Pulsed-field gel electrophoresis analysis of Bordetella pertussis isolates circulating in Europe from 1998 to 2009.

Between 1998 and 2009, Bordetella pertussis clinical isolates were collected during three periods, i.e., 1998 to 2001 (n = 102), 2004 to 2005 (n = 154), and 2007 to 2009 (n = 140), from nine countries with distinct vaccination programs, i.e., Denmark, Finland, France, Germany, The Netherlands, Norway, Poland, Sweden, and the United Kingdom. Pulsed-field gel electrophoresis (PFGE) analysis was performed according to standardized recommendations for epidemiological typing of B. pertussis. There were 81 different PFGE profiles, five of which (BpSR3, BpSR5, BpSR10, BpSR11, and BpSR12) were observed in 61% of the 396 isolates and shown to be predominant in almost all countries. The major profile, BpSR11, showed a decreasing trend from 25% to 30% in 1998 to 2005 to 13% in 2007 to 2009, and there were increases in BpSR3 and BpSR10 from 0% and 8% to 21% and 22%, respectively. One difference between these profiles is that BpSR11 contains isolates harboring the fim3-2 allele and BpSR3 and BpSR10 contain isolates harboring the fim3-1 allele. The total proportion of the five predominant profiles increased from 44% in 1998 to 2001 to 63% in 2004 to 2005 to 70% in 2007 to 2009. In conclusion, common PFGE profiles were identified in B. pertussis populations circulating in European countries with different vaccination programs and different vaccine coverages. These prevalent isolates contain the novel pertussis toxin promoter ptxP3 allele. However, there is evidence for diversifying selection between ptxP3 strains characterized by distinct PFGE profiles. This work shows that, even within a relatively short time span of 10 years, successful isolates which spread through Europe and cause large shifts in B. pertussis populations may emerge.

Recovery of Bordetella pertussis from PCR-positive nasopharyngeal samples is dependent on bacterial load.

Viable Bordetella pertussis isolates are essential for surveillance purposes. We performed culture of 223 PCR-positive nasopharyngeal samples. B. pertussis was recovered from 45 (20.2%) of the samples. Growth was associated with a high bacterial load, as determined by PCR. Culture from PCR-positive samples is a feasible approach to recover B. pertussis isolates, and culture can be limited to samples with a high bacterial load.

Multilocus sequence typing of serial Candida albicans isolates from children with cancer, children with cystic fibrosis and healthy controls.

Candida albicans is a fungal pathogen, but also a commensal in many individuals. Since detailed molecular studies of children carrying C. albicans are lacking, we longitudinally investigated fecal and tonsillopharyngeal samples from 10 children undergoing treatment for cancer, six children treated for cystic fibrosis (CF), and seven healthy children during the time period of 1999-2008. Multilocus sequence typing (MLST) was performed on 62 C. albicans isolates. Only three of the 23 children (13%) were colonized with genetically unrelated strains in the longitudinal follow-up. We identified 32 different diploid sequence types (DSTs), but only one (409) was shared by two siblings. Most often, the fecal strain types were identical or closely related to the tonsillopharyngeal reservoirs. We found no closely related strain types in children who were hospitalized in the same ward or in children attending the same day care center. There was no sign of resistance to fluconazole, caspofungin, amphotericin B or flucytosine over time. This study shows that both children with cancer or CF, and healthy children usually harbor the same C. albicans strain over time. We did not find indications of clonal spread between children in the same environments, except in a pair of siblings.

RFLP clusters of Mycobacterium tuberculosis strains from the Indian Ocean Region: local and South Asian characteristics.

This is the first study describing the genetic polymorphism of Mycobacterium tuberculosis strains in the Indian Ocean Region. Using IS6110 RFLP analysis, 475 M. tuberculosis isolates from Madagascar, Comoros, Mauritius, Mozambique and La Reunion were compared. Of the 332 IS6110 profiles found, 43 were shared by clusters containing 2-65 strains. Six clusters were common to at least two countries. Of 52 families of strains with similar IS6110 profiles, 10 were common to at least two countries. Interestingly, another characteristic was the frequency (16.8%) of IS6110 single-copy strains. These strains could be distinguished using the DR marker. This preliminary evaluation suggests genetic similarity between the strains of the Indian Ocean Region. However, additional markers would be useful for epidemiological studies and to assess the ancient transmission of strains between countries of this region.

