Hanna Soini

Single-Nucleotide Polymorphism–Based Population Genetic Analysis of Mycobacterium tuberculosis Strains from 4 Geographic Sites

We studied genetic relationships among 5069 Mycobacterium tuberculosis strains recovered from patients enrolled in 4 population-based studies in the United States and Europe, by analysis of 36 synonymous single-nucleotide polymorphisms (SNPs). All strains were assigned to 1 of 9 major genetic clusters based on sSNP profile. The same 9 genetic clusters were revealed by analysis of 227 nonsynonymous SNPs, 121 intergenic SNPs, and concatenated profiles of 578 SNPs available for a subset of 48 representative strains. IS6110 profiles, spoligotypes, and mycobacterial interspersed repetitive unit patterns were nonrandomly associated with SNP-based phylogenetic lineages, together indicating a strongly clonal population structure. Isolates of the 9 genetic clusters were not distributed with equal frequency in all localities, reflecting geographic subdivision. The SNP-based phylogenetic framework provides new insight into the worldwide evolution of M. tuberculosis and a gateway for investigating genotype-disease phenotype relationships in large samples of strains.

Comparison of Two Commercially Available DNA Line Probe Assays for Detection of Multidrug-Resistant Mycobacterium tuberculosis

ABSTRACT Two commercially available DNA line probe assays, Genotype MTBDR and INNO-LiPA Rif. TB, were evaluated for their abilities to detect resistance to isoniazid (INH) and rifampin (RIF) in 52 Mycobacterium tuberculosis isolates. The test results were compared to those obtained by phenotypic drug susceptibility testing and sequencing. Compared to the results of phenotypic drug susceptibility testing, the Genotype MTBDR test results were concordant for INH for 47 of the 52 (90.4%) isolates, and both the Genotype MTBDR and the INNO-LiPA Rif. TB test results were concordant for RIF for 51 of the 52 (98.1%) isolates. The Genotype MTBDR test results correlated with the sequencing results for 48 of the 52 (92.3%) isolates and the INNO-LiPA Rif. TB results for 50 of the 52 (96.2%) isolates. Both assays are useful for the rapid screening of M. tuberculosis isolates obtained from patients suspected of having multidrug-resistant tuberculosis, but the GenoType MTBDR assay has the advantage of being able to detect resistance to both INH and RIF simultaneously.

Complex Transmission Dynamics of Clonally Related Virulent Mycobacterium tuberculosis Associated with Barhopping by Predominantly Human Immunodeficiency Virus-Positive Gay Men

Limited data suggest that measures to reduce tuberculosis transmission should be based on locations rather than on personal contacts. Molecular epidemiologic methods (analysis of IS6110 patterns, spoligotypes, variable numbers of tandem DNA repeats, and automated DNA sequence data) identified a cohort of 48 persons who were infected with progeny of the same Mycobacterium tuberculosis strain. Epidemiologic investigation documented that a large proportion of the patients were gay white human immunodeficiency virus-positive men. Most practiced barhopping, an activity that involved patronizing many bars in the same neighborhood each night. Few subjects were directly linked to more than 1 or 2 other persons by conventional investigation methods, which shows that the transmission dynamics were unusually complex compared with most previously described episodes of strain spread. The data support the concept that identification of locations where pathogen dissemination likely occurs may provide additional strategies for targeted tuberculosis control.

Transmission Dynamics and Molecular Characterization of Mycobacterium tuberculosis Isolates with Low Copy Numbers of IS6110

ABSTRACT Population-based analysis of Mycobacterium tuberculosistransmission in Houston, Tex., over 5 years identified 377 patients infected with an isolate containing one to four copies of IS6110. The isolates were analyzed by spoligotyping and assigned to one of three major genetic groups based on nucleotide polymorphisms in codons katG 463 and gyrA 95. Prospectively obtained patient interviews were reviewed to assess epidemiologic links between apparently clustered patients. A total of 13 groups of isolates with the same IS6110 profile were identified, representing 326 of the 377 patients (86.5%; range 2 to 113 patients). In contrast, 28 groups of isolates containing 334 patients (88.6%) had the same spoligotype (range, 2 to 143 patients). Combination of IS6110 profile and spoligotype data identified 31 clusters with 300 patients (79.6%; range, 2 to 82 patients). All 377 isolates belonged to major genetic group 1 (77 patients) or genetic group 2 (300 patients); no major genetic group 3 isolates were identified. Among the 228 patients interviewed, 33 patients (14.5%) were directly linked to another patient in the same cluster. Possible epidemiologic links were also found among 11 patients. Moreover, many clusters consisted of individuals with the same ethnicity. In conclusion, we confirmed that IS6110profiling and spoligotyping together provide enhanced molecular discrimination of M. tuberculosis isolates with low copy numbers of IS6110. Identification of epidemiologic links among some of the patients verified that the combination of these two methods reliably indexes tuberculosis transmission.

Mycobacterium simiae Pseudo-outbreak Resulting from a Contaminated Hospital Water Supply in Houston, Texas

Various species of nontuberculous mycobacteria are known to cause nosocomial pseudo-outbreaks, but there have been no detailed reports of nosocomial Mycobacterium simiae pseudo-outbreaks. From April 1997 through February 2001, we recovered 65 M. simiae isolates from 62 patients at a community teaching hospital in Houston, Texas. The organism was grown in various water samples obtained in the hospital building and in professional building 1 but not in professional building 2, which has a separate water supply system. Thirty-one environmental and human outbreak-related M. simiae isolates had indistinguishable or closely related patterns on pulsed-field gel electrophoresis and were considered clonal. M. simiae can be a cause of nosocomial pseudo-outbreaks. The reservoir for this pseudo-outbreak was identified as a contaminated hospital water supply.

