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1.  Better Tests, Better Care: Improved Diagnostics for Infectious Diseases 
In this IDSA policy paper, we review the current diagnostic landscape, including unmet needs and emerging technologies, and assess the challenges to the development and clinical integration of improved tests. To fulfill the promise of emerging diagnostics, IDSA presents recommendations that address a host of identified barriers. Achieving these goals will require the engagement and coordination of a number of stakeholders, including Congress, funding and regulatory bodies, public health agencies, the diagnostics industry, healthcare systems, professional societies, and individual clinicians.
doi:10.1093/cid/cit578
PMCID: PMC3820169  PMID: 24200831
diagnostics; rapid diagnostics; point-of-care testing; molecular diagnostics; clinical microbiology; infectious diseases
2.  Controlled Clinical Comparison of New Pediatric Medium with Adsorbent Polymeric Beads (PF Plus) versus Charcoal-Containing PF Medium in the BacT/Alert Blood Culture System 
Journal of Clinical Microbiology  2014;52(6):1898-1900.
We conducted a controlled clinical comparison of PF Plus, the new pediatric medium with adsorbent polymeric beads, versus the charcoal-containing PF medium in the BacT/Alert blood culture system. A total of 2,381 pediatric cultures were enrolled, and 1,703 (71.5%) were deemed to be compliant and acceptable for analysis. Seventy-two cultures (4.2%) had a positive result with 80 clinically significant microorganisms. The results showed that the PF Plus medium yielded more clinically significant microorganisms than the BacT/Alert system (P < 0.05). In addition, the PF Plus bottle yielded positive results an average of 5.0 h earlier than the PF bottle for compliant clinically significant cultures (18.3 h versus 23.2 h, P = 0.004). PF Plus is an improved medium for detecting microorganisms that cause pediatric bloodstream infections.
doi:10.1128/JCM.00175-14
PMCID: PMC4042798  PMID: 24648564
3.  Bacteremic Disseminated Tuberculosis in Sub-Saharan Africa: A Prospective Cohort Study 
Even with provision of antiretroviral therapy and tuberculosis treatment, almost 50% of patients with bacteremic disseminated tuberculosis die within one month of hospitalization. This study characterizes survival, predictors of Mycobacterium tuberculosis bacteremia, and predictors of death.
Background. Disseminated tuberculosis is a major health problem in countries where generalized human immunodeficiency virus (HIV) infection epidemics coincide with high tuberculosis incidence rates; data are limited on patient outcomes beyond the inpatient period.
Methods. We enrolled consecutive eligible febrile inpatients in Moshi, Tanzania, from 10 March 2006 through 28 August 2010; those with Mycobacterium tuberculosis bacteremia were followed up monthly for 12 months. Survival, predictors of bacteremic disseminated tuberculosis, and predictors of death were assessed. Antiretroviral therapy (ART) and tuberculosis treatment were provided.
Results. A total of 508 participants were enrolled; 29 (5.7%) had M. tuberculosis isolated by blood culture. The median age of all study participants was 37.4 years (range, 13.6–104.8 years). Cough lasting >1 month (odds ratio [OR], 13.5; P < .001), fever lasting >1 month (OR, 7.8; P = .001), weight loss of >10% (OR, 10.0; P = .001), lymphadenopathy (OR 6.8; P = .002), HIV infection (OR, undefined; P < .001), and lower CD4 cell count and total lymphocyte count were associated with bacteremic disseminated tuberculosis. Fifty percent of participants with M. tuberculosis bacteremia died within 36 days of enrollment. Lower CD4 cell count (OR, 0.88; P = .049) and lower total lymphocyte count (OR, 0.76; P = .050) were associated with death. Magnitude of mycobacteremia tended to be higher among those with lower CD4 cell counts, but did not predict death.
Conclusions. In the era of free ART and access to tuberculosis treatment, almost one half of patients with M. tuberculosis bacteremia may die within a month of hospitalization. Simple clinical assessments can help to identify those with the condition. Advanced immunosuppression predicts death. Efforts should focus on early diagnosis and treatment of HIV infection, tuberculosis, and disseminated disease.
doi:10.1093/cid/cis409
PMCID: PMC3491770  PMID: 22511551
4.  Methicillin-Susceptible Staphylococcus aureus Endocarditis Isolates Are Associated With Clonal Complex 30 Genotype and a Distinct Repertoire of Enterotoxins and Adhesins 
The Journal of Infectious Diseases  2011;204(5):704-713.
Background. Using multinational collections of methicillin-susceptible Staphylococcus aureus (MSSA) isolates from infective endocarditis (IE) and soft tissue infections (STIs), we sought to (1) validate the finding that S. aureus in clonal complex (CC) 30 is associated with hematogenous complications and (2) test the hypothesis that specific genetic characteristics in S. aureus are associated with infection severity.
Methods. IE and STI isolates from 2 cohorts were frequency matched by geographic origin. Isolates underwent spa typing to infer CC and multiplex polymerase chain reaction for presence of virulence genes.
