Biomedical subjects

Jeffrey Driscoll

Publications and source records attributed to Jeffrey Driscoll.

11 recordsLinked to original sources

PubMed2006

Identifying Mycobacterium tuberculosis complex strain families using spoligotypes.

We present a novel approach for analysis of Mycobacterium tuberculosis complex (MTC) strain genotyping data. Our work presents a first step in an ongoing project dedicated to the development of decision support tools for tuberculosis (TB) epidemiologists exploiting both genotyping and epidemiological data. We focus on spacer oligonucleotide typing (spoligotyping), a genotyping method based on analysis of a direct repeat (DR) locus. We use mixture models to identify strain families of MTC based on their spoligotyping patterns. Our algorithm, SPOTCLUST, incorporates biological information on spoligotype evolution, without attempting to derive the full phylogeny of MTC. We applied our algorithm to 535 different spoligotype patterns identified among 7166 MTC strains isolated between 1996 and 2004 from New York State TB patients. Two models were employed and validated: a 36-component model based on global spoligotype database SpolDB3, and a randomly initialized model (RIM) containing 48 components. Our analysis both confirmed previously expert-defined families of MTC strains and suggested certain new families. SPOTCLUST, which is available online, can be further improved by incorporating data obtained using additional strain genetic markers and epidemiological information. We demonstrate on New York City (NYC) patient data how the resulting models can potentially form the basis of TB control tools using genotyping.

Adolescent↗

PubMed2006

Which patients' factors predict the rate of growth of Mycobacterium tuberculosis clusters in an urban community?

Factors influencing tuberculosis cluster growth are poorly understood. The authors examined clusters of two or more culture-confirmed Mycobacterium tuberculosis cases between January 1, 2001, and December 31, 2003, that had insertion sequence 6110 (IS6110) restriction fragment length polymorphism and spoligotype patterns identical to those of another study case. Genotypes first seen in New York, New York, before or during 1993 were considered historical; recent strains were those first seen after 1993. The authors examined the effect of the combined characteristics of infectiousness of the first two cases in a cluster on the rate of cluster growth. Genotyping was performed for 2,408 (91.8%) of the 2,623 tuberculosis cases diagnosed; 873 cases were in 212 clusters. Thirty-one clusters had historical strains, 153 were recent, and 28 were of unknown period. Patients' infectiousness was not associated with the rate of cluster growth among historical strain clusters. Among recent strain clusters, infectiousness of both of the initial cases was associated with a higher rate of cluster growth compared with clusters in which neither initial case was infectious, upon adjustment for male sex (rate ratio = 2.62, 95% confidence interval: 1.19, 5.78). The rate of genotype cluster growth should be monitored regardless of how long the strain has been present in the community. However, infectiousness in the first two cases may be useful to prioritize genotype cluster investigations.

AIDS-Related Opportunistic Infections↗

PubMed2006

Strain-specific differences in two large Mycobacterium tuberculosis genotype clusters in isolates collected from homeless patients in New York City from 2001 to 2004.

We studied two large Mycobacterium tuberculosis genotype clusters associated with recent outbreaks in homeless persons to determine factors associated with these tuberculosis (TB) strains. Isolates from all culture-positive TB cases diagnosed from 1 January 2001 to 31 December 2004 were genotyped. Patients whose isolates had identical restriction fragment length polymorphism patterns and spoligotypes were considered clustered. Health department records were reviewed and reinterviews attempted for clustered cases. Patients with the Cs30 and BEs75 strains were compared to other genotypically clustered cases and to each other. The two largest genotype clusters among homeless persons were the Cs30 strain (n = 105) and the BEs75 strain (n = 47). Fifty-one (49%) patients with the Cs30 strain and 28 (60%) with the BEs75 strain were homeless. Compared to patients with the BEs75 strain, patients with the Cs30 strain were less likely to be respiratory acid-fast bacillus smear positive (51% versus 72%). Furthermore, patients with the BEs75 strain were more likely to be HIV infected (74% versus 42%), which suggests that most patients with this strain advanced to disease after recent infection. Cases in clusters of strains that have been circulating in the community over a long time period, such as the Cs30 strain, require additional investigation to determine whether clustering is a result of recent transmission or reactivation of remote infection.

Adolescent↗

PubMed2005

First-generation hybrid MEMS gas chromatograph.

The fabrication, assembly, and initial testing of a hybrid microfabricated gas chromatograph (microGC) is described. The microGC incorporates capabilities for on-board calibration, sample preconcentration and focused thermal desorption, temperature-programmed separations, and "spectral" detection with an integrated array of microsensors, and is designed for rapid determinations of complex mixtures of environmental contaminants at trace concentrations. Ambient air is used as the carrier gas to avoid the need for on-board gas supplies. The microsystem is plumbed through an etched-Si/glass microfluidic interconnection substrate with fused silica capillaries and employs a miniature commercial pump and valve subsystem for directing sample flow. The latest performance data on each system component are presented followed by first analytical results from the working microsystem. Tradeoffs in system performance as a function of volumetric flow rate are explored. The determination of an 11-vapor mixture of typical indoor air contaminants in less than 90 s is demonstrated with projected detection limits in the low part-per-billion concentration range for a preconcentrated air-sample volume of 0.25 L.

