scholarly journals Diversity and Global Distribution of IncL/M Plasmids Enabling Horizontal Dissemination ofβ-Lactam Resistance Genes among the Enterobacteriaceae

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Marcin Adamczuk ◽  
Piotr Zaleski ◽  
Lukasz Dziewit ◽  
Renata Wolinowska ◽  
Marta Nieckarz ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Western Europe ◽  
Phylogenetic Analyses ◽  
Horizontal Transmission ◽  
Treatment Plant ◽  
Clinical Strain ◽  
Ecological Niches ◽  
Broad Host Range ◽  
Genes Encoding

Antibiotic resistance determinants are frequently associated with plasmids and other mobile genetic elements, which simplifies their horizontal transmission. Several groups of plasmids (including replicons of the IncL/M incompatibility group) were found to play an important role in the dissemination of resistance genes encodingβ-lactamases. The IncL/M plasmids are large, broad host range, and self-transmissible replicons. We have identified and characterized two novel members of this group: pARM26 (isolated from bacteria inhabiting activated sludge from a wastewater treatment plant) and pIGT15 (originating from a clinical strain ofEscherichia coli). This instigated a detailed comparative analysis of all available sequences of IncL/M plasmids encodingβ-lactamases. The core genome of these plasmids is comprised of 20 genes with conserved synteny. Phylogenetic analyses of these core genes allowed clustering of the plasmids into four separate groups, which reflect their antibiotic resistance profiles. Examination of the biogeography of the IncL/M plasmids revealed that they are most frequently found in bacteria of the family Enterobacteriaceae originating from the Mediterranean region and Western Europe and that they are able to persist in various ecological niches even in the absence of direct antibiotic selection pressure.

scholarly journals Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria

2021 ◽  
Vol 12 ◽  
Author(s):  
Aaron Law ◽  
Olubunmi Solano ◽  
Celeste J. Brown ◽  
Samuel S. Hunter ◽  
Matt Fagnan ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Treatment Plant ◽  
Antibiotic Resistance Genes ◽  
Broad Host Range ◽  
Human Pathogens ◽  
Current Crisis ◽  
Acquired Drug Resistance ◽  
Resistance Plasmids

Antibiotic resistance (AR) is a threat to modern medicine, and plasmids are driving the global spread of AR by horizontal gene transfer across microbiomes and environments. Determining the mobile resistome responsible for this spread of AR among environments is essential in our efforts to attenuate the current crisis. Biosolids are a wastewater treatment plant (WWTP) byproduct used globally as fertilizer in agriculture. Here, we investigated the mobile resistome of biosolids that are used as fertilizer. This was done by capturing resistance plasmids that can transfer to human pathogens and commensal bacteria. We used a higher-throughput version of the exogenous plasmid isolation approach by mixing several ESKAPE pathogens and a commensal Escherichia coli with biosolids and screening for newly acquired resistance to about 10 antibiotics in these strains. Six unique resistance plasmids transferred to Salmonella typhimurium, Klebsiella aerogenes, and E. coli. All the plasmids were self-transferable and carried 3–6 antibiotic resistance genes (ARG) conferring resistance to 2–4 antibiotic classes. These plasmids-borne resistance genes were further embedded in genetic elements promoting intracellular recombination (i.e., transposons or class 1 integrons). The plasmids belonged to the broad-host-range plasmid (BHR) groups IncP-1 or PromA. Several of them were persistent in their new hosts when grown in the absence of antibiotics, suggesting that the newly acquired drug resistance traits would be sustained over time. This study highlights the role of BHRs in the spread of ARG between environmental bacteria and human pathogens and commensals, where they may persist. The work further emphasizes biosolids as potential vehicles of highly mobile plasmid-borne antibiotic resistance genes.

scholarly journals Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes

2013 ◽  
Vol 79 (24) ◽  
pp. 7684-7695 ◽  
Author(s):  
Celeste J. Brown ◽  
Diya Sen ◽  
Hirokazu Yano ◽  
Matthew L. Bauer ◽  
Linda M. Rogers ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Host Range ◽  
Resistance Genes ◽  
Treatment Plant ◽  
Antibiotic Resistance Genes ◽  
Broad Host Range ◽  
Accessory Gene ◽  
Freshwater Habitats ◽  
Beneficial Traits ◽  
Broad Host Range Plasmids

