up to 4.0-log). The oxidation methods were then applied to an unsterilized pond water matrix in order to study and evaluate the indigenous ARB and ARGs disinfection efficiencies in aquaculture, which reached 1.4-log and 1.0-log during treatment with fishery oxidants used in pond preparation at high concentrations before stocking (5-15 mg/L), respectively. A high chlorine concentration (15 mg/L) could efficiently remove ARGs (or iARGs) from pond water, and the iARG removal efficiency was higher than that of eARGs in pond water. The method and results of this study could aid in guiding future research and practical disinfection to control the spread of ARGs and ARB in aquaculture.


Asunto(s)
Genes Bacterianos , Purificación del Agua , Antagonistas de Receptores de Angiotensina , Inhibidores de la Enzima Convertidora de Angiotensina , Antibacterianos/farmacología , Farmacorresistencia Microbiana/genética , Humanos , Estrés Oxidativo , Aguas Residuales
14.
Artículo en Inglés | MEDLINE | ID: mdl-33999788

RESUMEN

A total of 27 Listeria isolates that could not be classified to the species level were obtained from soil samples from different locations in the contiguous United States and an agricultural water sample from New York. Whole-genome sequence-based average nucleotide identity blast (ANIb) showed that the 27 isolates form five distinct clusters; for each cluster, all draft genomes showed ANI values of <95 % similarity to each other and any currently described Listeria species, indicating that each cluster represents a novel species. Of the five novel species, three cluster with the Listeria sensu stricto clade and two cluster with sensu lato. One of the novel sensu stricto species, designated L. cossartiae sp. nov., contains two subclusters with an average ANI similarity of 94.9%, which were designated as subspecies. The proposed three novel sensu stricto species (including two subspecies) are Listeria farberi sp. nov. (type strain FSL L7-0091T=CCUG 74668T=LMG 31917T; maximum ANI 91.9 % to L. innocua), Listeria immobilis sp. nov. (type strain FSL L7-1519T=CCUG 74666T=LMG 31920T; maximum ANI 87.4 % to L. ivanovii subsp. londoniensis) and Listeria cossartiae sp. nov. [subsp. cossartiae (type strain FSL L7-1447T=CCUG 74667T=LMG 31919T; maximum ANI 93.4 % to L. marthii) and subsp. cayugensis (type strain FSL L7-0993T=CCUG 74670T=LMG 31918T; maximum ANI 94.7 % to L. marthii). The two proposed novel sensu lato species are Listeria portnoyi sp. nov. (type strain FSL L7-1582T=CCUG 74671T=LMG 31921T; maximum ANI value of 88.9 % to L. cornellensis and 89.2 % to L. newyorkensis) and Listeria rustica sp. nov. (type strain FSL W9-0585T=CCUG 74665T=LMG 31922T; maximum ANI value of 88.7 % to L. cornellensis and 88.9 % to L. newyorkensis). L. immobilis is the first sensu stricto species isolated to date that is non-motile. All five of the novel species are non-haemolytic and negative for phosphatidylinositol-specific phospholipase C activity; the draft genomes lack the virulence genes found in Listeria pathogenicity island 1 (LIPI-1), and the internalin genes inlA and inlB, indicating that they are non-pathogenic.


Asunto(s)
Riego Agrícola , Listeria/clasificación , Filogenia , Microbiología del Agua , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Genes Bacterianos , Listeria/aislamiento & purificación , New York , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
15.
Artículo en Inglés | MEDLINE | ID: mdl-33999791