RFLP clusters of Mycobacterium tuberculosis strains from the Indian Ocean Region: local and South Asian characteristics

This is the first study describing the genetic polymorphism of Mycobacterium tuberculosis strains in the Indian Ocean Region. Using IS6110 RFLP analysis, 475 M. tuberculosis isolates from Madagascar, Comoros, Mauritius, Mozambique and La Reunion were compared. Of the 332 IS6110 profiles found, 43 were shared by clusters containing 2-65 strains. Six clusters were common to at least two countries. Of 52 families of strains with similar IS6110 profiles, 10 were common to at least two countries. Interestingly, another characteristic was the frequency (16.8 percent) of IS6110 single-copy strains. These strains could be distinguished using the DR marker. This preliminary evaluation suggests genetic similarity between the strains of the Indian Ocean Region. However, additional markers would be useful for epidemiological studies and to assess the ancient transmission of strains between countries of this region.

Diagnostics of fungal infections in the Nordic countries: we still need to improve!

A Nordic External Quality Assessment programme in medical mycology was established in 2005. In order to monitor not 'best practice' but the level of routine diagnostics, specimens were designed to resemble clinical samples and laboratories were asked to handle the samples like routine samples. Five simulated clinical samples were distributed to 59 participating Nordic laboratories of clinical microbiology. The specimens contained the following microorganisms: 1) Candida glabrata and C. albicans in a ratio of 1:20; 2) Cryptococcus neoformans; 3) Aspergillus fumigatus, C. albicans and Enterobacter cloacae; 4) C. tropicalis, Klebsiella pneumonia and Enterococcus faecium; 5) None. 66% of the laboratories failed to detect the C. glabrata isolate in sample no. 1. 34% of the laboratories reporting susceptibility results incorrectly reported the Cryptococcus neoformans isolate as fluconazole susceptible. 24% of the laboratories failed to detect Aspergillus fumigatus in specimen no. 3 despite the accompanying clinical information notifying that it was a BAL sample from a neutropenic patient in an ICU. In conclusion, this distribution of simulated clinical samples illustrates that the traditional quality assessment programmes may give a false sense of satisfactory performance, that mycological diagnosis is difficult, and that there is a need of further improvement and attention.

Candidemia in Norway (1991 to 2003): results from a nationwide study.

A long-term, nationwide prospective candidemia study has been ongoing in Norway since 1991. All medical microbiological laboratories in the country have participated. During the period 1991 to 2003 a total of 1,393 episodes of candidemia occurred in 1,348 patients. The incidence of candidemia episodes per 100,000 inhabitants increased from approximately 2 episodes in the early 1990s to 3 episodes in 2001 to 2003. The average annual incidences varied markedly between the age groups. The incidence was high in patients aged < 1 year and in patients aged > or = 70 years. In patients > or = 80 years of age, the incidence has increased during the last 3 years from an annual average of 6.5 to 15.6 cases/100,000 inhabitants in 2003. Four Candida species (C. albicans [70%], C. glabrata [13%], C. tropicalis [7%], and C. parapsilosis [6%]) accounted for 95.5% of the isolates. The species distribution has been constant during the 13-year study period. The distribution of the most important species varied with the age of the patient. In patients < 1 year of age, the majority of episodes were caused by C. albicans (91%). The occurrence of C. glabrata increased with age. In patients > or = 80 years of age, approximately 1/3 of all episodes were due to this species. All C. albicans strains were susceptible to fluconazole. The percentage of yeast isolates with decreased susceptibility to fluconazole (MICs > or = 16 microg/ml) was 10.7% during the first period of this study (1991 to 1996) and 11.7% during the second period (1997 to 2003).

18S rDNA polymerase chain reaction and sequencing in onychomycosis diagnostics.

Diagnostic approaches to onychomycosis have traditionally been based on a combination of culture and microscopy. In the present study clinical specimens from 346 patients with suspected onychomycosis were analysed by 18S polymerase chain reaction (detection) followed by sequencing and subsequent database search (identification) in parallel with routine culture on agar (detection and identification). In 49 samples Trichophyton rubrum was identified by culture and sequencing. In 67 additional culture negative samples, a positive dermatophyte sequence was obtained (T. rubrum in 54, T. mentagrophytes in 5, and T. species in 8 samples). Fifteen samples cultured positive while no sequence was obtained. Two hundred and seven samples were negative by culture as well as by sequencing. Nails from 10 healthy controls were negative by culture and sequencing. In conclusion, the number of specimens that were positive by polymerase chain reaction was more than double the number that were positive by culture alone.