ABSTRACTBroad-host-range self-transferable plasmids are known to facilitate bacterial adaptation by spreading genes between phylogenetically distinct hosts. These plasmids typically have a conserved backbone region and a variable accessory region that encodes host-beneficial traits. We do not know, however, how well plasmids that do not encode accessory functions can survive in nature. The goal of this study was to characterize the backbone and accessory gene content of plasmids that were captured from freshwater sources without selecting for a particular phenotype or cultivating their host. To do this, triparental matings were used such that the only required phenotype was the plasmid's ability to mobilize a nonconjugative plasmid. Based on complete genome sequences of 10 plasmids, only 5 carried identifiable accessory gene regions, and none carried antibiotic resistance genes. The plasmids belong to four known incompatibility groups (IncN, IncP-1, IncU, and IncW) and two potentially new groups. Eight of the plasmids were shown to have a broad host range, being able to transfer into alpha-, beta-, and gammaproteobacteria. Because of the absence of antibiotic resistance genes, we resampled one of the sites and compared the proportion of captured plasmids that conferred antibiotic resistance to their hosts with the proportion of such plasmids captured from the effluent of a local wastewater treatment plant. Few of the captured plasmids from either site encoded antibiotic resistance. A high diversity of plasmids that encode no or unknown accessory functions is thus readily found in freshwater habitats. The question remains how the plasmids persist in these microbial communities.

scholarly journals Strain-Specific Transfer of Antibiotic Resistance from an Environmental Plasmid to Foodborne Pathogens

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Eva Van Meervenne ◽  
Els Van Coillie ◽  
Frederiek-Maarten Kerckhof ◽  
Frank Devlieghere ◽  
Lieve Herman ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Antibiotic Resistance ◽  
Human Health ◽  
Resistance Genes ◽  
Foodborne Pathogens ◽  
Pathogenic Bacteria ◽  
Treatment Plant ◽  
Diffusion Method ◽  
Broad Host Range ◽  
Transfer Ratio

Pathogens resistant to multiple antibiotics are rapidly emerging, entailing important consequences for human health. This study investigated if the broad-host-range multiresistance plasmid pB10, isolated from a wastewater treatment plant, harbouring amoxicillin, streptomycin, sulfonamide, and tetracycline resistance genes, was transferable to the foodborne pathogensSalmonellaspp. orE. coliO157:H7 and how this transfer alters the phenotype of the recipients. The transfer ratio was determined by both plating and flow cytometry. Antibiotic resistance profiles were determined for both recipients and transconjugants using the disk diffusion method. For 14 of the 15 recipient strains, transconjugants were detected. Based on plating, transfer ratios were between6.8×10−9and3.0×10−2while using flow cytometry, transfer ratios were between <1.0×10−5and1.9×10−2. With a few exceptions, the transconjugants showed phenotypically increased resistance, indicating that most of the transferred resistance genes were expressed. In summary, we showed that an environmental plasmid can be transferred into foodborne pathogenic bacteria at high transfer ratios. However, the transfer ratio seemed to be recipient strain dependent. Moreover, the newly acquired resistance genes could turn antibiotic susceptible strains into resistant ones, paving the way to compromise human health.

scholarly journals Molecular Characterization and Comparative Genomics of IncQ-3 Plasmids Conferring Resistance to Various Antibiotics Isolated from a Wastewater Treatment Plant in Warsaw (Poland)

Antibiotics ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 613 ◽  
Author(s):  
Marta Piotrowska ◽  
Lukasz Dziewit ◽  
Rafał Ostrowski ◽  
Cora Chmielowska ◽  
Magdalena Popowska
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Resistance Genes ◽  
Wastewater Treatment Plant ◽  
Treatment Plant ◽  
Antibiotic Resistance Genes ◽  
Fluoroquinolone Resistance ◽  
Broad Host Range ◽  
Aminoglycoside Resistance ◽  
Core Genes

