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Treatment of Escherichia coli infections has become increasingly challenging due to the emergence of multidrug‐resistant mechanisms within the bacterial genome. Integrons play an essential role in spreading antibiotic resistance. This study is aimed at detecting the prevalence of Class 1, 2, and 3 integrons among E. coli associated with urinary tract infections (UTIs). A total of 90 E. coli strains were isolated from UTI samples and tested for antibiotic susceptibility using phenotypic methods. Biofilm formation was conducted using the microtiter plate method. Conventional PCR was used to detect the integrase genes. Overall, 48.9% of E. coli isolates (44/90) were MDR, and 58.9% (53/90) were resistant to ampicillin. A total of 60% (54/90) of E. coli isolates were biofilm producers. PCR results showed that 22.2% (20/90), 6.7% (6/90), and 3.3% (3/90) of E. coli isolates were positive for Class 1, Class 2, and both classes of integrons, respectively. However, Class 3 integron was not detected in all E. coli isolates. A significant correlation was observed between the MDR and Class 1 integron ( p < 0.05). There is no statistical significance between the presence of integrons and biofilm formation among E. coli isolates. Our findings revealed that the presence of Class 1 integron among E. coli isolates was associated with antibiotic resistance.

The unique genetic makeup and remarkable competency of Vibrio cholerae are the key factors that help the cholera pathogen adapt rapidly to adverse environmental conditions and resist the detrimental effect of antimicrobial agents. In the last few decades, V. cholerae that causes acute watery diarrhoeal disease cholera has emerged as a notorious multidrug resistant (MDR) enteric pathogen. Although chromosomal mutations can contribute to antimicrobial resistance (AMR), the frequent acquisition of extrachromosomal mobile genetic elements (MGEs) from closely/distantly related bacterial species are major players in V. cholerae drug resistance. Whole genome sequence analysis of clinical and environmental V. cholerae strains revealed that the genome of most of the recent isolates harbour integrating conjugative elements (ICEs), plasmids, superintegron, transposable elements and insertion sequences, which are the key carriers of genetic traits encoding antimicrobial resistance function. Different antimicrobial resistance genes identified in V. cholerae can contribute in antibiotic resistance by facilitating one of the following three mechanisms; (i) reduced permeability or active efflux of the antibiotics, (ii) alteration of the antibiotic targets by introducing post-transcriptional/translational modifications and (iii) hydrolysis or chemical modification of antibiotics. Here, we present an overview of the present insights on the emergence and mechanisms of AMR in V. cholerae.

Mobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to ‘evolve on demand’ in response to antibiotic pressure. To test this hypothesis, we inserted a custom three-cassette integron into Pseudomonas aeruginosa and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. In summary, integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity. From urinary tract infections to bacterial pneumonia, many diseases can now be treated through a course of antibiotics. Yet bacteria have evolved to respond to this threat, gaining new antibiotic resistance genes that allow them to evade the drugs. Addressing this growing issue requires to either discover new antibiotics, or to stop resistance before it emerges – a strategy that can only work if scientists know exactly how this mechanism takes place. For bacteria, it is a waste of resources to produce the proteins that confer resistance if antibiotics are absent. In fact, doing so can decrease their chance to survive and reproduce. A genetic element known as an integron can help to manage that burden. This piece of genetic information is formed of a succession of ‘cassettes’ containing antibiotic resistance genes. More proteins are made from the genes present at the start of the integron, compared to the ones towards the end. When bacteria encounter antibiotics, an enzyme called integrase is activated, allowing the organisms to shuffle the order of their cassettes in the integron. It is thought – but not yet proven – that this mechanism helps bacteria to activate their resistance ‘on demand’. To find out, Souque et al. engineered the bacteria Pseudomonas aeruginosa to carry a custom integron with three cassettes, each helping the organism to resist to a different antibiotic. In addition, only half of the bacteria had a working integrase and could therefore shuffle their gene cassettes. The organisms were then exposed to an increasing amount of the antibiotics for which the cassette in the last position provided resistance. The bacteria with a working integrase survived longer than those without, as they were able to shuffle their cassettes and move the useful antibiotic resistance gene into top position. In addition, the cassettes carrying the genes to resist to other types of antibiotics were excised from the genetic information and lost. Understanding integrons could guide future antibiotic treatment strategies, for instance by combining antibiotics with chemicals that block integrase activity. It might also be possible to force bacteria to delete resistance cassettes by cycling through different antibiotics.

