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Class I integrons have garnered significant attention due to pivotal roles in the dissemination of antimicrobial resistance genes (ARGs), which impose risks to public health and food safety. Here, the prevalence and characteristics of class I integrons in Escherichia coli isolates derived from food-producing animals and human patients were assessed. Of 721 E. coli isolates collected from human patients (113), pigs (298), and poultry (310), 93 (12.90%) carried the class I integrase gene (intI1). Multilocus sequence typing identified 39 sequence types from 93 intI1-postive isolates, including three novel types. Sequence analysis revealed that 59 classical class I integrons encompassed six distinct gene cassettes arrangements [dfrA17-aadA5, dfrA12-aadA2, dfrA1-aadA1, dfrA7, aac(6')-Ib, and aadA1-aac(3)-VIa]. Six insertion sequences (IS1, IS6, IS21, IS91, IS110, and IS256) and one transposon (Tn3) were harbored in proximity to the integrons. A comparison with sequences retrieved from the National Center for Biotechnology Information database demonstrated that E. coli isolates with integron sequences were detected in various food-producing animals and human hosts in environmental niches across Asia, Europe, and North America. These findings indicate the potential risk of ARG transmission between food-producing animals and humans by bacteria populations and provide useful baseline data for monitoring of ARGs. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance (AMR) impacts environmental processes and poses a threat to public health even in remote glacierized areas. In this study, we aimed to (i) investigate the diversity of antibiotic resistance genes (ARGs) and integrons in culturable bacteria, and to (ii) present a snapshot of microbial resistance on a glacier and its adjacent habitats in Scandinavia. We collected samples from glacier mice, spheroidal-to-ovoidal shaped bryophyte on the glacier surface, and from a proglacial lake at Austerdalsbreen in central Norway. We found variable bacterial counts ranging from 1.6 × 103 CFU/ml in water to 4.8 × 103 CFU/ml in glacier mice, with coliforms and aminoglycoside-resistant coliforms prevalent in microalgae bloom in the proglacial lake. Class 1 integrons were more frequently observed in glaciolacustrine sediment. Integron variable regions encompassing cassettes conferring resistance to macrolides and aminoglycosides in intI1-positive strains isolated from glacier mice and associated with multidrug resistance in aminoglycoside-resistant coliforms from microalgae bloom were found. The culturable bacteria carrying variable regions of integrons were identified as Pseudomonas sp., Paenibacillus sp., Escherichia coli, Klebsiella sp., Enterobacter sp., and Citrobacter sp. Additionally, we identified other ARGs, including sul1, aadA1, ampC, blaTEM, and blaOXA, indicating the presence of multiple mechanisms of antibiotic resistance. Our findings contribute to understanding of the distribution and dissemination of antibiotic resistance via glacial bryophytes to downstream ecosystem of proglacial lake in Norway.Highlights: Glacier mice and proglacial lake are habitats for ARB and bacteria with class 1 integrons. The co-occurrence of multiple ARGs in bacteria indicates a potential for co-selection. The variable regions of integrons contain genes determining resistance to macrolides, aminoglycosides and multidrug resistance. [ABSTRACT FROM AUTHOR]

Antibiotic resistance is a significant global health concern, leading to increased morbidity, mortality, and health care costs. Integrons are genetic elements that could acquire and express gene cassettes, including those that confer antibiotic resistance. This comprehensive study focused on the distribution of integrons and their gene cassettes in clinical isolates. This study explored the structure and classification of integrons with particular emphasis on Class I, II, III, and IV integrons. It also discussed the role of integrons in antibiotic resistance. The findings of this study contribute to a better understanding of the mechanisms underlying antibiotic resistance and provide valuable insights for developing strategies to combat this public health crisis. [ABSTRACT FROM AUTHOR]

Objective: This study aimed to determine the carriage of transferable integron-associated drug resistance in Escherichia coli (E. coli) strains isolated from blood cultures. Materials and Methods: A total of 111 E. coli isolates were included in this study. Antimicrobial susceptibility testing of the isolates against 17 antibiotics was performed using an automated microbiology system. Integron-specific polymerase chain reactions (PCR) were used to detect the presence of integrons. The antibiotic resistance gene cassettes in the variable regions of integrons were analyzed by DNA sequencing. Plasmid transfer assays were performed using the broth mating method. The clonal relationships among integron-carrying strains were evaluated by pulsed-field gel electrophoresis (PFGE). Results: Resistance rates to antibiotics ranged from 0.9% to 63%. Thirty-eight strains carried gene cassettes encoding dfrA7, dfr17-aadA5, dfrV, dfrA1-aadA1, and dfrA12-aadA2. Seven strains possessed class 2 integrons with gene arrays dfrA1-sat2-aadA1 and dfrA1-sat2-aadA30. Twenty-two integron-carrying isolates harbored conjugative resistance plasmids, three of which were identified as belonging to the IncN group. Two strains with class 1 integrons, isolated from different clinics, exhibited similar patterns in the PFGE analysis. Conclusion: Approximately 50% of E. coli isolates from blood cultures at our hospital were found to carry integron-associated transferable drug resistance, suggesting their potential role in the horizontal dissemination of resistance genes. Further research is needed to understand the prevalence of E. coli strains of blood origin and the role of integrons and gene cassette arrays in the spread of resistance. [ABSTRACT FROM AUTHOR]

Integrons, which are genetic components commonly found in bacteria, possess the remarkable capacity to capture gene cassettes, incorporate them into their structure, and thereby contribute to an increase in genomic complexity and phenotypic diversity. This adaptive mechanism allows integrons to play a significant role in acquiring, expressing, and spreading antibiotic resistance genes in the modern age. To assess the current challenges posed by integrons, it is necessary to have a thorough understanding of their characteristics. This review aims to elucidate the structure and evolutionary history of integrons, highlighting how the use of antibiotics has led to the preferential selection of integrons in various environments. Additionally, it explores their current involvement in antibiotic resistance and their dissemination across diverse settings, while considering potential transmission factors and routes. This review delves into the arrangement of gene cassettes within integrons, their ability to rearrange, the mechanisms governing their expression, and the process of excision. Furthermore, this study examines the presence of clinically relevant integrons in a wide range of environmental sources, shedding light on how anthropogenic influences contribute to their propagation into the environment. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Integrons, which are genetic components commonly found in bacteria, possess the remarkable capacity to capture gene cassettes, incorporate them into their structure, and thereby contribute to an increase in genomic complexity and phenotypic diversity. This adaptive mechanism allows integrons to play a significant role in acquiring, expressing, and spreading antibiotic resistance genes in the modern age. To assess the current challenges posed by integrons, it is necessary to have a thorough understanding of their characteristics. This review aims to elucidate the structure and evolutionary history of integrons, highlighting how the use of antibiotics has led to the preferential selection of integrons in various environments. Additionally, it explores their current involvement in antibiotic resistance and their dissemination across diverse settings, while considering potential transmission factors and routes. This review delves into the arrangement of gene cassettes within integrons, their ability to rearrange, the mechanisms governing their expression, and the process of excision. Furthermore, this study examines the presence of clinically relevant integrons in a wide range of environmental sources, shedding light on how anthropogenic influences contribute to their propagation into the environment.

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.

ABSTRACT: Objectives: Current research shows that the resistance of Escherichia coli (E. coli) is mainly related to integron gene cassettes. To assess the resistance of E. coli of goose origin and the carriage of its integron genes in four farms in Heilongjiang Province, antibiotic resistance phenotypes and the presence of various types of integrons were investigated. Methods: In this study, test strains were sampled and isolated from the farms, and 109 test strains were tested for drug sensitivity of 15 different antimicrobial drugs by the Kb disc diffusion method. Polymerase chain reaction was used to detect E. coli in three types of integrase genes (intI1, intI2, and intI3) and for sequencing analysis of the class I integron gene cassette. Results: Susceptibility test results show that more than 70% of tested strains exhibit resistant phenotypes to ampicillin, amoxicillin, imipenem, tetracycline, and doxycycline. The detection rate of class I integrons was 68.91%, while class II integrons and class III integrons were not detected. The detection rate of class I integrin gene cassette was 7.42%. Sequence analysis showed that strains carried different integron gene cassettes: dfrA17-aadA5, dfrA1-aadA1, dfrA27-arr-3, and aminoglycoside 3′'-nucleotidyltransferase. Conclusions: Results suggest that the detection rate of class I integrons is highly correlated with their drug resistance. Class I integrons provide a valuable guide to studying the spread and the expression of resistance genes and thus finding effective measures to prevent bacterial resistance.

