Plasmids of the same Inc groups in Enterobacteria before and after the medical use of antibiotics. - Related Documents




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494901.0000Plasmids of the same Inc groups in Enterobacteria before and after the medical use of antibiotics. Conjugative plasmids were common in enterobacteria isolated before the medical use of antibiotics. Plasmid F of Escherichia coli K-12 was one example and we identified others in over 20% of a collection of strains isolated between 1917 and 1954, the Murray collection. In the past 25 years, conjugative plasmids encoding antibiotic resistances have become common in bacteria of the same genera as those of the Murray Collection--Salmonella, Shigella, Klebsiella, Proteus, Escherichia. The present study was made to show whether the 'pre-antibiotic' plasmids belonged to the same groups, as defined by incompatibility tests (Inc groups), as modern R plasmids. Of 84 such plasmids established in E. coli K-12, none with antibiotic resistance determinants, 65 belonged to the same groups as present resistance (R) plasmids. Thus the remarkable way in which medically important bacteria have acquired antibiotic resistance in the past 25 years seems to have been by the insertion of new genes into existing plasmids rather than by the spread of previously rare plasmids.19836316165
495510.9999Evidence of extensive interspecies transfer of integron-mediated antimicrobial resistance genes among multidrug-resistant Enterobacteriaceae in a clinical setting. Multidrug resistance in gram-negative bacteria appears to be primarily the result of the acquisition of resistance genes by horizontal transfer. To what extent horizontal transfer may be responsible for the emergence of multidrug resistance in a clinical setting, however, has rarely been investigated. Therefore, the integron contents of isolates collected during a nosocomial outbreak of genotypically unrelated multidrug-resistant Enterobacteriaceae were characterized. The integron was chosen as a marker of transfer because of its association with multiresistance. Some genotypically identical isolates harbored different integrons. Grouping patients carrying the same integron yielded 6 epidemiologically linked clusters, with each cluster representing a different integron. Several patients carried multiple species harboring the same integron. Conjugation experiments with these strains resulted in the transfer of complete resistance patterns at high frequencies (10(-2) to 10(-4)). These findings provide strong evidence that the horizontal transfer of resistance genes contributed largely to the emergence of multidrug-resistant Enterobacteriaceae in this clinical setting.200212089661
495720.9999Plasmid-mediated quinolone resistance gene detected in Escherichia coli from cattle. Fluoroquinolones resistance in bacteria can be due to chromosomal and plasmid-mediated mechanisms. Of growing concern is the acquisition of genes encoding quinolone resistance in combination with other resistance mechanisms such as extended-spectrum beta-lactamases. In this study we describe the identification of an isolate of Escherichia coli from cattle which carried qnrS1 in combination with a blaCTX-M gene, although they were not co-localised on the same plasmid. In addition, using a DNA array it was possible to identify several other antimicrobial resistance genes in this isolate. This is the first report of a qnr gene in E. coli from cattle in the UK and highlights the need for surveillance of these emerging resistance mechanisms.201120884136
446430.9999Class 1 integrons, gene cassettes, mobility, and epidemiology. Integrons are genetic elements that, although unable to move themselves, contain gene cassettes that can be mobilized to other integrons or to secondary sites in the bacterial genome. The majority of approximately 60 known gene cassettes encode resistance to antibiotics. Recently, a number of gene cassettes encoding extended-spectrum beta-lactamases or carbapenemases have been described. Up to at least five cassettes may be present in an integron, which leads to multiresistance. Frequently, more than one integron is observed within the same bacterial cell. Integrons are widespread in their species distribution. Although integrons are normally reported from Enterobacteriaceae and other gram-negative bacteria, an integron has been described in Corynebacterium glutamicum, a gram-positive species. The gene cassette in this integron showed even higher expression when compared to the expression in Escherichia coli. Integrons have been reported from all continents and are found frequently. The widespread occurrence of integrons is thought to be due to their association with transposon plasmids, conjugative plasmids, or both. Integrons form an important source for the spread of antibiotic resistance, at least in gram-negative bacteria but also potentially in gram-positive bacteria. The aim of this review is to describe the versatility of integrons, especially their mobility and their ability to collect resistance genes.199910614949