Epidemiologic Differences between United States— and Foreign-Born Tuberculosis Patients in Houston, Texas

The proportion of foreign-born tuberculosis patients in the United States is increasing. To analyze the epidemiology of tuberculosis in foreign-born people, culture-positive patients with tuberculosis in Houston, Texas, were interviewed from October 1995 through September 1998, and their isolates were molecularly characterized. Of the 1131 patients included in the study, 795 (70.3%) were US born and 336 (29.7%) were foreign born. The decrease in tuberculosis case rate among US-born people was 3.5 times that of foreign-born people. Significantly more US-born than foreign-born patients belonged to strain clusters (71.3% vs. 29.5%; P<.001). Risk factors associated with strain clustering were as follows: black ethnicity, low income, and homelessness in US-born patients and homelessness in foreign-born patients. Isolates from foreign-born patients were more likely to be resistant to >/=1 drug (15.4% vs. 8.4%; P=.001) and to be multidrug resistant (2.4% vs. 0.7%; P=.027) than isolates from US-born patients. These observations warrant increased emphasis on this distinct subpopulation of tuberculosis patients.

Evaluation of GenoType and LiPA MYCOBACTERIA Assays for Identification of Finnish Mycobacterial Isolates

ABSTRACT Two DNA strip assays, INNO-LiPA MYCOBACTERIA and GenoType Mykobakterien, were evaluated for identification of 81 Finnish mycobacterial isolates. The LiPA assay correctly identified 89.4% of the 66 isolates studied, and the GenoType assay identified 95.1% of 81 isolates. The GenoType assay had a wider selection of species and less stringent temperature requirements.

Early dissemination of Borrelia burgdorferi without generalized symptoms in patients with erythema migrans

The diagnosis of erythema migrans (EM) is not always easy, and reports of culture‐ or PCR‐confirmed diagnosis as well as reports of EM with simultaneous disseminated disease are few. Characteristics and incidence of EM in addition to frequency of early dissemination of B. burgdorferi were studied in the archipelago of South‐Western Finland prospectively using questionnaires, skin biopsies and blood samples. Clinical EM was recognized in 82 patients (incidence 148/100000 inhabitants/year). Of skin biopsy samples, 35.5% were positive by PCR (the majority B. garinii), and 21.5% by cultivation (all B. garinii). Of blood samples, 3.8% were positive by PCR, and 7.7% by cultivation. Of the patients, 30.9% were seropositive at the first visit, and 52.9% 3 weeks later. Of the patients with laboratory confirmed diagnosis, the EM lesion was ring‐like in 31.8% and homogenous in 65.9%. Dissemination of B. burgdorferi, based on culture or PCR positivity of blood samples, was detected in 11.0% of the patients. The frequency of generalized symptoms was nearly the same in patients with as in those without dissemination (22.2% vs 27.4%). Only 21.4% of the patients with culture‐positive EM recalled a previous tick bite at the site of the EM lesion. We conclude that EM lesions are more often homogenous than ring‐like. B. burgdorferi may disseminate early without generalized symptoms.

High rates of disseminated infection due to non-tuberculous mycobacteria among AIDS patients in Finland.

OBJECTIVE to determine the rate of disseminated infection due to non-tuberculous mycobacteria (NTM) among Finnish AIDS patients, and to analyse the epidemiology of these infections. METHODS in a prospective cohort study HIV-infected patients with CD4 counts < 200 x 10(6)/l were interviewed, and had mycobacterial blood cultures performed at baseline and at 6 months, then subsequently for clinical indications; autopsies were performed on patients who died. The cohort was followed at least for 24 months or to death. Water samples were collected from the homes of patients and from the environment and cultured for organisms of the Myobacterium avium complex (MAC). Environmental and clinical isolates were compared using pulsed field gel electrophoresis (PFGE). RESULTS NTM infection occurred in 22 (43%) of 51, 19 isolates were Mycobacterium avium, two M. genavense and one M. intracellulare. Multivariate analysis identified urban residence (P=0.04) and eating raw fish (P=0.04) as independent risk factors. Molecular analysis revealed two clusters of related isolates (three M. avium, two M. genavense) among urban residents. CONCLUSION AIDS patients in Finland have high rates of disseminated infection due to NTM. Clusters of identical organisms and association with urban residence suggests that these are newly acquired infections in advanced AIDS.

Prospective evaluation of the GenoType assay for routine identification of mycobacteria.

In order to evaluate the proficiency of the GenoType Mycobacteria strip hybridization assay (Hain Lifescience, Nehren, Germany) for the routine identification of mycobacteria, the assay was used to identify 178 clinical isolates during a 6-month prospective study. The GenoType results were compared to the identification results obtained with AccuProbe (GenProbe, San Diego, CA, USA) or 16S rDNA sequencing, and an overall agreement of 89.3% between GenoType and the two reference methods was reached. The GenoType assay is, thus, a rapid and reliable method for the identification of clinically important mycobacteria, and it is well suited for use in a routine laboratory.