Antibiotic resistance in the ECOR collection: integrons and identification of a novel aad gene

Integrons containing the VIM-2 metallo-beta-lactamase gene among imipenem-resistant Pseudomonas aeruginosa strains from different Chinese hospitals

A total of 140 nonrepetitive strains of imipenem-resistant Pseudomonas aeruginosa were isolated from five different Chinese hospitals. Fourteen isolates were confirmed to contain the VIM-2 metallo-beta-lactamase gene. Twelve isolates harbored two kinds of class 1 integron, containing both VIM-2- and aminoglycoside-resistant genes.

Incidence of class 1 integrons in multiple antibiotic-resistant Gram-negative copiotrophic bacteria from the River Torsa in India

The presence of class 1 integrons in multiple-antibiotic-resistant (MAR) Gram-negative copiotrophic bacteria from the River Torsa in India was detected using a polymerase chain reaction (PCR)-based screening method. Among 100 isolates that were resistant to at least five of the twelve antibiotics tested, 40 carried class 1 integrons, with inserted DNA regions of 0.7-3.2 kb. Carriage of integrons in strains of higher MAR index was found to be statistically significant. DNA sequencing was used to identify the genetic content of the integron-variable regions. In addition to the identification of gene cassettes dfrA1, dfrA5, dfrA7, dfrA17 and a variant of dfrA12 for trimethoprim, aac(6')-Ib for amikacin and tobramycin and aadA1 and aadA6 for streptomycin and spectinomycin resistance, a novel ORF predicted from a sequence of Morganella sp. TR 90 bearing homology with the Vibrio cholerae dfrA1 gene cassette was characterized. To our knowledge, this is the first report of the incidence and abundance of class 1 integrons in copiotrophic river water bacteria from India.

In117, an unusual In0-like class 1 integron containing CR1 and bla(CTX-M-2) and associated with a Tn21-like element

An unusual In0-like class 1 integron containing a common region that includes the putative recombinase gene named orf513 (CR1) and bla(CTX-M-2) was characterized from Escherichia coli. The integron contained an unusual gene cassette array, estX-aadA1, embedded between the 5'-conserved segment (5'-CS) and 3'-CS1 regions and was flanked by mer-Tn21 sequences downstream of the tni truncated module. This element constitutes one of the few examples of CR1-bearing class 1 integrons that has been fully characterized.

Multiplex PCR for screening of integrons in bacterial lysates

Bacterial integrons are a useful PCR amplification target in epidemiological surveys of bacterial antibiotic resistance, and a variety of primers have been published. We describe multiplex PCR methodology to test for classes 1, 2 and 3 integron-associated integrases in boiled lysates of Gram-negative bacteria. We report on performance in Acinetobacter spp. (n=50), Enterobacteriaceae (n=76), Pseudomonas aeruginosa (n=15), Bacteroidesspp. (n=69), and in undifferentiated mixed cultures derived from perineal swabs (n=50) and endotracheal aspirates (n=8). This method achieved 100% sensitivity and specificity in simple lysates made from a range of bacteria, without requiring DNA extraction, and is recommended as an efficient screening tool for surveys of integron cassettes.

Integron content of extended-spectrum-beta-lactamase-producing Escherichia coli strains over 12 years in a single hospital in Madrid, Spain

The contribution of integrons to the dissemination of extended-spectrum beta-lactamases (ESBL) was analyzed on all ESBL-producing Escherichia coli isolates from 1988 to 2000 at Ramon y Cajal Hospital. We studied 133 E. coli pulsed-field gel electrophoresis types: (i) 52 ESBL-producing clinical strains (C-ESBL) (16 TEM, 9 SHV, 21 CTX-M-9, 1 CTX-M-14, and 5 CTX-M-10); (ii) 43 non-ESBL blood clinical strains (C-nESBL); and (iii) 38 non-ESBL fecal isolates from healthy volunteers (V-nESBL). Class 1 integrons were more common among C-ESBL (67%) than among C-nESBL (40%) or V-nESBL (26%) (P < 0.001) due to the high number of strains with bla(CTX-M-9), which is linked to an In6-like class 1 integron. Without this bias, class 1 integron occurrence would be similar in C-ESBL and C-nESBL groups (47% versus 40%). Occurrence of class 2 integrons was similar among clinical and community isolates (13 to 18%). No isolates contained class 3 integrons. The relatively low rate of class 1 integrons within transferable elements carrying bla(TEM) (23%) or bla(SHV) (33%) and the absence of class 2 integrons in all ESBL transconjugants mirror the assembly of translocative pieces containing bla(TEM) or bla(SHV) on local available transferable elements lacking integrons. The low diversity of class 1 integrons (seven types recovered in all groups) might indicate a wide dissemination of specific genetic elements in which they are located. In our environment, the spread of genetic elements encoding ESBL has no major impact on the dispersion of integrons, nor do integrons have a major impact on the spread of ESBL, except when bla(ESBL) genes are within an integron platform such as bla(CTX-M-9).