495040.9999Molecular bases for multidrug resistance in Yersinia pseudotuberculosis. The enteropathogen Yersinia pseudotuberculosis causes gastrointestinal infections in humans. Although this species is usually susceptible to antibiotics active against Gram-negative bacteria, we identified three multidrug resistant (MDR) strains of Y. pseudotuberculosis that were isolated from the environment in Russia and from a patient in France. The resistance traits of the two Russian isolates were transferable at high frequencies (≈2×10(-1)/donor CFU) to Y. pseudotuberculosis. In contrast no transfer of the antibiotic resistances carried by the French strain was observed. Sequencing of the plasmid extracts of the Y. pseudotuberculosis transconjugants for the Russian isolates revealed the presence of conjugative plasmids of the IncN group that carried genes conferring resistance to four to six classes of antibiotics. The French strain harbored a large MDR plasmid of the IncHI2 group that carried resistance genes to six families of antibiotics, and contained a truncated set of transfer genes, accounting for the lack of plasmid transfer. All three Y. pseudotuberculosis plasmids were homologous to MDR plasmids found in various enterobacteria. A phylogenetic analysis showed that the two Russian strain plasmids were closely related to each other and were more distant from the French plasmid. To the best of our knowledge, this is the first molecular characterization of MDR plasmids in Y. pseudotuberculosis. Due to the propensity of this species to acquire exogenous plasmids, the risk of emergence of new MDR Y. pseudotuberculosis isolates should be seriously taken into consideration.201728830739
597850.9998Evidences of gentamicin resistance amplification in Klebsiella pneumoniae isolated from faeces of hospitalized newborns. The intestinal microbiota, a barrier to the establishment of pathogenic bacteria, is also an important reservoir of opportunistic pathogens. It plays a key role in the process of resistance-genes dissemination, commonly carried by specialized genetic elements, like plasmids, phages, and conjugative transposons. We obtained from strains of enterobacteria, isolated from faeces of newborns in a university hospital nursery, indication of phenotypical gentamicin resistance amplification (frequencies of 10(-3) to 10(-5), compatible with transposition frequencies). Southern blotting assays showed strong hybridization signals for both plasmidial and chromosomal regions in DNA extracted from variants selected at high gentamicin concentrations, using as a probe a labeled cloned insert containing aminoglycoside modifying enzyme (AME) gene sequence originated from a plasmid of a Klebsiella pneumoniae strain previously isolated in the same hospital. Further, we found indications of inactivation to other resistance genes in variants selected under similar conditions, as well as, indications of co-amplification of other AME markers (amikacin). Since the intestinal environment is a scenario of selective processes due to the therapeutic and prophylactic use of antimicrobial agents, the processes of amplification of low level antimicrobial resistance (not usually detected or sought by common methods used for antibiotic resistance surveillance) might compromise the effectiveness of antibiotic chemotherapy.199910585658
996760.9998The biology of IncI2 plasmids shown by whole-plasmid multi-locus sequence typing. IncI2 type plasmids are medium-sized (~55-80 kb) conjugative plasmids that have been found carrying important antimicrobial resistance genes but have also been frequently found as cryptic plasmids. The DNA sequences for 147 fully sequenced IncI2 plasmids were studied by a whole-plasmid multi-locus sequence typing (wpMLST) scheme. A total of 171 loci were identified of which 52 were considered core (carried by greater than 95% of the plasmids). Most of the plasmids carrying the antimicrobial gene mcr-1 were in a distinct clade while most of the antimicrobial gene free plasmids were more distantly related. However, the host strains of bacteria were disparate for both groups of plasmids, showing that conjugal transfer of IncI2 plasmid is frequent. The mcr-1 gene was likely to have been introduced into IncI2 plasmids multiple times. It was also observed that the genes for conjugation showed significant linkage disequilibrium despite substantial diversity for most of those genes. Genes associated with biofilm formation were also among the core genes. The core genes can be considered the cohesive unit that defines the IncI2 plasmid group. Given the role conjugation can play in biofilm formation, it was concluded that conjugation is an active survival strategy for IncI2 plasmids. The IncI2 plasmid will have selective advantage when the plasmid-bearing bacteria are introduced to a new animal host that carries potential conjugal mates.201931629716