Antibiotic resistance genes (ARGs) are classified as emerging environmental pollutants of global public health concern. These ARGs are disseminated through genetic elements such as integrons. Integrons can acquire, integrate, and express various rearrangeable gene cassettes (GCs), harboring different ARGs that may be readily spread to other bacteria in widely varied niches. Different classes of integrons possessing diverse arrays of ARGs located within its GCs are commonly distributed in the Enterobacteriaceae family and are responsible for the high rate of multidrug resistance observed. The members of this family are natural commensals of the gastrointestinal tracts of humans and animals released into the different aquatic environments. Various water sources further disseminate the organisms and their diverse resistance gene repertoires. Thus, understanding the distribution and diversity of the significant integron classes in the clinically relevant Enterobacteriaceae members will be of utmost importance. It will provide a framework for health authorities to make decisions on surveillance of these contaminants in the environment.

Piotr Celejewski-Marciniak,1 Renata Wolinowska,2 Marta Wróblewska1,3 1Department of Dental Microbiology, Medical University of Warsaw, Warsaw, Poland; 2Department of Pharmaceutical Microbiology, Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland; 3Department of Microbiology, Central Clinical Hospital, University Clinical Centre, Medical University of Warsaw, Warsaw, PolandCorrespondence: Marta Wróblewska; Piotr Celejewski-MarciniakDepartment of Dental Microbiology, Medical University of Warsaw, 1a Banacha street, Warsaw, 02-097, PolandTel +48225991777; +48665101188Email marta.wroblewska@wum.edu.pl; piotrcm@onet.plPurpose: Gram-negative rods of the genus Serratia play an increasing role as etiological agents of healthcare-associated infections (HAI) in humans. These bacteria are characterized by natural and acquired resistance to several groups of antibacterial agents. The aim of the study was to characterize class 1, 2 and 3 integrons in the clinical isolates of Serratia spp. in Poland.Methods: The study comprised 112 clinical strains of Serratia, isolated from patients hospitalized in Poland in 2010– 2012. Identification of strains was confirmed using MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) system. Detection of class 1, 2 and 3 integrase DNA sequence was performed by multiplex-PCR. Amplicons obtained in the PCR reactions were purified and then sequenced bidirectionally.Results: Among the analyzed strains, Serratia marcescens was a predominant species (103/112, 92.0%). All three classes of integrase DNA sequence were detected in the analyzed strains of Serratia spp. DNA sequence of class 3 integron, besides integrase gene, revealed three gene cassettes (dfrB3, blaGES-7,blaOXA/aac(6ʹ)-Ib-cr). BLAST analysis of DNA sequence revealed that class 3 integron was carried on 9448 bp plasmid which was named pPCMI3 – whole sequence of its DNA was submitted to GenBank NCBI (National Center for Biotechnology Information) – NCBI MH569711.Conclusion: In this study, we identified a new plasmid pPCMI3 harboring class 3 integron. This is the first report of a gene oxa/aac(6ʹ)-Ib-cr coding for a novel fusion protein, which consists of OXA β-lactamase and acetyltransferase aac(6ʹ)-Ib-cr. In the analyzed strains, class 1 and 2 integrons were also detected. Among the strains with class 1 integron, nine contained cassette array 5ʹCS-aadA2-ORF-dfrA12-3ʹCS, and two – cassette array 5ʹCS-aacC1-ORF-ORF-aadA1-3ʹCS, which were not previously reported in Serratia spp.Keywords: Serratia marcescens, gene cassettes, antibiotic resistance, carbapenemase, fusion protein

Abstract Background Productions of metallo-β-lactamases enzymes are the most common mechanism of antibiotic resistance to all beta-lactam classes (except monobactams) in Acinetobacter baumannii. MBLs are usually associated with gene cassettes of integrons and spread easily among bacteria. The current study was performed to detect the genes encoding MBLs and integron structures in A. baumannii isolates from burn patients. Methods This study was performed on 106 non-duplicate A. baumannii isolates from burn patients referred to Shahid Motahari Hospital in Tehran. Antibiotic susceptibility of A. baumannii isolates was performed using disk diffusion and broth microdilution method in accordance with the CLSI guidelines. The presence of class 1 integron and associated gene cassettes as well as MBLs-encoding genes including bla VIM, and bla IMP were investigated using PCR and sequencing techniques. Results In this cross-sectional study all (100%) of the A. baumannii isolates examined were multidrug resistant. All isolates were sensitive to colistin and simultaneously all were resistant to imipenem. PCR assays showed the presence of bla VIM and bla IMP genes in 102 (96.2%) and 62 (58.5%) isolates of A. baumannii respectively. In addition, 62 (58.5%) of the A. baumannii isolates carried integron class 1, of which 49 (79.0%) were identified with at least one gene cassette. Three types of integron class 1 gene cassettes were identified including: arr2, cmlA5, qacE1 (2300 bp); arr-2, ereC, aadA1, cmlA7, qacE1 (4800 bp); and aac(3)-Ic, cmlA5 (2250 bp). Conclusion A high prevalence of MBLs genes, especially bla VIM, was identified in the studied MDR A. baumannii isolates. In addition, most of the strains carried class 1 integrons. Furthermore, the gene cassettes arrays of integrons including cmlA5 and cmlA7 were detected, for the first time, in A. baumannii strains in Iran.

In recent years, different acquired resistance mechanisms, including transposons, bacteriophages, plasmids, and integrons have been identified as involved in the spread of resistance genes in bacteria. The role of integrons as mobile genetic elements playing a central role in antibiotic resistance has been well studied and documented. Integrons are the ancient structures that mediate the evolution of bacteria by acquiring, storing, disposing, and resorting to the reading frameworks in gene cassettes. The term integron describes a large family of genetic elements, all of which are able to capture gene cassettes. Integrons were classified into three important classes based on integrase intI gene sequence. Integrons can carry and spread the antibiotic resistance genes among bacteria and are among the most significant routes of distribution of resistance genes via horizontal transfer. All integrons have three essential core features. The first feature is intI, the second one is an integron-associated recombination site, attI, and an integron-associated promoter, Pc, is the last feature. Among them, the class 1 integron is a major player in the dissemination of antibiotic resistance genes across pathogens and commensals. Various classes of integrons possessing a wide variety of gene cassettes are distributed in bacteria throughout the world. This review thus focuses on the distribution of integrons among important bacteria.

Integrons are genetic components that are critically involved in bacterial evolution and antimicrobial resistance by assisting in the propagation and expression of gene cassettes. In recent decades, biochar has been introduced as a fertilizer to enhance physiochemical properties and crop yield of soil, while manure has been used as a fertilizer for centuries. The current study aimed to investigate the impact of biochar, manure, and a combination of biochar and manure on integrons, their gene cassettes, and relative antimicrobial resistance in paddy soil. Field experiments revealed class 1 (CL1) integrons were prevalent in all samples, with higher concentration and abundance in manure-treated plots than in biochar-treated ones. The gene cassette arrays in the paddy featured a broad pool of cassettes with a total of 35% novel gene cassettes. A majority of gene cassettes encoded resistance to aminoglycosides, heat shock protein, heavy metals, pilus secretory proteins, and twin-arginine translocases (Tat), TatA, TatB, and TatC. Both in combination and solo treatments, the diversity of gene cassettes was increased in the manure-enriched soil, however, biochar reduced the gene cassettes' diversity and their cassettes array. Manure considerably enhanced CL1 integrons abundance and antimicrobial resistance, whereas biochar amendments significantly reduced integrons and antimicrobial resistance. The results highlighted the differential effects of biochar and manure on integrons and its gene cassette arrays, showing increased abundance of integrons and antibiotic resistance upon manure application and decrease of the same with biochar. The use of biochar alone or in combination with manure could be a beneficial alternative to mitigate the spread of antimicrobial resistance and bacterial evolution in the environment, specifically in paddy soils. [ABSTRACT FROM AUTHOR]

Abstract Background Integrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging. Results Here, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants. Conclusions Our results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes.