Mobile genetic elements (MGEs) are associated with the emergence of multidrug resistance in extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae. This study explores the role of class 1 integrons and IS26 elements in breaching taxonomic barriers. A total of 110 E. coli bacteria were isolated from 300 clinical mastitis milk samples. The 98% E. coli isolates were extended-spectrum beta-lactamase- producers. About 83% of these isolates carried co-resistance for fluoroquinolones. The co-existence of (extended-spectrum beta-lactamase + quinolone resistance determining region mutations) and (extended-spectrum beta-lactamase + plasmid-mediated quinolone resistance genes) was found in 76% and 44% of isolates, respectively. The MGEs were detected in 88% of isolates with IS26 in 82% and class 1 integrase in 40% of isolates. The types of class 1 integron gene cassettes detected includes dfrA7, (dfrA17 + aadA5), and (dfrA1 + aadA1). We discovered 2 and 4 novel variants of the dfrA17 and aadA5 genes, respectively. We report a variant of aadA5 with mutation E235G in the Indian subcontinent earlier reported only in a human clinical isolate from Belgium. About 19 isolates carried IS26 linked to integrase gene intI1 with an internal deletion of 265 bp in the 5`CS of integrase gene intI1, earlier reported only in E. coli ST131 isolates from human clinical, wastewater samples. This study suggests intercontinental dissemination of antibiotic resistant genes (ARGs) across different microbiomes via mobile genetic elements.Key points• The role of mobile genetic elements in the emergence of multidrug-resistant E. coli in bovine mastitis.• Novel variants of the aadA5 (aminoglycoside adenyl transferase) and dfrA17 (dihydrofolate reductase) genes were identified in pathogenic E. coli isolated from bovine mastitis in class 1 integron gene cassette.• Sequence analysis of mobile genetic components revealed the physical connection between IS26 and intI1 genes with an internal deletion in 5'CS of class 1 integrase.

Background The aim of this study was to characterize class 1,2 and 3 integrons in clinical MDR Klebsiella pneumoniae isolates in Kashan, Iran. Methods One hundred-eighty one Klebsiella pneumoniae were recovered from clinical specimens during November 2013 to October 2014. Antimicrobial susceptibility patterns were determined by disk diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) guidelines for detection of MDR strains. Of the 181  Klebsiella pneumoniae, 146 (80.7%) of isolates were isolated from nosocomial infected patients and 150 (82.9%) identified as MDR isolates. The PCR amplification was used to show presence of class 1, 2 and 3 integrons among MDR strains. The PCR method and sequencing were used for evaluation of cassette content of integrons. Results Of the MDR K. pneumoniae isolates, 150 (100%) and 55 (36.7%) carried intI1 and intI2 genes, respectively. None of the MDR Klebsiella pneumoniae isolates carried class 3 integrons. Amplification of conserved segment (CS) of class 1 and class 2 integrons revealed 10 different arrays including: No. cassette; dfrA5 , dfrA30 ; aadA2 ; aadA2 , dfrA12 ; dfrA17 , aadA5 , aadA4 ; dfrA5 , dfrA30 , aadA2 ; dfrA5 , dfrA30 , aadA2 , dfrA12, dfrA5 , dfrA30 , dfrA17 , aadA5 , aadA4 ; aadA2 , aadA2 , dfrA12 ; dfrA5 , dfrA30 , aadA2 , aadA2 , dfrA12 and 4 arrays including: No. cassette; aadA1 ; dfrA1-sat1 ; aadA1 , dfrA1-sat1 , respectively. Conclusions The finding of present study revealed a high prevalence of integrons especially class 1 among MDR K. pneumoniae isolates from nosocomial infections in Kashan, which led to rapid extension of MDR strains.

