Predominant VNTR family of strains of Mycobacterium tuberculosis isolated from South Asian patients.

SETTING: Despite the low incidence of tuberculosis in the UK, some minority ethnic groups, particularly those originating from South Asia, experience very high incidence rates. OBJECTIVE: Comparison of the variable number tandem repeat (VNTR) profiles of strains of Mycobacterium tuberculosis circulating in an immigrant community in the UK with those found in the country of ethnic origin. DESIGN: Isolates of M. tuberculosis were collected from samples obtained from patients attending clinics in Leeds and Bradford, UK and Rawalpindi, Pakistan. Strains were compared using VNTR analysis and mixed-linker PCR. RESULTS: Comparison of VNTR profiles found that one profile (42235) represented 37% of patient isolates from Rawalpindi and 23% of patient isolates in Leeds and Bradford, where it was associated exclusively with patients with South Asian names. A second profile (02235) represented 15% of patient isolates in Leeds and Bradford, and was also exclusively associated with the South Asian community. These profiles could be subdivided by mixed-linker PCR analysis. CONCLUSION: The VNTR profile 42235 may represent a family of strains commonly found in communities associated with South Asia.

Comparison of variable number tandem repeat and IS6110-restriction fragment length polymorphism analyses for discrimination of high- and low-copy-number IS6110 Mycobacterium tuberculosis isolates.

The present study was designed to evaluate the use of variable number tandem repeat (VNTR) and IS6110-restriction fragment length polymorphism (RFLP) analyses in combination as a two-step strategy for discrimination (as measured by the Hunter-Gaston Discrimination Index [HGDI]) of both high- and low-copy-number IS6110 Mycobacterium tuberculosis isolates compared to IS6110-RFLP alone with an unselected collection of isolates. Individually, IS6110-RFLP fingerprinting produced six clusters that accounted for 69% of the low-copy-number IS6110 isolates (five clusters) and 5% of the high-copy-number IS6110 isolates (one cluster). A total of 39% of all the isolates were clustered (HGDI = 0.97). VNTR analysis generated a total of 35 different VNTR allele profile sets from 93 isolates (HGDI = 0.938). Combining IS6110-RFLP analysis with VNTR analysis reduced the overall percentage of clustered isolates to 29% (HGDI = 0.988) and discriminated a further 27% of low-copy-number isolates that would have been clustered by IS6110-RFLP alone. The use of VNTR analysis as an initial typing strategy facilitates further analysis by IS6110-RFLP, and more importantly, VNTR analysis subdivides some IS6110-RFLP-defined clusters containing low- and single-copy IS6110 isolates.

Rapid identification of laboratory contamination with Mycobacterium tuberculosis using variable number tandem repeat analysis.

Compared with solid media, broth-based mycobacterial culture systems have increased sensitivity but also have higher false-positive rates due to cross-contamination. Systematic strain typing is rarely undertaken because the techniques are technically demanding and the data are difficult to organize. Variable number tandem repeat (VNTR) analysis by PCR is rapid and reproducible. The digital profile is easily manipulated in a database. We undertook a retrospective study of Mycobacterium tuberculosis isolates collected over an 18-month period following the introduction of the BACTEC MGIT 960 system. VNTR allele profiles were determined with early positive broth cultures and entered into a database with the specimen processing date and other specimen data. We found 36 distinct VNTR profiles in cultures from 144 patients. Three common VNTR profiles accounted for 45% of true-positive cases. By combining VNTR results with specimen data, we identified nine cross-contamination incidents, six of which were previously unsuspected. These nine incidents resulted in 34 false-positive cultures for 29 patients. False-positive cultures were identified for three patients who had previously been culture positive for tuberculosis and were receiving treatment. Identification of cross-contamination incidents requires careful documentation of specimen data and good communication between clinical and laboratory staff. Automated broth culture systems should be supplemented with molecular analysis to identify cross-contamination events. VNTR analysis is reproducible and provides timely results when applied to early positive broth cultures. This method should ensure that patients are not placed on unnecessary tuberculosis therapy or that cases are not falsely identified as treatment failures. In addition, areas where existing procedures may be improved can be identified.