RESUMEN

The taxonomic relationships and genome features of the type strains in the Streptomyces aurantiacus clade, including Streptomyces aurantiacus, Streptomyces ederensis, Streptomyces glomeroaurantiacus, Streptomyces umbrinus, Streptomyces phaeochromogenes, Streptomyces dioscori and Streptomyces tauricus, were investigated. Type strains of these species shared high 16S rRNA gene sequence similarity to each other. Multilocus sequence analysis (MLSA) based on atpD, gyrB, recA, rpoB and trpB genes revealed that S. ederensis and S. umbrinus belong to the same species. Also, S. aurantiacus and S. glomeroaurantiacus belong to the same species, but the remaining species are not closely related to each other. MLSA results were verified by the results average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses; while the ANI and dDDH values between S. ederensis and S. umbrinus are 98.1 and 85.4 %, respectively, these values between S. aurantiacus and S. glomeroaurantiacus are 98.9 and 90.7 %, respectively. The presence of almost the same set of biosynthetic gene clusters and highly consistent phenotypic test results also supported the synonymy between S. ederensis and S. umbrinus, as well as between S. aurantiacus and S. glomeroaurantiacus. Therefore, S. ederensis should be reclassified as a later heterotypic synonym of S. umbrinus and S. glomeroaurantiacus should be reclassified as a later heterotypic synonym of S. aurantiacus.


Asunto(s)
Filogenia , Streptomyces/clasificación , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Genes Bacterianos , Genómica , Tipificación de Secuencias Multilocus , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
16.
Artículo en Inglés | MEDLINE | ID: mdl-34016249

RESUMEN

A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas. The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes. Computation of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas campi sp. nov. (type strain S1-A32-2T=LMG 31521T=DSM 110222T) is proposed.


Asunto(s)
Pradera , Filogenia , Pseudomonas/clasificación , Microbiología del Suelo , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Genes Bacterianos , Alemania , Nitratos/metabolismo , Hibridación de Ácido Nucleico , Pseudomonas/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
17.
Int J Mol Sci ; 22(9)2021 Apr 27.
Artículo en Inglés | MEDLINE | ID: mdl-33925677

RESUMEN

pCTX-M3 is the archetypic member of the IncM incompatibility group of conjugative plasmids (recently referred to as IncM2). It is responsible for the worldwide dissemination of numerous antibiotic resistance genes, including those coding for extended-spectrum ß-lactamases and conferring resistance to aminoglycosides. The IncM plasmids acquired during evolution diverse mobile genetic elements found in one or two multiple resistance regions, MRR(s), grouping antibiotic resistance genes as well as mobile genetic elements or their remnants. The IncM plasmids can be found in bacteria inhabiting various environments. The information on the structure and biology of pCTX-M3 is integrated in this review. It focuses on the functional modules of pCTX-M3 responsible for its replication, stable maintenance, and conjugative transfer, indicating that the host range of the pCTX-M3 replicon is limited to representatives of the family Enterobacteriaceae (Enterobacterales ord. nov.), while the range of recipients of its conjugation system is wide, comprising Alpha-, Beta-, and Gammaproteobacteria, and also Firmicutes.


Asunto(s)
Farmacorresistencia Bacteriana/genética , Plásmidos/genética , Proteínas Bacterianas/genética , Conjugación Genética , ADN Bacteriano/genética , Enterobacteriaceae/genética , Transferencia de Gen Horizontal , Genes Bacterianos , Especificidad del Huésped/genética , beta-Lactamasas/genética
18.
Bioresour Technol ; 333: 124988, 2021 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-33894444

RESUMEN

The metagenomic and quantitative polymerase chain reaction approaches were combined to evaluate the profiles of ARGs and plasmids in anaerobically digested dairy manure in situ and reveal the persistence and elevation of typical ARGs and plasmids in its subsequent disposal facilities in CAFOs, respectively. Our results indicated that the typical ARGs and plasimd were mainly sul2, mefa, tetm-01, tetm-02, tetw, aph3iiia, and clostridioides difficile strain 12,038 plasmid unnamed in CAFOs, some of which greatly enriched in AD residue after its storage, especially sul1 and sul2. Meantime, the AD slurry recycling introduced the bacteria carrying ARGs into soil, especially Romboutsia genus, which greatly enriched sul2, tetm-01, tetm-02, aphiiia, and mefa. In the present study, ARGs occurrence, persistence and distribution were understood through in situ analysis of their profiles during dairy manure AD treatment and subsequent disposals in CAFOs, which are helpful for controlling the potential environmental risks from dairy manure recycling.