Efficacy and safety of linezolid in multidrug resistant tuberculosis (MDR-TB)--a report of ten cases.

OBJECTIVES: Multidrug resistant tuberculosis (MDR-TB) is an increasing problem in many parts of the world and in Norway the increase has been substantial since 1998. New therapies for MDR-TB have not been introduced since the fluoroquinolones in the 1970s. The cure rate of this disease has been reported to be lower than for non-drug resistant TB, and the use of new experimental drugs in combination therapy is warranted. METHODS: Ten consecutive patients with culture proven MDR-TB were treated with the novel antibiotic drug linezolid in combination regimens for 6-40 (median 17) weeks and followed up 11-50 (median 24) months after end of treatment. All strains were sensitive to linezolid with MIC<4 mg/l. Treatment was given as direct observed therapy (DOT) and sputum cultures, blood chemistry and neurologic examination were undertaken on a regular basis. RESULTS: Nine patients were cured, one patient with poor adherence to treatment and advanced AIDS died. Seven of 10 patients experienced serious adverse events, which led to withdrawal of linezolid in all seven. Six patients developed peripheral neuropathy and five patients bone marrow depression, blood transfusions were given to three patients and in all five patients bone marrow function normalized after cessation of linezolid. Peripheral neuropathy was not fully reversed in all patients. CONCLUSION: Linezolid seems highly active in combination treatment of MDR-TB. Cultures became negative 10-37 days after the introduction of the drug. However, peripheral neuropathy and bone marrow depression led to linezolid withdrawal in seven patients, and neuropathy may not be fully reversible in all patients.

Invasive fungal infections at The Norwegian Radium Hospital 1998-2003.

The study evaluates the clinical and microbiological data from patients with documented invasive fungal infections at a comprehensive cancer centre in Norway. Relevant microbiology and pathology databases were screened and medical records were reviewed. 17 yeast infections, including 1 case of cryptococcal meningitis, and no mould infections were found. Diagnostically, in 30% of the positive blood cultures Candida only grew in the Mycosis IC/F bottle. Half of the patients had febrile neutropenia, and 30% had undergone complicated abdominal or pelvic surgery. 12 out of 13 positive blood cultures were Candida albicans. 30% of the patients died of acute septic candidiasis. Within 14 months 90% of the patients were dead from their underlying diseases. A diagnosis of invasive fungal infection is an ominous sign for the patient's overall prognosis.

Clostridium tertium: 3 case reports.

Clostridium tertium is infrequently isolated from blood in patients with underlying diseases. Laboratory diagnosis is often delayed because Clostridium tertium is aerotolerant and resistant to metronidazole. Clinically it is a problem because it is commonly resistant to metronidazole, clindamycin and cephalosporins. We present 3 cases illustrating these characteristics.

Impact of drug resistance on fitness of Mycobacterium tuberculosis strains of the W-Beijing genotype.

Mycobacterium tuberculosis strains of the W-Beijing genotype became a common cause of tuberculosis during the past years and they are often associated with drug resistance. The biological factors facilitating the selection and wide dissemination of these strains are not known. To determine how acquisition of drug resistance affected growth of strains of the W-Beijing genotype, the growth of 55 M. tuberculosis isolates were studied using the BBL MGIT Mycobacteria Growth Indicator Tube and the BACTEC MGIT 960 System. Susceptible strains of non-Beijing genotypes were found to be the most fit strains. Drug-resistant strains of non-Beijing genotypes were more likely to grow slower than susceptible strains (P=0.001). Drug-resistant strains of the W-Beijing genotype had two tendencies of growth: some of them showed reduced growth compared to susceptible strains, while others did not show loss of fitness measured as growth.

Molecular epidemiology and drug resistance of Mycobacterium tuberculosis isolates in the Archangel prison in Russia: predominance of the W-Beijing clone family.

