scholarly journals Diversity and Distribution of Potential Pathogens and Antibiotic Resistance Genes in Anthropogenic Disturbances Aquatic Environment and Their Relationship with Microbial Indicators

2021 ◽  
Author(s):  
Xiang-Long Zhao ◽  
Zhao Qi ◽  
Hao Huang ◽  
Jian Tu ◽  
Xiang-Jun Song ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Antibiotic Resistance Genes ◽  
Chaohu Lake ◽  
Lake Basin ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Potential Health ◽  
Microbial Indicators

Abstract Microbial indicators are often used as alternative indicators of microbial safety in water. However, information regarding the correlation between microbial indicators and ecotoxicological factors such as potential pathogens and antibiotic resistance genes (ARGs) in anthropogenically impacted waters remains highly limited. Combining 16S rRNA and metagenomic sequencing data, we investigated the composition of bacterial community and potential pathogens, ARGs diversity, ARGs host and horizontal gene transfer (HGT) potential in water samples under the influence of different exogenous pollutants in Chaohu Lake basin. The water body that receives a large amount of domestic sewage showed a significant decrease in microbial diversity and a significant enrichment of potential pathogens. A total of 14 main types and 461 subtypes of ARGs were detected in all samples, dominated by multidrug resistance (MDR) efflux pump (53.6%), aminoglycoside (6.0%), fluoroquinolone (5.8%) and polymyxin (5.46%). Host-tracking analysis showed that Escherichia coli and Bacteroides graminisolvens carried a wealth of ARG subtypes. Correlation analysis showed that potential pathogens and some ARG subtypes such as dfrE, sul2, PmrE exhibits significant correlation with indicator bacteria. Overall, next-generation sequencing (NGS) has the ability to conduct preliminary surveys of environmental samples to access potential health risks, thus providing ideas for water resources management.

scholarly journals Exploring the prevalence and distribution patterns of antibiotic resistance genes in bovine gut microbiota using a metagenomic approach

2020 ◽  
Author(s):  
Zhen Zhu ◽  
Mingze Cao ◽  
Weiwei Wang ◽  
Liwei Zhang ◽  
Tenghe Ma ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Beef Cattle ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Distribution Patterns ◽  
Antibiotic Consumption ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Illumina Hiseq

Abstract Background: Antibiotic resistance genes (ARGs) have become recognized contaminants and pose a high public health risk. The animal gut microbiota is a reservoir of ARGs, but the knowledge of the origin and dissemination of ARGs remains unclear.Methods: 30 of the fecal samples were obtained from bovine and were immediately frozen in liquid nitrogen. Total metagenomic DNA was extracted by cetyltrimethylammonium bromide (CTAB) method and sequenced by Illumina HiSeq X Ten platform. After quality control and assembled, the sequence were annotated by NR, CARD and ISfinder. Statistical analysis was performed using SPSS 19.0.Results: A total of 42 ARG types were detected by annotating the metagenomic sequencing data from the Comprehensive Antibiotic Resistance Database (CARD). We found that the diversity and abundance of ARGs in individual yaks were significantly lower than those in dairy and beef cattle. The results of heat map and single-nucleotide polymorphism (SNP) clustering suggest that ARGs from dairy and beef cattle are more similar, while those from yaks cluster separately. Conclusion: The long-term use of antibiotics may contribute to this difference, suggesting that antibiotic consumption is the main cause of ARG prevalence. Furthermore, abundant insertions and integrations were also found in this study, signifying a strong potential for horizontal transfer of ARGs among microbes, especially pathogens.

scholarly journals Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ishi Keenum ◽  
Robert K. Williams ◽  
Partha Ray ◽  
Emily D. Garner ◽  
Katharine F. Knowlton ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Land Application ◽  
Multidimensional Analysis ◽  
Small Scale ◽  
Antibiotic Administration ◽  
Metagenomic Sequencing ◽  
Combined Effects ◽  
Bacterial Microbiota