New integron-associated gene cassette encoding a 3-N-aminoglycoside acetyltransferase

A fifth gene cassette containing an aacC gene, aacCA5, was found in an aacCA5-aadA7 cassette array in a class 1 integron isolated from a multiply drug resistant Salmonella enterica serovar Kentucky strain. The AacC-A5 or AAC(3)-Ie acetyltransferase encoded by aacCA5 is related to other AAC(3)-I enzymes and confers resistance to gentamicin.

Dissemination of sulfonamide resistance genes (sul1, sul2, and sul3) in Portuguese Salmonella enterica strains and relation with integrons

In 200 sulfonamide-resistant Portuguese Salmonella isolates, 152 sul1, 74 sul2, and 14 sul3 genes were detected. Class 1 integrons were always associated with sul genes, including sul3 alone in some isolates. The sul3 gene has been identified in isolates from different sources and serotypes, which also carried a class 1 integron with aadA and dfrA gene cassettes.

Mechanisms of resistance in multiple-antibiotic-resistant Escherichia coli strains of human, animal, and food origins

Seventeen multiple-antibiotic-resistant nonpathogenic Escherichia coli strains of human, animal, and food origins showed a wide variety of antibiotic resistance genes, many of them carried by class 1 and class 2 integrons. Amino acid changes in MarR and mutations in marO were identified for 15 and 14 E. coli strains, respectively.

Variant Salmonella genomic island 1 antibiotic resistance gene cluster containing a novel 3'-N-aminoglycoside acetyltransferase gene cassette, aac(3)-Id, in Salmonella enterica serovar newport

Salmonella genomic island 1 (SGI1) harbors an antibiotic resistance gene cluster and was previously identified in the multidrug-resistant Salmonella enterica serovars Typhimurium DT104, Agona, Paratyphi B, and Albany. This antibiotic resistance gene cluster is a complex class 1 integron and most often confers resistance to ampicillin (Ap), chloramphenicol (Cm)/florfenicol (Ff), streptomycin (Sm)/spectinomycin (Sp), sulfonamides (Su), and tetracycline (Tc) (ApCmFfSmSpSuTc profile). Recently, variant SGI1 antibiotic resistance gene clusters conferring different antibiotic resistance profiles have been identified in several S. enterica serovars and were classified as SGI1-A to -G. We identified a new variant SGI1 antibiotic resistance gene cluster in two multidrug-resistant S. enterica serovar Newport strains isolated from humans in France. In these strains, the Sm/Sp resistance gene cassette aadA2 inserted at the first attI1 site was replaced by two other aminoglycoside resistance gene cassettes. The first one contains a new resistance gene encoding an AAC(3)-I aminoglycoside 3-N-acetyltransferase that confers resistance to gentamicin (Gm) and sisomicin (Sc). This gene has been named aac(3)-Id. The second one harbors the Sm/Sp resistance gene aadA7. This gene cassette replacement in the SGI1 complex integron of serovar Newport strains constitutes a new variant SGI1 antibiotic resistance gene cluster named SGI1-H. The occurrence of SGI1 in different S. enterica serovars, now including serovar Newport, strengthens the hypothesis of horizontal transfer of SGI1.

Integron-associated antibiotic resistance in enteroaggregative and enteroinvasive Escherichia coli

Ten enteroinvasive (EIEC) and 25 enteroaggregative (EaggEC) E. coli strains isolated from Senegalese patients were analyzed for their integron content. All strains were resistant to at least two antibiotics. Four EIEC and 15 EaggEC were found to carry a class 1 integron. An identical integron carrying a single dfrA5 cassette, conferring resistance to trimethoprim, was identified in all four EIEC strains. Five EaggEC strains harbored an integron with a single cassette, dfrA7, while the remaining 10 strains carried two integrons, one with a single cassette, aadA1a conferring resistance to streptomycin and spectinomycin, and the second one bearing two cassettes, dfrA13 and oxa5, the later being a beta-lactam resistance cassette. The presence of these integrons is worrying, because trimethoprim is largely used for diarrheal disease therapy in Africa. Thus, the presence of integrons in diarrheagenic strains is of public health importance because a limited number of antibiotics are available in developing countries.