PCR single strand conformational polymorphism can be used to detect the gene encoding SHV-7 extended-spectrum beta-lactamase and to identify different SHV genes within the same strain.

The PCR single strand conformational polymorphism (PCR-SSCP) technique described to identify mutants of the SHV beta-lactamases was extended to identify an SHV-7 type beta-lactamase. This was found in a strain of Klebsiella pneumoniae, the first recorded isolate in the UK to produce this type of enzyme. We also demonstrate that PCR-SSCP can be used to identify more than one SHV beta-lactamase gene in a single strain.

Molecular evolution of the tet(M) gene in Gardnerella vaginalis.

Five clinical isolates of Gardnerella vaginalis known to carry the tetracycline resistance determinant Tet M were examined by hybridization and nucleotide sequencing. Four of the strains carried tet(M) genes with identical sequences. The two versions of the tet(M) gene found in G. vaginalis did not show complete identity with other published tet(M) sequences, but showed mosaic structures with regions of homology to tet(M) gene sequences from Tn916, Tn1545 and the American type plasmid found in Neisseria gonorrhoeae. Hybridization studies showed that all isolates carried the tet(M) gene on a single HindII restriction fragment of variable length. No evidence was found for the presence of sequences homologous to the transposition functions of Tn916.

Prevalence and mechanism of resistance to 'third-generation' cephalosporins in clinically relevant isolates of Enterobacteriaceae from 43 hospitals in the UK, 1990-1991.

In a UK survey of the occurrence of extended spectrum beta-lactamases, 96 hospitals submitted a total of 3951 non-selected, non-duplicate isolates of Enterobacteriaceae from 100 patients in each hospital, 206 of these cultures being mixed and, therefore, discarded. These isolates were initially screened for strains likely to produce extended-spectrum beta-lactamases (ESBLs) by MIC determination of beta-lactams followed by a bioassay, then disc approximation test and isoelectric focusing (IEF). Isolates were further examined using two pairs of PCR primers for both blaTEM and blaSHV genes. The ability of isolates to transfer resistance to both cefotaxime and ceftazidime by conjugation and transformation were examined. Four hundred and nine cefotaxime/ceftazidime-resistant isolates (10.9%) were identified from the 3745 submitted isolates, of which 338 (9.0%) were Enterobacteriaceae, 29 Escherichia coli, 35 Klebsiella spp. and seven Hafnia alveii. IEF suggested that 17 isolates produced an ESBL, which was confirmed in most cases by PCR and hydrolysis, five isolates produced an SHV enzyme by IEF, but not confirmed by PCR, and 11 had isoelectric points in the range 8-9 suggesting a possible AmpC enzyme. Only two isolates transferred the determinants. In the case of the Klebsiella spp., 19 of the 24 ceftazidime-resistant/clavulanate-sensitive isolates were positive by PCR for a blaSHV gene. No isolates were identified as carrying blaTEM, although eight isolates had isoelectric points of 5-6.3, suggesting the presence of a possible TEM beta-lactamase. The results for the H. alveii isolates suggest that either an AmpC-like enzyme or a transferable beta-lactamase which is not TEM/SHV is present. This study shows that a wide range of genotypically and phenotypically different isolates of Enterobacteriaceae producing ESBL-like enzymes is present throughout the UK at a frequency of about 1% of unselected isolates. It is important that surveillance of resistance to these clinically important antibiotics is maintained as the occurrence of localized or more widespread outbreaks caused by bacteria producing ESBLs is to be expected.

Transcontinental importation into the UK of Escherichia coli expressing a plasmid-mediated AmpC-type beta-lactamase exposed during an outbreak of SHV-5 extended-spectrum beta-lactamase in a Leeds hospital.

