Integron-associated Gene Cassettes Research Articles

Integrons in the development of antimicrobial resistance: critical review and perspectives.

Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, the key players capable of transferring genes from bacterial chromosomes to plasmids and their integration by integrase to the target pathogenic host. Moreover, integrons play a central role in disseminating and assembling genes connected with antibiotic resistance in pathogenic and commensal bacterial species. They exhibit a large and concealed diversity in the natural environment, raising concerns about their potential for comprehensive application in bacterial adaptation. They should be viewed as a dangerous pool of resistance determinants from the "One Health approach." Among the three documented classes of integrons reported viz., class-1, 2, and 3, class 1 has been found frequently associated with AMRs in humans and is a critical genetic element to serve as a target for therapeutics to AMRs through gene silencing or combinatorial therapies. The direct method of screening gene cassettes linked to pathogenesis and resistance harbored by integrons is a novel way to assess human health. In the last decade, they have witnessed surveying the integron-associated gene cassettes associated with increased drug tolerance and rising pathogenicity of human pathogenic microbes. Consequently, we aimed to unravel the structure and functions of integrons and their integration mechanism by understanding horizontal gene transfer from one trophic group to another. Many updates for the gene cassettes harbored by integrons related to resistance and pathogenicity are extensively explored. Additionally, an updated account of the assessment of AMRs and prevailing antibiotic resistance by integrons in humans is grossly detailed-lastly, the estimation of AMR dissemination by employing integrons as potential biomarkers are also highlighted. The current review on integrons will pave the way to clinical understanding for devising a roadmap solution to AMR and pathogenicity. Graphical AbstractThe graphical abstract displays how integron-aided AMRs to humans: Transposons capture integron gene cassettes to yield high mobility integrons that target res sites of plasmids. These plasmids, in turn, promote the mobility of acquired integrons into diverse bacterial species. The acquisitions of resistant genes are transferred to humans through horizontal gene transfer.

Detection of class 1 integron-associated gene cassettes of multi-drug resistant Salmonella strains isolated from food at conventional markets in Ho Chi Minh city

After Salmonella strains were isolated from food samples collected randomly at conventional markets in several districts in Ho Chi Minh city, we evaluated antibiotic resistance by Kirby-Bauer methods, and the serotype name was assigned according to ISO/TR 6579-3:2014 and class 1 integron was investigated by PCR technique. As a result, there were seven distinguished serovars, including S. Kentucky (8 strains); S. Infantis (4 strains); S. Agona and S. Potsdam (2 strains); S. Saintpaul, S. Braenderup, S. Indiana (01 strain); OMF:1,z6:UT and 7:1,z6:UT (01 strain). The rate of multidrug-resistance Salmonella serovars carrying class 1 integron was 100% (21/21). The gene cassette region of class 1 integron accounted for 85.71% (18/21). The presence of mobile genetic factors in Salmonella in the study suggests that the bacteria can transmit or receive antibiotic resistance genes from other bacterial species in the natural environment. In addition, the research results provide scientific evidence for management decisions and raise awareness of effective antibiotic use in Ho Chi Minh City, Vietnam.

Multiple antibiotic resistance and DNA methylation in Enterobacteriaceae isolates from different environments

Antibiotic resistant bacteria with diverse resistance phenotypes and genotypes are ubiquitous in the environments that have become a global health concern. The role of DNA methylation in the dissemination of antibiotic resistance among different environments is currently unclear. We recovered 646 Enterobacteriaceae (Eb) isolates from hospital, livestock manure, municipal wastewater-treatment plants, river sediment and soil for comprehensive analysis of resistance phenotypes, β-lactamase genes, integrons, integron-associated gene cassettes and the levels of DNA methylation. Antibiotic susceptibility testing revealed that approximately 87.31 % isolates were multidrug resistant Eb. The β-lactamase genes were positively detected in 473 isolates with greater diversity in human or animal sourced Eb, while its prevalence was found to be highest in the Eb isolates from the natural environments. Forty-three gene cassettes (28 different types mediated by intI1) were detected in 53 (19.63 %) isolates, with greater diversity in Eb isolates from hospital and livestock manure. The multiple antibiotic resistance index of single strain was positively correlated with the 5-methylcytosine and showed a negative correlation with 6-methylademine. We conclude that the development of antibiotic resistance could possibly be coupled with DNA methylation, which might enhance the antimicrobial resistance and survival capacity of Eb.