Prevalence and characterization of integrons in blood culture Enterobacteriaceae and gastrointestinal Escherichia coli in Norway and reporting of a novel class 1 integron-located lincosamide resistance gene

Background

Class 1 integrons contain genetic elements for site-specific recombination, capture and mobilization of resistance genes. Studies investigating the prevalence, distribution and types of integron located resistance genes are important for surveillance of antimicrobial resistance and to understand resistance development at the molecular level.

Methods

We determined the prevalence and genetic content of class 1 integrons in Enterobacteriaceae (strain collection 1, n = 192) and E. coli (strain collection 2, n = 53) from bloodstream infections in patients from six Norwegian hospitals by molecular techniques. Class 1 integrons were also characterized in 54 randomly selected multiresistant E. coli isolates from gastrointestinal human infections (strain collection 3).

Results

Class 1 integrons were present in 10.9% of the Enterobacteriaceae blood culture isolates of collection 1, all but one (S. Typhi) being E. coli. Data indicated variations in class 1 integron prevalence between hospitals. Class 1 integrons were present in 37% and 34% of the resistant blood culture isolates (collection 1 and 2, respectively) and in 42% of the resistant gastrointestinal E. coli. We detected a total of 10 distinct integron cassette PCR amplicons that varied in size between 0.15 kb and 2.2 kb and contained between zero and three resistance genes. Cassettes encoding resistance to trimethoprim and aminoglycosides were most common. We identified and characterized a novel plasmid-located integron with a cassette-bound novel gene (linF) located downstream of an aadA2 gene cassette. The linF gene encoded a putative 273 aa lincosamide nucleotidyltransferase resistance protein and conferred resistance to lincomycin and clindamycin. The deduced LinF amino acid sequence displayed approximately 35% identity to the Enterococcus faecium and Enterococcus faecalis nucleotidyl transferases encoded by linB and linB'

Conclusions

The present study demonstrated an overall low and stable prevalence of class 1 integron gene cassettes in clinical Enterobacteriaceae and E. coli isolates in Norway. Characterization of the novel lincosamide resistance gene extends the growing list of class 1 integron gene cassettes that confer resistance to an increasing number of antibiotics.

Resistance integrons and super-integrons

Integrons are genetic elements composed of a gene encoding an integrase, gene cassettes and an integration site for the gene cassettes (att). The integrase excises and integrates the gene cassettes from and into the integron, but integrons themselves are not mobile. Two groups of integrons are known: resistance integrons and super-integrons. Nearly all known gene cassettes from resistance integrons encode resistance to antibiotics or disinfectants. These integrons are found on transposons, plasmids and the bacterial chromosome. Gene cassettes in super-integrons encode a variety of different functions. Super-integrons are located on the bacterial chromosome. More than 100 gene cassettes may be present, in contrast to resistance integrons where less than ten cassettes are present. Many species harbour super-integrons, which are species-specific, whereas particular resistance integrons can be found in a variety of species. The gene cassettes in resistance integrons probably originated from super-integrons. In the last few years, a variety of new gene cassettes have been described. Many of these encode resistance against newer antibiotics such as cephalosporins and carbapenems. Resistance integrons have been found in isolates from a wide variety of sources, including food.

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.

Newdfr2Gene As a Single-Gene Cassette in a Class 1 Integron from a Trimethoprim-ResistantEscherichia coliIsolate

Resistance to trimethoprim among Enterobacteriaceae is increasing in spite of a stable or decreasing use of the drug. Integrons are common among these bacteria and many of them contain dfr gene cassettes. A clinical isolate of Escherichia coli from a urine specimen obtained at the Karolinska Hospital in Stockholm was resistant to trimethoprim, ampicillin, sulfonamides, chloramphenicol, streptomycin, and norfloxacin. PCR analysis with primers specific for the 5' and 3' sequences flanking the cassettes in class 1 integrons, detected a very short cassette region of no more than approximately 400 bp. Sequence analysis of the entire integron was performed, revealing a single-gene cassette of 411 bp encoding a new dihydrofolate reductase. The gene cassette comprised all sequences between the flanking conserved sequences and encoded only 78 amino acids. By homology it belongs to the unique group of dfr2 gene cassettes and being the fourth described gene in this group the new gene is called dfr2d. The enzymes encoded by the dfr2 genes are 67% identical and are not related to any other known dfr gene products.

