Distribution Of Integrons Research Articles

Integrons in uropathogenic Escherichia coli and their relationship with phylogeny and virulence

Uropathogenic Escherichia coli (UPEC) comprise a heterogeneous group of strains. In a previous epidemiological survey performed on 230 UPEC isolates, five virulence profiles were described, each one defined by the presence of some virulence determinants and by the absence of others. Phylogenetic groups and antibiotic resistances distributed non-randomly among the isolates with different profiles. Based on these results, the presence of class 1 and 2 integrons was now investigated in these UPEC isolates in order to analyze the distribution of integrons among the phylogenetic groups and virulence profiles. As detected by PCR reactions targeted to the corresponding integrase genes, the class 1 integrons prevailed (22%) followed by those of class 2 (8%). Integrons distributed unevenly among the four main E. coli phylogenetic groups: class 1 integrons predominated in the isolates belonging to group D while class 2 were almost absent in this group. In relation to virulence, integrons frequently appeared in some virulence profiles and were particularly scarce in others. Concerning the class 1 integrons, the most notable findings were that they highly concentrated in isolates presenting one of the virulence profiles (profile V) and were absent in isolates bearing the K1 capsule. The analysis of the Pc promoter variants of the class 1 integrons revealed that all isolates with virulence profile V contained the same Pc version; PcH1. Findings in this work support the idea that, among UPEC strains, integrons would encounter constraints for their installation in some genetic backgrounds while other backgrounds would be propitious for their permanence.

Genotypic characteristics of multidrug‐resistant Escherichia coli isolates associated with urinary tract infections

Escherichia coli is an important pathogen involved in community-acquired urinary tract infections (CA-UTIs). In this study, we analyzed the prevalence of frequently occurring genes and the distribution of integrons in 51 multidrug-resistant (MDR) E.coli isolates associated with CA-UTIs. The clonality of these strains was investigated by phylogrouping, multi-locus sequence typing, and pulsed-field gel electrophoresis (PFGE). All these strains were found to produce two or more resistance determinants, ceftazidime-hydrolyzing CTX-M-type extended-spectrum β-lactamases (ESBLs) and plasmid-mediated quinolone resistance determinants were the most prevalent (92.2% and 51.0%, respectively). A sulfhydryl variable-61-producing E.coli strain was identified for the first time in China. The prevalence of class 1 integrons was 54.9%, class 2 integrons were detected in three isolates but no isolate contained a class 3 integron. Phylogenetic group D was the dominant, observed in 70.6% of the isolates. PFGE analysis revealed a high level of diversity. Twenty-four distinctive sequence types (STs) including four major STs (ST648, ST224, ST38, and ST405) were identified. To our knowledge, this is the first report on the characterization of MDR E.coli isolates associated with CA-UTIs in China; our results suggest that an MDR D-ST648 clone producing CTX-M-ESBLs has emerged as a major clone in the community setting.

Detection of Class 1 and 2 Integrons Among Enteropathogenic Escherichia coli Isolates

Background:: Integrons are frequently detected in clinical isolates of Enterobacteriaceae. These elements are able to capture and express gene cassettes encoding antibiotic resistance. Numerous studies have examined the distribution of integrons in Escherichia coli. Despite this, there is a paucity of epidemiological data on the occurrence of integrons as well as extended spectrum β-lactamases (ESBLs) among enteropathogenic E. coli isolates. Objectives:: The main aim of this study was to investigate the prevalence of integrons as well as ESBLs among enteropathogenic E. coli isolates obtained from children with diarrhea in Tehran, Iran. Patients and Methods:: In total, 42 enteropathogenic E. coli strains were isolated from children with diarrhea and examined for the presence of class 1 and 2 integrons. The combined disk method was also performed to detect ESBL production. Statistical analysis was used for the comparison of the categorical data. Results:: Class 1 integron was identified in 24 (57.1%) isolates, while only 2 (4.8%) isolates harbored class 2 integron. Integrons were significantly associated with resistance to certain antibiotics, including; co-trimoxazole (P = 0.016) and tetracycline (P = 0.006). Of the 42 enteropathogenic E. coli isolates, 9 (21.4%) isolates were ESBL producers. However, no significant association was observed between the existence of integrons and ESBL production (P = 0.26). Conclusions:: Class 1 integrons are prevalent among enteropathogenic E. coli isolates, regardless of whether or not they produce ESBLs. This study emphasizes the alarming role of integrons in antibiotic resistance within diarrheagenic E. coli strains.

Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons

BackgroundIntegrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens. The SOS response is a regulatory network under control of the repressor protein LexA targeted at addressing DNA damage, thus promoting genetic variation in times of stress. We recently reported a direct link between the SOS response and the expression of integron integrases in Vibrio cholerae and a plasmid-borne class 1 mobile integron. SOS regulation enhances cassette swapping and capture in stressful conditions, while freezing the integron in steady environments. We conducted a systematic study of available integron integrase promoter sequences to analyze the extent of this relationship across the Bacteria domain.ResultsOur results showed that LexA controls the expression of a large fraction of integron integrases by binding to Escherichia coli-like LexA binding sites. In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons. There was a significant correlation between lack of LexA control and predicted inactivation of integrase genes, even though experimental evidence also indicates that LexA regulation may be lost to enhance expression of integron cassettes.ConclusionsAncestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA. The data also indicated that SOS regulation has been actively preserved in mobile integrons and large chromosomal integrons, suggesting that unregulated integrase activity is selected against. Nonetheless, additional adaptations have probably arisen to cope with unregulated integrase activity. Identifying them may be fundamental in deciphering the uneven distribution of integrons in the Bacteria domain.

Stenotrophomonas maltophilia resistance to trimethoprim/sulfamethoxazole mediated by acquisition of sul and dfrA genes in a plasmid-mediated class 1 integron

Stenotrophomonas maltophilia is becoming a more and more common cause of infections. In this study, the minimal inhibitory concentrations of trimethoprim/sulfamethoxazole (SXT), ceftazidime, minocycline, levofloxacin, chloramphenicol and ticarcillin/clavulanic acid were determined and the distribution of integrons and sul1, sul2 and dfrA genes was investigated in 102 S. maltophilia isolates collected from patients treated in 31 hospitals in Anhui, China, in the month of September in 2006–2008. The rate of resistance to SXT was up to 30.4%, and 64.7% of isolates were class 1 integron-positive. Sequencing data revealed the following novel gene cassettes embedded in class 1 integrons: dfrA17–aadA5; dfrA12–aadA2; aacA4–catB8–aadA1; aadB–aac(6′)-II–blaCARB-8; and arr-3–aacA4. This is the first report of the gene cassettes dfrA17–aadA5 and dfrA12–aadA2 and of sul2 genes in SXT-resistant S. maltophilia isolates in China. None of the SXT-susceptible S. maltophilia isolates were positive for sul2 or dfrA gene products by polymerase chain reaction (PCR), but PCR products for sul1 were detected in 27 SXT-susceptible and 25 SXT-resistant isolates. The findings from this study indicate that the sul1 gene, in combination with dfrA17 and dfrA12 gene cassettes and sul2 genes located within a 7.3kb plasmid, lead to a high rate of SXT resistance and also confirm the need for ongoing resistance surveillance.

Occurrence and Distribution of Various Genetic Structures of Class 1 and Class 2 Integrons inSalmonella entericaIsolates from Foodborne Disease Patients in Korea for 16 Years

We have investigated the distribution of integrons among 752 multidrug-resistant Salmonella isolates from human febrile and/or diarrheal patients during 1992-2007 and analyzed their genetic characteristics. Here, we report extensive integron analysis results within human isolates during the last 16 years. The gene or gene cassette(s) in the class 1 integrons found in the isolates were dfrA7, dfrA12-orfF-aadA2, aadA2, bla(PSE1), dfrA1-aadA1, dfrA17-aadA5, bla(OXA1)-aadA1, aadB-aadA1, aadA22, aadA1, and aac6'Ib-bla(OXA1)-aadA2. Class 2 integrons harboring dfrA1-sat2-aadA1 gene cassette were also found in four isolates. Twenty-nine isolates including one Salmonella Schleissheim isolate had two integrons harboring aadA2 and bla(PSE1) in their variable regions of 1.0 and 1.2 kb amplicons, respectively, which have been also found in Salmonella genomic island 1 (SGI1) of multidrug-resistant Salmonella Typhimurium DT104. The presence of SGI1 in Salmonella Schleissheim isolate was proved by SGI1-specific polymerase chain reaction. We first report a Salmonella Schleissheim having SGI1, Salmonella Typhimurium and Salmonella Heidelberg having the class 2 integron with dfrA1-sat2-aadA1 cassettes, Salmonella London with the aac6'Ib-bla(OXA1)-aadA2 gene cassette, Salmonella Chailey with the gene cassette of aadA22, and coexistence of two class 1 integrons carrying aadA22 and dfrA12-orfF-aadA2 in Salmonella Typhimurium.