Detection of class 1 integron-associated gene cassettes and tetracycline resistance genes in Escherichia coli isolated from ready to eat vegetables

BackgroundReady to eat (RTE) vegetables are easily accessible healthy foods that are commonly consumed globally, including in Indonesia. However, these RTE vegetables contain potential contamination from pathogens and multi-drug resistant bacteria. Therefore, in the present study, we examined the presence of tetracycline-resistant E. coli (TRE) isolates from RTE vegetables. MethodsSusceptibility to antimicrobial agents was determined using the Kirby-Bauer disc diffusion method. Characterisation of antibiotic resistant genes was performed using PCR and sequencing of tetracycline resistant gene, integron and gene cassette from the TRE isolates. ResultsThe isolates collected in this study were resistant not only to tetracycline, but also to streptomycin. Some isolates also displayed resistance to kanamycin (77.8%), chloramphenicol (11.1%), and ciprofloxacin (5.6%). All of the isolates contained integrons (intI1) and the tetA gene; tetB was not detected in our study. Further analysis showed that some isolates (38.8%) contained the dfrA7 gene cassette, which encodes dihydrofolate reductase, which is responsible for resistance to trimethoprim. Of all the isolates that presented integrons, 11 isolates (61.1%) did not carry gene cassettes. These empty integrons have the potential to convert themselves rapidly into multigraviton strains. ConclusionsTRE isolates contain the tetA gene and integron 1. Only 38.8% of the isolates that have been identified contain the dfrA7 gene cassette, which is responsible for trimethoprim antibiotic resistance. Further identification of genes conferring resistance to other antibiotics is necessary to better characterise antibiotic resistance.

The Relationship of Class I Integron Gene Cassettes and the Multidrug-Resistance in Extended -Spectrum β-Lactamase Producing Isolates of Escherichia coli

Background: Integron is an important element in creating multi-drug resistant (MDR) bacteria. This study evaluated the relationship of class I integron and antibiotic resistance in extended-spectrum beta-lactamase producing (ESBL) isolates of Escherichia coli (E. coli). Methods: A total of 66 ESBL-producing E. coli were isolated from urinary tract infection in Kermanshah and their antimicrobial susceptibility was assessed. The incidence of class I integron was determined in isolates using PCR. The class I integron-associated gene cassettes were also verified by DNA sequencing. Data were analyzed using statistical methods. Results: Of 66 ESBL-producing isolates, 65 (98.5%) were MDR. The most prevalent antibiotic resistance of the isolates was observed for ampicillin (98.4%), ceftriaxone (98.4%), cefotaxime (95.4%), and co-trimoxazole (86.3%). The frequency of class I integron in isolates was 92.3%. The relationship between class I integron and resistance to streptomycin, co-trimoxazole, and ceftazidime was statistically significant. The genes encoding resistance to streptomycin and co-trimoxazole, as well as a gene encoding a protein with unknown function, were associated with class I integron. The most common gene cassette was dfrA17-aadA5. Conclusions: The results indicate a high prevalence of antibiotic resistance among ESBL-producing isolates to the antibiotics commonly used for the empirical treatment of urinary tract infections. The frequency of class I integron and associated gene cassettes involving resistance to antibiotics is high. There is a high percentage of MDR among the ESBL-producing isolates, which mostly contain gene cassettes. These findings suggest a strong association of integron and ESBL genes in the isolates.

Molecular Detection of Class 1 Integron-Associated Gene Cassettes in KPC-2-Producing Klebsiella pneumoniae Clones by Whole-Genome Sequencing.