Sixteen strains of Escherichia coli with high-level resistance to extended-spectrum cephalosporins and other classes of antibiotic have been isolated at St James' University Hospital, Leeds. They produce up to three separate beta-lactamases: TEM-1, SHV-5 and, in five isolates, a plasmid-mediated AmpC-type enzyme. With the exception of carbapenems, the isolates reported in this study were resistant to all beta-lactam antibiotics including extended-spectrum cephalosporins and the monobactam aztreonam. There was evidence of the spread of a plasmid encoding SHV-5, particularly amongst patients on the liver transplant unit. Sensitivity to beta-lactam antibiotics in five isolates expressing the AmpC-type beta-lactamase was not restored by the beta-lactamase inhibitor clavulanic acid. These bacteria also carried blaSHV-5 on a large plasmid. PCR-amplification of the structural gene and digestion with restriction endonucleases demonstrated that the plasmid-mediated blaAmpC probably identified as BIL-1 using the criteria available. Four of the five patients carrying isolates that carried the plasmid-located blaAmpC gene had recently visited the Indian subcontinent and we presume that they returned carrying these bacteria. Restriction fragment length polymorphism analysis using pulsed field gel electrophoresis (PFGE) suggests that at least four distinct strains existed amongst these five isolates. The two isolates that had very similar PFGE patterns had different plasmid profiles and were isolated from different locations in the hospital and at different times. This study demonstrates the ease with which highly resistant bacteria can be imported into the UK and spread within hospitals.

Influence of relative humidity and suspending menstrua on survival of Acinetobacter spp. on dry surfaces.

Acinetobacter spp. are being reported with increasing frequency as a cause of nosocomial infection and have been isolated from the skin of healthy individuals, patients, hospital staff, dry nonbiotic objects, and different pieces of medical equipment. Factors affecting the survival of Acinetobacter spp. under conditions closely similar to those found in the hospital environment were investigated in the present study to help us understand the epidemiology of nosocomial Acinetobacter infection. Bacterial cells were suspended in distilled water or bovine serum albumin and were dried onto glass coverslips and kept at different relative humidities. Cells washed from coverslips were used to determined viable counts. Freshly isolated strains of Acinetobacter spp. belonging to the clinically important Acinetobacter calcoaceticus-Acinetobacter baumannii complex were found to be more resistant to drying conditions (e.g., 30 days for A. baumannii 16/49) than American Type Culture Collection strains (e.g., 2 days for A. baumannii ATCC 9955). The majority of strains belonging to the Acb complex had survival times similar to those observed for the gram-positive organism Staphylococcus aureus tested in the experiment. Survival times were prolonged for almost all the strains tested when they were suspended in bovine serum albumin (e.g., 60 days for A. baumannii R 447) compared with those for strains suspended in distilled water (11 days for R 447). The survival times for strains at higher relative humidity (31 or 93%) were longer than those for strains of Acinetobacter kept at a relative humidity of 10% (11 days at 31% relative humidity and 4 days at 10% relative humidity for R447). These findings are consistent with the observed tendency of Acinetobacter spp. to survive on dry surfaces, and they can be transferred not only by moist vectors but also under dry conditions in a hospital environment during nosocomial infection outbreaks. The results obtained in the experiment support the previously suggested airborne spread of Acinetobacter spp. in hospital wards and repeated outbreaks after incomplete disinfection of contaminated dry surfaces.

Detection of mutations conferring extended-spectrum activity on SHV beta-lactamases using polymerase chain reaction single strand conformational polymorphism (PCR-SSCP).

Single strand conformational polymorphism (SSCP) is a recently developed technique used to detect single base mutations in short PCR-generated amplimers. The method has been adapted and applied to differentiation of beta-lactamase genes. Each of the five standard SHV strains used produced a unique SSCP pattern, allowing the possibility of rapid identification of the SHV genes of other isolates. A clinical isolate that phenotypically produced SHV-5 yielded a pattern of major bands indistinguishable from that of the SHV-5 standard strain, illustrating the applicability of this technique. We therefore report a reliable and reproducible technique that can be applied to the characterisation of the SHV beta-lactamases.