Nosocomial bacterial Isolates collected within 2003-2004 (n=411) and 2005-2007 (n=422) were highly resistant to cephalosporins III-IV and antibacterials of other groups (aminoglycosides, fluoroquinolons, chloramphenicol, and co-trimoxazole). Genes encoding TEM, SHV, CTX-M, OXA-2, and AmpC types of beta-lactamases (BLs) in the E.coli, Klebsiella spp., and Enterobacter spp. isolates were detected using polymerase chain reaction (PCR). Prevalent CTX-M-type BLs were detected in 85% of the E.coli, 87% of the Klebsiella spp., and 38% of the Enterobacter spp. isolates of the first strain collection and in 94% of the E.coli, 91% of the Klebsiella spp., and 38% of the Enterobacter spp. isolates of the second one. Genes belonging to three subtypes of blaCTX-M genes were identified: blaCTX-M-1 (228 blaCTX-M-15 and six blaCTX-M-3 of the first strain collection; 275 blaCTX-M-15, three blaCTX-M-3, and one blaCTX-M-22 of the second one), blaCTX-M-2 (one blaCTX_M_5 of the first strain collection and one blaCTX-M-2 of the second one), blaCTX-M-9 (17 blaCTX-M-14 and one blaCTX-M-9 of the first strain collection; seven blaCTX-M-14 and one blaCTX-M-9 of the second one). Three isolates of the first strain collection and one isolate of the second one carried two genes belonging to two different subtypes i. e. blaCTX-M-15 and blaCTX-M-14 simultaneously. The bacterial isolates had high levels of associative resistance to ciprofloxacin, co-trimoxazole, gentamicin, amikacin, and chloramphenicol associated with the resistance gene cassettes aadA1, aadA2, aadA5, aadB, aacA4, aac(6)Ib; dfrA1, dfrA5, dfrA12, dfrA17, cmlA1, ereA2, and catB8 in the class 1 integrons and the resistance gene cassettes dfrA1, sat1, and aadA1 in the class 2 integrons.

Integrons are genetic components that are critically involved in bacterial evolution and antimicrobial resistance by assisting in the propagation and expression of gene cassettes. In recent decades, biochar has been introduced as a fertilizer to enhance physiochemical properties and crop yield of soil, while manure has been used as a fertilizer for centuries. The current study aimed to investigate the impact of biochar, manure, and a combination of biochar and manure on integrons, their gene cassettes, and relative antimicrobial resistance in paddy soil. Field experiments revealed class 1 (CL1) integrons were prevalent in all samples, with higher concentration and abundance in manure-treated plots than in biochar-treated ones. The gene cassette arrays in the paddy featured a broad pool of cassettes with a total of 35% novel gene cassettes. A majority of gene cassettes encoded resistance to aminoglycosides, heat shock protein, heavy metals, pilus secretory proteins, and twin-arginine translocases (Tat), TatA, TatB, and TatC. Both in combination and solo treatments, the diversity of gene cassettes was increased in the manure-enriched soil, however, biochar reduced the gene cassettes’ diversity and their cassettes array. Manure considerably enhanced CL1 integrons abundance and antimicrobial resistance, whereas biochar amendments significantly reduced integrons and antimicrobial resistance. The results highlighted the differential effects of biochar and manure on integrons and its gene cassette arrays, showing increased abundance of integrons and antibiotic resistance upon manure application and decrease of the same with biochar. The use of biochar alone or in combination with manure could be a beneficial alternative to mitigate the spread of antimicrobial resistance and bacterial evolution in the environment, specifically in paddy soils.

Harmonious ecological environment is a major concern with rising feeding and consumption of ducks, as these waterfowl birds can promote the spread of antibiotic resistant genes (ARGs). Therefore, this study was conducted to know diversity of antimicrobial resistance (AMR), integrons, and mobile genetic elements (MGEs) in Escherichia coli (E. coli) isolated from intestinal contents or pericardial effusion of diseased ducks from 2018 to 2020 in Sichuan, China. The AMR phenotype was determined via disk diffusion test in 165 E. coli isolates. Further, the integrase genes of integron (intI1, intI2 and intI3 genes), gene cassettes (GCs) and MGEs were screened by PCR and sequencing. The results indicated 100% isolates were resistant to at least one antibiotic and 98.8% were multidrug-resistant strains. Highest AMR phenotype was recorded to rifampin (97.0%) followed by ampicillin (95.8%), chloramphenicol (89.7%), trimethoprim-sulfamethoxazole (84.2%), ciprofloxacin (83.0%), cefotaxime (80.0%), streptomycin (75.8%), doxycycline (49.7%), amikacin (10.3%), amoxicillin/clavulanic acid (3.6%), polymyxin B (1.2%) and ertapenem (0.6%). Further, class 1 and 2 integrons were found in 87.3% and 17.6% isolates, respectively. All isolates were negative for intI3 gene. The variable region of class 1 and 2 integrons contained total 13 different GCs, including arr-3+dfrA27, dfrA1+aadA1, dfrA17+aadA5, dfrA12, dfrA1+sat2+aadA1, dfrA12+aadA2, dfrA5, aadA2+ere(A)+dfrA32, aac(6’)-Ib-cr, aadA22, aadA5, dfrA17, and dfrA27. Moreover, 13 MGEs in 69 different combinations were observed with predominance of IS26 followed by tnpA/Tn21, trbC, ISEcp1, merA, ISAba1, tnsA, tnsB, tnsC, IS1133, tnsD, ISCR3/14, and tnsE. Thus, the monitoring of integrons, MGEs and ARGs is important to understand the complex mechanism of AMR, which might help to introduce interventions for prevention and control of AMR in duck farms in China.

The drug resistance pattern of infectious A. baumannii isolates of Saudi Arabia was evaluated and the integrons in samples were characterized. The isolates were obtained from patients of King Abdulaziz University Hospital, Jeddah, Saudi Arabia. The aim of this study was to investigate the association between drug resistance and the presence of integrons in A. baumannii isolates. A total 84 A. baumannii isolates were collected from different sources. Identification of isolates was carried out by conventional methods as well as by VITEK 2 technology system. Antibiotic resistance of A. baumannii isolates was determined by disc diffusion method. PCR amplification was conducted to detect the presence of intI1, intI2, intI3 in isolates. Majority of the isolates (66.7%) were found resistant to 5 or more antibiotics while gentamicin was proved to be most inhibitory. All resistant A. baumannii isolates were also positive for class 1 integrons with gene cassettes of different sizes. On the other hand, all except one antibiotic sensitive isolate was devoid of any class 1 integrons. The DNA sequencing of PCR amplified class I integrons revealed the presence of different gene cassettes such as aac(3)-Ia, dfrA15, aac(6')-Ib, dfrA17, dfrA7, aadA5 etc. The obtained results are compelling for a strong association between antibiotic resistance and the presence of class 1 integrons in these A. baumannii isolates. [ABSTRACT FROM AUTHOR]

Integrons are a segment of dsDNA that play a major role in bacterial adaptation and evolution. These genetic determinants are known by the presence of three necessary apparatuses: an integrase (intI gene), Pc (a promoter) and attI (a recombination site). These elements are able to acquire gene cassettes, which can carry antibiotic resistance factors, via site-specific recombination mechanism. The most common types of resistance integrons are class I (Tn402 derivatives), followed by class II and III. In recent years, the role of integrons as an important factor in the transmission and spread of resistance factors has been considered. Therefore, the ongoing threats posed by integrons require an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons. It shows how antibiotics use selected particular integrons from the environmental pool, so that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens.

Background: Productions of metallo-β-lactamases enzymes are the most common mechanism of antibiotic resistance to all beta-lactam classes (except monobactams) in Acinetobacter baumannii. MBLs are usually associated with gene cassettes of integrons and spread easily among bacteria. The current study was performed to detect the genes encoding MBLs and integron structures in A. baumannii isolates from burn patients.Methods: This study was performed on 106 non-duplicate A. baumannii isolates from burn patients referred to Shahid Motahari Hospital in Tehran. Antibiotic susceptibility of A. baumannii isolates was performed using disk diffusion and broth microdilution method in accordance with the CLSI guidelines. The presence of class 1 integron and associated gene cassettes as well as MBLs-encoding genes including blaVIM, and blaIMP were investigated using PCR and sequencing techniques.Results: In this cross-sectional study all (100%) of the A. baumannii isolates examined were multidrug resistant. All isolates were sensitive to colistin and simultaneously all were resistant to imipenem. PCR assays showed the presence of blaVIM and blaIMP genes in 102 (96.2%) and 62 (58.5%) isolates of A. baumannii respectively. In addition, 62 (58.5%) of the A. baumannii isolates carried integron class 1, of which 49 (79.0%) were identified with at least one gene cassette. Three types of integron class 1 gene cassettes were identified including: arr2, cmlA5, qacE1 (2300 bp); arr-2, ereC, aadA1, cmlA7, qacE1 (4800 bp); and aac(3)-Ic, cmlA5 (2250 bp).Conclusion: A high prevalence of MBLs genes, especially blaVIM, was identified in the studied MDR A. baumannii isolates. In addition, most of the strains carried class 1 integrons. Furthermore, the gene cassettes arrays of integrons including cmlA5 and cmlA7 were detected, for the first time, in A. baumannii strains in Iran. [ABSTRACT FROM AUTHOR]