The dissemination of antimicrobial resistance genes and the bacterium that harbor them have increasingly become a public concern, especially in low- and middle-income countries. The present study used whole-genome sequencing to analyze 10 KPC-2-producing Klebsiella pneumoniae isolates obtained from clinical specimens originated from Brazilian hospitals. The study documents a relevant "snapshot" of the presence of class 1 integrons in 90% of the strains presenting different gene cassettes (dfrA30, dfrA15, dfrA12, dfrA14, aadA1, aadA2, and aac(6')Iq), associated or not with transposons. Two strains presented nonclassical integron (lacking the normal 3'conserved segment). In general, most strains showed a complex resistome, characterizing them as highly resistant. Integrons, a genetically stable and efficient system, confer to bacteria as highly adaptive and low cost evolution potential to bacteria, even more serious when associated with high-risk clones, indicating an urgent need for control and prevention strategies to avoid the spread of resistance determinants in Brazil. Despite this, although the class 1 integron identified in the KPC-2-producing K. pneumoniae clones is important, our findings suggest that other elements probably have a greater impact on the spread of antimicrobial resistance, since many of these important genes were not related to this cassette.

Spread of multidrug-resistant Escherichia coli harboring integron via swine farm waste water treatment plant

Wastewater treatment plants (WWTPs) that release treated wastewater into the environment have emerged as a major threat to public health. In this study, we investigated Escherichia coli load and antibiotic-resistance profiles across different treatment processes at a swine farm WWTP. The frequency of the detection of class 1 and 2 integrons, and their association with antibiotic resistance, were also analyzed. Samples were obtained at each of five sampling sites that represented each processing step within the WWTP. The largest decrease in E. coli load was observed during the anaerobic digestion step (from 4.86 to 2.89log CFU/mL). Isolates resistant to β-lactam antibiotics were efficiently removed after a series of treatment steps, whereas the proportions of isolates resistant to non-β-lactam antibiotics and multidrug-resistant strains were maintained across treatments. The occurrence of integron-positive strains was not significantly different at the various sampling sites (43.4–70%; p>0.05). Of the class 1 integron-positive isolates, 17.9% harbored the integron-associated gene cassettes aadA2, aadA12, aadA22, and dfrA15. To the best of our knowledge, this is the first description of a class 1 integron containing the aadA12 gene cassette from a swine farm and the presence of a class 1 integron containing dfrA15 in E. coli. This suggests that novel antibiotic-resistance gene cassette arrays could be generated in swine farm WWTPs. Moreover, 75% of integron-positive strains were categorized as multidrug resistant, whereas only 15.4% of integron-negative strains were multidrug resistant (p<0.05), indicating that integrons may be responsible for mediating resistance in WWTPs. With regard to the occurrence of multidrug-resistant, integron-positive E. coli recovered from the final effluent, our results highlighted the potential risks associated with wastewater discharge from swine farm WWTPs in terms of the spread of antibiotic-resistant bacteria to the aquatic environment.

Antimicrobial resistance and class 1 integron-associated gene cassettes in Salmonella enterica serovar Typhimurium isolated from pigs at slaughter and abattoir environment

Forty-five multi-resistant Salmonella enterica subsp. enterica serovar (S.) Typhimurium isolates obtained at five pig abattoirs in Southern Brazil were characterized. Their relatedness was determined by XbaI-macrorestriction analysis. Resistance genes, integrons and plasmid-mediated quinolone resistance genes (PMQR) were investigated by PCR. Amplicons for the variable part of class 1 integrons and the quinolone resistance-determining regions (QRDR) were sequenced. Plasmids were characterized by conjugation assays and replicon typing. Eighteen XbaI-macrorestriction patterns and 19 plasmid profiles were seen. Resistance to ampicillin (blaTEM), chloramphenicol (catA1 and floR), streptomycin (strA-strB), streptomycin/spectinomycin (aadA variants), sulphonamides (sul1, sul2, sul3) and tetracyclines [tet(A) and tet(B)] were commonly found. A trimethoprim resistance gene, dfrA8, was identified on a 100-kb plasmid. Single substitutions in the QRDR of GyrA but no PMQR genes were found. Twenty-five isolates carried class 1 integrons with an aadA23 gene cassette or unusual class 1 integrons with a dfrA12-orfF-aadA27 gene cassette array. Both integrons were found on large conjugative plasmids. Salmonella plasmid-located virulence genes spvR, spvA, spvB, rck and pefA were found on an IncFIB resistance plasmid. Hybrid virulence-resistance plasmids or plasmids harbouring class 1 integrons may play a role in the maintenance and dissemination of antimicrobial resistance among S. Typhimurium in this pig production system.