Abstract Background Research is needed to delineate the relative and combined effects of different antibiotic administration and manure management practices in either amplifying or attenuating the potential for antibiotic resistance to spread. Here, we carried out a comprehensive parallel examination of the effects of small-scale (> 55 °C × 3 days) static and turned composting of manures from dairy and beef cattle collected during standard antibiotic administration (cephapirin/pirlimycin or sulfamethazine/chlortetracycline/tylosin, respectively), versus from untreated cattle, on “resistomes” (total antibiotic resistance genes (ARGs) determined via shotgun metagenomic sequencing), bacterial microbiota, and indicator ARGs enumerated via quantitative polymerase chain reaction. To gain insight into the role of the thermophilic phase, compost was also externally heated to > 55 °C × 15 days. Results Progression of composting with time and succession of the corresponding bacterial microbiota was the overarching driver of the resistome composition (ANOSIM; R = 0.424, p = 0.001, respectively) in all composts at the small-scale. Reduction in relative abundance (16S rRNA gene normalized) of total ARGs in finished compost (day 42) versus day 0 was noted across all conditions (ANOSIM; R = 0.728, p = 0.001), except when externally heated. Sul1, intI1, beta-lactam ARGs, and plasmid-associated genes increased in all finished composts as compared with the initial condition. External heating more effectively reduced certain clinically relevant ARGs (blaOXA, blaCARB), fecal coliforms, and resistome risk scores, which take into account putative pathogen annotations. When manure was collected during antibiotic administration, taxonomic composition of the compost was distinct according to nonmetric multidimensional analysis and tet(W) decayed faster in the dairy manure with antibiotic condition and slower in the beef manure with antibiotic condition. Conclusions This comprehensive, integrated study revealed that composting had a dominant effect on corresponding resistome composition, while little difference was noted as a function of collecting manure during antibiotic administration. Reduction in total ARGs, tet(W), and resistome risk suggested that composting reduced some potential for antibiotic resistance to spread, but the increase and persistence of other indicators of antibiotic resistance were concerning. Results indicate that composting guidelines intended for pathogen reduction do not necessarily provide a comprehensive barrier to ARGs or their mobility prior to land application and additional mitigation measures should be considered.

scholarly journals Correlation between the Antibiotic Resistance Genes and Susceptibility to Antibiotics among the Carbapenem-Resistant Gram-Negative Pathogens

Antibiotics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 255
Author(s):  
Salma M. Abdelaziz ◽  
Khaled M. Aboshanab ◽  
Ibrahim S. Yahia ◽  
Mahmoud A. Yassien ◽  
Nadia A. Hassouna
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Antibiotic Resistance Genes ◽  
Multiple Drug ◽  
P Value ◽  
Multidrug Efflux ◽  
Multidrug Efflux Pump ◽  
Gram Negative ◽  
Carbapenem Resistant

In this study, the correlation between the antibiotic resistance genes and antibiotic susceptibility among the carbapenem-resistant Gram-negative pathogens (CRGNPs) recovered from patients diagnosed with acute pneumonia in Egypt was found. A total of 194 isolates including Klebsiella pneumoniae (89; 46%), Escherichia coli (47; 24%) and Pseudomonas aeruginosa (58; 30%) were recovered. Of these, 34 (18%) isolates were multiple drug resistant (MDR) and carbapenem resistant. For the K. pneumoniae MDR isolates (n = 22), blaNDM (14; 64%) was the most prevalent carbapenemase, followed by blaOXA-48 (11; 50%) and blaVIM (4; 18%). A significant association (p value < 0.05) was observed between the multidrug efflux pump (AcrA) and resistance to β-lactams and the aminoglycoside acetyl transferase gene (aac-6’-Ib) gene and resistance to ciprofloxacin, azithromycin and β-lactams (except for aztreonam). For P. aeruginosa, a significant association was noticed between the presence of the blaSHV gene and the multidrug efflux pump (MexA) and resistance to fluoroquinolones, amikacin, tobramycin, co-trimoxazole and β-lactams and between the aac-6’-Ib gene and resistance to aminoglycosides. All P. aeruginosa isolates (100%) harbored the MexAB-OprM multidrug efflux pump while 86% of the K. pneumoniae isolates harbored the AcrAB-TolC pump. Our results are of great medical importance for the guidance of healthcare practitioners for effective antibiotic prescription.

scholarly journals Improved Electrotransformation and Decreased Antibiotic Resistance of the Cystic Fibrosis Pathogen Burkholderia cenocepacia Strain J2315