The emergence of multidrug (MDR) isolates of Escherichia coli has made the treatment of urinary tract infections (UTI) very challenging. Integrons are considered to be one of the most important mechanisms in the dissemination of resistance genes. In the current study, we sought to investigate the antibiotic resistance patterns, class 1–3 integrons and corresponding gene cassettes in urinary isolates of E. coli in the southwest of Iran. A total of 144 E. coli isolates were collected from the patients with UTIs. Antibiotic susceptibility test conducted by the disc diffusion method using 12 different antibiotics. The polymerase chain reaction (PCR) was used for the detection of intl1, intI2, and intI3 genes. To analyze the gene cassettes, variable regions of class 1 integron were amplified by PCR and subjected to sequencing. The highest rates of resistance were exhibited to amoxicillin/clavulanic (73.6%), trimethoprim-sulfamethoxazole (63.9%) and tetracycline (63.2%). Totally, intI1 and intI2 genes were identified in 62.5 and 9% of isolates. One-hundred and nine (75.7%) E. coli isolates were multidrug resistance (MDR), among which 78% harbored intI1 gene. Also, all of the intI2 positive E. coli isolates were MDR. Ten different gene cassette arrays were found in intl1 positive E. coli including dfrA5, dfrA25, dfrA7, aacA4, aadA1, aadB-catB3, dfrA17-aadA5, dfrA12-orfF-aadA2, aadA1-blaOXA-30, and dfrA5-catB3-aacA4. The dfrA17-aadA5 was the most prominent gene cassette array among E. coli isolates. Characterization of resistance gene cassettes located in integrons in this study showed a high frequency of dfrA and aad genes which confer resistance to trimethoprim and aminoglycosides. The obtained result from this study could be useful in planning to prevent the rising rate of antibiotic resistance. [ABSTRACT FROM AUTHOR]

The objective was to investigate the multidrug resistance and presence of class 1 and 2 integrons in 300 Escherichia coli isolates obtained from 20 broiler farms during three rearing periods (one-day-old chicks, thirty-day-old chickens, and one day before slaughter) in Fars, South Iran. Results showed that 81.00%, 82.00%, and 85.00% of isolates were multidrugresistant on the first day, thirty-day-old chickens, and one day before slaughter, respectively. Multidrug-resistant E. coli isolates were further examined for the presence of class 1 and 2 integrons using PCR assay. The existence of class 1 integron-integrase gene (intI1) was confirmed in 68.40%, 72.70%, and 60.90% of multidrug-resistant isolates from stage 1, stage 2, and stage 3 of the rearing period, respectively. The frequency of class 2 integron-integrase gene (intI2) during the first to the third stage of sampling was 2.60%, 25.50%, and 30.40%. Also, sequence analysis of the cassette arrays within class 1 integron revealed the presence of the genes associated with resistance for trimethoprim (dfrA), streptomycin (aadA), erythromycin (ereA), and orfF genes. The results revealed that percentages of antimicrobial resistance in E. coli isolates were significantly higher in the middle and end stages of the rearing period. In conclusion, widespread dissemination of class 1 integrons in all three stages and rising trends of class 2 integrons existence in E. coli isolates during the rearing period of broiler chickens could exacerbate the spread of resistance factors among bacteria in the poultry industry. Future research is needed to clarify its implication for human health. [ABSTRACT FROM AUTHOR]

Background: Integrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging. Results: Here, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants. Conclusions: Our results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance had become a serious worldwide health problem. Antimicrobial resistance may result through several mechanisms that have been attributed to genetic mutation with low frequencies, and specific bacterial genes that have been associated with resistance against several antimicrobials used against host microorganisms. Transfer of the genes responsible for antimicrobial resistance horizontally is a central mechanism for the wide spread of the resistance among bacteria. This mechanism includes the transfer of transposons and plasmids that mediate antimicrobial resistance from one bacterium to others. Integrons are groups of genetic entities that can exchange combine, and lead to the expression of unique DNA elements that are called Gene cassettes. These cassettes contain a site-specific recombination mechanism. A particular bacterial genome portion, Integrons are considered to play an important role in transmission of antimicrobial resistance. This review addresses how integrons and multidrug resistance spread among different bacteria. [ABSTRACT FROM AUTHOR]

[Objective】The antibiotic resistance and the carrying status of integron-gene cassettes were detected in Vibrio parahaemolyticus from Litopenaeus vannamei in Guangi, in order to provide basic data for control of V. parahaemolyticus disease in L. vannamei and research of the molecular resistance mechanism of the germ. [Method】 The antibiotic resistance of V parahaemolyticus to 16 kinds of antil)iotics was evaluated by K-Bdisk diffusion test. The carrying status of integrons of class I, II and III, and the gene cassettes in the variable area of class I integron were detected byPCR method. Correlation of the carrying status of integron-gene cassette and the antibiotic resistance of the strains was analyzed. [Result 】The results showed different levels of susceptibility of 104 strains of V. parahaemolyticus to 16 kinds of antibiotics. The highest sensi¬tivity was shown toward florfenicolFFC) with the rate of 82. 7 %.And the strongest resistance was shown t〇%ward sulfamono- methoxine! SMM), sulfamethazine SM2) and compound sulfa¬diazine! SD) withi the rates of 93. 3 [- 100. 0 %. From the year 2013 to 2018 , there were 20 kinds of antil)iogram p2tems among which SD/SM2/SMM/SMD/SXT/RAD was the dominant one in V. parahaemolyticus from L. vannamei of Guangxi. The PCR resialts showed that tlie detection rate of fntl gene class I integrase) was 64. 4 %, and the ones of sull and qacEAl were 25. 0 [and 27. 9 [respectively. The detection rate of strains harboring all of the —l, s; and qacEAl genes was 22. 1 %. Among these strains, there were 6 strains detected to occupy the gene cassettes incliading blaCTX-M-2-aadAl and blaVIM-60-aadAl-aacA. There were no integron genes of class II or III found in all the isolates. Therewereremarkabledifferencesa- mong the detection rates of fntl and qacEAl genes in Beiliai, Qinzhou and Fangchenggang cities% < 0. 05 , the same as below?). The resist¬ance rates of tliiamphenicol^ TAP) in —/-positive strains were significantly bigger than the ones in —/-negative strains. But the correlations between resistance phenotypes of the rest antibiotics and the gene were not significant % > 0 • 05 , the same as below). There were no sig¬ nificant detected correlations between the resistance phenotype of cefradine RAD) and gene baCTU-M-Z+yF/M-O, the one of neomycin NEO) and gene aadAl/aacA , and the one of sulfanilamides and gene sl•【Conclusion】 The highest sensitivity was shown toward floifeni- col which could be considered as the alternative antibiotic for controlling the V parahaemolyticus disease in L. vannamei of Guangi. But the correlations between the carrying status of gene and the most of antibiotics were not significant. There were also no significant correla¬tions between the gene cassettes and the related antibiotic resistance. Nevertheless, the prevalence of class I integron increased the possibility of generation of multidrug resistance in V parahaemolyticus from L. vannamei of Guangxi, thus monitoring of integron-gene cassettes in Vibri¬ os should be strengtliened [ABSTRACT FROM AUTHOR]

Abstract Background Integrons are mobile DNA elements and they have an important role in acquisition and dissemination of antimicrobial resistance genes. However, there are limited data available on integrons of Staphylococcus aureus (S. aureus) from bovine mastitis, especially from Chinese dairy cows. To address this knowledge gap, bovine mastitis-inducing S. aureus isolates were investigated for the presence of integrons as well as characterization of gene cassettes. Integrons were detected using PCR reactions and then further characterized by a restriction fragment-length polymorphism analysis and amplicon sequencing. Results All 121 S. aureus isolates carried the class 1 integrase gene intI1, with no intI2 and intI3 genes detected. One hundred and three isolates were positive for the presence of 12 resistance genes, either alone or in combination with other gene cassettes. These resistance genes encoded resistance to trimethoprim (dhfrV, dfrA1, dfrA12), aminoglycosides (aadA1, aadA5, aadA4, aadA24, aacA4, aadA2, aadB), chloramphenicol (cmlA6) and quaternary ammonium compound (qacH) and were organized into 11 different gene cassettes arrangements (A-K). The gene cassette arrays dfrA1-aadA1 (D, 44.6%), aadA2 (K, 31.4%), dfrA12-orfX2-aadA2 (G, 27.3%) and aadA1 (A, 25.6%) were most prevalent. Furthermore, 74 isolates contained combinations of 2 to 4 gene cassette arrays. Finally, all of the integron/cassettes-positive isolates were resistant to aminoglycoside antibiotics. Conclusions This is the first study on the integrons and gene cassette arrays in S. aureus isolates from milk of mastitic cows from Northwestern China and provide the evidence for class 1 integron as possible antibiotic resistance determinants on dairy farms.