Prisons play a significant role in the epidemiology of drug-resistant tuberculosis. A total of 114 Mycobacterium tuberculosis isolates recovered from patients in the Archangel prison (Archangel, Russia) in 2001 were studied using restriction fragment-length polymorphism analysis and spoligotyping. Drug susceptibility was analyzed by the radiometric broth method (BACTEC; Becton Dickinson Diagnostic Systems). According to genotyping studies, 87 (76.3%) of the isolates belonged to the W-Beijing family. Nearly all (96.6%) W-Beijing isolates were part of a cluster, whereas only 25.9% of the other isolates were clustered (P<.001). The largest cluster comprised 43 patients. Multidrug resistance was high among new (34.0%) and previously treated (55.0%) cases. Resistance to ethambutol (OR, 3.4; 95% CI, 1.0-12.7; P=.03) and streptomycin (OR, 4.2; 95% CI, 1.5-11.6; P=.001) was significantly associated with infection with W-Beijing isolates. Tuberculosis due to drug-resistant W-Beijing isolates is a major problem in the Archangel prison.

Continued low rates of transmission of Mycobacterium tuberculosis in Norway.

In this study, we determined the genetic diversity of Mycobacterium tuberculosis isolated in Norway from 1999 to 2001. The results were compared to those for strains isolated from 1994 to 1998. A total of 818 patients were diagnosed with tuberculosis (TB) during the last 3-year period. Of these cases, 576 (70%) were verified by culturing, and strains from 551 patients (96%) were analyzed by the IS6110 restriction fragment length polymorphism (RFLP) method. We excluded 13 strains (2.4%) from the analyses, since they were found to represent false-positive samples. A total of 67 strains (12%) that carried fewer than five copies of IS6110 were analyzed by spoligotyping. The strains were from 157 patients (29%) of Norwegian origin and 381 patients (71%) of foreign origin. The rate of diversity among all of the strains was 90%, while in 1994 to 1998 it was 87%. Clusters were assumed to have arisen from recent transmission; the degree of such transmission was 10% in 1999 to 2001, while for the whole 8-year period (1994 to 2001), it was 11%. Of the 109 patients diagnosed as being part of a cluster in 1999 to 2001, 89 were infected with a strain that carried more than four copies of IS6110. Among these 89 patients, 52 (58%) were infected with a strain that had already been identified in 1994 to 1998. The results indicated that most cases of TB in Norway were due to the import of new strains rather than to transmission within the country. This finding demonstrates that screening of immigrants for TB upon arrival in Norway needs to be improved. Outbreaks, however, were caused mainly by strains that have been circulating in Norway for many years.

Deciphering an outbreak of drug-resistant Mycobacterium tuberculosis.

There have been ample warnings that multidrug-resistant (MDR) tuberculosis (TB) will continue to emerge if countries do not strengthen their control of TB. In low-incidence European countries, however, these warnings have been substantiated mainly by outbreaks in association with human immunodeficiency virus (HIV)-positive patients. The aim of this study was to investigate an outbreak of infection with MDR and drug-resistant Mycobacterium tuberculosis that was diagnosed among 20 HIV-negative patients living in Norway. Of these, 19 were immigrants from East Africa and one was an ethnic Norwegian. We wanted to find out if transmission had taken place in Norway or abroad and to identify the genetic basis of drug resistance. The strains were analyzed by IS6110 restriction fragment length polymorphism, antibiotic susceptibility tests, spoligotyping, reverse hybridization to regions of the rpoB gene, and sequencing of the katG gene. Epidemiological links between the patients were mapped, and the strains were compared to those isolated in 36 other countries and regions. All strains were resistant to isoniazid and carried Ala234Gly, Ser315Thr, and Arg463Leu substitutions in the katG gene. Eleven strains were MDR and carried a Ser531Leu substitution in the rpoB gene. MDR was acquired in the index patient after arrival in Norway. Links were found among 14 patients. The strain was imported from Somalia but acquired MDR and was transmitted in Norway. This demonstrated that MDR strains are not necessarily imported from high-incidence countries and can be highly communicable. The outbreak underscores a deficiency in the TB control measures employed in many countries and challenges the adequacy of the policy of screening immigrants for TB only on arrival.

Significance of Candida recovered from intraoperative specimens in patients with intra-abdominal perforations.