2009 ◽  
Vol 76 (4) ◽  
pp. 1095-1102 ◽  
Author(s):  
Nelly Dubarry ◽  
Wenli Du ◽  
David Lane ◽  
Franck Pasta
Keyword(s):  
Cystic Fibrosis ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Antibiotic Resistance Genes ◽  
Burkholderia Cenocepacia ◽  
The Poor ◽  
High Level

ABSTRACT The bacterium Burkholderia cenocepacia is pathogenic for sufferers from cystic fibrosis (CF) and certain immunocompromised conditions. The B. cenocepacia strain most frequently isolated from CF patients, and which serves as the reference for CF epidemiology, is J2315. The J2315 genome is split into three chromosomes and one plasmid. The strain was sequenced several years ago, and its annotation has been released recently. This information should allow genetic experimentation with J2315, but two major impediments appear: the poor potential of J2315 to act as a recipient in transformation and conjugation and the high level of resistance it mounts to nearly all antibiotics. Here, we describe modifications to the standard electroporation procedure that allow routine transformation of J2315 by DNA. In addition, we show that deletion of an efflux pump gene and addition of spermine to the medium enhance the sensitivity of J2315 to certain commonly used antibiotics and so allow a wider range of antibiotic resistance genes to be used for selection.

Ultraviolet irradiation sensitizes Pseudomonas aeruginosa PAO1 to multiple antibiotics

2018 ◽  
Vol 4 (12) ◽  
pp. 2051-2057 ◽  
Author(s):  
Fuzheng Zhao ◽  
Qing Hu ◽  
Hongqiang Ren ◽  
Xu-Xiang Zhang
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Uv Irradiation ◽  
Resistance Genes ◽  
Ultraviolet Irradiation ◽  
Efflux Pump ◽  
Antibiotic Resistance Genes ◽  
Regulatory System ◽  
Pseudomonas Aeruginosa Pao1 ◽  
Multiple Antibiotics

UV irradiation disturbs the regulatory system of efflux pump proteins to sensitize P. aeruginosa to multiple antibiotics. The increasing susceptibility to rifampicin and vancomycin might be caused by UV-mediated mutations in antibiotic resistance genes.

Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics

2020 ◽  
Vol 96 (10) ◽  
Author(s):  
Bo Li ◽  
Zeng Chen ◽  
Fan Zhang ◽  
Yongqin Liu ◽  
Tao Yan
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Soil Samples ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Metagenomic Sequencing ◽  
Clinical Issue ◽  
Abundance And Diversity

ABSTRACT Widespread occurrence of antibiotic resistance genes (ARGs) has become an important clinical issue. Studying ARGs in pristine soil environments can help to better understand the intrinsic soil resistome. In this study, 10 soil samples were collected from a high elevation and relatively pristine Tibetan area, and metagenomic sequencing and bioinformatic analyses were conducted to investigate the microbial diversity, the abundance and diversity of ARGs and the mobility potential of ARGs as indicated by different mobile genetic elements (MGEs). A total of 48 ARG types with a relative abundance of 0.05–0.28 copies of ARG/copy of 16S rRNA genes were detected in Tibetan soil samples. The observed ARGs were mainly associated with antibiotics that included glycopeptide and rifamycin; the most abundant ARGs were vanRO and vanSO. Low abundance of MGEs and potentially plasmid-related ARGs indicated a low horizontal gene transfer risk of ARGs in the pristine soil. Pearson correlation and redundancy analyses showed that temperature and total organic carbon were the major environmental factors controlling both microbial diversity and ARG abundance and diversity.

scholarly journals Detection of bacteriophages and cyanophages for water quality control of a water supply system in Amazônia

2021 ◽  
Author(s):  
Bruna Verônica Azevedo Gois ◽  
Kenny da Costa Pinheiro ◽  
Wylerson Guimarães Nogueira ◽  
Andressa de Oliveira Aragão ◽  
Ana Lídia Cavalcante Queiroz ◽  
...  
Keyword(s):  
Water Quality ◽  
Resistance Genes ◽  
High Throughput Sequencing ◽  
Antibiotic Resistance Genes ◽  
Taxonomic Diversity ◽  
Metropolitan Region ◽  
Human Consumption ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Water Quality Control

