Insertion Sequence IS6110 Research Articles

A comparison of DNA extraction procedures for the detection of Mycobacterium ulcerans, the causative agent of Buruli ulcer, in clinical and environmental specimens

Mycobacterium ulcerans is the causative agent of Buruli ulcer, the third most common mycobacterial disease in humans after tuberculosis and leprosy. Although the disease is associated with aquatic ecosystems, cultivation of the bacillus from the environment is difficult to achieve. Therefore, at the moment, research is based on the detection by PCR of the insertion sequence IS 2404 present in M. ulcerans and some closely related mycobacteria. In the present study, we compared four DNA extraction methods for detection of M. ulcerans DNA, namely the one tube cell lysis and DNA extraction procedure (OT), the FastPrep procedure (FP), the modified Boom procedure (MB), and the Maxwell® 16 Procedure (M16). The methods were performed on serial dilutions of M. ulcerans, followed by PCR analysis with different PCR targets in M. ulcerans to determine the detection limit (DL) of each method. The purity of the extracted DNA and the time and effort needed were compared as well. All methods were performed on environmental specimens and the two best methods (MB and M16) were tested on clinical specimens for detection of M. ulcerans DNA. When comparing the DLs of the DNA extraction methods, the MB and M16 had a significantly lower DL than the OT and FP. For the different PCR targets, IS 2404 showed a significantly lower DL than mls A, MIRU1, MIRU5 and VNTR6. The FP and M16 were considerably faster than the MB and OT, while the purity of the DNA extracted with the MB was significantly higher than the DNA extracted with the other methods. The MB performed best on the environmental and clinical specimens. This comparative study shows that the modified Boom procedure, although lengthy, provides a better method of DNA extraction than the other methods tested for detection and identification of M. ulcerans in both clinical and environmental specimens.

Association between Mycobacterium avium subsp. paratuberculosis DNA in blood and cellular and humoral immune response in inflammatory bowel disease patients and controls

Similarities between human inflammatory bowel disease (IBD) and ruminant paratuberculosis have fueled a heated discussion on the role of Mycobacterium avium subsp. paratuberculosis (MAP) in the etiology of IBD. In order to determine microbiological and immunological evidence of an association between MAP and IBD, blood from 222 inflammatory bowel disease patients and 80 healthy donors from the Basque Country (Spain) were subjected to nested PCR for MAP-specific insertion sequence IS900, interferon-gamma (IFN-gamma) release test with PPA-3 MAP antigen (IFNMAP) or phosphate-buffered saline (IFNPBS), and antibody ELISA with PPA-3 MAP antigen (ABMAP). Highly significant differences in the proportion of PCR-positive IBD patients (17%) and healthy controls (43%) as well as lower IFNMAP and higher ABMAP and IFNPBS responses were observed. Treatment was associated with decreases in IFNMAP and PCR-positive frequency. These results indicate the existence of immune responses and treatment interactions with MAP that strongly support an etiological role of this agent in IBD.

Promising loci of variable numbers of tandem repeats for typing Beijing family Mycobacterium tuberculosis

We analysed the genotypes of 325 Mycobacterium tuberculosis clinical isolates obtained during 2002 throughout Japan. The genotyping methods included insertion sequence IS6110 RFLP, spoligotyping and variable number of tandem repeat (VNTR) analyses. Clustered isolates revealed by IS6110 RFLP analysis accounted for 18.5 % (60/325) of the isolates. Beijing genotype tuberculosis (TB) accounted for 73.8 % (240/325) of the isolates. Using VNTR, we analysed 35 loci, including 12 standard mycobacterial interspersed repetitive units and 4 exact tandem repeats. The discriminatory power of these 16 loci was low. Using VNTR analyses of the 35 loci, 12 loci (VNTRs 0424, 0960, 1955, 2074, 2163b, 2372, 2996, 3155, 3192, 3336, 4052 and 4156) were selected for the genotyping of Beijing genotype strains. Comparison of the discriminatory power of the 12-locus VNTR [Japan Anti-Tuberculosis Association (JATA)] to that of the 15-locus and 24-locus VNTRs proposed by Supply et al. (2006) showed that our established VNTR system was superior to the reported 15-locus VNTR and had almost equal discriminatory power to the 24-locus VNTR. This 12-locus VNTR (JATA) can therefore be used for TB genotyping in areas where Beijing family strains are dominant.