As small, mobilizable replicons with a broad host range, IncQ plasmids are widely distributed among clinical and environmental bacteria. They carry antibiotic resistance genes, and it has been shown that they confer resistance to β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, sulphonamides, and tetracycline. The previously proposed classification system divides the plasmid group into four subgroups, i.e., IncQ-1, IncQ-2, IncQ-3, and IncQ-4. The last two subgroups have been poorly described so far. The aim of this study was to analyze five newly identified IncQ-3 plasmids isolated from a wastewater treatment plant in Poland and to compare them with all known plasmids belonging to the IncQ-3 subgroup whose sequences were retrieved from the NCBI database. The complete nucleotide sequences of the novel plasmids were annotated and bioinformatic analyses were performed, including identification of core genes and auxiliary genetic load. Furthermore, functional experiments testing plasmid mobility were carried out. Phylogenetic analysis based on three core genes (repA, mobA/repB, and mobC) revealed the presence of three main clusters of IncQ-3 replicons. Apart from having a highly conserved core, the analyzed IncQ-3 plasmids were vectors of antibiotic resistance genes, including (I) the qnrS2 gene that encodes fluoroquinolone resistance and (II) β-lactam, trimethoprim, and aminoglycoside resistance genes within integron cassettes.

scholarly journals Characterization of a Multiresistant Mosaic Plasmid from a Fish Farm Sediment Exiguobacterium sp. Isolate Reveals Aggregation of Functional Clinic-Associated Antibiotic Resistance Genes

2013 ◽  
Vol 80 (4) ◽  
pp. 1482-1488 ◽  
Author(s):  
Jing Yang ◽  
Chao Wang ◽  
Jinyu Wu ◽  
Li Liu ◽  
Gang Zhang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Mobile Elements ◽  
Fish Farms ◽  
Significant Similarity ◽  
Content Type ◽  
Genes Encoding ◽  
The Mean

ABSTRACTThe genusExiguobacteriumcan adapt readily to, and survive in, diverse environments. Our study demonstrated thatExiguobacteriumsp. strain S3-2, isolated from marine sediment, is resistant to five antibiotics. The plasmid pMC1 in this strain carries seven putative resistance genes. We functionally characterized these resistance genes inEscherichia coli, and genes encoding dihydrofolate reductase and macrolide phosphotransferase were considered novel resistance genes based on their low similarities to known resistance genes. The plasmid G+C content distribution was highly heterogeneous. Only the G+C content of one block, which shared significant similarity with a plasmid fromExiguobacterium arabatum, fit well with the mean G+C content of the host. The remainder of the plasmid was composed of mobile elements with a markedly lower G+C ratio than the host. Interestingly, five mobile elements located on pMC1 showed significant similarities to sequences found in pathogens. Our data provided an example of the link between resistance genes in strains from the environment and the clinic and revealed the aggregation of antibiotic resistance genes in bacteria isolated from fish farms.

scholarly journals Metagenomic Community Composition and Resistome Analysis in a Full-scale Cold Climate Wastewater Treatment Plant

2021 ◽  
Author(s):  
Miguel Uyaguari
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Activated Sludge ◽  
Relative Abundance ◽  
Resistance Genes ◽  
Wastewater Treatment Plant ◽  
Treatment Plant ◽  
Antibiotic Resistance Genes ◽  
Gene Copies ◽  
Final Effluent

Abstract Background: Wastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we characterized the resistome, the distribution of classes 1-3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba. Samples were collected from raw sewage, returned activated sludge, final effluent, and dewatered sludge. A total of 28 bacterial and viral metagenomes were sequenced over two seasons, fall and winter. Integron-integrase genes, the 16S rRNA gene, and the coliform beta-glucuronidase gene were also quantified during this time period. Results: Bacterial classes observed above 1% relative abundance in all treatments were Actinobacteria (39.24% ± 0.25%), Beta-proteobacteria (23.99% ± 0.16%), Gamma-proteobacteria (11.06% ± 0.09%), and Alpha-proteobacteria (9.18 ± 0.04%). Families within the Caudovirales order: Siphoviridae (48.69% ± 0.10%), Podoviridae (23.99% ± 0.07%), and Myoviridae (19.94% ± 0.09%) were the dominant phage observed throughout the NESTP. The most abundant bacterial genera (in terms of average percent relative abundance) in influent, returned activated sludge, final effluent, and sludge, respectively, includes Mycobacterium (37.4%, 18.3%, 46.1%, and 7.7%), Acidovorax (8.9%, 10.8%, 5.4%, and 1.3%), and Polaromonas (2.5%, 3.3%, 1.4%, and 0.4%).The most abundant class of antibiotic resistance in bacterial samples was tetracycline resistance (17.86% ± 0.03%) followed by peptide antibiotics (14.24% ± 0.03%), and macrolides (10.63% ± 0.02%). Similarly, the phage samples contained a higher prevalence of macrolide (30.12% ± 0.30%), peptide antibiotic (10.78% ± 0.13%), and tetracycline (8.69% ± 0.11%) resistance. In addition, intI1 was the most abundant integron-integrase gene throughout treatment (1.14x104 gene copies/mL) followed by intI3 (4.97x103 gene copies/mL) while intI2 abundance remained low (6.4x101 gene copies/mL).Conclusions: The wastewater treatment plant successfully reduced the abundance of bacteria, DNA bacteriophages, and antibiotic resistance genes although many of them still remained in effluent and biosolids. The presence of integron-integrase genes throughout treatment and in effluent suggests that antibiotic resistance genes could be actively disseminating resistance between both environmental and pathogenic bacteria.