Air↗

PubMed2005

Phenotypic and molecular characterization of Mycobacterium tuberculosis isolates resistant to both isoniazid and ethambutol.

In performing radiometric susceptibility testing on over 2,000 patient isolates of Mycobacterium tuberculosis during the past 6 years, we found that resistance to 7.5 microg/ml ethambutol (EMB) occurred only in isolates that are also resistant to 0.4 microg/ml isoniazid (INH). Using 157 selected isolates in the present study, we performed radiometric and agar proportion susceptibility tests and DNA sequencing of genetic regions associated with resistance to these two drugs. The goal was to study the occurrence of the common mutations associated with resistance to each drug and also to determine whether any particular INH-resistance-associated mutation occurred more often in combination with any particular EMB-resistance-associated mutation. In an analysis of 128 isolates resistant to 0.4 microg/ml INH, we found that a mutation at katG Ser315 was more common in isolates also resistant to 7.5 microg/ml EMB (61 of 67=91.0%) than in isolates either susceptible to EMB or resistant to 2.5 microg/ml EMB (39 of 60=65.0%). These observations suggest that INH-resistant strains with a mutation at katG Ser315 are more likely to acquire resistance to 7.5 microg/ml EMB than are isolates with INH-resistance-associated mutations at other sites. In addition, we found that 64 of 67 (95.5%) isolates resistant to 7.5 microg/ml EMB contained a mutation in either codon 306 or codon 406 of embB. Met306Val was the most common embB mutation, present in 52 (77.6%) of the 67 isolates. Most occurrences of this mutation (49 of 52=94.2%) were found in isolates that also contained the katG Ser315Thr mutation. Finally, sequencing this region of embB appears to be sufficiently sensitive for use as a rapid screening tool for detection of high-level resistance to EMB.

Antitubercular Agents↗

PubMed2003

Potential nosocomial exposure to Mycobacterium tuberculosis from a bronchoscope.

OBJECTIVE: To investigate a possible nosocomial outbreak of tuberculosis (TB). DESIGN: Retrospective cohort study. SETTING: Community hospital. METHODS: We reviewed medical records, hospital infection control measures, and potential locations of nosocomial exposure. We examined the results of acid-fast bacilli (AFB) smears, cultures, and drug susceptibility testing, and performed a DNA fingerprint analysis. We observed laboratory specimen processing procedures and bronchoscope disinfection procedures. We also reviewed bronchoscopy records. RESULTS: In October 2000, three patients had bronchoscopy specimen cultures that were positive for Mycobacterium tuberculosis. Of the three, only one had clinical signs and symptoms consistent with TB and positive AFB sputum smears. The other two did not have signs and symptoms consistent with TB and had no known exposure to individuals with infectious TB. The three M. tuberculosis isolates had matching DNA fingerprints. No evidence of laboratory cross-contamination was identified. The three culture-positive specimens of M. tuberculosis were collected with the same bronchoscope within 9 days. This bronchoscope was inadequately cleaned and disinfected between patients, and the automated reprocessor used was not approved for use with the hospital bronchoscope. CONCLUSIONS: One of the bronchoscopes at this hospital was contaminated with M. tuberculosis during bronchoscopy of an AFB-smear-positive patient. Subsequent specimen contamination likely occurred because the bronchoscope had been inadequately cleaned and disinfected. Patients who subsequently underwent bronchoscopy were also potentially exposed to M. tuberculosis from this bronchoscope.

Aged↗

PubMed2002

Identification and evolution of an IS6110 low-copy-number Mycobacterium tuberculosis cluster.

A cohort of 56 patients infected with related strains of Mycobacterium tuberculosis, the S75 group, was identified in a New Jersey population-based study of all isolates with a low number of copies of the insertion element IS6110. Genotyping was combined with surveillance data to identify the S75 group and to elucidate its recent evolution. The S75 group had similar demographic and geographic characteristics. Seventeen persons (30%) were linked epidemiologically. The S75 group was segregated from other low-copy-number isolates on the basis of several independent molecular methods. This group included 3 IS6110 genotype variants: BE, H6, and C28, containing 1, 2, and 3 IS6110 insertions, respectively. IS6110 insertion site mapping and comparative sequence analysis strongly suggest a stepwise acquisition of IS6110 elements from BE to H6 to C28. S75 represents a locally produced strain cluster that has recently evolved. The combination of multiple molecular tools with traditional epidemiology provides novel insights into dissemination, local transmission, and evolution of M. tuberculosis.

