ISCR Elements Research Articles

Genomic insights into evolution of extensive drug resistance in Stenotrophomonas maltophilia complex

We report first complete genomic investigation of extensive drug resistance (XDR) in a nosocomial Stenotrophomonas maltophilia complex strain that is resistant to mainstream drugs (trimethoprim/sulfamethoxazole and levofloxacin). Comprehensive genomic investigation revealed its exclusive fourteen dynamic regions and highly enriched resistome comprising of two sulfonamide resistance genes on two diverse super-integrons of chromosomal origin. In addition, both these integrons harbour array of antibiotic resistance and commonly used disinfectant's resistance genes linked to ISCR elements. Isolation of a novel XDR strain from Indian tertiary care unit belonging to novel ST with diverse array of resistance genes on ISCR linked super-integrons indicates extent and nature of selection pressure in hospitals. Since, repetitive elements have major role in their spread and due to limitations of draft genomes, there is an urgent need to employ complete genome-based investigation for tracking the emergence of XDR at global level and designing strategies of antimicrobial stewardship and disinfection. ImportanceHospital settings in India have one of the highest usages of antimicrobials and a heavy patient load. We hereby report a novel clinical isolate of S. maltophilia complex with two super-integrons that harbour array of antimicrobial resistance genes along with biocide and heavy metal resistance genes. Further, the presence of ISCR type of transposable elements on both the integrons indicates their propensity to transfer resistome while their chromosomal origin suggests possibilities for further genomic/phenotypic complexities according to selection pressure. Such complex mobile cassettes in a novel strain is a potential threat to global health care. Hence, to understand the evolution of opportunistic nosocomial pathogen, there is an urgent need to employ cost-effective long read technologies to keep vigilance on novel and XDR pathogens in populous countries. There is also need for surveillance of the usage of disinfectants and other antimicrobials for environmental hygiene and linked/rapid co-evolution of XDR in nosocomial pathogens.Repositories: Complete genome sequence of Stenotrophomonas maltophilia SM866: CP031058.

Metagenomic exploration reveals a marked change in the river resistome and mobilome after treated wastewater discharges.

Mobile genetic elements (MGEs) are key agents in the spread of antibiotic resistance genes (ARGs) across environments. Here we used metagenomics to compare the river resistome (collection of all ARGs) and mobilome (e.g., integrases, transposases, integron integrases and insertion sequence common region "ISCR" elements) between samples collected upstream (n=6) and downstream (n=6) of an urban wastewater treatment plant (UWWTP). In comparison to upstream metagenomes, downstream metagenomes showed a drastic increase in the abundance of ARGs, as well as markers of MGEs, particularly integron integrases and ISCR elements. These changes were accompanied by a concomitant prevalence of 16S rRNA gene signatures of bacteria affiliated to families encompassing well-known human and animal pathogens. Our results confirm that chronic discharges of treated wastewater severely impact the river resistome affecting not only the abundance and diversity of ARGs but also their potential spread by enriching the river mobilome in a wide variety of MGEs.

Mobile ISCR elements: Structure, functions, and role in emergence, increase, and spread of blocks of bacterial multiple antibiotic resistance genes

The recently discovered method of horizontal distribution of bacterial genes with ISCR atypical insertion sequences is reviewed using the example of drug-resistance genes. The mechanism of transposition of such elements including rolling circle replication, formation of autonomous nonreplicable circular structures, and homologous recombination provides mobilization of any section of the adjacent DNA. ISCR elements represent a more powerful gene mobilization system than transposons and integrons and provide formation of groups of mobile genes, including antibiotic resistance genes of pathogenic bacteria. The structure and functions of ISCR elements are discussed together with their similarity and dissimilarity to IS91-like elements and their role in emergence of blocks of multiple antibiotic resistance genes and their contribution to evolution of bacteria and plasmids.

Combinatorial events of insertion sequences and ICE in Gram-negative bacteria

The emergence of antibiotic and antimicrobial resistance in Gram-negative bacteria is incremental and linked to genetic elements that function in a so-called 'one-ended transposition' manner, including ISEcp1, ISCR elements and Tn3-like transposons. The power of these elements lies in their inability to consistently recognize one of their own terminal sequences, while recognizing more genetically distant surrogate sequences. This has the effect of mobilizing the DNA sequence found adjacent to their initial location. In general, resistance in Gram-negatives is closely linked to a few one-off events. These include the capture of the class 1 integron by a Tn5090-like transposon; the formation of the 3' conserved segment (3'-CS); and the fusion of the ISCR1 element to the 3'-CS. The structures formed by these rare events have been massively amplified and disseminated in Gram-negative bacteria, but hitherto, are rarely found in Gram-positives. Such events dominate current resistance gene acquisition and are instrumental in the construction of large resistance gene islands on chromosomes and plasmids. Similar combinatorial events appear to have occurred between conjugative plasmids and phages constructing hybrid elements called integrative and conjugative elements or conjugative transposons. These elements are beginning to be closely linked to some of the more powerful resistance mechanisms such as the extended spectrum β-lactamases, metallo- and AmpC type β-lactamases. Antibiotic resistance in Gram-negative bacteria is dominated by unusual combinatorial mistakes of Insertion sequences and gene fusions which have been selected and amplified by antibiotic pressure enabling the formation of extended resistance islands.