scholarly journals Accumulation and expression of multiple antibiotic resistance genes in Arcobacter cryaerophilus that thrives in sewage

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3269 ◽  
Author(s):  
Jess A. Millar ◽  
Rahul Raghavan
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Resistance Genes ◽  
Treatment Plant ◽  
Antibiotic Resistance Genes ◽  
Environmental Water ◽  
Multidrug Resistant ◽  
Municipal Sewage ◽  
Animal Origin ◽  
Resistant Bacteria

We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also determined that a majority of ARGs was being expressed in sewage, suggestive of trace levels of antibiotics or other stresses that could act as a selective force that amplifies multidrug resistant bacteria in municipal sewage. Because all bacteria are not eliminated even after several rounds of wastewater treatment, ARGs in sewage could affect public health due to their potential to contaminate environmental water.

scholarly journals Unearthing the Boreal Soil Resistome Associated with Permafrost Thaw

2020 ◽  
Author(s):  
Tracie J. Haan ◽  
Devin M. Drown
Keyword(s):  
Antibiotic Resistance ◽  
Active Layer ◽  
Resistance Genes ◽  
Soil Bacteria ◽  
Bacterial Community Composition ◽  
Ecological Niches ◽  
Whole Genome ◽  
Near Surface ◽  
Permafrost Thaw ◽  
Insight Into

ABSTRACTUnderstanding the distribution and mobility of antibiotic resistance genes (ARGs) in soil bacteria from diverse ecological niches is critical in assessing their impacts on the global spread of antibiotic resistance. In permafrost associated soils, climate and human driven forces augment near-surface thaw altering the overlying active layer. Physiochemical changes shift bacterial community composition and metabolic functioning, however, it is unknown if permafrost thaw will affect ARGs comprising the boreal soil resistome. To assess how thaw shifts the resistome, we performed susceptibility testing and whole genome sequencing on soil isolates from a disturbance-induced thaw gradient in Interior Alaska. We found resistance was widespread in the Alaskan isolates, with 87% of the 90 isolates resistant to at least one of the five antibiotics. We also observed positive trends in both the proportion of resistant isolates and the abundance of ARGs with permafrost thaw. However, the number of ARGs per genome and types of genes present were shown to cluster more strongly by bacterial taxa rather than thaw emphasizing the evolutionary origins of resistance and the role vertical gene transfer has in shaping the predominantly chromosomally encoded ARGs. The observed higher proportion of plasmid-borne and distinct ARGs in our isolates compared to RefSoil+ suggests local conditions affect the composition of the resistome along with selection for ARG mobility. Overall taxonomy and geography shape the resistome, suggesting that as microbial communities shift in response to permafrost thaw so will the ARGs in the boreal active layer.IMPORTANCEAs antibiotic resistance continues to emerge and rapidly spread in clinical settings, it is imperative to generate studies that build insight into the ecology of environmental resistance genes that pose a threat to human health. This study provides insight into the occurrence of diverse ARGs found in Alaskan soil bacteria which is suggestive of the potential to compromise health. The observed differences in ARG abundance with increasing permafrost thaw suggest the role of soil disturbance in driving the distribution of resistant determinants and the predominant taxa that shape the resistome. Moreover, the high-quality whole genome assemblies generated in this study are an extensive resource for microbial researchers interested in permafrost thaw and will provide a steppingstone for future research into ARG mobility and transmission risks.