460770.9998Genetics of resistance to trimethoprim in cotrimoxazole resistant uropathogenic Escherichia coli: integrons, transposons, and single gene cassettes. Cotrimoxazole, the combined formulation of sulfamethoxazole and trimethoprim, is one of the treatments of choice for several infectious diseases, particularly urinary tract infections. Both components of cotrimoxazole are synthetic antimicrobial drugs, and their combination was introduced into medical therapeutics about half a century ago. In Gram-negative bacteria, resistance to cotrimoxazole is widespread, being based on the acquisition of genes from the auxiliary genome that confer resistance to each of its antibacterial components. Starting from previous knowledge on the genotype of resistance to sulfamethoxazole in a collection of cotrimoxazole resistant uropathogenic Escherichia coli strains, this work focused on the identification of the genetic bases of the trimethoprim resistance of these same strains. Molecular techniques employed included PCR and Sanger sequencing of specific amplicons, conjugation experiments and NGS sequencing of the transferred plasmids. Mobile genetic elements conferring the trimethoprim resistance phenotype were identified and included integrons, transposons and single gene cassettes. Therefore, strains exhibited several ways to jointly resist both antibiotics, implying different levels of genetic linkage between genes conferring resistance to sulfamethoxazole (sul) and trimethoprim (dfrA). Two structures were particularly interesting because they represented a highly cohesive arrangements ensuring cotrimoxazole resistance. They both carried a single gene cassette, dfrA14 or dfrA1, integrated in two different points of a conserved cluster sul2-strA-strB, carried on transferable plasmids. The results suggest that the pressure exerted by cotrimoxazole on bacteria of our environment is still promoting the evolution toward increasingly compact gene arrangements, carried by mobile genetic elements that move them in the genome and also transfer them horizontally among bacteria.202438946902
452380.9998Mosaic structure of a multiple-drug-resistant, conjugative plasmid from Campylobacter jejuni. Partial sequence analysis of a tet(O) plasmid from a multiple-drug-resistant clinical isolate of Campylobacter jejuni revealed 10 genes or pseudogenes encoding different aminoglycoside inactivating enzymes, transposase-like genes, and multiple unknown genes from a variety of pathogenic and commensal bacteria. The plasmid could be mobilized by a P incompatibility group plasmid into Escherichia coli, where it apparently integrated into the chromosome and expressed high-level resistance to multiple aminoglycoside antibiotics. This work provides new information about both the nature of drug resistance in C. jejuni and the ability of C. jejuni to exchange genes with other bacterial species.200515917546
574590.9998F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli. The evolution and propagation of antibiotic resistance by bacterial pathogens are significant threats to global public health. Contemporary DNA sequencing tools were applied here to gain insight into carriage of antibiotic resistance genes in Escherichia coli, a ubiquitous commensal bacterium in the gut microbiome in humans and many animals, and a common pathogen. Draft genome sequences generated for a collection of 101 E. coli strains isolated from healthy undergraduate students showed that horizontally acquired antibiotic resistance genes accounted for most resistance phenotypes, the primary exception being resistance to quinolones due to chromosomal mutations. A subset of 29 diverse isolates carrying acquired resistance genes and 21 control isolates lacking such genes were further subjected to long-read DNA sequencing to enable complete or nearly complete genome assembly. Acquired resistance genes primarily resided on F plasmids (101/153 [67%]), with smaller numbers on chromosomes (30/153 [20%]), IncI complex plasmids (15/153 [10%]), and small mobilizable plasmids (5/153 [3%]). Nearly all resistance genes were found in the context of known transposable elements. Very few structurally conserved plasmids with antibiotic resistance genes were