FosI Is a New Integron-Associated Gene Cassette Encoding Reduced Susceptibility to Fosfomycin.

In this work, we demonstrate that the fosI gene encodes a predicted small protein with 134 amino acids and determines reduced susceptibility to fosfomycin. It raised the MIC from 0.125 to 6 μg/ml when the pBRA100 plasmid was introduced into Escherichia coli TOP10 and to 16 μg/ml when the gene was cloned into the pBC_SK(-) vector and expressed in E. coli TOP10.

Identification of integrons and phylogenetic groups of drug-resistant Escherichia coli from broiler carcasses in China

The dissemination of drug-resistant Escherichia coli in poultry products is becoming a public concern, as it endangers food security and human health. It is very common for E. coli to exhibit drug resistance in the poultry industry in China due to the excessive use of antibiotics. However, few studies have examined the drug resistance endowed by integrons and integron-associated gene cassettes in different phylogenetic groups of E. coli isolated from broiler carcasses. In this study, 373 antibiotic-resistant E. coli strains were isolated from the surfaces or insides of broiler carcasses from a slaughterhouse in Shandong Province, China. According to phylogenetic assays of chuA, yjaA, and an anonymous DNA fragment, TSPE4-C2, these isolates belong to four phylogenetic groups (A, B1, B2, and D) and seven subgroups (A0, A1, B1, B21, B22, D1, and D2). Of the tested isolates, 95.71% (n=357) are multi-drug resistant, among which group B1 was predominant, accounting for 33.51% (n=125) of the tested isolates. A high percentage of the E. coli isolates were resistant to amoxicillin–clavulanic acid (99.20%, n=370), doxycycline (92.23%, n=344), sulfamethoxazole–trimethoprim (90.88%, n=339), ciprofloxacin, (64.61%, n=241), sulbactam–cefoperazone (51.21%, n=191), and amikacin (33.78%, n=126). Furthermore, among the 373 isolates, class 1 and 2 integrons were identified in 292 (78.28%) and 49 (13.14%) of the isolates, respectively, while no class 3 integrons were detected. The most prevalent gene cassette arrays were dfrA17–aadA5 and dfrA12–orfF–aadA2 in the variable region of class 1 integrons, while only one gene cassette array (dfrA1–sat2–aadA1) was detected in the variable region of class 2 integrons. Class 1 integrons were distributed in various physiological subtypes, whereas no predominant phylogenetic groups could be identified. The presence of class 2 integrons in the B21 subtype was significantly higher than in the other subtypes, and it coexisted with the class 1 integron. This study suggests that broiler products are potential sources of multi-drug resistant E. coli, and that resistance genes could be spread by lateral gene transfer.

Analysis of Integron-associated Gene Cassettes in Clinical Acinetobacter Calcoaceticus-Baumannii Complex Isolates from Central Taiwan