Versatility of aminoglycosides and prospects for their future

Aminoglycoside antibiotics have had a major impact on our ability to treat bacterial infections for the past half century. Whereas the interest in these versatile antibiotics continues to be high, their clinical utility has been compromised by widespread instances of resistance. The multitude of mechanisms of resistance is disconcerting but also illuminates how nature can manifest resistance when bacteria are confronted by antibiotics. This article reviews the most recent knowledge about the mechanisms of aminoglycoside action and the mechanisms of resistance to these antibiotics.

Antimicrobial resistance markers of class 1 and class 2 integron-bearing Escherichia coli from irrigation water and sediments

Municipal and agricultural pollution affects the Rio Grande, a river that separates the United States from Mexico. Three hundred and twenty-two Escherichia coli isolates were examined for multiple antibiotic resistance phenotypes and the prevalence of class 1 and class 2 integron sequences. Thirty-two (10%) of the isolates were resistant to multiple antibiotics. Four (13%) of these isolates contained class 1-specific integron sequences; one isolate contained class 2 integron-specific sequences. Sequencing showed that the class 1 integron-bearing strain contained two distinct gene cassettes, sat-1 and aadA. Although three of the four class 1 integron-bearing strains harbored the aadA sequence, none of the strains was phenotypically resistant to streptomycin. These results suggest that integron-bearing E. coli strains can be present in contaminated irrigation canals and that these isolates may not express these resistance markers.

Analysis of gene cassettes of streptomycin-spectinomycin resistance of Hungarian Salmonella enterica serotype Typhimurium strains

By PCR using the ant(3")-Ia primer pair the aadA gene was detected in 34 streptomycin- and spectinomycin-resistant Salmonella enterica serotype Typhimurium strains. Out of them 12 belonged to DT104 and 22 to non-DT104 phage type. Using different primer combinations it was demonstrated that this gene was integron-associated in all cases: in the DT104 strains it was generally contained by a 1 kb integron while in the majority of the non-DT104 strains by a 2.05 kb (less often by a 1.9 or 1 kb) integron. In the case of integrons carrying multiple cassettes the cassette containing the aadA gene was located closer to the 3' end of the integron. The aadA genes of DT104 and non-DT104 strains were different: in the former group the aadA2 gene, while in the latter group (constituted by strains of five different phages types as well as unclassifiable and untypable strains) the aadA1 gene could be identified. The RH50/RH51 primer pair described by Collis and Hall (1992) proved to be suitable for rapid discrimination between the aadA1 and aadA2 genes on the basis that the RH51 primer bound exclusively to the aadA2 gene.

Integron-associated antibiotic resistance in Salmonella enterica serovar typhi from Asia

Eighteen of 25 isolates of Salmonella enterica serovar Typhi were multidrug resistant and contained class 1 integrons with a single cassette, dfrVII or aadA1. The dfrVII-containing integron was likely borne on an IncHI1 plasmid. Salmonella serovar Typhi could become resistant to broad-spectrum cephalosporins by integrating cassettes, such as veb-1, a common cassette in Asia.

Mercury resistance determinants related to Tn21, Tn1696, and Tn5053 in enterobacteria from the preantibiotic era

Three mer transposons from the Murray collection of preantibiotic enterobacteria show >99% sequence identity to current isolates. Tn5073 is most closely related to Tn5036 and Tn1696, and Tn5074 is most closely related to Tn5053. Tn5075 is most closely related to Tn21 but lacks integron In2 and is flanked by insertion elements.

Detection and characterization of class 1 integrons in enterohemorrhagic Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) strains isolated from humans, cattle, and food and belonging to serogroups O26 (7 strains), O111 (19 strains), and O157 (70 strains) were examined for susceptibility to 11 antimicrobial drugs. Fifty-nine strains showing resistance to at least one of the drugs were examined by PCR for the presence of class 1 integrons, which were identified in 17 strains. Integrons were found more frequently in strains belonging to serogroups O111 and O26 than in the O157 isolates. DNA sequence analysis demonstrated that most of the integrons contained the aadA1 gene cassette conferring resistance to streptomycin/ spectinomycin, alone or associated with the drfA1 gene cassette conferring resistance to trimethoprim. One integron, identified in a O157:H7 strain, carried the aadA2 and dfrA12 gene cassettes, conferring resistance to streptomycin/spectinomycin and trimethoprim, and the open reading frame F (OrfF) encoding unknown functions. Most of the integrons were carried by Tn21 derivative transposons and were transferable by conjugation to an E. coli K-12 strain. In conclusion, integrons and antibiotic resistance genes can be frequently found in EHEC strains, particularly E. coli O111 and E. coli O26, and their presence could complicate therapeutic trials.