identified, with the exception of an ∼90-kb F plasmid in sequence type 1193 (ST1193) isolates that appears to serve as a platform for resistance genes and may have virulence-related functions as well. Carriage of antibiotic resistance genes on transposable elements and mobile plasmids in commensal E. coli renders the resistome highly dynamic.IMPORTANCE Rising antibiotic resistance in human-associated bacterial pathogens is a serious threat to our ability to treat many infectious diseases. It is critical to understand how acquired resistance genes move in and through bacteria associated with humans, particularly for species such as Escherichia coli that are very common in the human gut but can also be dangerous pathogens. This work combined two distinct DNA sequencing approaches to allow us to explore the genomes of E. coli from college students to show that the antibiotic resistance genes these bacteria have acquired are usually carried on a specific type of plasmid that is naturally transferrable to other E. coli, and likely to other related bacteria.202032759337
4472100.9998Conjugative plasmids in bacteria of the 'pre-antibiotic' era. Antibiotic resistance is common in bacteria that cause disease in man and animals and is usually determined by plasmids. The prevalence of such plasmids, and the range of drugs to which they confer resistance, have increased greatly in the past 25 yr. It has become clear from work in many laboratories that plasmids have acquired resistance genes, of ultimately unknown origin, as insertions into their circular DNA. The intensive use of antibiotics since their introduction in the 1940s can explain the spread of plasmids that have acquired such genes but little is known of the incidence of plasmids in pathogenic bacteria before the widespread use of antibiotics in medicine. E.D.G. Murray collected strains of Enterobacteriaceae from 1917 to 1954; we now report that 24% of these encode information for the transfer of DNA from one bacterium to another. From at least 19% of the strains, conjugative plasmids carrying no antibiotic resistance were transferred to Escherichia coli K-12.19836835408
4605110.9998Self-transmissible multidrug resistance plasmids in Escherichia coli of the normal intestinal flora of healthy swine. The resistance genes and their surroundings on three self-transmissible plasmids found in Escherichia coli of the enteric normal flora of healthy pigs have been characterized. The resistance elements found are similar to those commonly found in clinical isolates, like the transposon Tn1721 including the Tet A tetracycline resistance determinant, Tn10 with the Tet B determinant, Tn21 including a class 1 integron with the aadA1a cassette inserted, sulII encoding sulfonamide resistance, and the strA-strB genes responsible for streptomycin resistance. The plasmids were able to mobilize into various recipients, including swine pathogens, zoonotic bacteria, and commensals when conjugation experiments were carried out. Transfer of plasmids did not require optimal conditions concerning nutrition and temperature as plasmids were transferred in 0.9% saline at room temperature, suggesting that in vivo transfer might be possible. This study shows that transferable resistance elements appearing in normal flora bacteria from animals are similar to those commonly found in clinical isolates of human origin. The results indicate a probable communication between pathogens and the normal flora with respect to exchange of resistance factors.200111442346
3356120.9998Conjugative multiple-antibiotic resistance plasmids in Escherichia coli isolated from environmental waters contaminated by human faecal wastes. AIMS: To better understand the involvement of faecal contamination in the dissemination of antibiotic resistance genes, we investigated the genetic supports of resistances in nine multi-resistant Escherichia coli strains originating from human faecal contamination, and isolated from three different aquatic environments used for producing drinking water. METHODS AND RESULTS: Seven strains harboured at least one large plasmid that we have characterized (size, antibiotic resistance patterns, incompatibility group, capacity of autotransfer, presence of integron). Most of these plasmids were conjugative and carried numerous resistances. One of the plasmids studied, belonging to the IncP incompatibility group, was able to transfer by conjugation to Pseudomonas fluorescens and Aeromonas sp. Only two of the plasmids we studied carried class 1 and/or 2 integron(s). CONCLUSIONS: Conjugative plasmids isolated from multi-resistant E. coli strains explained most of the resistances of their host strains and probably contribute to the spread of antibiotic resistance genes coming from human faecal contamination. SIGNIFICANCE AND IMPACT OF THE STUDY: These results highlight the key role played by plasmids in the multi-resistance phenotype of faecal bacteria and the diversity of these genetic structures. Contaminated water, especially accidentally contaminated drinking water, could be a path back to humans for these plasmids.201525387599