High prevalence of trimethoprim-resistance cassettes in class 1 and 2 integrons in Senegalese Shigella spp isolates

Integrons have a well-established role in the dissemination of resistance among Gram-negative pathogens and are thus a useful marker of antibiotic resistance. Shigellae are noteworthy for their multiple drug resistance, having gradually acquired resistance to most widely use and inexpensive antimicrobial drugs. A total of 32 Shigella strains belonging to serotypes flexneri, dysenteriae, and boydii 20, a new Shigella serovar, resistant to at least four antibiotics were analyzed by molecular techniques. Class 1 integrons were the most prevalent (92.8%); class 2 integrons were found in 16 strains (57.1%). Fifty percent of the strains harboured both class 1 and 2 integrons (intI1 and intI2 genes); this combination of integrase genes was most prevalent in S. boydii 20 and S. dysenteriae strains. The class 1 integrons detected contained dfr and aadA cassettes, alone or in combination (dfrA5/dfrA15, or dfrA15-aadA1, dfrA1-aadA2), and an atypical cassette array with an insertion sequence (oxa30-aadA1-IS1). For class 2 integrons, we detected either the same cassettes as those found in Tn7 (dfrA1-sat1-aadA1-orfX) or truncated class 2 integrons without aadA1 or orfX. The tns genes were absent from all class 2 integrons.The distribution of integrons among RAPD profiles and serotypes revealed a clonal spread of integrons into serotypes and a transfer of integrons between different serotypes. The detection of integrons in a new Shigella serovar, in addition with a high integron prevalence among Shigella strains, confirms the propensity of shigellae to acquire and disseminate resistance determinants.

Distribution of integron-associated trimethoprim-sulfamethoxazole resistance determinants amongEscherichia colifrom humans and food-producing animals

To compare the distribution of integrons and trimethoprim-sulfamethoxazole resistance genes among Escherichia coli isolates from humans and food-producing animals. A collection of 174 multidrug-resistant E. coli isolates obtained from faecal samples of food-producing animals (n = 64) and humans (n = 59), and patients with urinary tract infections (n = 51) in Hong Kong during 2002-2004 were studied. The strains were analysed for their phylogenetic groups, the presence of sul genes (sul1 and sul2), integrons (intl1 and intl2) and class 1 integron-associated dfr cassette genes by PCR, restriction enzyme analysis and sequencing. Integrons were identified in 110 (63.2%) isolates. The prevalence of integrons was significantly different according to the specimen sources (animal faecal 84.4%, human faecal 67.8% and human urinary 31.4%) and phylogenetic groups (B1 80.8%, A 77.6%, D 54.1% and B2 11.5%). Faecal isolates (both human and animal) are more likely to belong to group A and B1. In contrast, most urinary isolates were either groups B2 and D. Among dfr containing isolates, dfrA1 and dfrA12 were almost exclusively found in strains of phylogenetic groups A and B1; and were present in animal and human faecal isolates. In contrast, dfrA17 was found in both faecal and urinary isolates and comprised strains from all phylogenetic groups. The sul1 and sul2 genes were equally prevalent among the isolates irrespective of the specimen source and phylogenetic group status. Pulsed-field gel electrophoresis analysis of isolates with identical cassette genes showed that they were genetically diverse. More animal faecal isolates carry class 1 integrons than human faecal and human urinary isolates, and the distribution of phylogenetic groups is common across animal and human faecal isolates but different from human urinary isolates. Commensal isolates from food-producing animals are an important reservoir for integrons carrying antibiotic resistance genes.

Distribution of integrons and SGI1 among antibiotic-resistant Salmonella enterica isolates of animal origin

In Salmonella enterica, resistance to antibiotics can be caused by the presence of SGI1, transposons or conjugative plasmids. In this study we were interested in the relative contribution of these genetic elements to the antibiotic resistance of S. enterica isolates collected within a single year in the Czech Republic from animal sources. Altogether 123 antibiotic-resistant isolates belonging to 16 different S. enterica serovars were classified into 3 groups according to the presence of SGI1 and the presence of integrons. The first group consisted of 62 strains in which neither SGI1 nor class 1 integron was detected. A high diversity among serovars and resistance phenotypes was found in this group. The second group consisted of 56 strains positive for both the SGI1 and class 1 integron, out of which 55 belonged to serovar Typhimurium and one to a nonmotile serovar [4,12] which harboured the SGI1-B variant. The third group comprised five strains which were positive for class 1 integron but negative for the SGI1. Sequencing of the integrons in these isolates identified integron with sat1 and aadA1 gene cassettes in S. Sandiego and S. Pullorum, dfrA1 and aadA1 gene cassettes in S. Typhimurium integron, and aadA21 gene cassette in S. Braenderub and S. Zanzibar.

