scholarly journals Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Qi Zhang ◽  
Zhenyan Zhang ◽  
Tao Lu ◽  
Yitian Yu ◽  
Josep Penuelas ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Rapid Development ◽  
Antibiotic Resistance Genes ◽  
Soil Invertebrates ◽  
The Core ◽  
Environmental Concentrations ◽  
Global Soil ◽  
Colonization Potential ◽  
Biochemical Analyses ◽  
And Function

Abstract Background The ubiquitous gut microbiotas acquired from the environment contribute to host health. The gut microbiotas of soil invertebrates are gradually assembled from the microecological region of the soil ecosystem which they inhabit, but little is known about their characteristics when the hosts are under environmental stress. The rapid development of high-throughput DNA sequencing in the last decade has provided unprecedented insights and opportunities to characterize the gut microbiotas of soil invertebrates. Here, we characterized the core, transient, and rare bacterial taxa in the guts of soil invertebrates using the core index (CI) and developed a new theory of global microbial diversity of soil ecological microregions. Results We found that the Gammaproteobacteria could respond indiscriminately to the exposure to environmental concentrations of soil pollutants and were closely associated with the physiology and function of the host. Meanwhile, machine-learning models based on metadata calculated that Gammaproteobacteria were the core bacteria with the highest colonization potential in the gut, and further identified that they were the best indicator taxon of the response to environmental concentrations of soil pollution. Gammaproteobacteria also closely correlated with the abundance of antibiotic resistance genes. Conclusions Our results determined that Gammaproteobacteria were an indicator taxon in the guts of the soil invertebrates that responded to environmental concentrations of soil pollutants, thus providing an effective theoretical basis for subsequent assessments of soil ecological risk. The results of the physiological and biochemical analyses of the host and the microbial-community functions, and the antibiotic resistance of Gammaproteobacteria, provide new insights for evaluating global soil ecological health.

scholarly journals Chloramphenicol Resistance in Clostridium difficile Is Encoded on Tn4453 Transposons That Are Closely Related to Tn4451 from Clostridium perfringens

1998 ◽  
Vol 42 (7) ◽  
pp. 1563-1567 ◽  
Author(s):  
Dena Lyras ◽  
Christine Storie ◽  
Andrea S. Huggins ◽  
Paul K. Crellin ◽  
Trudi L. Bannam ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Clostridium Difficile ◽  
Transposable Elements ◽  
Clostridium Perfringens ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Nucleotide Sequencing ◽  
Chloramphenicol Resistance ◽  
Circular Form ◽  
And Function

ABSTRACT The chloramphenicol resistance gene catD fromClostridium difficile was shown to be encoded on the transposons Tn4453a and Tn4453b, which were structurally and functionally related to Tn4451 fromClostridium perfringens. Tn4453a and Tn4453b excised precisely from recombinant plasmids, generating a circular form, as is the case for Tn4451. Evidence that this process is mediated by Tn4453-encodedtnpX genes was obtained from experiments which showed that in trans these genes complemented a Tn4451tnpXΔ1 mutation for excision. Nucleotide sequencing showed that the joint of the circular form generated by the excision of Tn4453a and Tn4453b was similar to that from Tn4451. These results suggest that the Tn4453-encoded TnpX proteins bind to similar DNA target sequences and function in a manner comparable to that of TnpX from Tn4451. Furthermore, it has been shown that Tn4453a and Tn4453b can be transferred to suitable recipient cells by RP4 and therefore are mobilizable transposons. It is concluded that, like Tn4451, they must encode a functional tnpZ gene and a targetoriT or RSA site. The finding that related transposable elements are present in C. difficile andC. perfringens has implications for the evolution and dissemination of antibiotic resistance genes and the mobile elements on which they are found within the clostridia.

scholarly journals Occurrence and Distribution Characteristics of Antibiotic Resistance Genes in Sediments Between Urban and Rural of the Liaohe River Basin, China

2021 ◽  
Author(s):  
Guangshui Na ◽  
Keyu Zhang ◽  
Hui Gao ◽  
Ruijing Li ◽  
Shuaichen Jin ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
River Basin ◽  
Resistance Genes ◽  
Rural Areas ◽  
Human Activities ◽  
Rapid Development ◽  
River Sediments ◽  
Antibiotic Resistance Genes ◽  
Liaohe River ◽  
Liaohe River Basin