Bacteria have existed on Earth for three billion years or so and have become adept at protecting themselves against toxic chemicals. Antibiotics have been in clinical use for a little more than 6 decades. That antibiotic resistance is now a major clinical problem all over the world attests to the success and speed of bacterial adaptation. Mechanisms of antibiotic resistance in bacteria are varied and include target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Acquisition of genes needed to elaborate the various mechanisms is greatly aided by a variety of promiscuous gene transfer systems, such as bacterial conjugative plasmids, transposable elements and integron systems, that move genes from one DNA system to another and from one bacterial cell to another, not necessarily one related to the gene donor. Bacterial plasmids serve as the scaffold on which are assembled arrays of antibiotic resistance genes, by transposition (transposable elements and ISCR mediated transposition) and site‐specific recombination mechanisms (integron gene cassettes). The evidence suggests that antibiotic resistance genes in human bacterial pathogens originate from a multitude of bacterial sources, indicating that the genomes of all bacteria can be considered as a single global gene pool into which most, if not all, bacteria can dip for genes necessary for survival. In terms of antibiotic resistance, plasmids serve a central role, as the vehicles for resistance gene capture and their subsequent dissemination. These various aspects of bacterial resistance to antibiotics will be explored in this presentation. British Journal of Pharmacology (2008) 153, S347–S357; doi:10.1038/sj.bjp.0707607; published online 14 January 2008

Background Antimicrobial resistance (AMR) is a global threat. Escherichia coli is an important reservoir of resistance genes, and the coexistence of mcr with class 1 integron ( intI 1) is alarming, mcr confers resistance to colistin, a last-resort antibiotic, while intI1 often carries multiple transferable resistance determinants. Although colistin use in livestock is banned in Bangladesh, data on colistin-resistant E. coli in food animals, particularly cattle, remain scarce. This study investigated multidrug-resistance patterns, biofilm formation, and the prevalence of intI 1 and its association with mcr and other resistance determinants in E. coli from Bangladeshi cattle. Methods A total of 254 samples (feces, rectal swabs, soil, and water) were collected from cattle farms across three divisions of Bangladesh (Dhaka, Sylhet, and Barisal). E. coli isolates were identified using culture methods and confirmed with the VITEK-2 system and PCR. Antimicrobial susceptibility testing was performed using VITEK-2 system following CLSI guidelines. The presence of class 1 integron and mcr ( mcr-1 to mcr-5 ) genes was detected by PCR. Biofilm formation was assessed using the crystal violet assay. Statistical analysis was conducted in R using Chi-square exact test, with significance set at p  < 0.05. Results E. coli was detected in 76.4% of samples, with the highest prevalence in feces (86.8%). Antimicrobial testing revealed complete sensitivity to several antibiotics, but resistance occurred to cefuroxime (33%), ciprofloxacin (26.8%), and amoxicillin-clavulanic acid (22.2%), with all isolates showing intermediate response to colistin. Overall, 29.4% of isolates were MDR, though no XDR or PDR were detected. Class 1 integron was present in 52.6% and the mcr-1 gene in 21.7%, both significantly associated with MDR ( p  < 0.001). Water isolates showed the highest proportion of strong biofilm producers (25.5%). Conclusion This study reveals a high prevalence of class 1 integron and the mcr-1 gene in MDR E. coli from food animals in Bangladesh, highlighting their role in resistance dissemination and the public health risk of colistin resistance. The strong association of integron with MDR and mcr-1 underscores the need for prudent antibiotic use, routine surveillance, and stronger antimicrobial stewardship in livestock to limit the spread of resistance to humans.

Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4000 Klebsiella pneumoniae genomes for the presence of integrons and antibiotic resistance genes within them. Our data show that K. pneumoniae has a large diversity of integrons and the largest mobile integron in our database of plasmids. The pangenome of these integrons contains a total of 165 different gene families with most of the largest families being related with resistance to numerous types of antibiotics. IntegronFinder is a free and open-source software available on multiple public platforms.

Background Antimicrobial resistance (AMR) is a global threat driven mainly by horizontal gene transfer (HGT) mechanisms through mobile genetic elements (MGEs) including integrons. The variable region (VR) of an integron can acquire or excise gene cassettes (GCs) that confer resistance to antibiotics based on the selection pressure. Escherichia coli plays a significant role in the genetic transfer of resistance determinants to other Gram-negative bacteria. Current study is aimed to detect and compare integron-mediated resistance in clinical isolates of E. coli . Unique isolates of E. coli from urine or blood cultures were studied for their antimicrobial resistance patterns and integrons were detected using polymerase chain reaction assays followed by Sanger sequencing of GCs. Results During the study period, a total of 470 E. coli isolates were obtained, 361 (76.8%) from urinary and 109 (23.1%) from bacteremic sources. Class 1 integrons were detected in 66 (18.2%) and 26 (23.8%) isolates respectively. Urinary isolates of E. coli harbouring Class 1 integrons demonstrated significantly higher rates of resistance ( p  < 0.05) for most antibiotics (12/16, 75%) compared to integron negative isolates. Although not statistically significant, similar differences were observed in bacteremic isolates. Among the urinary isolates, 27 (40.9%) had a VR, in which the most common GC array detected was DfrA17-AadA5 ( n  = 14), followed by DfrA5 ( n  = 4) and DfrA12 ( n  = 3). Among bacteremic isolates, only 4 (15.3%) had a VR, all of which were carrying DfrA17 . The detected GC array correlated with the respective isolates’ phenotypic resistance patterns. Conclusion We found a strong correlation between integron positivity and trimethoprim resistance among E. coli from urinary sources. Although higher rates of resistance were observed in bacteremic isolates, they mostly carried empty integrons.

Background Nosocomial infections and persistence of multidrug resistant biofilm forming Acinetobacter baumannii in hospitals has made it as a serious problem in healthcare settings worldwide. Methods A total of 100 A. baumannii clinical isolates from immunocompromised patients hospitalized in ICU were investigated for biofilm formation, the presence of biofilm related genes ( bap, ompA, csuE, fimH, epsA, bla PER-1 , bfmS, ptk, pgaB, csgA, kpsMII ), integron characterization and molecular typing based on REP-PCR. Results All isolates were resistant to three or more categories of antibiotics and considered as multidrug resistant (MDR). A total of 32 isolates were resistant to all tested antibiotics and 91% were extensively drug-resistance (XDR). All isolates were able to produce biofilm and 58% of isolates showed strong ability to biofilm formation. All strong biofilm forming A. baumannii isolates were XDR. All A. baumannii isolates carried at least one biofilm related gene. The most prevalent gene was csuE (100%), followed by pgaB (98%), epsA and ptk (95%), bfmS (92%) and ompA (81%). 98% of isolates carried more than 4 biofilm related genes, simultaneously. Class I integron (67%) was more frequent in comparison with class II (10%) ( P  < 0.05). The REP-PCR patterns were classified as 8 types (A-H) and 21 subtypes. The A1 (23%) and C1 (15%) clusters were the most prevalent among A. baumannii isolates ( P  < 0.05). According to the REP-PCR patterns, 23% of all isolates had a clonal relatedness. Conclusion Our study revealed the high frequency of biofilm forming XDR A. baumannii in ICU patients, with a high prevalence of biofilm related genes of csuE and pgaB. It seems that the appropriate surveillance and control measures are essential to prevent the emergence and transmission of XDR A. baumannii in our country.