ABSTRACT Whole-genome sequencing of trimethoprim-resistant Escherichia coli strains MF2165 and PF9285 from healthy Swiss fattening calves revealed a so far uncharacterized dihydrofolate reductase gene, dfrA36. Functionality and association with trimethoprim resistance were demonstrated by cloning and expressing dfrA36 in E. coli. The DfrA36 protein showed the closest amino acid identity (49.4%) to DfrA20 from Pasteurella multocida and to the Dfr determinants DfrG (41.2%), DfrD (40.8%), and DfrK (40.0%) found in Gram-positive bacteria. The dfrA36 gene was integrated within a florfenicol/chloramphenicol-sulfonamide resistance ISCR2 element (floR-ISCR2-dfrA36-sul2) next to a Tn21-like transposon that contained genes with resistance to sulfonamides (sul1), streptomycin (aadA1), gentamicin/tobramycin/kanamycin (aadB), and quaternary ammonium compounds (qacEΔ1). A search of GenBank databases revealed that dfrA36 was present in 26 other E. coli strains from different origins as well as in Acinetobacter. IMPORTANCE The presence of dfrA36 associated with ISCR2 in Escherichia coli from animals, as well as its presence in other E. coli strains from different sources and countries and in Acinetobacter, highlights the global spread of this gene and its potential for further dissemination. The genetic link of ISCR2-dfrA36 with other antibiotic and disinfectant resistance genes showed that multidrug-resistant E. coli may be selected and maintained by the use of either one of several antimicrobials.

ObjectiveTo describe the polymorphisms of gene cassette promoters of the class 1 integron in clinical Proteus isolates and their relationship with antibiotic resistance.MethodsPolymorphisms of the gene cassette promoter in 153 strains of Proteus were analyzed by PCR and nucleotide sequencing. Variable regions of atypical class 1 integrons were detected by inverse PCR and nucleotide sequencing. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was used to analyze the phylogenetic relationships of class 1 integron-positive clinical Proteus isolates. Representative beta-lactamase genes (bla), including blaTEM,blaSHV,blaCTX-M-1,blaCTX-M-2,blaCTX-M-8,blaCTX-M-9,blaCTX-M-25 and blaOXA-1, and plasmid-mediated quinolone resistance (PMQR) genes including qnrA, qnrB, qnrC, qnrD, qnrS, oqxA, oqxB, qepA, and aac(6′)-Ib were also screened using PCR and sequence analysis.ResultsFifteen different gene cassette arrays and 20 different gene cassettes were detected in integron-positive strains. Of them, aadB-aadA2 (37/96) was the most common gene cassette array. Two of these gene cassette arrays (estX-psp-aadA2-cmlA1, estX-psp-aadA2-cmlA1-aadA1a-qacI-tnpA-sul3) have not previously been reported. Three different Pc-P2 variants (PcS, PcWTGN-10, PcH1) were detected among the 96 Proteus strains, with PcH1 being the most common (49/96). Strains carrying the promoters PcS or PcWTGN-10 were more resistant to sulfamethoxazole, gentamicin and tobramycin than those carrying PcH1. Strains with weak promoter (PcH1) harbored significantly more intra- and extra-integron antibiotic resistance genes than isolates with strong promoter (PcWTGN-10). Further, among 153 isolates, representative beta-lactamase genes were detected in 70 isolates (blaTEM-1, 54; blaOXA-1, 40; blaCTX-M-3, 12; blaCTX-M-14, 12; blaCTX-M-65, 5; blaCTX-M-15, 2) and representative PMQR genes were detected in 87 isolates (qnrA, 6; qnrB, 3; qnrC, 5; qnrD, 46; qnrS, 5; oqxA, 7; aac(6′)-Ib, 13; aac(6′)-Ib-cr, 32).ConclusionTo the best of our knowledge, this study provides the first evidence for polymorphisms of the class 1 integron variable promoter in clinical Proteus isolates, which generally contain relatively strong promoters. Resistance genotypes showed a higher coincidence rate with the drug-resistant phenotype in strong-promoter-containing strains, resulting in an ability to confer strong resistance to antibiotics among host bacteria and a relatively limited ability to capture gene cassettes. Moreover, strains with relatively weak integron promoters can “afford” a heavier “extra-integron antibiotic resistance gene load”. Furthermore, the gene cassettes estX, psp and the gene cassette arrays estX-psp-aadA2-cmlA1, estX-psp-aadA2-cmlA1-aadA1a-qacI-tnpA-sul3 have been confirmed for the first time in clinical Proteus isolates. Beta-lactamase genes and PMQR were investigated, and blaTEM-1 and blaOXA-1 were the most common, with qnrD and aac (6′)-Ib-cr also being dominant.

The pork production chain is an important reservoir of antimicrobial resistant bacteria. This study identified and characterized integrons in Salmonella isolates from a Brazilian pork production chain and associate them with their antibiotic resistance pattern. A total of 41 whole-genome sequencing data of nontyphoidal Salmonella were analyzed using PlasmidSPAdes and IntegronFinder software. Nine isolates (21.9%) had some integrons identified (complete and/or incomplete). Six complete class 1 integrons were found, with streptomycin resistance genes ( aadA1 , aadA2 ) alone or downstream of a trimethoprim resistance gene ( dfrA1 , dfrA12) , and some also containing resistance genes for sulfonamides ( sul1 , sul3 ) and chloramphenicol ( cmlA1 ). Class 2 integron was detected in only one isolate, containing dfrA1 - sat2 - aadA1 gene cassettes. Five isolates harbored CALINs-clusters attC but lacking integrases-with antimicrobial resistance genes typically found in integron structures. In all, integrons were observed among four serotypes: Derby, Bredeney, Panama, and monophasic var. Typhimurium I 4,[5],12:i:-. The association of integrons with antibiotic resistance phenotype showed that these elements were predominantly identified in multidrug resistance isolates, and six of the seven gentamicin-resistant isolates had integrons. So, surveillance of integrons in Salmonella should be performed to identify the potential for the spread of antimicrobial resistance genes among bacteria.

Integrons are a segment of dsDNA that play a major role in bacterial adaptation and evolution. These genetic determinants are known by the presence of three necessary apparatuses: an integrase (intI gene), Pc (a promoter) and attI (a recombination site). These elements are able to acquire gene cassettes, which can carry antibiotic resistance factors, via site-specific recombination mechanism. The most common types of resistance integrons are class I (Tn402 derivatives), followed by class II and III. In recent years, the role of integrons as an important factor in the transmission and spread of resistance factors has been considered. Therefore, the ongoing threats posed by integrons require an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons. It shows how antibiotics use selected particular integrons from the environmental pool, so that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. [ABSTRACT FROM AUTHOR]