A multiresistant clone of Shiga toxin-producing Escherichia coli O118:[H16] is spread in cattle and humans over different European countries

Multiresistant Shiga toxin-producing Escherichia coli (STEC) O118:H16 and O118 nonmotile strains (designated O118:[H16]) were detected by examination of 171 STEC isolates for their antimicrobial sensitivity. Of 48 STEC O118:[H16] strains, 98% were resistant to sulfonamide, 96% were resistant to streptomycin, 79% were resistant to kanamycin, 75% were resistant to tetracycline, 67% were resistant to ampicillin, 60% were resistant to chloramphenicol, 48% were resistant to trimethoprim, and 10% each were resistant to gentamicin and nalidixic acid. Nalidixic acid resistance and reduced susceptibility to ciprofloxacin were associated with the mutation gyrA(LEU-83). The STEC O118:[H16] strains were found to belong to a single genetic clone as investigated by multilocus enzyme electrophoresis and by multilocus sequence analysis of E. coli housekeeping genes. The STEC O118:[H16] strains originated from humans and cattle and were isolated in seven different countries of Europe between 1986 and 1999. Strains showing multiresistance to up to eight different antimicrobials predominated among the more recent STEC O118:[H16] strains. The genes in parentheses were associated with resistance to kanamycin (aphA1-Ia), chloramphenicol (catA1), tetracycline [tet(A)], and ampicillin (bla(TEM-1)). Class 1 integrons containing sulI (sulfonamide resistance), aadA1a (streptomycin resistance), or dfrA1 (trimethoprim resistance)-aadA1a gene cassettes were detected in 28 strains. The bla(TEM-1b) gene was present in 18 of 21 strains that were examined by nucleotide sequencing. Class 1 integrons and bla(TEM) genes were localized on plasmids and/or on the chromosome in different STEC O118:[H16] strains. Hybridization of XbaI-digested chromosomal DNA separated by pulsed-field gel electrophoresis revealed that bla(TEM) genes were integrated at different positions in the chromosome of STEC O118:[H16] strains that could have occurred by Tn2 insertion. Our data suggest that strains belonging to the STEC O118:[H16] clonal group have a characteristic propensity for acquisition and maintenance of resistance determinants, thus contrasting to STEC belonging to other serotypes.

Class 1 integron containing a new gene cassette, aadA10, associated with Tn1404 from R151

The carbenicillin, gentamicin, kanamycin, streptomycin, spectinomycin, sulfonamide, and tobramycin resistance determinants found on Pseudomonas aeruginosa plasmid R151 have previously been shown to translocate to another plasmid, R388, and it was inferred that a transposon, Tn1404, carried the resistance determinants. Sequencing of the cassette array from the plasmid known as R388::Tn1404 revealed two known gene cassettes, oxa10 and aadB, and a previously unidentified cassette determining resistance to streptomycin and spectinomycin, here designated aadA10, in the order oxa10-aadB-aadA10. These cassettes replaced the dfrB2-orfA cassette array of R388, indicating that movement of the resistance determinants from R151 to R388 resulted from recombinational exchange between two class 1 integrons rather than transposition. The AadA10 protein is most closely related to AadA6 (85% identical) and AadA7 (80% identical). The aadA10 cassette found here has only a simple site containing a 7-bp spacer derived from attI1 in place of a 59-base element and is likely to represent a derivative of the complete cassette. IntI1-mediated deletion of the aadA10 cassette was not detected, indicating that this single simple site is either inactive or only weakly active.

Generally overlooked fundamentals of bacterial genetics and ecology

Several important aspects of the antimicrobial resistance problem have not been treated extensively in previous monographs on this subject. This section very briefly updates information on these topics and suggests how this information is of value in assessing the contributions of human and agricultural use of antimicrobial agents on the problem of increasing antimicrobial resistance. The overall themes are (1) that propagation of resistance is an ecological problem, and thus (2) that ameliorating this problem requires recognition of long-established information on the commensal microbiota of mammals, as well as that of recent molecular understanding of the genetic agents involved in the movement of resistance genes.

