scholarly journals Metagenomics Analysis Reveals the Microbial Communities, Antimicrobial Resistance Gene Diversity and Potential Pathogen Transmission Risk of Two Different Landfills in China

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 230
Author(s):  
Shan Wan ◽  
Min Xia ◽  
Jie Tao ◽  
Yanjun Pang ◽  
Fugen Yu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Communities ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Gene Diversity ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Pathogen Transmission ◽  
Transmission Risk ◽  
Antimicrobial Resistance Gene

In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in the two landfills, and archaea and fungi were also detected. The genera Methanoculleus, Lysobacter, and Pseudomonas were predominantly present in all samples. sul2, sul1, tetX, and adeF were the four most abundant antibiotic resistance genes. Sixty-nine bacterial pathogens were identified from the two landfills, with Klebsiella pneumoniae, Bordetella pertussis, Pseudomonas aeruginosa, and Bacillus cereus as the major pathogenic microorganisms, indicating the existence of potential environmental risk in landfills. In addition, KEGG pathway analysis indicated the presence of antibiotic resistance genes typically associated with human antibiotic resistance bacterial strains. These results provide insights into the risk of pathogens in landfills, which is important for controlling the potential secondary transmission of pathogens and reducing workers’ health risk during landfill excavation.

scholarly journals Molecular Analysis of Antibiotic Resistance Gene Clusters in Vibrio cholerae O139 and O1 SXT Constins

2001 ◽  
Vol 45 (11) ◽  
pp. 2991-3000 ◽  
Author(s):  
Bianca Hochhut ◽  
Yasmin Lotfi ◽  
Didier Mazel ◽  
Shah M. Faruque ◽  
Roger Woodgate ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Vibrio Cholerae ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Dna Sequences ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Gene Clusters ◽  
Vibrio Cholerae O139 ◽  
El Tor

ABSTRACT Many recent Asian clinical Vibrio cholerae E1 Tor O1 and O139 isolates are resistant to the antibiotics sulfamethoxazole (Su), trimethoprim (Tm), chloramphenicol (Cm), and streptomycin (Sm). The corresponding resistance genes are located on large conjugative elements (SXT constins) that are integrated into prfC on the V. cholerae chromosome. We determined the DNA sequences of the antibiotic resistance genes in the SXT constin in MO10, an O139 isolate. In SXTMO10, these genes are clustered within a composite transposon-like structure found near the element's 5′ end. The genes conferring resistance to Cm (floR), Su (sulII), and Sm (strA and strB) correspond to previously described genes, whereas the gene conferring resistance to Tm, designated dfr18, is novel. In some other O139 isolates the antibiotic resistance gene cluster was found to be deleted from the SXT-related constin. The El Tor O1 SXT constin, SXTET, does not contain the same resistance genes as SXTMO10. In this constin, the Tm resistance determinant was located nearly 70 kbp away from the other resistance genes and found in a novel type of integron that constitutes a fourth class of resistance integrons. These studies indicate that there is considerable flux in the antibiotic resistance genes found in the SXT family of constins and point to a model for the evolution of these related mobile elements.

scholarly journals Longitudinal assessment of antibiotic resistance gene profiles from the infant gut microbiome

2019 ◽  
Author(s):  
Evelyn Loo ◽  
Amanda Zain ◽  
Gaik Chin Yap ◽  
Rikky W Purbojati ◽  
Daniela I Drautz-Moses ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Cohort Study ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Longitudinal Cohort Study ◽  
First Year ◽  
Beta Lactam ◽  
First Year Of Life

Abstract Background: The rapid spread of multidrug- resistant pathogenic bacteria is a worldwide public health concern. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)- producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence and dynamics by studying the longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing E coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants. Methods: We analysed the antibiotic resistance genes profile in the first year of life among 75 infants who had stool samples collected at multiple timepoints using metagenomics. Results: The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively. Conclusion: In this longitudinal cohort study of healthy infants living in a region with high endemic antibacterial resistance, we demonstrate that majority of the infants harboured a number of antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.