Insights and inferences about integron evolution from genomic data

BackgroundIntegrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign DNA. These are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse suite of genes unrelated to pathogenicity. Here, we provide a systematic analysis of the distribution and diversity of integron intI genes and integron-containing bacteria.ResultsWe found integrons in 103 different pathogenic and non-pathogenic bacteria, in six major phyla. Integrons were widely scattered, and their presence was not confined to specific clades within bacterial orders. Nearly 1/3 of the intI genes that we identified were pseudogenes, containing either an internal stop codon or a frameshift mutation that would render the protein product non-functional. Additionally, 20% of bacteria contained more than one integrase gene. dN/dS ratios revealed mutational hotspots in clades of Vibrio and Shewanella intI genes. Finally, we characterized the gene cassettes associated with integrons in Methylobacillus flagellatus KT and Dechloromonas aromatica RCB, and found a heavy metal efflux gene as well as genes involved in protein folding and stability.ConclusionOur analysis suggests that the present distribution of integrons is due to multiple losses and gene transfer events. While, in some cases, the ability to integrate and excise foreign DNA may be selectively advantageous, the gain, loss, or rearrangment of gene cassettes could also be deleterious, selecting against functional integrases. Thus, such a high fraction of pseudogenes may suggest that the selective impact of integrons on genomes is variable, oscillating between beneficial and deleterious, possibly depending on environmental conditions.

Origin of Class 1 and 2 Integrons and Gene Cassettes in a Population-Based Sample of Uropathogenic Escherichia coli

The prevalence of urinary tract infections (UTI) caused by trimethoprim-sulfamethoxazole (TMP-SMX)-resistant Escherichia coli is increasing and varies geographically in the United States. Recent community-based UTI studies have demonstrated geographic clustering of an Escherichia coli clonal group, suggesting occurrence of a community outbreak of UTI. A large proportion of this clonal group (designated CgA) isolated from women in a California college community was found to be resistant to TMP-SMX. We wished to determine if the acquisition of TMP-SMX resistance by CgA occurred before or after the CgA strains were introduced into this community. Between October 1999 and January 2000 and between October 2000 and January 2001, 482 E. coli isolates were consecutively collected from the urine samples of women with UTI at a student health clinic and analyzed for determinants of TMP-SMX resistance. In particular, the distribution of integrons harboring resistance cassettes for TMP-SMX (dfr) was examined. Among 95 TMP-SMX-resistant isolates, 68 and 27 isolates carried class 1 and class 2 integrons, respectively. A class 1 integron was found in 25 (93%) of 27 TMP-SMX-resistant CgA isolates but in only 43 (63%) of 68 TMP-SMX-resistant non-CgA isolates (P < 0.001) and in none of 44 TMP-SMX-susceptible E. coli isolates (P < 0.0001). CgA strains carried only a single arrangement of class 1 gene cassettes (dfrA17-aadA5), while the non-clonal group strains carried nine different cassette arrangements. These results support the idea that CgA strains acquired their resistance at a common site prior to their spread to the college community.

Integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution.

Integrons are horizontal gene transfer (HGT) systems containing elements necessary for site-specific recombination and expression of foreign DNA. The overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. This report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. First, using culture-independent techniques, we explored the diversity of integrons and integron-transferred genes in heavy-metal-contaminated mine tailings. Using degenerate primers, we amplified integron integrase genes from the tailings. We discovered 14 previously undescribed integrase genes, including six novel gene lineages. In addition, we found 11 novel gene cassettes in this sample. One of the gene cassettes that we sequenced is similar to a gene that codes for a step in a pathway for nitroaromatic catabolism, a group of compounds associated with mining activity. This suggests that integrons may be important for gene transfer in response to selective pressures other than the presence of antibiotics. We also investigated the evolution of integrons by statistically comparing the phylogenies of 16S rRNA and integrase genes from the same organisms, using sequences from GenBank and various sequencing projects. We found significant differences between the organismal (16S rRNA) and integrase trees, and we suggest that these differences may be due to HGT.

Detection of integrons in worldwide nosocomial isolates of Acinetobacter spp.

OBJECTIVE: To examine the distribution of integrons in genotypically unrelated worldwide multiresistant clinical isolates of Acinetobacter spp. METHODS: The presence and genetic location of class 1, 2 and 3 integrons were examined in a genotypically heterogeneous collection of 25 nosocomial isolates of Acinetobacter spp., from 15 locations in 11 different countries worldwide, by hybridization and PCR-based methods. Class 1 integron structures were characterized genetically by a PCR mapping technique. RESULTS: Class 1 integrons were detected in 17 of the 25 Acinetobacter isolates examined. Only one isolate contained a class 2 integron. No class 3 integrons were detected. The integrons varied in size and in the number of inserted cassettes, but similar integrons were found in genotypically distinct isolates from different locations worldwide. These structures were integrated into the chromosome in all isolates where they were detected, although some integrons were capable of subsequent transfer or mobilization. Genes coding for aminoglycoside-modifying enzymes formed the predominant cassettes identified within the integrons. CONCLUSIONS: Clinical isolates of Acinetobacter spp. from diverse locations seem to share resistance mechanisms acquired from other genera by a variety of mechanisms, including dissemination of integrons. Once integrons are incorporated into the bacterial genome, Acinetobacter spp. are potentially able to act as a reservoir of resistance genes for other species and genera.