IS CR Elements Are Key Players in IncA/C Plasmid Evolution

In the recent paper by Call et al. (1), the authors show that sequence analysis of their IncA/C plasmids revealed that antimicrobial resistance genes were grouped in four main regions in addition to the region that harbors the blaCMY gene in an otherwise highly related plasmid backbone structure. The authors show that the floR resistance region is found in all three plasmids as well as in the pSN254 plasmid and is found in close proximity to what the authors (and also a previous paper [9]) call insA. The authors also note that another antibiotic resistance gene cluster includes the resistance gene aadA which is found in three of these plasmids and is always found adjacent to an insertion sequence termed insE (9). These two insertions, insE and insA, are typical of insertion sequences previously designated ISCR elements (6, 7). ISCR elements are closely related to an unusual family of insertion sequences called the IS91 family (6, 7). These elements are known to move by a process called rolling-circle replication, and a function of this process is the concomitant movement of additional sequences found upstream of their transposase genes (5). To be specific, insE is indeed ISCR2, and insF is ISCR16 (8). ISCR elements are now recognized as powerful antibiotic resistance gene capture and movement systems that are also capable of constructing extended clusters of antibiotic resistance genes on plasmids as well as on chromosomes (7). The IncA/C plasmid group is now known to be very widely distributed both geographically and in many species of bacteria because of the plasmids' promiscuous behavior (3, 4). The IncA/C reference plasmid, pRA1, isolated in 1971 from the fish pathogen Aeromonas hydrophila harbors ISCR2 (2), indicating that this element has been closely involved in recruiting antibiotic resistance genes with IncA/C plasmids for some time. ISCR2 is often found in close proximity to the sul2 gene and a truncated glmM gene as a conserved resistance array among IncA/C plasmids; ISCR2 is often called an ISVsa3-like IS element or simply orfA (2). Interestingly, a recent publication has indicated that the ICE element SXT shares a common ancestor with the IncA/C plasmids (2), and ISCR2 together with truncated copies of this element are always found as part as SXT, implicating ISCR2 in the construction of this element (6). The ISCR16 element appears to be a more recent addition to the IncA/C plasmids and has been found in only three plasmids so far and always adjacent to groEL or groES gene(s) (8). This also is very interesting as this element and the closely related elements ISCR3 and ISCR4 are also found adjacent to sections of groEL as well as resistance genes, which has allowed us to track the evolutionary history of this element (8). Therefore, it appears that ISCR elements are key players in the recent evolution of the IncA/C plasmid group. Furthermore, gene capture systems such as ISCR elements allied with the promiscuous nature of IncA/C plasmids provides a new and powerful combination for rapid dissemination of antibiotic resistance genes.

First Report of the Metallo-β-Lactamase SPM-1 in Europe

In 1997, the first SPM-1-positive Pseudomonas aeruginosa isolate (48-1997A) from a 4-year-old leukemic girl in San Paulo, Brazil, was characterized. bla SPM-1 was flanked by two IS CR elements, designated IS CR4 , and probably transposes via a mechanism called rolling-circle replication ([8][1]).

Evolution of the ISCR3 group of ISCR elements.

The ISCR elements ISCR3, ISCR4, ISCR5, ISCR14, and ISCR16 all share a percent G+C of 68 to 69%. They also share between 75% and 97% identity in their transposase open reading frames. Furthermore, with the exception of ISCR5, they are all found adjacent to sections of groEL that display the highest identity to the same gene from Xanthomonas spp. The combined information is consistent with the descent from an ancestral ISCR element in a Xanthomonas-like organism.

First detection of plasmid-mediated quinolone resistance in the community setting and in hospitalized patients in Switzerland

1. Eckert C, Gautier V, Arlet G. DNA sequence analysis of the genetic environment of blaCTX-M genes. J Antimicrob Chemother 2006; 57: 14–23. 2. Canton R, Coque TM. The CTX-M b-lactamase pandemic. Curr Opin Microbiol 2006; 9: 466–75. 3. Partridge SR, Hall RM. In34, a complex In5 family class 1 integron containing orf513 and dfrA10. Antimicrob Agents Chemother 2003; 47: 342–9. 4. Valverde A, Canton R, Galan JC et al. In117, an unusual In0-like class 1 integron containing CR1 and blaCTX-M-2 and associated with a Tn21-like element. Antimicrob Agents Chemother 2006; 50: 799–802. 5. Arduino SM, Roy PH, Jacoby GA et al. blaCTX-M-2 is located in an unusual class 1 integron (In35) which includes Orf513. Antimicrob Agents Chemother 2002; 46: 2303–6. 6. Jarlier V, Nicolas MH, Fournier G et al. Extended broad-spectrum b-lactamases conferring transferable resistance to newer b-lactam agents in Enterobacteriaceae: hospital prevalence and susceptibility patterns. Rev Infect Dis 1988; 10: 867–78. 7. Toleman MA, Bennett PM, Walsh TR. ISCR elements: novel gene-capturing systems of the 21st century? Microbiol Mol Biol Rev 2006; 70: 296–316.

Comparison of Etest with agar dilution for testing the susceptibility of Pseudomonas aeruginosa and other multidrug-resistant bacteria to colistin

ISCR elements in S. maltophilia. Therefore, the possibility of trimethoprim resistance genes located on ISCR elements beyond class 1 integrons in clinical isolates in the present study merits further elucidation. However, chromosome-mediated trimethoprim resistance cannot be ruled out. Furthermore, selection of QAC resistance in the natural environment has the potential to co-select for antibiotic resistance. In this study, the incidence of trimethoprim/sulfamethoxazole resistance was significantly associated with the presence of QAC resistance genes carried on integrons. Therefore, it is possible that introduction of QAC into hospital settings to prevent bacterial infection might enhance the selection of trimethoprim/ sulfamethoxazole-resistant isolates. In conclusion, this study indicates that isolates with resistance to trimethoprim/sulfamethoxazole are associated with the presence of class 1 integrons and QAC resistance genes located on integrons.