Abstract Antibiotic Resistance Genes (ARGs) are considered to be emerging pollutants related to human activities. The rapid development of global urbanization has expanded human activities, thereby exacerbating the global human health risks caused by antibiotic resistance genes. The effects of urban and rural environments are multifarious, which makes the source and distribution of ARGs in the environment diversification. Understanding the distribution and spread of ARGs is essential for studying the environmental behavior of ARGs. In this study, the occurrence 296 genes were detected by the high-throughput qPCR technology, and FC value was used to analyze the diversity of ARGs and Mobile Genetic Elements (MGEs) in sediments between urban and rural areas of the Liaohe River Basin, China. The co-occurrence of MGEs and ARGs was analyzed using network to decipher core genes. A total of 187 ARGs and 10 MGEs were detected in all sediment samples. The average number of genes detected in urban sites is 89 higher than that in rural sites. The high abundance and various types of ARGs and MGEs detected in urban river sediments indicates that the occurrence of urban ARGs is more complex. MGEs were detected high levels and were significantly correlated with the abundance and diversity of ARGs in river sediments providing evidence that MGEs were related to the occurrence and distribution of ARGs and tnpA(tnpA-07, tnpA-01 and tnpA-03) gene were at the key position of co-occurrence of various types of ARGs.

scholarly journals Evolution of Antibiotic Resistance and the Relationship between the Antibiotic Resistance Genes and Microbial Compositions under Long-Term Exposure to Tetracycline and Sulfamethoxazole

2019 ◽  
Vol 16 (23) ◽  
pp. 4681 ◽  
Author(s):  
Bingbing Du ◽  
Qingxiang Yang ◽  
Ruifei Wang ◽  
Ruimin Wang ◽  
Qiang Wang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
The Core ◽  
Aerobic Wastewater Treatment ◽  
The Relationship ◽  
Bacterial Groups ◽  
Wastewater Treatment Systems

The removal of antibiotics and widespread of antibiotic resistance genes (ARGs) have received continuous attention due to the possible threats to environment. However, little information is available on the evolution of antibiotic resistance and the relationship between ARGs and microbial communities under long-term exposure to sub-inhibitory concentrations of antibiotics. In our study, two laboratory-scale anoxic-aerobic wastewater treatment systems were established and operated for 420 days to investigate the evolution of antibiotic resistance under exposure of 5 mg·L−1 tetracycline (TC) or 5 mg·L−1 TC and 1 mg·L−1 sulfamethoxazole (SMX). The average removal rates of TC and SMX were about 59% and 72%, respectively. The abundance of the main ARGs responsible for resistance to TC and SMX increased obviously after antibiotics addition, especially when TC and SMX in combination (increased 3.20-fold). The tetC and sul1 genes were the predominant genes in the development of TC and SMX resistance, in which gene sul1 had the highest abundance among all the detected ARGs. Network analysis revealed that under antibiotic pressure, the core bacterial groups carrying multiple ARGs formed and concentrated in about 20 genera such as Dechloromonas, Candidatus Accumulibacter, Aeromonas, Rubrivivax, in which intI1 played important roles in transferring various ARGs except sul3.

scholarly journals Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

2020 ◽  
Author(s):  
Alyssa Kent ◽  
Albert Vill ◽  
Qiaojuan Shi ◽  
Michael J. Satlin ◽  
Ilana Lauren Brito
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiome ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Healthy Individuals ◽  
Hematopoietic Stem ◽  
Culture Independent ◽  
Neutropenic Patients ◽  
Mobile Ar ◽  
And Function

AbstractThe gut microbiome harbors a ‘silent reservoir’ of antibiotic resistance (AR) genes that is thought to contribute to the emergence of multidrug-resistant pathogens through the process of horizontal gene transfer (HGT). To counteract the spread of AR genes, it is paramount to know which organisms harbor mobile AR genes and with which organisms they engage in HGT. Despite methods to characterize the bulk presence1, abundance2 and function3 of AR genes in the gut, technological limitations of short-read sequencing have precluded linking bacterial taxa to specific mobile genetic elements (MGEs) and their concomitant AR genes. Here, we apply and evaluate a high-throughput, culture-independent method for surveilling the bacterial carriage of MGEs, based on bacterial Hi-C protocols. We compare two healthy individuals with a cohort of seven neutropenic patients undergoing hematopoietic stem cell transplantation, who receive multiple courses of antibiotics throughout their prolonged hospitalizations, and are thus acutely vulnerable to the threat of multidrug-resistant infections4. We find that the networks of HGT are surprisingly distinct between individuals, yet AR and mobile genes are more dispersed across taxa within the neutropenic patients than the healthy subjects. Our data further suggest that HGT is occurring throughout the course of treatment in the microbiomes of neutropenic patients and within the guts of healthy individuals over a similar timeframe. Whereas most efforts to understand the spread of AR genes have focused on pathogenic species, our findings shed light on the role of the human gut microbiome in this process.

scholarly journals Positive and Negative Effects of Metal Oxide Nanoparticles on Antibiotic Resistance Genes Transfer

Antibiotics ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 742
Author(s):  
Georgy D. Otinov ◽  
Alina V. Lokteva ◽  
Anastasia D. Petrova ◽  
Irina V. Zinchenko ◽  
Maria V. Isaeva ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Metal Oxide ◽  
Resistance Genes ◽  
Rapid Development ◽  
Metal Oxide Nanoparticles ◽  
Antibiotic Resistance Genes ◽  
Biological Synthesis ◽  
Oxide Nanoparticles ◽  
E Coli