Objective: To describe the polymorphisms of gene cassette promoters of the class 1 integron in clinical Proteus isolates and their relationship with antibiotic resistance. Methods: Polymorphisms of the gene cassette promoter in 153 strains of Proteus were analyzed by PCR and nucleotide sequencing. Variable regions of atypical class 1 integrons were detected by inverse PCR and nucleotide sequencing. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was used to analyze the phylogenetic relationships of class 1 integron-positive clinical Proteus isolates. Representative beta-lactamase genes (bla), including bla TEM, bla SHV, bla CTX-M-1, bla CTX-M-2, bla CTX-M-8, bla CTX-M-9, bla CTX-M-25 and bla OXA-1, and plasmid-mediated quinolone resistance (PMQR) genes including qnrA, qnrB, qnrC, qnrD, qnrS, oqxA, oqxB, qepA , and aac(6′)-Ib were also screened using PCR and sequence analysis. Results: Fifteen different gene cassette arrays and 20 different gene cassettes were detected in integron-positive strains. Of them, aadB-aadA2 (37/96) was the most common gene cassette array. Two of these gene cassette arrays (estX-psp-aadA2-cmlA1, estX-psp-aadA2-cmlA1-aadA1a-qacI-tnpA-sul3) have not previously been reported. Three different Pc-P2 variants (PcS, PcWTGN-10, PcH1) were detected among the 96 Proteus strains, with PcH1 being the most common (49/96). Strains carrying the promoters PcS or PcWTGN-10 were more resistant to sulfamethoxazole, gentamicin and tobramycin than those carrying PcH1. Strains with weak promoter (PcH1) harbored significantly more intra- and extra-integron antibiotic resistance genes than isolates with strong promoter (PcWTGN-10). Further, among 153 isolates, representative beta-lactamase genes were detected in 70 isolates (bla TEM-1, 54; bla OXA-1, 40; bla CTX-M-3, 12; bla CTX-M-14, 12; bla CTX-M-65, 5; bla CTX-M-15, 2) and representative PMQR genes were detected in 87 isolates (qnrA , 6; qnrB , 3; qnrC , 5; qnrD , 46; qnrS , 5; oqxA , 7; aac(6′)-Ib , 13; aac(6′)-Ib-cr , 32). Conclusion: To the best of our knowledge, this study provides the first evidence for polymorphisms of the class 1 integron variable promoter in clinical Proteus isolates, which generally contain relatively strong promoters. Resistance genotypes showed a higher coincidence rate with the drug-resistant phenotype in strong-promoter-containing strains, resulting in an ability to confer strong resistance to antibiotics among host bacteria and a relatively limited ability to capture gene cassettes. Moreover, strains with relatively weak integron promoters can "afford" a heavier "extra-integron antibiotic resistance gene load". Furthermore, the gene cassettes estX , psp and the gene cassette arrays estX-psp-aadA2-cmlA1, estX-psp-aadA2-cmlA1-aadA1a-qacI-tnpA-sul3 have been confirmed for the first time in clinical Proteus isolates. Beta-lactamase genes and PMQR were investigated, and bla TEM-1 and bla OXA-1 were the most common, with qnrD and aac (6′)-Ib-cr also being dominant. [ABSTRACT FROM AUTHOR]

A novel carbapenem-hydrolyzing beta-lactamase, called IMP-63, was identified in three clonally distinct strains of Pseudomonas aeruginosa and two strains of Pseudomonas putida isolated within a 4 year timeframe in three French hospitals. The bla IMP–63 gene that encodes this carbapenemase turned out to be located in the variable region of four integrons (In 1297 , In 1574 , In 1573 , and In 1572) and to coexist with novel or rare gene cassettes (fosM , gcu170 , gcuF1) and insertion elements (IS Psp7v , IS Pa16v). All these integrons except one (In 1574) were flanked by a copy of insertion sequence IS Pa17 next to the orf6 putative gene, and were carried by non-conjugative plasmids (pNECK1, pROUSS1, pROUSS2, pROUE1). These plasmids exhibit unique modular structures and partial sequence homologies with plasmids previously identified in various non-fermenting environmental Gram-negative species. Lines of evidence suggest that IS Pa17 promoted en bloc the transposition of IMP-63-encoding integrons on these different plasmids. As demonstrated by genotyping experiments, isolates of P. aeruginosa harboring the 28.9-kb plasmid pNECK1 and belonging to international "high-risk" clone ST308 were responsible for an outbreak in one hospital. Collectively, these data provide an insight into the complex and unpredictable routes of diffusion of some resistance determinants, here bla IMP–63, among Pseudomonas species. [ABSTRACT FROM AUTHOR]

Our study was conducted to investigate the antibiotic susceptibility profiles, integrons and their associated gene cassettes (GCs), and insertion sequence common regions of Escherichia coli isolates from Penaeus vannamei collected at a large-scale freshwater shrimp farm in Zhejiang Province, People’s Republic of China. A total of 182 E. coli isolates were identified from 200 samples. With the exception of imipenem, isolates were most commonly resistant to β-lactams, followed by tetracylines and sulfonamides. Fifty-two (28.6%) E. coli isolates were classified as multidrug resistant, and the patterns were highly diverse, with 29 types represented. The multiple-antibiotic resistance indices of the isolates were 0.17 to 0.56; 9.3% (17) of the 182 isolates were positive for class 1 integrons, 0.5% (1 isolate) was positive for class 2 integrons, and an insertion sequence common region 1 element was found upstream of the intI1 (integrase) gene in one of the intI1-positive isolates. Four GC arrays were detected in class 1 integrons, and one GC array was detected in class 2 integrons. Although the overall prevalence of antimicrobial-resistant bacteria in P. vannamei was lower than that previously reported for poultry and livestock farms in China, concerns about the inappropriate use of antibiotics and the transmission of antimicrobial-resistant bacteria in aquaculture were raised. Alternative approaches to reducing or replacing the use of antibiotics should be further studied. [ABSTRACT FROM AUTHOR]

Abstract The pork production chain and raw pork products are among the most important reservoirs of antimicrobial-resistant microorganisms. This study investigated the antimicrobial resistance profiles and integrons and their associated gene cassettes of Escherichia coli isolated from a large-scale centralized swine slaughterhouse in Zhejiang, China and its downstream markets. A total of 300 E. coli isolates were identified from 720 samples. No E. coli isolates were detected on the slaughtering line or at downstream supermarkets. Of the 300 E. coli isolates collected from lairages and downstream open markets, 242 (80.67%) were classified as multi-drug resistant (MDR). In addition, the prevalence of multi-drug resistance was significantly different (p < 0.05) and antimicrobial resistance profiles varied among the different sampling points. Furthermore, of 300 E. coli strains, 76 (25.33%) were positive for class 1 integrons and nine (3.00%) were positive for class 2 integrons. Three different gene cassettes were detected in class 1 integrons and one gene cassette was detected in class 2 integrons. Our study demonstrates that E. coli isolates from lairages and open markets are frequently MDR, and suggests that precautionary measures and hygienic environments are necessary to prevent the spread of antimicrobial-resistant microorganisms and their mobile genetic elements through the food chain. Highlights • No E. coli isolate was detected on the slaughtering line or at supermarkets. • E. coli from lairages and open markets were highly multi-drug resistant. • Multi-drug resistance rates of E. coli differed significantly among sampling sites. • Antimicrobial resistance profiles of E. coli varied between sampling sites. • Class 1 and 2 integrons and various gene cassettes were identified. [ABSTRACT FROM AUTHOR]

Natural systems of cloning and expression of mobile gene cassettes caught by site-specific recombination, class 1 and 2 integrons, play an important role in mobilization and spread of genetic determinants of antibiotic resistance in gram-negative bacterial human pathogens, especially in a hospital environment. The gene cassettes localized in variable parts of integrons determine resistance to antibacterial drugs (AD) of different functional classes. The aim of the work is the detection and characteristic of class 1 and 2 integrons in gram-negative bacteria isolated in multidisciplinary hospitals of Moscow and other regions of the Russian Federation in 2003–2015. Clinical strains of gram-negative bacteria (n = 1248) mainly had multidrug resistance phenotype (94%). An amount of 10% of strains were resistant to AD of three functional groups; 19%, four; 42%, five; 17%, six; and 7%, seven. A high level of resistance of the studied strains to beta-lactams is associated with the presence of beta-lactamase genes of blaTEM (35% strains), blaSHV (25%), blaCTX-M (38%), blaOXA (31%), blaVIM (3%), and blaNDM (2%) types; to AD of other functional groups, with the presence of class 1 integrons (59%) and class 2 integrons (8%). Most class 1 integrons (54%) and class 2 integrons (88%) contained in its variable part 22 variants of gene cassette arrays in class 1 integrons and 4 variants in class 2 integrons. During the study, 31 types of gene cassettes were identified (including the most widespread, aadB, aacA4, aacC1, aadA1, aadA2, aadA5, blaVIM-2, dfrA1, dfrA7, dfrA12, orfC, orfE, orfY, and sat1) associated with the resistance of strains to aminoglycosides, chloramphenicol, sulfonamides, and beta-lactams, as well as orf cassettes encoding the proteins with unknown functions. New gene cassette arrays were identified: dfrA12s-orfF-aadA2 (In1249) and dfrA1-IS911-sat1-aadA1 (not numbered). [ABSTRACT FROM AUTHOR]

