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

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.

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Movement of IS26-Associated Antibiotic Resistance Genes Occurs via a Translocatable Unit That Includes a Single IS26 and Preferentially Inserts Adjacent to Another IS26

mBio ◽

10.1128/mbio.01801-14 ◽

2014 ◽

Vol 5 (5) ◽

Cited By ~ 121

Author(s):

Christopher J. Harmer ◽

Robert A. Moran ◽

Ruth M. Hall

Keyword(s):

Antibiotic Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Class I ◽

Resistant Bacteria ◽

Gram Negative Bacteria ◽

Unusual Structure ◽

Gram Negative

ABSTRACTThe insertion sequence IS26plays a key role in disseminating antibiotic resistance genes in Gram-negative bacteria, forming regions containing more than one antibiotic resistance gene that are flanked by and interspersed with copies of IS26. A model presented for a second mode of IS26movement that explains the structure of these regions involves a translocatable unit consisting of a unique DNA segment carrying an antibiotic resistance (or other) gene and a single IS copy. Structures resembling class I transposons are generated via RecA-independent incorporation of a translocatable unit next to a second IS26such that the ISs are in direct orientation. Repeating this process would lead to arrays of resistance genes with directly oriented copies of IS26at each end and between each unique segment. This model requires that IS26recognizes another IS26as a target, and in transposition experiments, the frequency of cointegrate formation was 60-fold higher when the target plasmid contained IS26. This reaction was conservative, with no additional IS26or target site duplication generated, and orientation specific as the IS26s in the cointegrates were always in the same orientation. Consequently, the cointegrates were identical to those formed via the known mode of IS26movement when a target IS26was not present. Intact transposase genes in both IS26s were required for high-frequency cointegrate formation as inactivation of either one reduced the frequency 30-fold. However, the IS26target specificity was retained. Conversion of each residue in the DDE motif of the Tnp26 transposase also reduced the cointegration frequency.IMPORTANCEResistance to antibiotics belonging to several of the different classes used to treat infections is a critical problem. Multiply antibiotic-resistant bacteria usually carry large regions containing several antibiotic resistance genes, and in Gram-negative bacteria, IS26is often seen in these clusters. A model to explain the unusual structure of regions containing multiple IS26copies, each associated with a resistance gene, was not available, and the mechanism of their formation was unexplored. IS26-flanked structures deceptively resemble class I transposons, but this work reveals that the features of IS26movement do not resemble those of the IS and class I transposons studied to date. IS26uses a novel movement mechanism that defines a new family of mobile genetic elements that we have called “translocatable units.” The IS26mechanism also explains the properties of IS257(IS431) and IS1216, which belong to the same IS family and mobilize resistance genes in Gram-positive staphylococci and enterococci.

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High levels of antibiotic resistance gene expression among birds living in a wastewater treatment plant

10.1101/462366 ◽

2018 ◽

Cited By ~ 2

Author(s):

Vanessa R. Marcelino ◽

Michelle Wille ◽

Aeron C. Hurt ◽

Daniel González-Acuña ◽

Marcel Klaassen ◽

...

Keyword(s):

Antibiotic Resistance ◽

Wastewater Treatment ◽

Resistance Gene ◽

Resistance Genes ◽

Wastewater Treatment Plant ◽

Antibiotic Resistance Gene ◽

Treatment Plant ◽

Antibiotic Resistance Genes ◽

Resistant Bacteria ◽

Chloramphenicol Resistance

AbstractAntibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. We used bulk RNA-sequencing (meta-transcriptomics) to assess the diversity and expression levels of functionally active resistance genes in the microbiome of birds with aquatic behavior. We sampled birds across a range of habitats, from penguins in Antarctica to ducks in a wastewater treatment plant in Australia. This revealed 81 antibiotic resistance genes in birds from all localities, including β-lactam, tetracycline and chloramphenicol resistance in Antarctica, and genes typically associated with multidrug resistance plasmids in areas with high human impact. Notably, birds feeding at a wastewater treatment plant carried the greatest resistance gene burden, suggesting that human waste, even if it undergoes treatment, contributes to the spread of antibiotic resistance genes to the wild. Differences in resistance gene burden also reflected the birds’ ecology, taxonomic group and microbial functioning. Ducks, which feed by dabbling, carried a higher abundance and diversity of resistance genes than turnstones, avocets and penguins, that usually prey on more pristine waters. In sum, this study helps to reveal the complex factors explaining the distribution of resistance genes and their exchange routes between humans and wildlife.

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

Diversity ◽

10.3390/d13060230 ◽

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.