Description of an unusual class 2 integron in Shigella sonnei isolates in Senegal (sub-Saharan Africa)

Description of an unusual class 2 integron in Shigella sonnei isolates in Senegal (sub-Saharan Africa)

Neonatal pertussis presenting as acute bronchiolitis: direct detection of the Bordetella pertussis genome using loop-mediated isothermal amplification

We report a 28-day-old female infant with pertussis presenting as severe acute bronchiolitis with cyanosis. On admission, the patient's symptoms were similar to those of acute bronchiolitis. However, occasional apneic episodes with cyanosis and peripheral lymphocytosis suggested neonatal pertussis and prompted us to examine the presence of Bordetella pertussis using loop-mediated isothermal amplification (LAMP) based on the insertion sequence IS481. LAMP of the nasopharyngeal and intratracheal aspirates was positive for B. pertussis and a diagnosis of neonatal pertussis was made. As the clinical features of pertussis in neonates and early infancy are not characteristic, LAMP is a useful tool for rapid diagnosis of B. pertussis infection.

Insertion sequence-based cassette PCR: cultivation-independent isolation of γ-hexachlorocyclohexane-degrading genes from soil DNA

gamma-Hexachlorocyclohexane (gamma-HCH) is a highly chlorinated pesticide that has caused serious environmental problems. Based on the frequently observed association of insertion sequence IS6100 with lin genes for gamma-HCH degradation in several gamma-HCH-degrading bacterial strains isolated to date, DNA fragments flanked by two copies of IS6100 were amplified by nested polymerase chain reaction (PCR) technique using a DNA sample extracted from soil contaminated with HCH. Four distinct DNA fragments with sizes of 6.6, 2.6, 1.6, and 1.3 kb were obtained, three of which carried lin genes: the 6.6-kb fragment carried linD and linE as well as linR; the 2.6-kb fragment showed a truncated form of linF; and the 1.6-kb fragment carried linB. Our approach, named as insertion sequence (IS)-based cassette PCR, was successful in the isolation of the lin genes from HCH-contaminated soil without cultivation of host cells and is applicable for the culture-independent isolation of other functional genes bordered by other IS elements.

Spontaneous Amplification of the Actinorhodin Gene Cluster in Streptomyces coelicolor Involving Native Insertion Sequence IS 466

We observed a spontaneous amplification of the Streptomyces coelicolor chromosome, including genes encoding biosynthetic enzymes of the antibiotic actinorhodin. A new junction of two tandem segments has, inserted within it, a third copy of a transposable element existing in two places elsewhere in the chromosome, suggesting its involvement in the amplification mechanism.

First Isolation of Mycobacterium ulcerans from an Aquatic Environment: The End of a 60-Year Search?

First Isolation of Mycobacterium ulcerans from an Aquatic Environment: The End of a 60-Year Search?

Coexistence of qnrB4 and qnrS1 in a clinical strain of Klebsiella pneumoniae

To identify the location and the relationship, and to analyze the genetic background of 2 plasmid-mediated quinolone resistance genes, qnrB4 and qnrS1, carried by a clinical strain of Klebsiella pneumoniae (K pneumoniae). The plasmids carrying qnrB4 or qnrS1 were identified by Southern blotting. A HindIII fragment containing qnrB4 or qnrS1 was cloned into plasmid puc18 and sequenced. qnrB4 and qnrS1 were located on 2 different plasmids, pHS7 and pHS8, and were 180 and 45 kb in size, respectively. A transconjugant carrying plasmid pHS7 bearing qnrB4 and another transconjugant carrying pHS9 bearing qnrB4 and qnrS1 were obtained by conjugation. Plasmid pHS8 bearing qnrS1 was also transferred to J53 by transformation. The ciprofloxacin minimal inhibitory concentrations (MIC) for J53 transconjugants or the transformant carrying qnrB4 only, qnrS1 only, and both qnrB4 and qnrS1 were 0.19, 0.25, and 0.25 mg/L, respectively, while the parent clinical strain of K pneumoniae had a MIC of 0.75 mg/L. qnrB4 was located in a sul1-type integron with blaDHA-1, ampR and psp genes in upstream and insertion sequence IS26, and sap genes in downstream of qnrB4. qnrS1 was not located in an integron, but IS26 was found both upstream and downstream, and IS2 was found directly upstream of qnrS1. qnrB and qnrS can be harbored simultaneously by a single clinical strain of K pneumoniae. These 2 genes are carried by 2 different plasmids and have different genetic environments in plasmid DNA structure.