Molecular epidemiology of ceftazidime resistant Enterobacteriaceae from patients on a paediatric oncology ward.

Between the autumn of 1989 and January 1990, 21 of the 44 children on the paediatric oncology ward of St. James's University Hospital, Leeds, UK were infected or colonised with Enterobacteriaceae producing extended-spectrum beta-lactamases. This represents 48% of the patients on the ward. Only six patients (14%) had microbiologically proven septicaemia caused by such bacteria during this period. Eighty-one isolates of Enterobacteriaceae producing extended-spectrum beta-lactamases derived from blood culture (7 isolates from 6 patients) or faecal samples (74 isolates) were available for examination. These comprised 28 Escherichia coli, 28 Klebsiella oxytoca, 11 Klebsiella pneumoniae, 10 Citrobacter freundii, 3 Enterobacter spp. and 1 Serratia marcescens. Clinical isolates were resistant to penicillins and to ceftazidime. Strains isolated in this study also showed multiple resistance to a range of antimicrobial agents. Transfer to a nalidixic acid resistant laboratory strain of E. coli UB5201 was attempted, but transfer of the ceftazidime resistance determinant was only successful in 25 isolates (31%). Examination of plasmid DNA revealed sequences in each isolate that hybridised with the TEM beta-lactamase gene probe used on a variety of plasmids ranging in size from 2.5- > 150 kb, sometimes found on several replicons in a single isolate. The TEM gene probe also hybridised with chromosomal DNA in a large number of isolates. Nucleotide sequence analysis demonstrated the presence of three extended-spectrum beta-lactamases: TEM-10B produced by two isolates, TEM-12B produced by 37 isolates and TEM-26B produced by 40 isolates. In two cases, isolates produced two beta-lactamases, and it proved impossible to identify these enzymes unequivocally. The genes encoding TEM-10B and TEM-26B both differ from TEM-12B by single nucleotide substitutions. Analysis of the ribotype patterns derived from the clinical isolates provided evidence for cross-colonisation between patients, and this was confirmed by analysis of the plasmid profiles. Four years after discontinuing ceftazidime and other extended-spectrum cephalosporins on this ward, patients were still colonised with bacteria that produced extended-spectrum beta-lactamases.

Nucleotide sequences of the tet(M) genes from the American and Dutch type tetracycline resistance plasmids of Neisseria gonorrhoeae.

High-level tetracycline-resistant Neisseria gonorrhoeae (TRNG) has been associated with the presence of a plasmid approximately 25.2 MDa in size which carries a Tet M tetracycline resistance determinant. Two different plasmid types, American and Dutch, have previously been described, based on the restriction endonuclease digestion pattern. In this study, the tet(M) genes from the two plasmid types have been amplified by the polymerase chain reaction (PCR) and then sequenced. The gene sequences from the two plasmids shared 96.8% identity, and showed similarities with different segments of the tet(M) gene sequences from Tn1545, Tn916 and Ureaplasma urealyticum. The data suggest that it is highly likely that the Tet M determinant found in the American type plasmid has a different origin from that present in the Dutch plasmid.

PCR for the detection and typing of campylobacters.

The flaA gene of Campylobacter sp. was amplified using PCR. Primers were chosen which amplified 1.3 kb of the flaA gene in Camp. jejuni and Camp. coli. 'Campylobacter upsaliensis' amplimer was approximately 1.7 kb in size and was easily distinguishable. Other species of campylobacter failed to yield amplimer. The amplimer was digested with Alu 1 which demonstrated considerable restriction fragment length polymorphism and should allow the development of a rapid novel typing scheme which does not rely on previous culture of campylobacter strains.