Highlights • An IncP-1β group plasmid harbouring four identical bla GES-5 genes was identified. • The quadruple gene cassettes were embedded in an unusual class 1 integron. • A one to two dilution MIC difference was observed between single and four bla GES-5 genes. • The level of bla GES-5 expression in single and quadruple copies was not directly proportional to gene copy number. • The bla GES-5 gene cassette transfer frequency was characterised. ABSTRACT Integrons are genetic platforms responsible for the dissemination of antimicrobial resistance genes among Gram-negative bacteria, primarily due to their association with transposable elements and conjugative plasmids. In this study, a cassette array containing four identical bla GES-5 genes embedded in a class 1 integron located on an IncP-1β group plasmid from a clinical Pseudomonas aeruginosa strain was identified. Comparative genome analysis and conjugation assay showed that the plasmid pICP-4GES lacked the trbN, trbO and trbP genes but was conjugable. Antimicrobial susceptibility testing revealed that compared with single-copy bla GES-5 complementary strains, both the cloned and chromosome-targeted expression of four copies of bla GES-5 increased the minimum inhibitory concentration (MIC) by one to two dilutions for most of the selected antimicrobials. Quantitative real-time reverse transcription PCR (RT-qPCR) showed that the four consecutive cassettes increased bla GES-5 expression by approximately two-fold compared with the single-copy bla GES-5 strain, suggesting that the level of gene expression was not directly proportional to copy number. In addition, the gene cassette capture assay showed that the global bla GES-5 transfer frequency reached 5.38 × 10–4. [ABSTRACT FROM AUTHOR]

In this study, we collected different levels of altered rocks of a rocky mountain and the adjacent soil and characterized the abundance and weathering effectiveness of Bacillus strains. Based on qPCR and culture‐dependent approaches, the gene copies or the numbers of Bacillus strains were significantly higher in the soil than in the altered rocks, while the ratio of the gene copies or the numbers of Bacillus strains to those of total bacteria was higher in the less altered rock, followed by the more altered rock and the soil. The relative abundance of the highly active Al‐solubilizing Bacillus strains was higher in the more altered rock, followed by the less altered rock and the soil. Among the Al‐solubilizing Bacillus species, 30–36% of them were different between the altered rocks and the soil, however, similar Al‐solubilizing Bacillus species were found in the less altered rocks and the more altered ones. The results showed the alteration‐related changes in the abundance and mineral weathering effectiveness of Bacillus strains and suggested the ecological adaptation of the mineral‐weathering Bacillus populations and their role in mineral weathering in the rock and soil environments. [ABSTRACT FROM AUTHOR]

Turnovers of sex-determining systems represent important diversifying forces across eukaryotes. Shifts in sex chromosomes—but conservation of the master sex-determining genes—characterize distantly related animal lineages. Yet in plants, in which separate sexes have evolved repeatedly and sex chromosomes are typically homomorphic, we do not know whether such translocations drive sex-chromosome turnovers within closely related taxonomic groups. This phenomenon can only be demonstrated by identifying sex-associated nucleotide sequences, still largely unknown in plants. The wild North American octoploid strawberries (Fragaria) exhibit separate sexes (dioecy) with homomorphic, female heterogametic (ZW) inheritance, yet sex maps to three different chromosomes in different taxa. To characterize these turnovers, we identified sequences unique to females and assembled their reads into contigs. For most octoploid Fragaria taxa, a short (13 kb) sequence was observed in all females and never in males, implicating it as the sex-determining region (SDR). This female-specific “SDR cassette” contains both a gene with a known role in fruit and pollen production and a novel retrogene absent on Z and autosomal chromosomes. Phylogenetic comparison of SDR cassettes revealed three clades and a history of repeated translocation. Remarkably, the translocations can be ordered temporally due to the capture of adjacent sequence with each successive move. The accumulation of the “souvenir” sequence—and the resultant expansion of the hemizygous SDR over time—could have been adaptive by locking genes into linkage with sex. Terminal inverted repeats at the insertion borders suggest a means of movement. To our knowledge, this is the first plant SDR shown to be translocated, and it suggests a new mechanism (“move-lock-grow”) for expansion and diversification of incipient sex chromosomes. [ABSTRACT FROM AUTHOR]

Struvite recovered from wastewater is promising for recycling phosphorus into soil as fertilizers. However, struvite application may prompt the proliferation of antibiotic resistance in soil and plant. This study examined the impacts of struvite application and biochar amendment on integrons abundance and gene cassette contexts in rhizosphere soil and phyllosphere using quantitative PCR and clone library analysis. Microcosm experiments revealed that class 1 integron was the most prevalent in all samples, with higher concentration and higher relative abundance in rhizosphere than those in phyllosphere. The majority of resistance gene cassettes were associated with genes encoding resistance to aminoglycosides, beta-lactams and chloramphenicols. Struvite application significantly increased the genetic diversity of antibiotic resistance gene cassettes in both rhizosphere and phyllosphere. However, biochar amendment attenuated the increasing effect of struvite application exerting on the class 1 integron antibiotic resistance gene cassette pool in phyllosphere. These findings highlighted human activities to be the source of integron gene cassette pool and raised the possibility of using biochar amendment as an alternative mean for mitigating antibiotic resistance in environments. [ABSTRACT FROM AUTHOR]

Sphingobium sp. strain SYK-6 expresses the best characterized catabolic systems for lignin-derived aromatic compounds. However, the uptake systems for these aromatics remain unknown. In this study, we identified and characterized the protocatechuate (PCA) transporter gene SLG_12880 (pcaK) in SYK-6. Sequence comparisons revealed that PcaK belongs to the aromatic acid/H+ symporter family of major facilitator superfamily transporters. Further, pcaK was highly conserved among Sphingomonadales possessing catabolic genes for vanillate and PCA. The growth of an SYK-6 pcaK mutant was significantly delayed on PCA medium and PCA uptake rate was only 8% of wild type. In addition, vanillate uptake rate was 78% of wild type, although the pcaK mutant grew as well as the wild type on vanillate. When pcaK was expressed in Sphingobium japonicum UT26S, the transformant acquired the capacity to uptake both PCA and vanillate. These results indicate that pcaK is responsible for the major proportion of PCA uptake and a minor fraction of vanillate uptake in SYK-6. The productivity of 2-pyrone-4,6-dicarboxylate (PDC), a building block of functional polymers, was evaluated using a PDC hydrolase SYK-6 mutant harboring a pcaK plasmid. The mutant exhibited 1.27-fold greater PCA conversion and 1.24-fold greater PDC production compared to the control strain, suggesting that enhanced expression of transporter genes for lignin-derived aromatics can be used to increase the production of value-added metabolites. [ABSTRACT FROM AUTHOR]

Integrons are genetic platforms able to excise, integrate and express antibiotic resistance gene cassettes (GCs). Here we investigated the complete genetic organisation, genetic environment, location and conjugative transferability of a collection of class 2 integrons carried by Escherichia coli strains from different sources (poultry/pork meat, animals and humans). PCR cartography was conducted to determine the genetic arrangement of the integrons, their physical linkage to Tn 7 and chromosomal insertion at the attTn7 site. Clonal relatedness of specific isolates was determined by MLST and DO-PCR. Transferability of class 2 integrons was tested by conjugation. The resulting transconjugants were characterised by antimicrobial resistance genotyping, S1-PFGE and replicon typing. Although a limited diversity of GCs was shown, a high percentage of novel structures was identified owing to the integration of insertion sequence (IS) elements at different sites (IS 3 /IS 4 /IS 5 /IS 21 families). Insertion of IS 10 in the attI2 site of a class 2 integron, between Pc2B and Pc2C promoters, was likely mediated by a site-specific transposition event. Chromosomal insertion of integrons at attTn7 was confirmed in 80% of the isolates. Conjugation experiments demonstrated that 29% of class 2 integrons could be mobilised to E. coli CHS26, demonstrating that they can be located in conjugative/mobilisable elements at a low frequency. Reported structures evidence how class 2 integrons have evolved by the activity of integron integrases and the invasion of ISs. Since most of them are chromosomally located, dispersion is predominantly vertical, although conjugation events also contribute to the spread of class 2 integrons among bacterial communities. [ABSTRACT FROM AUTHOR]