scholarly journals Entry Exclusion of Conjugative Plasmids of the IncA, IncC, and Related Untyped Incompatibility Groups

2019 ◽  
Vol 201 (10) ◽  
Author(s):  
Malika Humbert ◽  
Kévin T. Huguet ◽  
Frédéric Coulombe ◽  
Vincent Burrus
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Phylogenetic Analyses ◽  
Antibiotic Resistance Genes ◽  
Genomic Islands ◽  
Pathogenic Species ◽  
Incompatibility Group ◽  
Content Type ◽  
Conjugative Plasmids ◽  
Type Iv

ABSTRACTConjugative plasmids of incompatibility group C (IncC), formerly known as A/C2, disseminate antibiotic resistance genes globally in diverse pathogenic species ofGammaproteobacteria. Salmonellagenomic island 1 (SGI1) can be mobilized by IncC plasmids and was recently shown to reshape the conjugative type IV secretion system (T4SS) encoded by these plasmids to evade entry exclusion. Entry exclusion blocks DNA translocation between cells containing identical or highly similar plasmids. Here, we report that the protein encoded by the entry exclusion gene of IncC plasmids (eexC) mediates entry exclusion in recipient cells through recognition of the IncC-encoded TraGCprotein in donor cells. Phylogenetic analyses based on EexC and TraGChomologs predicted the existence of at least three different exclusion groups among IncC-related conjugative plasmids. Mating assays using Eex proteins encoded by representative IncC and IncA (former A/C1) and related untyped plasmids confirmed these predictions and showed that the IncC and IncA plasmids belong to the C exclusion group, thereby explaining their apparent incompatibility despite their compatible replicons. Representatives of the two other exclusion groups (D and E) are untyped conjugative plasmids found inAeromonassp. Finally, we determined through domain swapping that the carboxyl terminus of the EexC and EexE proteins controls the specificity of these exclusion groups. Together, these results unravel the role of entry exclusion in the apparent incompatibility between IncA and IncC plasmids while shedding light on the importance of the TraG subunit substitution used by SGI1 to evade entry exclusion.IMPORTANCEIncA and IncC conjugative plasmids drive antibiotic resistance dissemination among several pathogenic species ofGammaproteobacteriadue to the diversity of drug resistance genes that they carry and their ability to mobilize antibiotic resistance-conferring genomic islands such as SGI1 ofSalmonella enterica. While historically grouped as “IncA/C,” IncA and IncC replicons were recently confirmed to be compatible and to abolish each other’s entry into the cell in which they reside during conjugative transfer. The significance of our study is in identifying an entry exclusion system that is shared by IncA and IncC plasmids. It impedes DNA transfer to recipient cells bearing a plasmid of either incompatibility group. The entry exclusion protein of this system is unrelated to any other known entry exclusion proteins.

scholarly journals Antibiotic Resistance Genes Dynamics at the Different Stages of the Biological Process in a Full-Scale Wastewater Treatment Plant

Proceedings ◽  
2018 ◽  
Vol 2 (11) ◽  
pp. 650 ◽  
Author(s):  
Ioanna Zerva ◽  
Ioanna Alexandropoulou ◽  
Maria Panopoulou ◽  
Paraschos Melidis ◽  
Spyridon Ntougias
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Resistance Genes ◽  
Wastewater Treatment Plant ◽  
Biological Process ◽  
Wastewater Treatment Plants ◽  
Treatment Plant ◽  
Antibiotic Resistance Genes ◽  
Additional Treatment ◽  
Full Scale

Wastewater treatment plants (WWTPs) highly contribute to the transmission of antibiotic resistance genes (ARGs) in the environment. In this work, the diversity of ermF, ermB, sul1 and int1-enconding genes was examined in the influent, the mixed liquor and the effluent of a full-scale WWTP. Based on the clones analyzed, similar genotypes were recorded at all process stages. However, distinct genotypes of int1 were responsible for the expression of sul1 and ermF genes in Gammaproteobacteria and Bacteroidetes, respectively. Due to the detection of similar ARGs profiles throughout the biological process, it is concluded that additional treatment is needed for their retention.

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