Purpose: Acinetobacter calcoaceticus-baumannii complex (ABC) has become a major infectious pathogen in Taiwan, and mobile DNA such as integrons and transposons often contribute to its multiple antibiotic resistance characteristics. Methods: A clinical epidemiological study of the cassette contents of the class 1 integron of ABC isolates in two central Taiwan hospitals was performed. Results: It was found that 78% (39/50) of strains possessed the IntI1 integrase gene, while four major different sizes of class 1 integron cassette arrays were found: 3.0 kb (aacC1-ORF1-ORF2- ORF3-aadA1) (aacC1: aminoglycoside 3'-N-acetyltransferase; aadA1: aminoglycoside 3'-adenyltransferase), 2.5 kb (aacA4- catB8-aadA1) (aacA4: aminoglycoside 6'-N-acetyl-transferase), 2.0 kb (dhfrXII-ORF-aadA2) (dhfrXII: dihydrofolate reductase; aadA2: aminoacyl-adenyltransferase A) and 1.2 kb (dhfrAI-ORF) (dhfrAI: dihydrofolate reductase type AI). Six different combinations of cassette arrays were also noted. The co-relationships between antibiotic-resistant phenotypes and genotypic combinations of cassettes were analyzed. As the 2.5-kb cassette array was found to be the most common in this study, the flanking regions of the specific integron of ABC were also analyzed by inverse PCR. In addition to antibiotic resistance genes, such as aphA1 (kanamycin resistance gene) (AphA1: aminoglycosidephosphotransferase), the transposase gene (tnpIS15/tnpAIS26) was found in the 2.5-kb cassette array flanking regions. Furthermore, PCR-RFLP confirmed that these flanking regions were conserved in all of the examined isolates. Conclusion: The SXT and GM resistance phenotypes of ABC isolates could be used in clinical screening for the IntI1- associated genotype. ABC isolates that carry a 2.5-kb cassette array have become dominant in Central Taiwan, and dissemination of this specific type of integron may derive from the involvement of mobile DNA.

Insight into the mobilome of Aeromonas strains.

The mobilome is a pool of genes located within mobile genetic elements (MGE), such as plasmids, IS elements, transposons, genomic/pathogenicity islands, and integron-associated gene cassettes. These genes are often referred to as “flexible” and may encode virulence factors, toxic compounds as well as resistance to antibiotics. The phenomenon of MGE transfer between bacteria, known as horizontal gene transfer (HGT), is well documented. The genes present on MGE are subject to continuous processes of evolution and environmental changes, largely induced or significantly accelerated by man. For bacteria, the only chance of survival in an environment contaminated with toxic chemicals, heavy metals and antibiotics is the acquisition of genes providing the ability to survive in such conditions. The process of acquiring and spreading antibiotic resistance genes (ARG) is of particular significance, as it is important for the health of humans and animals. Therefore, it is important to thoroughly study the mobilome of Aeromonas spp. that is widely distributed in various environments, causing many diseases in fishes and humans. This review discusses the recently published information on MGE prevalent in Aeromonas spp. with special emphasis on plasmids belonging to different incompatibility groups, i.e., IncA/C, IncU, IncQ, IncF, IncI, and ColE-type. The vast majority of plasmids carry a number of different transposons (Tn3, Tn21, Tn1213, Tn1721, Tn4401), the 1st, 2nd, or 3rd class of integrons, IS elements (e.g., IS26, ISPa12, ISPa13, ISKpn8, ISKpn6) and encode determinants such as antibiotic and mercury resistance genes, as well as virulence factors. Although the actual role of Aeromonas spp. as a human pathogen remains controversial, species of this genus may pose a serious risk to human health. This is due to the considerable potential of their mobilome, particularly in terms of antibiotic resistance and the possibility of the horizontal transfer of resistance genes.

Detection of integron-associated gene cassettes and other antimicrobial resistance genes in enterotoxigenic Bacteroides fragilis

Twenty seven Enterotoxigenic Bacteroides fragilis (ETBF) strains isolated from children in Kolkata, India, were tested for their antimicrobial resistance, presence of integrons and resistance encoding genes. Almost all the strains (>90%) were resistant to two or more antimicrobials. About 59–92% of the strains were resistant to ampicillin, amoxicillin, streptomycin, tetracycline, ciprofloxacin and norfloxacin. Most of these antimicrobial agents have been used in the treatment of diarrhea and other infectious diseases. In addition, about half a number of strains (48–55%) were resistant to clindamycin, cefotaxime, ceftazidime, ampicillin/sulbactam and trimethoprim/sulfamethoxazole. Moxifloxacin and metronidazole resistance ranged from 30 to 40%. All strains however, were found to be susceptible to chloramphenicol and imipenem. Class 1 integrase (intI1) was detected in seven and class 2 integrase (intI2) in one of the twenty seven ETBF strains. Resistance gene cassettes carried by these integrons had different alleles of dfr or aad genes. Beside these integron-borne genes, other genes encoding different antimicrobial resistance were also detected. Resistance genes such as cep(A) and tet(Q) were detected in most of the ETBF strains. To the best of our knowledge, this work constituted the first extensive report from India on the detection of integrons and antimicrobial resistance genes in ETBF.