Rapid development of antibiotic resistance in bacteria is a critical public health problem in the world. One of the main routes of resistance development is the transfer of genes containing antibiotic resistance cassettes. Gene transfer can be done through horizontal transfer of genes: transduction, conjugation, and transformation. Many factors in the environment influence these processes, and one of them is the action of metal oxide nanoparticles (MONPs), which can appear in the milieu through both biological synthesis and the release of engineered nanomaterial. In this study, the effect of AlOOH, CuO, Fe3O4, TiO2, and ZnO MONPs on the transformation (heat shock transformation) of bacteria Escherichia coli K12, and the conjugation between E. coli cc118 and E. coli Nova Blue were studied. The MONPs were synthesized by one method and fully characterized. ZnO nanoparticles (NPs) have significantly increased the efficiency of transformation (more than 9-fold), while the other NPs have reduced it to 31 times (TiO2 NPs). AlOOH NPs increased the number of transconjugants more than 1.5-fold, while CuO and Fe3O4 NPs did not have a significant effect on transformation and conjugation. Thus, the data shows that different types of MONPs can enhance or inhibit different gene transfer mechanisms, affecting the spread of antibiotic resistance genes.

scholarly journals Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda

2020 ◽  
Author(s):  
G. Ackers-Johnson ◽  
D. Kibombo ◽  
B. Kusiima ◽  
M.L. Nsubuga ◽  
E. Kigozi ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Population Structure ◽  
Rapid Development ◽  
Antibiotic Resistance Genes ◽  
Referral Hospital ◽  
Evidence Based ◽  
Time Data ◽  
Regional Referral Hospital ◽  
Western Uganda

AbstractTackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based improvement of antibiotic stewardship measures in the hospital. To address this, we combined existing antimicrobial susceptibility testing (AST) from FPRRH, with whole genome sequencing (WGS) of 41 Staphylococcus aureus isolates (2017-2019). AST revealed 73% (30/41) of isolates were resistant to one or more antibiotics and 29% (12/41) were multi-drug resistant (MDR). Resistance phenotypes were largely explained by the presence of antibiotic resistance genes in WGS data. Five isolates were methicillin-resistant S. aureus (MRSA) and MDR. Although all isolates were susceptible to clindamycin, a 24% carriage of erm genes suggests potential for rapid development of resistance. We inferred a population structure for the S. aureus isolates by comparing their core genomes. Twenty isolates formed a tight cluster corresponding to multilocus sequence typing clonal complex (CC) 152, a CC found to be particularly prevalent in northern Africa. The frequency of genes associated with methicillin, chloramphenicol and ciprofloxacin resistance were significantly lower among CC152 strains than non-CC152 strains; thus, in keeping with previous work, we find that CC152 is almost exclusively methicillin-sensitive S. aureus (MSSA). Also, in agreement with other studies, we observed that the occurrence of Panton-Valentine leukocidin toxin-encoding genes was significantly higher among CC152 strains than non-CC152 strains. However, we also observed that the coagulase gene was over-represented in this CC, further defining the virulence strategy of this important pathogen. By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, our study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.

scholarly journals Core Microbiota Drive the Prevalence of Extracellular Antibiotic Resistome in the Water Compartments

2022 ◽  
Author(s):  
Kai-Feng Yu ◽  
Peng Li ◽  
Yuansheng Huang ◽  
Jun Yang ◽  
Han Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Procrustes Analysis ◽  
Extracellular Dna ◽  
Core Microbiota ◽  
The Core ◽  
Water Compartments

Unlike intracellular chromosome, extracellular DNA (eDNA) may accelerate the spreading of antibiotic resistance genes (ARGs) through natural transformation, but one of the core issues regarding to the taxonomic characterization of eDNA in the complex water environments is largely unknown. Hence, Illumina Miseq sequencing was used to identify the genotype of eDNA from wastewater (WW), river water (RW) and stormwater (SW) runoff. High-throughput qPCR targeting 384 genes was implemented to detect extracellular ARGs (eARGs) and mobile genetic elements (eMGEs). We obtained 2,708,291 high quality sequences from 66 eDNA samples. The SW exhibited the significant higher Shannon Index. Subsequently, we identified 34 core bacteria sources of eDNA widely distributed in the three water compartments. Among which, Pseudomonas, Flavobacterium, Limnohabitans, Burkholderiaceae_unclassified, Methylotenera and Acinetobacter were the most prevalent. A total of 302 eARGs and eMGEs were detected, suggesting that eDNA is an important antibiotic resistance reservoir. Among the 127 shared genes of the three groups, 15 core resistance genes were filtered, including IS6100, sul1 NEW, intI1, ISPps1-pseud, aac3-Via, qacH_351 and ISSm2-Xanthob. The Procrustes analysis and Variance Partitioning Analysis (VPA) demonstrated that core bacteria and MGEs were significantly correlated with eARGs. These results suggested that the occurrence and changes of eARGs in the water compartments may be largely attributed to the core microbiota and eMGEs.

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