Molecular epidemiology of Mycobacterium tuberculosis in Lisbon

We conducted a molecular epidemiology study of Mycobacterium tuberculosis strains isolated from patients in Lisbon hospitals. We used restriction fragment length polymorphism (RFLP) to detect Lisbon family strains and to determine the genetic diversity of Mycobacterium tuberculosis strains isolated in Lisbon, through identification of the most important risk factors of tuberculosis transmission analysis, with the insertion sequence IS6110 as a probe to fingerprint isolates of Mycobacterium tuberculosis. 64.8% of the 290 Mycobacterium tuberculosis isolates were grouped in clusters. This figure was 60.7% if we excluded strains with five or fewer IS6110 copies. Multidrug-resistance was observed in 4.1% of the strains and they were all in clusters. Forty-five (18.2%) strains were included in the Lisbon family. Considering the relatively high percentage of strains in cluster detected in this study, we believe that active transmission is still taking place in Lisbon. Moreover, clusters of Lisbon strains represent the predominant strains circulating in Lisbon and are still related to drug resistance although presenting a lower percentage than that observed in previous studies.

Epidemiologia molecular de Mycobacterium tuberculosis em Lisboa

We conducted a molecular epidemiology study of Mycobacterium tuberculosis strains isolated from patients in Lisbon hospitals. We used restriction fragment length polymorphism (RFLP) to detect Lisbon family strains and to determine the genetic diversity of Mycobacterium tuberculosis strains isolated in Lisbon, through identification of the most important risk factors of tuberculosis transmission analysis, with the insertion sequence IS6110 as a probe to fingerprint isolates of Mycobacterium tuberculosis. 64.8% of the 290 Mycobacterium tuberculosis isolates were grouped in clusters. This figure was 60.7% if we excluded strains with five or fewer IS6110 copies. Multidrug-resistance was observed in 4.1% of the strains and they were all in clusters. Forty-five (18.2%) strains were included in the Lisbon family. Considering the relatively high percentage of strains in cluster detected in this study, we believe that active transmission is still taking place in Lisbon. Moreover, clusters of Lisbon strains represent the predominant strains circulating in Lisbon and are still related to drug resistance although presenting a lower percentage than that observed in previous studies.Rev Port Pneumol 2007; XIV (2): 239-259

Transposable modules generated by a single copy of insertion sequence ISPme1 and their influence on structure and evolution of natural plasmids of Paracoccus methylutens DM12.

We demonstrated that a single copy of insertion sequence ISPme1 can mobilize adjacent segments of genomic DNA of Paracoccus methylutens DM12, which leads to the generation of diverse transposable elements of various size and DNA contents. All elements (named transposable modules [TMos]) contain ISPme1 (placed at the 5' ends of the elements) and have variable 3'-end regions of between 0.5 and 5 kb. ISPme1 was shown to encode an outwardly oriented promoter, which may activate the transcription of genes transposed within TMos in evolutionarily distinct hosts. TMos may therefore be considered to be natural systems enabling gene capture, expression, and spread. However, unless these elements have been inserted into a highly conserved genetic context to enable a precise definition of their termini, it is extremely difficult or even impossible to identify them in bacterial genomes by in silico sequence analysis. We showed that TMos are present in the chromosome and plasmids of strain DM12. Sequence analysis of plasmid pMTH1 (32 kb) revealed that four TMos, previously identified with a trap vector, pMEC1, comprise 87% of its genome. Repeated TMos within pMTH1 may stimulate other structural rearrangements resulting from homologous recombination between long repeat sequences. This illustrates that TMos may play a significant role in shaping the structure of natural plasmids, which consequently may have a great impact on the evolution of plasmid genomes.

Microbiological and molecular analysis of Mycobabacterium tuberculosis complex strains isolated from patients with pulmonary tuberculosis

The aim of the study was to perform microbiological and molecular analysis of Mycobacterium tuberculosis complex strains isolated from patients with pulmonary tuberculosis originating from two different regions of Silesia voivodship in 2000 year. One of 135 strains subjected to the study lacked IS6110 insertion sequence. Its belonging to Mycobacterium tuberculosis complex was confirmedbypositivetestforspecificgyrBgenesequence. Strainresistanceanalysisrevealedthat in previously diagnosed patients resistance to streptomycin (16,2%) was more frequent than other. In contrast to never treated patients group where the prevalence of resistance to isoniazid was the most frequent (4,5%). In both group of patients resistance to rifampin or ethambutol was not detected. The multidrug resistance strains (4,6%) were detected only in the previously diagnosed group. Combined analysis of microbiological, epidemiological and molecular data are essential for creation of functional registry of patients infected with resistant Mycobacteria, giving the possibility of surveillance of drug resistant tuberculosis in populations. Pneumonol. Alergol. Pol. 2005, 73, 4-11 .