US Immigration Is Associated With Rapid and Persistent Acquisition of Antibiotic Resistance Genes in the Gut

2019 ◽  
Vol 71 (2) ◽  
pp. 419-421
Author(s):  
Quentin Le Bastard ◽  
Pajau Vangay ◽  
Eric Batard ◽  
Dan Knights ◽  
Emmanuel Montassier
Keyword(s):  
United States ◽  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
The United States ◽  
Human Migration ◽  
Metagenomics Analysis

Abstract Little is known about the effect of human migration on gut microbiome antibiotic resistance gene (ARG) carriage. Using deep shotgun stool metagenomics analysis, we found a rapid increase in gut microbiome ARG richness and abundance in women from 2 independent ethnic groups relocating from Thailand to the United States.

scholarly journals Is exposure to mercury a driving force for the carriage of antibiotic resistance genes?

2010 ◽  
Vol 59 (7) ◽  
pp. 804-807 ◽  
Author(s):  
David Skurnik ◽  
Raymond Ruimy ◽  
Derren Ready ◽  
Etienne Ruppe ◽  
Claire Bernède-Bauduin ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Driving Force ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Mercury Exposure ◽  
Mercury Resistance ◽  
High Exposure ◽  
E Coli

The mercury resistance gene merA has often been found together with antibiotic resistance genes in human commensal Escherichia coli. To study this further, we analysed mercury resistance in collections of strains from various populations with different levels of mercury exposure and various levels of antibiotic resistance. The first population lived in France and had no known mercury exposure. The second lived in French Guyana and included a group of Wayampi Amerindians with a known high exposure to mercury. Carriage rates of mercury resistance were assessed by measuring the MIC and by detecting the merA gene. Mercury-resistant E. coli was found significantly more frequently in the populations that had the highest carriage rates of antibiotic-resistant E. coli and in parallel antibiotic resistance was higher in the population living in an environment with a high exposure to mercury, suggesting a possible co-selection. Exposure to mercury might be a specific driving force for the acquisition and maintenance of mobile antibiotic resistance gene carriage in the absence of antibiotic selective pressure.

scholarly journals The Perfect Condition for the Rising of Superbugs: Person-to-Person Contact and Antibiotic Use Are the Key Factors Responsible for the Positive Correlation between Antibiotic Resistance Gene Diversity and Virulence Gene Diversity in Human Metagenomes

Antibiotics ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 605
Author(s):  
Célia P. F. Domingues ◽  
João S. Rebelo ◽  
Joël Pothier ◽  
Francisca Monteiro ◽  
Teresa Nogueira ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Loss Rate ◽  
Gene Diversity ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Virulence Gene ◽  
Transmission Probability ◽  
Positive Correlation ◽  
High Diversity

Human metagenomes with a high diversity of virulence genes tend to have a high diversity of antibiotic-resistance genes and vice-versa. To understand this positive correlation, we simulated the transfer of these genes and bacterial pathogens in a community of interacting people that take antibiotics when infected by pathogens. Simulations show that people with higher diversity of virulence and resistance genes took antibiotics long ago, not recently. On the other extreme, we find people with low diversity of both gene types because they took antibiotics recently—while antibiotics select specific resistance genes, they also decrease gene diversity by eliminating bacteria. In general, the diversity of virulence and resistance genes becomes positively correlated whenever the transmission probability between people is higher than the probability of losing resistance genes. The positive correlation holds even under changes of several variables, such as the relative or total diversity of virulence and resistance genes, the contamination probability between individuals, the loss rate of resistance genes, or the social network type. Because the loss rate of resistance genes may be shallow, we conclude that the transmission between people and antibiotic usage are the leading causes for the positive correlation between virulence and antibiotic-resistance genes.

scholarly journals Analytical Performance of Multiplexed Screening Test for 10 Antibiotic Resistance Genes from Perianal Swab Samples

2016 ◽  
Vol 62 (2) ◽  
pp. 353-359 ◽  
Author(s):  
G Terrance Walker ◽  
Tony J Rockweiler ◽  
Rossio K Kersey ◽  
Kelly L Frye ◽  
Susan R Mitchner ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Test Performance ◽  
Health Care Systems ◽  
Bacterial Species ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Resistant Bacteria ◽  
Gene Test