9974130.9998Role of Plasmids in Co-Selection of Antimicrobial Resistances Among Escherichia coli Isolated from Pigs. Co-selection is thought to occur when resistance genes are located on the same mobile genetic element. However, this mechanism is currently poorly understood. In this study, complete circular plasmids from swine-derived Escherichia coli were sequenced with short and long reads to confirm that resistance genes involved in co-resistance were co-transferred by the same plasmid. Conjugative transfer tests were performed, and multiple resistance genes were transmitted. The genes possessed by the donor, transconjugant, and plasmid of the donor were highly similar. In addition, the sequences of the plasmid of the donor and the plasmid of the transconjugant were almost identical. Resistance genes associated with statistically significant combinations of antimicrobial use and resistance were co-transmitted by the same plasmid. These results suggest that resistance genes may be involved in co-selection by their transfer between bacteria on the same plasmid.202337540099
4473140.9998The genetics of bacterial trimethoprim resistance in tropical areas. Resistance to trimethoprim in Gram-negative bacteria is largely manifested by two trimethoprim resistant dihydrofolate reductases (types I and II) encoded by genes originally located on resistance plasmids. Although trimethoprim resistance increased markedly after the clinical introduction of trimethoprim in the West, its spread has slowed and, in Edinburgh at least, has actually been declining. This reduction has been accompanied by the migration of a transposon, encoding the type I plasmid resistance gene, into the bacterial chromosome. In tropical areas, the incidence of trimethoprim resistance is very much higher. In Tanzania, it has spilled over into other bacteria outside the Enterobacteriaceae, but it was in India where the major problem existed. The majority (64%) of the Indian Enterobacteriaceae studied were resistant to the drug and most of the resistance genes were located on very large plasmids which also conferred resistance to many other antibacterial drugs. Some Indian plasmids carried a new trimethoprim resistance gene which is not detectable by conventional sensitivity tests and may be spreading unnoticed elsewhere. The proportion of trimethoprim resistance has been related to the volume of antibacterial drugs used.19873318025
4842150.9998Plasmid-borne AmpC beta-lactamases. Historically, it was thought that ampC genes encoding class C beta-lactamases were located solely on the chromosome but, within the last 12 years, an increasing number of ampC genes have been found on plasmids. These have mostly been acquired by ampC-deficient pathogenic bacteria, which consequently are supplied with new and additional resistance phenotypes. This review discusses the phylogenetic origin of the plasmid-encoded AmpC beta-lactamases, their occurrence, and mode of spread, as well as their hydrolytic properties.200212166675
4609160.9998The importance of integrons for development and propagation of resistance in Shigella: the case of Latin America. In Latin America, the disease burden of shigellosis is found to coexist with the rapid and rampant spread of resistance to commonly used antibiotics. The molecular basis of antibiotic resistance lies within genetic elements such as plasmids, transposons, integrons, genomic islands, etc., which are found in the bacterial genome. Integrons are known to acquire, exchange, and express genes within gene cassettes and it is hypothesized that they play a significant role in the transmission of multidrug resistance genes in several Gram-negative bacteria including Shigella. A few studies have described antibiotic resistance genes and integrons among multidrug resistant Shigella isolates found in Latin America. For example, in Brazil, Bolivia, Chile, Costa Rica and Peru, class 1 and class 2 integrons have been detected among multidrug resistant strains of Shigella; this phenomenon is more frequently observed in S. flexneri isolates that are resistant to trimethoprim, sulfamethoxazole, streptomycin, ampicillin, chloramphenicol, and tetracycline. The gene cassette sul2, which is frequently detected in Shigella strains resistant to the sulfonamides, suggests that the sulfonamide-resistant phenotype can be explained by the presence of