Biocides, drug resistance and microbial evolution

Antimicrobial biocides are widely used in critical human health situations in which rigorous infection control is needed. Increasingly, biocidal agents are being marketed for home use, although there is little evidence that they significantly improve home hygiene. Biocide resistance mechanisms share many themes with antibiotic resistance mechanisms.

The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons

Integrons are genetic elements that acquire and exchange exogenous DNA, known as gene cassettes, by a site-specific recombination mechanism. Characterized gene cassettes consist of a target recombination sequence (attC site) usually associated with a single open reading frame coding for an antibiotic resistance determinant. The affiliation of multiresistant integrons (MRIs), which contain various combinations of antibiotic resistance gene cassettes, with transferable elements underlies the rapid evolution of multidrug resistance among diverse Gram-negative bacteria. Yet the origin of MRIs remains unknown. Recently, a chromosomal super-integron (SI) harboring hundreds of cassettes was identified in the Vibrio cholerae genome. Here, we demonstrate that the activity of its associated integrase is identical to that of the MRI integrase, IntI1. We have also identified equivalent integron superstructures in nine distinct genera throughout the gamma-proteobacterial radiation. Phylogenetic analysis revealed that the evolutionary history of the system paralleled that of the radiation, indicating that integrons are ancient structures. The attC sites of the 63 antibiotic-resistance gene cassettes identified thus far in MRIs are highly variable. Strikingly, one-fifth of these were virtually identical to the highly related yet species-specific attC sites of the SIs described here. Furthermore, antimicrobial resistance homologues were identified among the thousands of genes entrapped by these SIs. Because the gene cassettes of SIs are substrates for MRIs, these data identify SIs as the source of contemporary MRIs and their cassettes. However, our demonstration of the metabolic functions, beyond antibiotic resistance and virulence, of three distinct SI gene cassettes indicates that integrons function as a general gene-capture system for bacterial innovation.

Long-term shifts in patterns of antibiotic resistance in enteric bacteria

Several mechanisms are responsible for the ability of microorganisms to tolerate antibiotics, and the incidence of resistance to these compounds within bacterial species has increased since the commercial use of antibiotics became widespread. To establish the extent of and changes in the diversity of antibiotic resistance patterns in natural populations, we determined the MICs of five antibiotics for collections of enteric bacteria isolated from diverse hosts and geographic locations and during periods before and after commercial application of antibiotics began. All of the pre-antibiotic era strains were susceptible to high levels of these antibiotics, whereas 20% of strains from contemporary populations of Escherichia coli and Salmonella enterica displayed high-level resistance to at least one of the antibiotics. In addition to the increase in the frequency of high-level resistance, background levels, conferred by genes providing nonspecific low-level resistance to multiple antibiotics, were significantly higher among contemporary strains. Changes in the incidence and levels of antibiotic resistance are not confined to particular segments of the bacterial population and reflect responses to the increased exposure of bacteria to antimicrobial compounds over the past several decades.

Integrons: an antibiotic resistance gene capture and expression system

Bacteria can transfer genetic information to provide themselves with protection against most antibiotics. The acquisition of resistance gene arrays involves genetic mobile elements like plasmids and transposons. Another class of genetic structures, termed integrons, have been described and contain one or more gene cassettes located at a specific site. Integrons are defined by an intl gene encoding an integrase, a recombination site attl and a strong promoter. At least six classes of integrons have been determined according to their intl gene. Classes 1, 2 and 3 are the most studied and are largely implicated in the dissemination of antibiotic resistance. A gene cassette includes an open reading frame and, at the 3'-end, a recombination site attC. Integration or excision of cassettes occur by a site-specific recombination mechanism catalyzed by the integrase. However, insertion can occur, albeit rarely, at non-specific sites leading to a stable situation for the cassette. Cassettes are transcribed from the common promoter located in the 5'-conserved segment and expression of distal genes is reduced by the presence of upstream cassettes. Most gene cassettes encode antibiotic resistant determinants but antiseptic resistant genes have also been described. Integrons seem to have a major role in the spread of multidrug resistance in gram-negative bacteria but integrons in gram-positive bacteria were described recently. Moreover, the finding of super-integrons with gene-cassettes coding for other determinants (biochemical functions, virulence factors) in Vibrio isolates dating from 1888 suggests the likely implication of this multicomponent cassette-integron system in bacterial genome evolution before the antibiotic era and to a greater extent than initially believed.