Analysis of class I integrons responsible for antibiotics resistance in Pseudomonas aeruginosa

An increase in resistance to antibiotics in Pseudomonasaeruginosa has become a major worldwide concern. Particularly, P. aeruginosa which produces carbapenemases, versatile metallo-β-lactamases (MBLs), causes limitation to treat infection. Class I integrons play an important role in the spread of antibiotic resistance determinants such as MBLs in P. aeruginosa. In the present study, we identified and characterized genetic contents of class I integrons in P. aeruginosa DK45 that was isolated from catheterized urine of patients at Chungbuk National University Hospital in South Korea and strongly exhibited carbapenemase activity. The correlation between integron-associated gene cassettes and antibiotics resistance was also investigated. Screening of the integrons in P. aeruginosa was performed by PCR and the integron-associated gene cassettes were further characterized by DNA sequencing. It was confirmed that three integrons (class I) harboring VIM-2, OXA-10, and OXA-30 type β-lactamase genes, respectively, existed on the bacterial plasmid. Each integron also contained genes encoding resistance determinants to various antibiotics such as aminoglycoside, fluoroquinolone and folate pathway inhibitors. Functional analysis by recombinant plasmids bearing each integron in Escherichiacoli indicated that each integron was associated to a high resistance rate to β-lactam and aminoglycoside antibiotics. The combined results suggest that genetic diversity of class I integrons is a major factor capable of increasing a broad spectrum resistance to the antibiotics.

Detection and characterization of class 1 integron-associated gene cassettes from Pseudomonas aeruginosa isolates in southern Taiwan

In this study, detection and characterization of class 1 integron-associated gene cassettes from Pseudomonas aeruginosa isolates in southern Taiwan were investigated. The study focused on the association between integron-associated resistance gene cassettes and multidrug resistance in P. aeruginosa isolates. Using polymerase chain reaction amplification, DNA sequencing, and basic local alignment search tool analysis, a total of 22 different types of gene cassette arrays were detected in 162 class 1 integron-positive P. aeruginosa isolates. We first identified 11 different types of new gene cassette arrays within class 1 integron in P. aeruginosa isolates, including aac(6′)-II-catB2-aadA2, aac(6′)-II-aadA2, aac(6′)-II-catB2, aacA4-aadA15, aacC1-orfA-orfB-aadA1, cm1A-aadA1, catB3-blaOxA-10-aadA15, aacA4-catB8-aadA1, aadB-orfF1-aadA11, dfrB1, and dfrB4a-aacA4-aacA4-aadA1. Of these, aac(6′)-II-catB2-aadA2 was the most frequently found gene cassette. Twenty-one (21/162, 12.9%) strains carrying two different types of gene cassette arrays of catB3-blaOxA-10-aadA15 and aac(6′)-II-catB2-aadA2 were also simultaneously present in the P. aeruginosa isolates. A novel dfrB4a gene, different from the dfrB4 gene detected in the gene cassette array of dfrB4a-aacA4-aacA4-aadA, was characterized. A metallo-β-lactamaseo gene was also found to be carried on the gene cassette of blaVIM-3-orf2a-aacA4-aadB-aacA4 inserted in a class 1 integron obtained from meropenem-resistant P. aeruginosa isolates.