Abstract BACKGROUND Multiantibiotic-resistant bacteria pose a threat to patients and place an economic burden on health care systems. Carbapenem-resistant bacilli and extended-spectrum β-lactamase (ESBL) producers drive the need to screen infected and colonized patients for patient management and infection control. METHODS We describe a multiplex microfluidic PCR test for perianal swab samples (Acuitas® MDRO Gene Test, OpGen) that detects the vancomycin-resistance gene vanA plus hundreds of gene subtypes from the carbapenemase and ESBL families Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), Verona integron-mediated metallo-β-lactamase (VIM), imipenemase metallo-β-lactamase (IMP), OXA-23, OXA-48, OXA-51, CTX-M-1, and CTX-M-2, regardless of the bacterial species harboring the antibiotic resistance. RESULTS Analytical test sensitivity per perianal swab is 11–250 CFU of bacteria harboring the antibiotic resistance genes. Test throughput is 182 samples per test run (1820 antibiotic resistance gene family results). We demonstrate reproducible test performance and 100% gene specificity for 265 clinical bacterial organisms harboring a variety of antibiotic resistance genes. CONCLUSIONS The Acuitas MDRO Gene Test is a sensitive, specific, and high-throughput test to screen colonized patients and diagnose infections for several antibiotic resistance genes directly from perianal swab samples, regardless of the bacterial species harboring the resistance genes.

scholarly journals Integron Mobilization Unit as a Source of Mobility of Antibiotic Resistance Genes

2009 ◽  
Vol 53 (6) ◽  
pp. 2492-2498 ◽  
Author(s):  
Laurent Poirel ◽  
Amélie Carrër ◽  
Johann D. Pitout ◽  
Patrice Nordmann
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Composite Structure ◽  
Antibiotic Resistance Gene ◽  
Shewanella Oneidensis ◽  
Antibiotic Resistance Genes ◽  
In Silico Analysis ◽  
Carbapenem Resistance ◽  
Class 1 Integron

ABSTRACT Antibiotic resistance genes are spread mostly through plasmids, integrons (as a form of gene cassettes), and transposons in gram-negative bacteria. We describe here a novel genetic structure, named the integron mobilization unit (IMU), that has characteristics similar to those of miniature inverted transposable elements (MITEs). Two IMUs (288 bp each) were identified from a carbapenem-resistant Enterobacter cloacae isolate that formed a composite structure encompassing a defective class 1 integron containing the carbapenem resistance gene bla GES-5. This ß-lactamase gene was located on a 7-kb IncQ-type plasmid named pCHE-A, which was sequenced completely. The plasmid pCHE-A was not self conjugative but was mobilizable, and it was successfully transferred from E. cloacae to Pseudomonas aeruginosa. The in silico analysis of the extremities of the IMU elements identified similarities with those of insertion sequence ISSod9 from Shewanella oneidensis MR-1. The mobilization of the IMU composite structure was accomplished by using the transposase activity of ISSod9 that was provided in trans. This is the first identification of MITE-type structures as a source of gene mobilization, implicating here a clinically relevant antibiotic resistance gene.

scholarly journals Distribution and Content of Class 1 Integrons in Different Vibrio cholerae O-Serotype Strains Isolated in Thailand

2000 ◽  
Vol 44 (5) ◽  
pp. 1315-1321 ◽  
Author(s):  
Anders Dalsgaard ◽  
Anita Forslund ◽  
Oralak Serichantalergs ◽  
Dorthe Sandvang
Keyword(s):  
Antibiotic Resistance ◽  
Vibrio Cholerae ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Gene Cassette ◽  
Gene Cassettes ◽  
Class 1 Integrons ◽  
Class 1