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Persistence of Transferable Extended-Spectrum-β-Lactamase Resistance in the Absence of Antibiotic Pressure

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00848-12 ◽

2012 ◽

Vol 56 (9) ◽

pp. 4703-4706 ◽

Cited By ~ 35

Author(s):

Jennifer L. Cottell ◽

Mark A. Webber ◽

Laura J. V. Piddock

Keyword(s):

Antibiotic Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Fitness Cost ◽

Resistant Bacteria ◽

Bacterial Host ◽

Antibiotic Resistant ◽

M 14 ◽

Host Strains

ABSTRACTThe treatment of infections caused by antibiotic-resistant bacteria is one of the great challenges faced by clinicians in the 21st century. Antibiotic resistance genes are often transferred between bacteria by mobile genetic vectors called plasmids. It is commonly believed that removal of antibiotic pressure will reduce the numbers of antibiotic-resistant bacteria due to the perception that carriage of resistance imposes a fitness cost on the bacterium. This study investigated the ability of the plasmid pCT, a globally distributed plasmid that carries an extended-spectrum-β-lactamase (ESBL) resistance gene (blaCTX-M-14), to persist and disseminate in the absence of antibiotic pressure. We investigated key attributes in plasmid success, including conjugation frequencies, bacterial-host growth rates, ability to cause infection, and impact on the fitness of host strains. We also determined the contribution of theblaCTX-M-14gene itself to the biology of the plasmid and host bacterium. Carriage of pCT was found to impose no detectable fitness cost on various bacterial hosts. An absence of antibiotic pressure and inactivation of the antibiotic resistance gene also had no effect on plasmid persistence, conjugation frequency, or bacterial-host biology. In conclusion, plasmids such as pCT have evolved to impose little impact on host strains. Therefore, the persistence of antibiotic resistance genes and their vectors is to be expected in the absence of antibiotic selective pressure regardless of antibiotic stewardship. Other means to reduce plasmid stability are needed to prevent the persistence of these vectors and the antibiotic resistance genes they carry.

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.45.11.2991-3000.2001 ◽

2001 ◽

Vol 45 (11) ◽

pp. 2991-3000 ◽

Cited By ~ 210

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.

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

10.21203/rs.2.18486/v1 ◽

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.

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What is the role of the environment in the emergence of novel antibiotic resistance genes? – A modelling approach

10.1101/2021.04.04.438392 ◽

2021 ◽

Author(s):

Johan Bengtsson-Palme ◽

Viktor Jonsson ◽

Stefanie Heß

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Quantitative Data ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Resistant Bacteria ◽

Minor Role ◽

Model Framework ◽

Animal Pathogens

AbstractIt is generally accepted that intervention strategies to curb antibiotic resistance cannot solely focus on human and veterinary medicine but must also consider environmental settings. While the environment clearly has a role in the transmission of resistant bacteria, it is less clear what role it plays in the emergence of novel types of resistance. It has been suggested that the environment constitutes an enormous recruitment ground for resistance genes to pathogens, but the extent to which this actually happens is unknown. In this study, we built a model framework for resistance emergence and used the available quantitative data on the relevant processes to identify the steps which are limiting the appearance of antibiotic resistance determinants in human or animal pathogens. We also assessed the effect of uncertainty in the available data on the model results. We found that in a majority of scenarios, the environment would only play a minor role in the emergence of novel resistance genes. However, the uncertainty around this role is enormous, highlighting an urgent need of more quantitative data to understand the role of the environment in antibiotic resistance development. Specifically, more data is most needed on the fitness costs of antibiotic resistance gene (ARG) carriage, the degree of dispersal of resistant bacteria from the environment to humans, but also the rates of mobilization and horizontal transfer of ARGs. Quantitative data on these processes is instrumental to determine which processes that should be targeted for interventions to curb development and transmission of resistance.

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

Clinical Infectious Diseases ◽

10.1093/cid/ciz1087 ◽

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.

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

Journal of Medical Microbiology ◽

10.1099/jmm.0.017665-0 ◽

2010 ◽

Vol 59 (7) ◽

pp. 804-807 ◽

Cited By ~ 31

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.

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Bacteriophage selection against a plasmid-encoded sex apparatus leads to the loss of antibiotic-resistance plasmids

Biology Letters ◽

10.1098/rsbl.2011.0384 ◽

2011 ◽

Vol 7 (6) ◽

pp. 902-905 ◽

Cited By ~ 41

Author(s):

Matti Jalasvuori ◽

Ville-Petri Friman ◽

Anne Nieminen ◽

Jaana K. H. Bamford ◽

Angus Buckling

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Species ◽

Low Frequency ◽

Antibiotic Resistance Genes ◽

Resistant Bacteria ◽

Bacterial Cells ◽

Antibiotic Resistant ◽

Resistance Plasmids ◽

Resistant Mutants

Antibiotic-resistance genes are often carried by conjugative plasmids, which spread within and between bacterial species. It has long been recognized that some viruses of bacteria (bacteriophage; phage) have evolved to infect and kill plasmid-harbouring cells. This raises a question: can phages cause the loss of plasmid-associated antibiotic resistance by selecting for plasmid-free bacteria, or can bacteria or plasmids evolve resistance to phages in other ways? Here, we show that multiple antibiotic-resistance genes containing plasmids are stably maintained in both Escherichia coli and Salmonella enterica in the absence of phages, while plasmid-dependent phage PRD1 causes a dramatic reduction in the frequency of antibiotic-resistant bacteria. The loss of antibiotic resistance in cells initially harbouring RP4 plasmid was shown to result from evolution of phage resistance where bacterial cells expelled their plasmid (and hence the suitable receptor for phages). Phages also selected for a low frequency of plasmid-containing, phage-resistant bacteria, presumably as a result of modification of the plasmid-encoded receptor. However, these double-resistant mutants had a growth cost compared with phage-resistant but antibiotic-susceptible mutants and were unable to conjugate. These results suggest that bacteriophages could play a significant role in restricting the spread of plasmid-encoded antibiotic resistance.

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