Epidemiological analysis of Salmonella isolates recovered from food animals and humans in eastern China

An epidemiological analysis of Salmonella spp. from food animals and humans in eastern China was conducted from 2008 to 2011. A total of 135 Salmonella isolates were recovered from 132 of 2566 tested fecal samples, representing 5.1% positives of the samples tested. Ten serotypes were identified among the 135 Salmonella enterica isolates, with Salmonella ser. Senftenberg, Salmonella ser. Enteritidis, Salmonella ser. Pullorum, and Salmonella ser. Typhimurium being the most common. Forty-seven pulsed-field gel electrophoresis (PFGE) profiles were generated among the 135 isolates, which grouped into six clusters (named A–F respectively). PFGE typing grouped the majority of isolates according to serotype, except for Salmonella ser. Senftenberg, Salmonella ser. Derby, and Salmonella ser. Saintpaul. And, more remarkable, no overlap in the PFGE patterns between the human and animal isolates was found. Antimicrobial testing revealed that 131 (97.0%) isolates were resistant to at least one antimicrobial. The highest prevalence of resistance was to carbenicillin (94.1%), followed by nalidixic acid (45.2%), sulfafurazole (37.0%), ampicillin (31.9%), and amoxicillin (28.9%). Additionally, blatem-1 (95.3%), blapse-1 (57.8%), sul2 (78.0%), and tetA (82.4%) were the most prevalent resistance genes, and other than the aminoglycoside resistance genes, the resistance phenotypes were consistent with the identified antimicrobial resistance genes. Finally, class 1 integrons were detected in eight (5.9%) of the 135 isolates, with all of the positive isolates containing int1 and qacEΔ1-sul I. Six positive isolates with a 1kb amplicon size harbored the aadA2 cassettes. However, class 1 integrons with a 600bp amplicon did not contain the integron-associated gene cassettes. Our findings showed the prevalence of Salmonella in food animals and humans in eastern China, and that the Salmonella isolates were phenotypically and genetically diverse. Additionally, many Salmonella isolates were resistant to multiple antimicrobial agents, which was consistent with the identified antimicrobial resistance genes.

Molecular Epidemiology of Integron-Associated Antimicrobial Gene Cassettes in the Clinical Isolates ofAcinetobacter baumanniifrom Northern Taiwan

BackgroundThe aims of this study were to understand the molecular epidemiology of integron-associated gene cassettes in Acinetobacter baumannii across four hospitals in northern Taiwan and to clarify the relationship between the presence of integrons and antibiotic-resistant phenotypes.MethodsSixty-five A. baumannii isolates, collected from the patients of four regional hospitals in northern Taiwan in 2009, were tested for the presence of integrons and their associated gene cassettes. The susceptibility difference between integron-positive and integron-negative A. baumannii strains was analyzed. Antibiotic-resistant phenotypes among A. baumannii with different types of gene cassette array combinations were also compared.ResultsAround 72% of the A. baumannii isolates carried class 1 integrase genes. Despite this, only three gene cassette arrays were found in the integrons. Integron-positive strains were significantly more resistant to all the tested antibiotics than the integrase-negative strains. All the four types of A. baumannii with different gene cassette array combinations were multidrug-resistant in nature. Gene cassette array aacA4-catB8-aadA1 existed in all the integron-positive A. baumannii isolates. Repetitive-sequence-based PCR (rep-PCR) results revealed the prevalence of one major cluster of imipenem-resistant A. baumannii strains (84%) in the four regional hospitals.ConclusionsThe presence of integrons with associated antimicrobial resistance gene cassettes can be used as a representative marker of multidrug resistance in A. baumannii. Some prevalent gene cassette arrays may exist among epidemiologically unrelated A. baumannii strains.

Deletion of Integron-Associated Gene Cassettes Impact on the Surface Properties of Vibrio rotiferianus DAT722