Abstract Background: Despite the importance of understanding the ecology of freshwater viruses, there are not many studies on the issue when compared to marine viruses. The microbiological interactions that occur in these environments are still poorly known, especially between bacteriophages and their host bacteria, as well as between cyanophages and cyanobacteria. Lake Bologna, from Belém, capital of the Brazilian State of Pará, is a source of water that supplies the city and its metropolitan region, yet it remains unexplored regarding the contents of its virome and viral diversity composition. Therefore, this work's main aim is to clarify in terms of taxonomic diversity the species of DNA viruses that are present in this lake, especially bacteriophages and cyanophages, since they can act both as transducers of resistance genes and reporters of water quality for human consumption. Results: For this work, we used the metagenomic sequencing data generated by Alves et al. (2020), and we analyzed it at the taxonomic level using the tools Kraken2, Bracken, and Pavian; later, the data was assembled using Genome Detective, which performs assembly of viruses. The results observed in this work suggest the existence of a widely diverse viral community and an established microbial phage regulated dynamics in the Lake Bolonha. Conclusions: This work is the first-ever to describe the virome of Lake Bolonha using a metagenomic approach based on high-throughput sequencing, as it contributes to the understanding of water-related public health concerns regarding the spreading of antibiotic resistance genes and population control of native bacteria and cyanobacteria.

scholarly journals Antibiotic Resistance Genes in Lemur Gut and Soil Microbiota Along a Gradient of Anthropogenic Disturbance

2021 ◽  
Vol 9 ◽  
Author(s):  
Sally L. Bornbusch ◽  
Christine M. Drea
Keyword(s):  
Antibiotic Resistance ◽  
Antibiotic Treatment ◽  
Resistance Genes ◽  
Anthropogenic Disturbance ◽  
Antibiotic Resistance Genes ◽  
Single Species ◽  
The United States ◽  
Metagenomic Sequencing ◽  
Natural Habitats ◽  
Human Contact

The overuse of man-made antibiotics has facilitated the global propagation of antibiotic resistance genes in animals, across natural and anthropogenically disturbed environments. Although antibiotic treatment is the most well-studied route by which resistance genes can develop and spread within host-associated microbiota, resistomes also can be acquired or enriched via more indirect routes, such as via transmission between hosts or via contact with antibiotic-contaminated matter within the environment. Relatively little is known about the impacts of anthropogenic disturbance on reservoirs of resistance genes in wildlife and their environments. We therefore tested for (a) antibiotic resistance genes in primate hosts experiencing different severities and types of anthropogenic disturbance (i.e., non-wildlife animal presence, human presence, direct human contact, and antibiotic treatment), and (b) covariation between host-associated and environmental resistomes. We used shotgun metagenomic sequencing of ring-tailed lemur (Lemur catta) gut resistomes and associated soil resistomes sampled from up to 10 sites: seven in the wilderness of Madagascar and three in captivity in Madagascar or the United States. We found that, compared to wild lemurs, captive lemurs harbored greater abundances of resistance genes, but not necessarily more diverse resistomes. Abundances of resistance genes were positively correlated with our assessments of anthropogenic disturbance, a pattern that was robust across all ten lemur populations. The composition of lemur resistomes was site-specific and the types of resistance genes reflected antibiotic usage in the country of origin, such as vancomycin use in Madagascar. We found support for multiple routes of ARG enrichment (e.g., via human contact, antibiotic treatment, and environmental acquisition) that differed across lemur populations, but could result in similar degrees of enrichment. Soil resistomes varied across natural habitats in Madagascar and, at sites with greater anthropogenic disturbance, lemurs and soil resistomes covaried. As one of the broadest, single-species investigations of wildlife resistomes to date, we show that the transmission and enrichment of antibiotic resistance genes varies across environments, thereby adding to the mounting evidence that the resistance crisis extends outside of traditional clinical settings.

scholarly journals Antibiotic resistance potential of the healthy preterm infant gut microbiome

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2928 ◽  
Author(s):  
Graham Rose ◽  
Alexander G. Shaw ◽  
Kathleen Sim ◽  
David J. Wooldridge ◽  
Ming-Shi Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Preterm Infant ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Antibiotic Resistance Genes ◽  
Taxonomic Diversity ◽  
Metagenomic Sequencing ◽  
Important Species ◽  
Antimicrobial Resistance Genes ◽  
Infant Gut Microbiome

Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.

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