A One-Step DNA PCR-based Method for the Detection of Mycobacterium tuberculosis Complex Grown on Lowenstein-Jensen Media

A simple, rapid, and sensitive direct colony polymerase chain reaction (PCR) method to detect Mycobacterium tuberculosis complex grown on Lowenstein-Jensen media is described. M. tuberculosis is killed by treating it for 2 hours with 70% ethanol. Whole Mycobacterium cells inactivated by ethanol are added to a PCR mix that is designed to amplify the IS6110 insertion sequence. All 44 isolates tested were positive by this method. Our results show that PCR can be performed directly on bacterial colonies without the need for DNA extraction before PCR. Moreover, inactivation of M. tuberculosis before DNA amplification reduces the potential exposure of workers to viable M. tuberculosis. The exclusion of DNA extraction and inactivation of colonies before PCR provide a safe and low-cost preparatory technique for PCR reaction compared with expensive conventional extraction protocols that are based on chemical and enzymatic lysis, especially for countries with limited resources.

Genotipos de aislados de campo de Brucella abortus de distintas regiones geográficas de Chile

SuMMAry Bovine brucellosis is an endemic, zoonotic disease of high economic impact. The genetic identification of the prevalent Brucella abortus strains, the pathogen, is key to pursue further epidemiological strategies for disease control. The insertion sequence IS711 has been used as genetic marker to differentiate among Brucella species, members of the same specie and within the same biovar. We have analyzed the IS711- RFLP pattern for 46 B. abortus isolates, collected during the period of 1997-2005 from 16 different geographical areas of Chile. All isolates were previously identified by conventional techniques as B. abortus biovar 1. Of these, 87% shared the same IS711 DNA profile, while an 8.7 % corresponded to the pattern of RB51 vaccine strain. We report the finding of two new strains, not differentiated by AMOS PCR, which showed unreported patterns of IS711-RFLP.

JIC Award 2007

Abstract A Klebsiella pneumoniae strain, KU6500, which showed resistance to extendedspectrum β-lactams and produced the plasmid-encoded AmpC β-lactamase CMY-4, was identifi ed from clinical isolates in Japan. The aim of this study was to identify the mechanism of the high-level expression of bla CMY-4 . Sequence analysis indicated that the promoter element of Citrobacter freundii was conserved, but the insertion sequence IS Ecp1 coding with the putative promoter element, was inserted into the AmpR binding site. We determined the infl uence of the promoter on bla CMY-4 expression and β-lactam resistance. Two recombinant plasmids containing the entire bla CMY-4 gene, with or without the IS Ecp1 - mediated promoter sequences, were constructed and named pMWampC and pMWISEcp1, respectively. Escherichia coli DH5α (pMWISEcp1) was resistant to almost all β-lactams tested and E. coli DH5α (pMWampC) was susceptible to all, except for cephalothin. In addition, the activity of each promoter was measured by subcloning the element into a promoterless luciferase plasmid pGL3-Basic vector. The expression of the putative promoter of IS Ecp1 was 18.9-fold higher than that of C. freundii . These results suggest that the putative promoter element of IS Ecp1 is necessary for the high-level expression of bla CMY-4 to confer resistance to extended-spectrum cephalosporins.