ABSTRACT In this study, 176 clinical and environmental Vibrio cholerae strains of different O serotypes isolated in Thailand from 1982 to 1995 were selected and studied for the presence of class 1 integrons, a new group of genetic elements which carry antibiotic resistance genes. Using PCR and DNA sequencing, we found that 44 isolates contained class 1 integrons harboring the aadB,aadA2, blaP1, dfrA1, anddfrA15 gene cassettes, which encode resistance to gentamicin, kanamycin, and tobramycin; streptomycin and spectinomycin; β-lactams; and trimethoprim, respectively. Each cassette array contained only a single antibiotic resistance gene. Although resistance genes in class 1 integrons were found in strains from the same epidemic, as well as in unrelated non-O1, non-O139 strains isolated from children with diarrhea, they were found to encode only some of the antibiotic resistance expressed by the strains. Serotype O139 strains did not contain class 1 integrons. However, the appearance and disappearance of the O139 serotype in the coastal city Samutsakorn in 1992 and 1993 were associated with the emergence of a distinct V. cholerae O1 strain which contained the aadA2resistance gene cassette. A 150-kb self-transmissible plasmid found in three O1 strains isolated in 1982 contained the aadB gene cassette. Surprisingly, several strains harbored two integrons containing different cassettes. Thus, class 1 integrons containing various resistance gene cassettes are distributed among differentV. cholerae O serotypes of mainly clinical origin in Thailand.

scholarly journals Molecular Identification and Quantification of Tetracycline and Erythromycin Resistance Genes in Spanish and Italian Retail Cheeses

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Ana Belén Flórez ◽  
Ángel Alegría ◽  
Franca Rossi ◽  
Susana Delgado ◽  
Giovanna E. Felis ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Gene Diversity ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Resistant Bacteria ◽  
Gene Pools ◽  
Erythromycin Resistance ◽  
Identification And Quantification

Large antibiotic resistance gene pools in the microbiota of foods may ultimately pose a risk for human health. This study reports the identification and quantification of tetracycline- and erythromycin-resistant populations, resistance genes, and gene diversity in traditional Spanish and Italian cheeses, via culturing, conventional PCR, real-time quantitative PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). The numbers of resistant bacteria varied widely among the antibiotics and the different cheese varieties; in some cheeses, all the bacterial populations seemed to be resistant. Up to eight antibiotic resistance genes were sought by gene-specific PCR, six with respect to tetracycline, that is,tet(K),tet(L),tet(M),tet(O),tet(S), andtet(W), and two with respect to erythromycin, that is,erm(B) anderm(F). The most common resistance genes in the analysed cheeses weretet(S),tet(W),tet(M), anderm(B). The copy numbers of these genes, as quantified by qPCR, ranged widely between cheeses (from 4.94 to10.18log⁡10/g). DGGE analysis revealed distinct banding profiles and two polymorphic nucleotide positions fortet(W)-carrying cheeses, though the similarity of the sequences suggests thistet(W) to have a monophyletic origin. Traditional cheeses would therefore appear to act as reservoirs for large numbers of many types of antibiotic resistance determinants.

scholarly journals The perfect condition for the rising of superbugs: person-to-person contagion and antibiotic use are the key factors responsible for the positive correlation between antibiotic resistance gene diversity and virulence gene diversity in human metagenomes

2020 ◽  
Author(s):  
Célia P. F. Domingues ◽  
João S. Rebelo ◽  
Teresa Nogueira ◽  
Joël Pothier ◽  
Francisca Monteiro ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Loss Rate ◽  
Gene Diversity ◽  
Recent Observation ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Antibiotic Use ◽  
Resistant Bacteria ◽  
Positive Correlation

1.AbstractThis study aims to understand the cause of the recent observation that humans with a higher diversity of virulence genes in their metagenomes tend to be precisely those with higher diversity of antibiotic-resistance genes. We simulated the transferring of virulence and antibiotic-resistance genes in a community of interacting people where some take antibiotics. The diversities of the two genes types became positively correlated whenever the contagion probability between two people was higher than the probability of losing resistant genes. However, no such positive correlations arise if no one takes antibiotics. This finding holds even under changes of several simulations’ parameters, such as the relative or total diversity of virulence and resistance genes, the contagion probability between individuals, the loss rate of resistance genes, or the social network type. Because the loss rate of resistance genes may be shallow, we conclude that the contagion between people and antibiotic usage is the leading cause of establishing the positive correlation mentioned above. Therefore, antibiotic use and something as prosaic as the contagion between people may facilitate the emergence of virulent and multi-resistant bacteria in people’s metagenomes with a high diversity of both gene types. These superbugs may then circulate in the community.

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