The integron platform allows the acquisition, expression, and dissemination of antibiotic resistance genes within gene cassettes. Wastewater treatment plants (WWTPs) contain abundant resistance genes; however, knowledge about the impacts of wastewater treatment on integrons and their gene cassettes is limited. In this study, by using clone library analysis and high-throughput sequencing, we investigated the abundance of class 1, 2, and 3 integrons and their corresponding gene cassettes in three urban WWTPs. Our results showed that class 1 integrons were most abundant in WWTPs and that wastewater treatment significantly reduced the abundance of all integrons. The WWTP influents harbored the highest diversity of class 1 integron gene cassettes, whereas class 3 integron gene cassettes exhibited highest diversity in activated sludge. Most of the gene cassette arrays detected in class 1 integrons were novel. Aminoglycoside, beta-lactam, and trimethoprim resistance genes were highly prevalent in class 1 integron gene cassettes, while class 3 integrons mainly carried beta-lactam resistance gene cassettes. A core class 1 integron resistance gene cassette pool persisted during wastewater treatment, implying that these resistance genes could have high potential to spread into environments through WWTPs. These data provide new insights into the impact of wastewater treatment on integron pools and highlight the need for surveillance of resistance genes within both class 1 and 3 integrons. IMPORTANCE Wastewater treatment plants represent a significant sink and transport medium for antibiotic resistance bacteria and genes spreading into environments. Integrons are important genetic elements involved in the evolution of antibiotic resistance. To better understand the impact of wastewater treatment on integrons and their gene cassette contexts, we conducted clone library construction and high-throughput sequencing to analyze gene cassette contexts for class 1 and class 3 integrons during the wastewater treatment process. This study comprehensively profiled the distribution of integrons and their gene cassettes (especially class 3 integrons) in influents, activated sludge, and effluents of conventional municipal wastewater treatment plants. We further demonstrated that while wastewater treatment significantly reduced the abundance of integrons and the diversity of associated gene cassettes, a large fraction of integrons persisted in wastewater effluents and were consequentially discharged into downstream natural environments. [ABSTRACT FROM AUTHOR]

Antibiotics, antibiotic-resistant bacteria (ARB), antibiotic-resistance genes (ARGs), and mobile genetic elements (MGEs) have been reported in many environments. However, the investigation of their occurrence and diversity in untreated hospital wastewater is still insufficient. High concentrations of antibiotic residues were found in hospital wastewater using solid-phase extraction and UPLC–MS/MS analysis. The concentrations of six of 14 antibiotics reached μg/L levels in the hospital wastewater, which is higher than reported in other aquatic environments. Results of high-throughput sequencing analysis indicated that sequences affiliated to genera Escherichia and Acinetobacter were the predominant in the cultivable multiple-antibiotic-resistant bacteria (CMARB) recovered from the wastewater of three hospitals in China, with compositions of 34%–74%. Notably, several genera containing clinically pathogenic or opportunistic CMARB (e.g., Escherichia , Acinetobacter , Aeromonas , Myroides , Enterococcus , Proteus , Pseudomonas , and Streptococcus ) were detected at high relative abundances in the wastewaters of the three hospitals. High-capacity quantitative PCR showed that 131–139 unique ARGs of the 178 targeted genes were detected in the hospital wastewaters. The high prevalence of five MGEs and 12 ARGs was confirmed with qPCR, and some positive correlations between ARGs and MGEs were identified, such as between int I1 and qnr D, int I2 and sul 3, int I3 and tet X, Tn 916 /Tn 1545 and sul 2, and IS CR1 and sul 3. These results suggest that highly abundant antibiotic-resistant pathogens and highly mobile ARGs already exist in the human body, and that their release from hospitals without effective treatment poses high risks to environments and human health. [ABSTRACT FROM AUTHOR]

Background and Objectives: Integrons play a major role in the transmission and accumulation of resistance factors in multidrug resistant bacteria. This study was aimed to evaluate the gene cassettes of class I integron and antimicrobial resistance in isolates of Citrobacter with multidrug resistance (MDR). Materials and Methods: Ninety isolates of Citrobacter spp. were collected from the largest hospital in Kermanshah, Iran. Antimicrobial resistance patterns were determined using disc diffusion method. The class I integron were detected by PCR. The integrase positive isolates were further analyzed for the presence of gene cassettes using 5' and 3' conserved sequences (CSs) primers and PCR products were sequenced. The data were analyzed using the chi-square test. Results: Of 90 Citrobacter isolates, 46 (51.1%) were multidrug resistant. Class I integron and gene cassettes were determined in 30 isolates (65.2%). Gene cassettes were found which contained genes encoded resistance to aminoglycosides and trimethoprim and a putative gene. Gene cassettes of dfrA12-orfF-aadA2, dfrA1-aadA1, aadA1 and dfrA15-aadA2 were also found in Citrobacter isolates. Conclusion: Our results indicate there is a high frequency of class I integron among multi-drug resistant strains of Citrobacter isolated from clinical settings. A high frequency of class I integron associated gene cassettes, in particular dfr and aadA, present in MDR strains of Citrobacter. This data indicates an important role of integrons in the creation and transmission of MDR strains in health care centers.

Novel class 1 integrons In1085 and In1086, containing the class D β-lactamase -encoding gene blaOXA, were identified in clinical enterobacterial strains. In this study, we aimed to characterize the genetic contexts of In1085 and In1086, with the goal of identifying putative mechanisms of integron mobilization. Four plasmids, approximately 5.3, 5.3, 5.7, and 6.6 kb, from 71 clinical Enterobacteriaceae strains were found to contain class 1 integrons (In37, In62, In1085, and In1086, respectively). Two of these plasmids, pEco336 and pNsa292, containing In1085 and In1086, respectively, were further characterized by antibiotic susceptibility testing, conjugation experiments, PCR, sequencing, and gene mapping. The OXA-type carbapenemase activities of the parental strains were also assessed. The results revealed that the novel integrons had different genetic environments, and therefore demonstrated diverse biochemical characteristics. Using evolutionary inferences based on the recombination of gene cassettes, we also identified a role for attCaadA16 structural features during attI1 × attC insertion reactions. Our analysis showed that gene cassette insertions in the bottom strand of attCaadA16 in the correct orientation lead to the expression the encoded genes from the Pc promoter. Our study suggests that the genetic features harbored within the integrons are inserted in a discernable pattern, involving the stepwise and parallel evolution of class 1 integron variations under antibiotic selection pressures in a clinical setting.

Background: In many developing countries, shigellosis is endemic and also occurs in epidemics and treatment of multidrug-resistant (MDR) isolates are important. The aims of this study were to determine the antimicrobial susceptibility, prevalence of class 1 and 2 integrons and the clonal relatedness of isolates. Materials and Methods: Antimicrobial susceptibility tests were performed by disc diffusion method. Polymerase chain reaction (PCR)-sequencing technique was employed for detection and characterization of integrons. The genetic relatedness was evaluated by using enterobacterial repetitive intergenic consensus (ERIC) PCR. Results: There was a high percentage of resistance to trimethoprim-sulfamethoxazole (TMP/SMX) (93.7%), ampicillin (AMP) (87.3%), streptomycin (STR) (84.5%) and tetracycline (TET) (78.9%). MDR phenotype was seen in 95.1% of total isolates. Most common MDR profile was TMP/SMX/STR/AMP resistant pattern. Among the 142 Shigella spp. analyzed in this study, 28 isolates were positive for class 1 integron with two types of gene cassette arrays (dfrA17/aadA5 = 31.7% and dfrA7 = 3.8%). The class 2 integron was more frequently detected among the isolates (94.7%) with dfrA1/sat1/aadA1 (69.4%) and dfrA1/sat1 (30.6%) gene cassettes. ERIC-PCR results showed 6, 5, 4 and 3 main genotypes among 5. flexneri, 5. sonnei, 5. boydii and S. dysenteriae isolates, respectively. Conclusion: Our findings revealed that multidrug resistant Shigella species with high prevalence of class 2 integron were very common in Iran. In addition, ERIC-PCR patterns showed limited variety of clones are responsible for shigellosis in the region of the study. [ABSTRACT FROM AUTHOR]

Rapid dissemination and emergence of novel antibiotic resistance genes among bacteria are rising problems worldwide. Since their discovery in clinical isolates in the late 1980s, class 1 integrons have been found in a wide range of bacterial genera and have been extensively studied as contributors to dissemination of antibiotic resistance. The present study aimed to investigate the presence and structure of class 1 integrons in plasmid-carrying bacterial isolates obtained from a biopurification system used for decontamination of pesticide-contaminated water as well as their possible role as reservoir of antimicrobial resistance gene cassettes. A total of 35 representative isolates were screened for the presence of class 1 integron integrase encoded by intI1. PCR and DNA sequencing revealed the presence of six class 1 integrons with four variable regions: 5'CS-aadA1b-3'CS, 5'CS-aadA2-3'CS, 5'CS-aadA11cΔ-3'CS and 5'CS-dfrB3-aadA1di-catB2-aadA6k-3'CS, the last two being unseen arrays of antimicrobial resistance gene cassettes associated with novel environmental alleles of intI1. These four class 1 integrons were identified as being present in four different genera, including Ochrobactrum, and Variovorax, where class 1 integrons have not been previously reported. The results provide evidence of the biopurification systems as a tank of class 1 integron carrying strains and novel environmental class 1 integron integrases associated with antimicrobial resistance gene cassette arrays. [ABSTRACT FROM AUTHOR]