OBJECTIVE: Determine the significance of recovering yeasts from intraoperative specimens from the abdominal cavity and to evaluate the effect of a single intraoperative dose of fluconazole on clinical outcome in patients with intra-abdominal perforations. DESIGN: Prospective, randomized, double-blind study. SETTING: Multicenter study from 13 hospitals in Norway. PATIENTS: One hundred nine patients with intra-abdominal perforations. INTERVENTIONS: Patients were randomized to receive either a single 400-mg fluconazole dose or placebo during the operation. MEASUREMENTS AND MAIN RESULTS: An intra-abdominal specimen for microbiological culture was obtained at the time of the operation. The primary response variable in the study was death. Secondary response variables were three parameters indicating a complicated postoperative period: mechanical ventilation for > or = 5 days, intensive care treatment for > or = 10 days, and use of a central venous catheter for > or = 10 days. Yeasts were recovered from a intraoperative intra-abdominal specimen from only 1 (3.5%) of 28 patients with perforated appendicitis and from 32 (39.5%) of 81 nonappendicitis patients. Excluding the appendicitis patients, the yeast recovery rate was high both for patients hospitalized at the time of the perforation (45%) and for nonhospitalized patients (32%). The overall mortality was 11% (12 patients). Single-dose intraoperative fluconazole prophylaxis did not reach a statistically significant effect on mortality (4 of 53 patients in the fluconazole group and 8 of 56 patients in the placebo group died [p = .059]). The only two explanatory variables significantly related to death were a intraoperative finding of yeast from an intra-abdominal specimen and the occurrence of a spontaneous perforation in a patient already hospitalized for nonsurgical cancer treatment. Detection of yeast was also a significant explanatory variable for a prolonged period of mechanical ventilation, intensive care treatment, and prolonged use of a central venous catheter. CONCLUSIONS: Single-dose intraoperative fluconazole prophylaxis did not have a statistically significant effect on overall mortality (odds ratio = 0.21; 95% confidence interval, 0.04-1.06; p = .059) in patients with intra-abdominal perforation. The recovery rate of yeast from intraoperative specimens from the abdominal cavity was high (>30%) and was associated with death and a complicated postoperative course.

[Genetic analysis of Mycobacterium tuberculosis in Norway 1994-98]. / Genetiske analyser av Mycobacterium tuberculosis-isolater i Norge 1994-98.

BACKGROUND: This study was undertaken to determine the genetic diversity in the population of Mycobacterium tuberculosis in Norway and to detect the degree of transmission between patients. The quality of the culturing work was ascertained by analysing the data for possible cross-contamination. MATERIAL AND METHODS: Genotypic relationships among 92% of all strains isolated in Norway in 1994-98 were assessed using IS6110-restriction fragment length polymorphism analysis. The strains had been isolated from 717 different patients. For isolates with less than five copies of IS6110 the directly repetitive element was also used. RESULTS: 20 isolates (2.8%) represented false positive samples. The isolates from 14.5% of the native Norwegian patients and 19.7% of the foreign patients were part of one of 35 clusters. INTERPRETATION: The results indicate that the degree of recent transmission of tuberculosis in Norway was low and that transmission between immigrants and native Norwegians was uncommon. The majority of cases were due to reactivation of previous disease.

Spread of drug-resistant Mycobacterium tuberculosis strains of the Beijing genotype in the Archangel Oblast, Russia.

A collection of 119 strains of Mycobacterium tuberculosis isolated from patients with pulmonary tuberculosis in the Archangel Oblast, Russia, in 1998 and 1999 were studied by using restriction fragment length polymorphism (RFLP) analysis with the IS6110 probe and spoligotyping. Resistance of the strains to antituberculosis drugs was analyzed by the BACTEC method, and mutations associated with rifampin resistance were detected by using the Inno-LiPA Rif. TB test. RFLP analysis and spoligotyping demonstrated that 53 (44.5%) of the strains belonged to the Beijing genotype. These strains showed a significantly higher rate of resistance than M. tuberculosis strains of other genotypes circulating in the region. In particular, 43.4% of the strains of the Beijing genotype were multidrug resistant; in contrast, only 10.6% of the other strains were. Of the strains of the Beijing genotype, 92.5% were part of a cluster, while only 33.3% of the remaining strains were clustered. Analysis of the medical records of the patients demonstrated that individuals infected with a strain of the Beijing genotype were significantly more likely to be alcohol abusers and to have chronic obstructive pulmonary disease prior to the tuberculosis diagnosis. Multivariate analysis showed that both variables were independently associated with infection by strains belonging to the Beijing genotype. Our study demonstrated that strains of the Beijing genotype are an important cause of tuberculosis in the Archangel Oblast and that dissemination of these strains is associated with the high incidence of drug resistance.