BackgroundThe integron is a genetic recombination system that catalyses the acquisition of genes on mobilisable elements called gene cassettes. In Vibrio species, multiple acquired gene cassettes form a cassette array that can comprise 1–3% of the bacterial genome. Since 75% of these gene cassettes contain genes encoding proteins of uncharacterised function, how the integron has driven adaptation and evolution in Vibrio species remains largely unknown. A feature of cassette arrays is the presence of large indels. Using Vibrio rotiferianus DAT722 as a model organism, the aim of this study was to determine how large cassette deletions affect vibrio physiology with a view to improving understanding into how cassette arrays influence bacterial host adaptation and evolution.Methodology/Principal FindingsBiological assays and proteomic techniques were utilised to determine how artificially engineered deletions in the cassette array of V. rotiferianus DAT722 affected cell physiology. Multiple phenotypes were identified including changes to growth and expression of outer membrane porins/proteins and metabolic proteins. Furthermore, the deletions altered cell surface polysaccharide with Proton Nuclear Magnetic Resonance on whole cell polysaccharide identifying changes in the carbohydrate ring proton region indicating that gene cassette products may decorate host cell polysaccharide via the addition or removal of functional groups.Conclusions/SignificanceFrom this study, it was concluded that deletion of gene cassettes had a subtle effect on bacterial metabolism but altered host surface polysaccharide. Deletion (and most likely rearrangement and acquisition) of gene cassettes may provide the bacterium with a mechanism to alter its surface properties, thus impacting on phenotypes such as biofilm formation. Biofilm formation was shown to be altered in one of the deletion mutants used in this study. Reworking surface properties may provide an advantage to the bacterium’s interactions with organisms such as bacteriophage, protozoan grazers or crustaceans.

The function of integron-associated gene cassettes in Vibrio species: the tip of the iceberg

The integron is a genetic element that incorporates mobile genes termed gene cassettes into a reserved genetic site via site-specific recombination. It is best known for its role in antibiotic resistance with one type of integron, the class 1 integron, a major player in the dissemination of antibiotic resistance genes across Gram negative pathogens and commensals. However, integrons are ancient structures with over 100 classes (including class 1) present in bacteria from the broader environment. While, the class 1 integron is only one example of an integron being mobilized into the clinical environment, it is by far the most successful. Unlike clinical class 1 integrons which are largely found on plasmids, other integron classes are found on the chromosomes of bacteria and carry diverse gene cassettes indicating a non-antibiotic resistance role(s). However, there is very limited knowledge on what these alternative roles are. This is particularly relevant to Vibrio species where gene cassettes make up approximately 1–3% of their entire genome. In this review, we discuss how emphasis on class 1 integron research has resulted in a limited understanding by the wider research community on the role of integrons in the broader environment. This has the capacity to be counterproductive in solving or improving the antibiotic resistance problem into the future. Furthermore, there is still a significant lack of knowledge on how gene cassettes in Vibrio species drive adaptation and evolution. From research in Vibrio rotiferianus DAT722, new insight into how gene cassettes affect cellular physiology offers new alternative roles for the gene cassette resource. At least a subset of gene cassettes are involved in host surface polysaccharide modification suggesting that gene cassettes may be important in processes such as bacteriophage resistance, adhesion/biofilm formation, protection from grazers and bacterial aggregation.

Role of Escherichia coli strain subgroups, integrons, and integron-associated gene cassettes in dissemination of antimicrobial resistance in aquatic environments of Jinan, China

Aquatic environments are known reservoirs of antibiotic-resistant bacteria, but little information is known about the role of Escherichia coli strain subgroups, integrons, and integron-associated gene cassettes in the prevalence of antimicrobial resistance. To address these knowledge gaps, the diversity and distribution of drug-resistant E. coli strains and their integrons in hospital wastewater (HWW) and XiaoQing River water (XQRW) in Jinan, China were compared. Phylogenetic assays showed that the isolates were distributed in every E. coli subgroup. The prevalence of antibiotic resistance in each E. coli subgroup from HWW was higher than in subgroups from XQRW, except for phylogenetic subgroup A(0). Classes 1 and 2 integrons were found in 327 strains (78.2% of the total 418 isolates) with a prevalence of 85.6% among the 209 isolates from HWW. Among 15 gene cassette arrays, dfrA17-aadA5 and dfrA12-orfF-aadA2 were the most prevalent. The prevalence of drug-resistance gene cassettes and diversity of arrays further proved that integrons were important contributors to the widespread occurrence of antibiotic resistance in E. coli among Jinan aquatic environments.