DNA Transposable Elements↗

PubMed2002

Sputum induction problems identified through genetic fingerprinting.

OBJECTIVE: To identify the contamination source of a cluster of eight positive Mycobacterium tuberculosis isolates from one laboratory session. METHODS: Spoligotyping was performed on M. tuberculosis isolates processed during one laboratory session. Laboratory and sputum induction protocols and records were reviewed. Sputum induction staff were interviewed. An environmental assessment of the sputum induction booth was performed. RESULTS: Spoligotyping identified a unique strain of susceptible M. tuberculosis from five induced sputa collected at Clinic A on the same day. Three specimens processed concurrently from other clinics had spoligotypes different from each other and from the cluster strain. A laboratory investigation revealed no procedural lapses. Sputum induction records from Clinic A indicated that patient 1 in the sputum induction booth had prior culture-confirmed tuberculosis. Patient 2 had a history of a drug-resistant strain. Patient 3 had completed tuberculosis treatment, with positive cultures 7 months earlier. Patients 4 and 5 were new to the clinic and had no subsequent positive M. tuberculosis specimens. The sputum induction booth was working within normal parameters. Sputum induction that day was overseen by a new employee with limited training and no supervision. A review of the sputum induction protocol identified ambiguity regarding care of the ultrasonic nebulizer between patients, which may have led to reuse of the discarded nebulizer solution from patient 1. CONCLUSIONS: A break in the sputum induction protocol may have contributed to contamination of patient specimens. Sputum induction is complicated, mandating adequate staff training and supervision and patient preparation. Spoligotyping identified a potential source of M. tuberculosis contamination.

Clinical Laboratory Techniques↗

PubMed2002

Molecular epidemiology of multidrug-resistant tuberculosis, New York City, 1995-1997.

From January 1, 1995, to December 31, 1997, we reviewed records of all New York City patients who had multidrug-resistant tuberculosis (MDRTB); we performed insertion sequence (IS) 6110-based DNA genotyping on the isolates. Secondary genotyping was performed for low IS6110 copy band strains. Patients with identical DNA pattern strains were considered clustered. From 1995 through 1997, MDRTB was diagnosed in 241 patients; 217 (90%) had no prior treatment history, and 166 (68.9%) were born in the United States or Puerto Rico. Compared with non-MDRTB patients, MDRTB patients were more likely to be born in the United States, have HIV infection, and work in health care. Genotyping results were available for 234 patients; 153 (65.4%) were clustered, 126 (82.3%) of them in eight clusters of >or=4 patients. Epidemiologic links were identified for 30 (12.8%) patients; most had been exposed to patients diagnosed before the study period. These strains were likely transmitted in the early 1990 s when MDRTB outbreaks and tuberculosis transmission were widespread in New York.

Adolescent↗

PubMed2002

Genotyping analyses of tuberculosis cases in U.S.- and foreign-born Massachusetts residents.

We used molecular genotyping to further understand the epidemiology and transmission patterns of tuberculosis (TB) in Massachusetts. The study population included 983 TB patients whose cases were verified by the Massachusetts Department of Public Health between July 1, 1996, and December 31, 2000, and for whom genotyping results and information on country of origin were available. Two hundred seventy-two (28%) of TB patients were in genetic clusters, and isolates from U.S-born were twice as likely to cluster as those of foreign-born (odds ratio [OR] 2.29, 95% confidence interval [CI] 1.69 to 3.12). Our results suggest that restriction fragment length polymorphism analysis has limited capacity to differentiate TB strains when the isolate contains six or fewer copies of IS6110, even with spoligotyping. Clusters of TB patients with more than six copies of IS6110 were more likely to have epidemiologic connections than were clusters of TB patients with isolates with few copies of IS6110 (OR 8.01, 95%; CI 3.45 to 18.93).

Adult↗

PubMed2002

Estimated costs of false laboratory diagnoses of tuberculosis in three patients.

We estimated direct medical and nonmedical costs associated with a false diagnosis of tuberculosis (TB) caused by laboratory cross-contamination of Mycobacterium tuberculosis cultures in Massachusetts in 1998 and 1999. For three patients who received misdiagnoses of active TB disease on the basis of laboratory cross-contamination, the costs totaled U.S. dollars 32618. Of the total, 97% was attributed to the public sector (local and state health departments, public health hospital and laboratory, and county and state correctional facilities); 3% to the private sector (physicians, hospitals, and laboratories); and <1% to the patient. Hospitalizations and inpatient tests, procedures, and TB medications accounted for 69% of costs, and outpatient TB medications accounted for 18%. The average cost per patient was dollars 10873 (range, dollars 1033-dollars 21306). Reducing laboratory cross-contamination and quickly identifying patients with cross-contaminated cultures can prevent unnecessary and potentially dangerous treatment regimens and anguish for the patient and financial burden to the health-care system.

Adult↗