Discriminative PCR of Bordetella pertussis from closely related Bordetella species using 16S rDNA Gene

Background : Polymerase-chain reaction (PCR) detection is useful to diagnosis of pertussis at initial stage because the growth rate of Bordetella pertussis (B. pertussis) is relatively slow. Currently, the primer set for the insertion sequence IS481 (BP primer) is used widely for PCR detection of B. pertussis. However, the cross-reactivity of BP primer set with Bordetella holmesii (B. holmesii) was reported recently. Therefore, discrimination of B. pertussis and B. holmesii is needed in PCR step. For this reason, we developed new primer sets based on 16S rDNA sequence for diagnostic use and estimated the efficiency of these new primer sets. Materials and Methods : The specific PCR primers were designed from the aligned sequence matrix of 16S rDNA genes of various Bordetella species. The specificity of designed primers were estimated using clinically important 4 Bordetella species, B. pertussis, B. holmesii, Bordetella parapertussis (B. parapertussis) and Bordetella bronchiseptica (B. bronchiseptica). The sensitivity to B. pertussis of designed primers was also estimated and compared with BP primer set. Results : As the results, the developed new primer set successfully distinguished B. pertussis and other Bordetella species containing B. holmesii. In the sensitivity assay, the detectable limits of 16S-F2/16S-R1 primer set for B. pertussis were revealed as 5 pg of genomic DNA and 10 5

PCR diagnostics of Mycobacterium tuberculosis in historic human long bone remains from 18th century burials in Kaiserebersdorf, Austria

BackgroundIn the present pilot study we applied recently published protocols for detecting Mycobacterium tuberculosis in human remains. We screened long bones from an 18th century cemetery and skulls from the anatomical "Weisbach collection" (19th century). In addition, besides the study of abundance of tuberculosis in inmates of the poorhouse itself, we were interested to test whether in this particular instance tuberculosis can be identified from cortical bones, which are rarely affected by tuberculosis, but mostly better preserved than the vertebral bodies or epiphyses.MethodThe DNA extractions from the bone samples were obtained following established ancient DNA protocols. Subsequently extracts were subjected to a series of PCR amplifications using primer pairs published previously [1,2]. PCR products of the expected size were subsequently sequenced.ResultsOnly primers targeting the repetitive IS6110 insertion sequence yielded PCR products of appropriate size. In one sample only (skull sample WB354 of the "Weisbach collection") sequence analysis revealed an authentic M. tuberculosis sequence that matched to a reference sequence from GenBank.ConclusionWith a variety of established PCR approaches we failed to detect M. tuberculosis DNA in historic human femurs from an 18th century cemetery relating to a poor house in Kaiserebersdorf, Austria. Our data may indicate that in this particular case, thoracic or lumbar vertebrae, i.e. bones that are severely affected by the disease, would be more suitable for molecular diagnostics than long bones. However, the unpredictable state of DNA preservation in bones from museum collections does not allow any general recommendation of any type of bone.

Mycobacterium ulcerans in mosquitoes captured during outbreak of Buruli ulcer, southeastern Australia.

Buruli ulcer (BU) occurs in >30 countries. The causative organism, Mycobacterium ulcerans, is acquired from the environment, but the exact mode of transmission is unknown. We investigated an outbreak of BU in a small coastal town in southeastern Australia and screened by PCR mosquitoes caught there. All cases of BU were confirmed by culture or PCR. Mosquitoes were trapped in multiple locations during a 26-month period. BU developed in 48 residents of Point Lonsdale/Queenscliff and 31 visitors from January 2001 through April 2007. We tested 11,504 mosquitoes trapped at Point Lonsdale (predominantly Aedes camptorhynchus). Forty-eight pools (5 species) were positive for insertion sequence IS2404 (maximum likelihood estimate 4.3/1,000), and we confirmed the presence of M. ulcerans in a subset of pools by detection of 3 additional PCR targets.

An evaluation of PCR methods to detect strains of Mycoplasma fermentans

A panel of 30 putative Mycoplasma fermentans strains, isolated from various sources including human, ovine and cell lines, were tested by a previously described polymerase chain reaction (PCR) to confirm their identity by amplification of a conserved 206 bp region of the insertion sequence IS 1550. In addition, the application of another PCR based on the major part of the IS 1550 element showed one or two products of different length (1144 and 1341 bp) enabling M. fermentans strains to be divided into two types designated as Type A and Type B. A PCR, which amplifies the macrophage activating lipopeptide gene ( malp), supported the identification of all the strains as M. fermentans. Thirteen other species of Mycoplasma from human sources gave negative results in these tests, with the exception of Mycoplasma orale, which was detected by both IS 1550-PCRs based on the major part and the conserved 206 bp region of the IS 1550 element. This study suggests that all M. fermentans isolates possess both the IS 1550 element and the malp gene. In contrast to the IS 1550, the malp gene is shown to be species-specific and the use of a malp PCR described here could prove to be a useful adjunct to IS 1550 detection as confirmation of the presence of M. fermentans in clinical material.