Asunto(s)
Antibacterianos , Estiércol , Antibacterianos/farmacología , Farmacorresistencia Microbiana , Genes Bacterianos , Suelo , Microbiología del Suelo
19.
Environ Pollut ; 281: 116980, 2021 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-33799209

RESUMEN

Coastal tourist and industrial cities are most likely to have differential effects on the distance dilution of antibiotic resistance genes (ARGs) in an estuary system. This study used high-throughput fluorescence quantitative polymerase chain reaction to identify sediment ARGs in two typical estuaries of coastal tourist and industrial cities (Xiamen and Taizhou) in China. The distance dilution of ARGs and its relationship with key environmental factors were analysed. The results indicated that along the river inlet towards the sea, the distance dilution effect on ARG abundance in estuary sediments of Taizhou was approximately double that in Xiamen, and the macrolide, lincosamide, and streptogramin B (MLSB) and vancomycin genes were replaced by the fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol (FCA) and ß-lactam genes in Taizhou, whereas ß-lactam genes succeeded the MLSB and sul genes in Xiamen. The abundance and number of ARGs and mobile genetic elements (MGEs) were positively correlated with the particle size and total organic carbon (TOC) contents of sediments, whereas they were negatively associated with the oxidation and reduction potential (Eh) and pH of sediments, as well as the seawater salinity. The sediment particle size (SPZ) was the dominant physicochemical factor affecting the abundance of ARGs (r = 0.826, p < 0.05) and MGEs (r = 0.850, p < 0.01). These findings suggest that although the distance dilution effect on the ARG abundance of estuary sediments of the industrial city is greater than that of the tourist city, the larger SPZ, higher TOC content, and lower salinity, pH, and Eh in estuary regions adjacent to the industrial city can more significantly facilitate the proliferation and propagation of ARGs in the sediments.


Asunto(s)
Antibacterianos , Estuarios , Antibacterianos/análisis , China , Ciudades , Farmacorresistencia Microbiana/genética , Genes Bacterianos , Sedimentos Geológicos
20.
Sci Total Environ ; 782: 146835, 2021 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-33838375

RESUMEN

Diminishing freshwater (FW) supplies necessitate the reuse of treated wastewater (TWW) for various purposes, like irrigation of agricultural lands. However, there is a growing concern that irrigation with TWW may transfer antibiotic resistance genes (ARGs) to the soil and crops. We hypothesized that TWW irrigation would increase the prevalence of antibiotic residues together with the corresponding ARGs in the irrigated soil. We further predicted that soil texture, especially pH, clay content, and organic matter variabilities, would change the antibiotic residues concentrations and thus ARGs dissemination. To test our predictions, three soils types (loamy-sand, loam, and clay) were irrigated with two water types (FW and TWW), over two consecutive seasons. We monitored physico-chemical parameters, the abundance of seven antibiotic residues, and their corresponding ARGs together with class 1 integron (intI1) in 54 water and soil samples collected at the end of the field experiments. The results revealed increase in antibiotics concentrations and ARGs relative abundance in TWW than FW. Yet, in the soil ARGs relative abundances were independent of the irrigation water quality, but dependent on the soil type, especially the clay content. Further, there were no clear associations between the targeted antibiotics or the presence of heavy metals and ARGs' relative abundance in the water or soil samples. Therefore, our results question the link between the discharge of antibiotics and heavy metals, and the dissemination of ARGs in soil environments.


Asunto(s)
Suelo , Aguas Residuales , Riego Agrícola , Antibacterianos/farmacología , Farmacorresistencia Microbiana/genética , Genes Bacterianos , Microbiología del Suelo , Aguas Residuales/análisis
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