the sul2 genes independent of the integron class detected. It is to be noted that sul3 was negative in all isolates analyzed in these studies. The high frequency of sulfonamide (as encoded by sul2) and trimethoprim resistance is likely to be a result of the recurrent use of trimethoprim sulfamethoxazole as a popular regimen for the treatment of shigellosis. The observed resistance profiles of Shigella strains confirm that ampicillin and trimethoprim-sulfamethoxazole are ineffective as therapeutic options. In-depth information regarding antibiotic resistance mechanism in this pathogen is needed in order to develop suitable intervention strategies. There is a pressing need for regional and local antimicrobial resistance profiling of Shigella to be included as a part of the public health strategy.201627528086
4954170.9998Integron class 1 reservoir among highly resistant gram-negative microorganisms recovered at a Dutch teaching hospital. Integrons play an important role in the dissemination of resistance genes among bacteria. Nearly 70% of highly resistant gram-negative bacteria isolated at a tertiary care hospital harbored an integron. Epidemiologic analysis suggests that horizontal gene transfer is an important mechanism of resistance spread and has a greater contribution than cross-transmission to levels of resistance in settings where highly resistant gram-negative bacteria are endemic.200919719415
9968180.9998Antibiotic Resistance, Core-Genome and Protein Expression in IncHI1 Plasmids in Salmonella Typhimurium. Conjugative plasmids from the IncHI1 incompatibility group play an important role in transferring antibiotic resistance in Salmonella Typhimurium. However, knowledge of their genome structure or gene expression is limited. In this study, we determined the complete nucleotide sequences of four IncHI1 plasmids transferring resistance to antibiotics by two different next generation sequencing protocols and protein expression by mass spectrometry. Sequence data including additional 11 IncHI1 plasmids from GenBank were used for the definition of the IncHI1 plasmid core-genome and pan-genome. The core-genome consisted of approximately 123 kbp and 122 genes while the total pan-genome represented approximately 600 kbp. When the core-genome sequences were used for multiple alignments, the 15 tested IncHI1 plasmids were separated into two main lineages. GC content in core-genome genes was around 46% and 50% in accessory genome genes. A multidrug resistance region present in all 4 sequenced plasmids extended over 20 kbp and, except for tet(B), the genes responsible for antibiotic resistance were those with the highest GC content. IncHI1 plasmids therefore represent replicons that evolved in low GC content bacteria. From their original host, they spread to Salmonella and during this spread these plasmids acquired multiple accessory genes including those coding for antibiotic resistance. Antibiotic-resistance genes belonged to genes with the highest level of expression and were constitutively expressed even in the absence of antibiotics. This is the likely mechanism that facilitates host cell survival when antibiotics suddenly emerge in the environment.201627189997
4948190.9998Yersinia pestis antibiotic resistance: a systematic review. Yersinia pestis, the cause of plague and a potential biological weapon, has always been a threatening pathogen. Some strains of Y. pestis have varying degrees of antibiotic resistance. Thus, this systematic review was conducted to alert clinicians to this pathogen's potential antimicrobial resistance. A review of the literature was conducted for experimental reports and systematic reviews on the topics of plague, Y. pestis, and antibiotic resistance. From 1995 to 2021, 7 Y. pestis isolates with 4 antibiotic resistance mechanisms were reported. In Y. pestis 17/95, 16/95, and 2180H, resistance was mediated by transferable plasmids. Each plasmid contained resistance genes encoded within specific transposons. Strain 17/95 presented multiple drug resistance, since plasmid 1202 contained 10 resistance determinants. Strains 16/95 and 2180H showed single antibiotic resistance because both additional plasmids in these strains carried only 1 antimicrobial determinant. Strains 12/87, S19960127, 56/13, and 59/13 exhibited streptomycin resistance due to an rpsl gene mutation, a novel mechanism that was discovered recently. Y. pestis can acquire antibiotic resistance in nature not only via conjugative transfer of antimicrobial-resistant plasmids from other bacteria, but also by gene point mutations. Global surveillance should be strengthened to identify antibiotic-resistant Y. pestis strains by whole-genome sequencing and drug susceptibility testing.202235255676