Results. 114 isolate pairs were genotyped. IE isolates were more likely to be CC30 (19.5% vs 6.2%; P = .005) and to contain 3 adhesins (clfB, cna, map/eap; P < .0001 for all) and 5 enterotoxins (tst, sea, sed, see, and sei; P ≤ .005 for all). CC30 isolates were more likely to contain cna, tst, sea, see, seg, and chp (P < .05 for all).
Conclusions. MSSA IE isolates were significantly more likely to be CC30 and to possess a distinct repertoire of virulence genes than MSSA STI isolates from the same region. The genetic basis of this association requires further study.
doi:10.1093/infdis/jir389
PMCID: PMC3156104  PMID: 21844296
5.  Performance of Nucleic Acid Amplification following Extraction of 5 Milliliters of Whole Blood for Diagnosis of Mycobacterium tuberculosis Bacteremia 
Journal of Clinical Microbiology  2012;50(1):138-141.
To investigate the performance of a nucleic acid amplification test (NAAT) for the diagnosis of Mycobacterium tuberculosis bacteremia, 5-ml aliquots of blood were inoculated into bioMérieux mycobacterial (MB) bottles and incubated, and 5-ml aliquots of blood were extracted and tested by real-time PCR. Of 25 samples from patients with M. tuberculosis bacteremia, 9 (36.0%) were positive and 1 (1.5%) of 66 control samples was positive by NAAT. The NAAT shows promise, but modifications should focus on improving sensitivity.
doi:10.1128/JCM.05963-11
PMCID: PMC3256687  PMID: 22031703
6.  Controlled Comparison of BacT/Alert MB System, Manual Myco/F Lytic Procedure, and Isolator 10 System for Diagnosis of Mycobacterium tuberculosis Bacteremia▿  
Journal of Clinical Microbiology  2011;49(8):3054-3057.
We compared the performance of the BacT/Alert MB system, that of the manual Bactec Myco/F Lytic procedure, and that of the Isolator 10 lysis-centrifugation system in the detection of Mycobacterium tuberculosis bacteremia. Mean times to detection were 16.4 days for BacT/Alert MB versus 20.0 days for Myco/F Lytic, 16.5 days for BacT/Alert MB versus 23.8 days for Isolator 10, and 21.1 days for Bactec Myco/F Lytic versus 22.7 days for Isolator 10. There were no significant differences in yields. The mean (range) magnitude of mycobacteremia was 30.0 (0.4, 90.0) CFU/ml and was correlated with the time to positivity in the BacT/Alert MB system (r = −0.4920). M. tuberculosis bacteremia was detected more rapidly in a continuously monitored liquid blood culture system, but the mean time to positivity exceeded 3 weeks.
doi:10.1128/JCM.01035-11
PMCID: PMC3147725  PMID: 21653761
7.  Quantitation of Candida CFU in Initial Positive Blood Cultures ▿  
Journal of Clinical Microbiology  2011;49(8):2879-2883.
One potential limitation of DNA-based molecular diagnostic tests for Candida bloodstream infection (BSI) is organism burden, which is not sufficiently characterized. We hypothesized that the number of CFU per milliliter (CFU/ml) present in an episode of Candida BSI is too low for reliable DNA-based diagnostics. In this study, we determined Candida burden in the first positive blood culture and explored factors that affect organism numbers and patient outcomes. We reviewed records of consecutive patients with a positive blood culture for Candida in the lysis-centrifugation blood culture system (Isolator, Wampole Laboratories, Cranbury, NJ) from 1987 to 1991. Descriptive statistics and logistic regression analyses were performed. One hundred fifty-two episodes of Candida BSI were analyzed. Patient characteristics included adult age (72%), indwelling central venous catheters (83%), recent surgery (29%), neutropenia (24%), transplant (14%), and other immune suppression (21%). Rates of treatment success and 30-day mortality for candidemia were each 51%. The median CFU/ml was 1 (mode 0.1, range 0.1 to >1,000). In the multivariate analysis, pediatric patients were more likely than adults to have high organism burdens (odds ratio [OR], 10.7; 95% confidence interval [95% CI], 4.3 to 26.5). Initial organism density did not affect patient outcome. Candida CFU/ml in the first positive blood culture of a BSI episode varies greatly; >50% of cultures had ≤1 CFU/ml, a concentration below the experimental yeast cell threshold for reliable DNA-based diagnostics. DNA-based diagnostics for Candida BSI will be challenged by low organism density and the need for sufficient specimen volume; future research on alternate targets is warranted.
doi:10.1128/JCM.00609-11
PMCID: PMC3147732  PMID: 21677065
8.  Transmission of MRSA between Companion Animals and Infected Human Patients Presenting to Outpatient Medical Care Facilities 
PLoS ONE  2011;6(11):e26978.
Methicillin-resistant Staphylococcus aureus (MRSA) is a significant pathogen in both human and veterinary medicine. The importance of companion animals as reservoirs of human infections is currently unknown. The companion animals of 49 MRSA-infected outpatients (cases) were screened for MRSA carriage, and their bacterial isolates were compared with those of the infected patients using Pulsed-Field Gel Electrophoresis (PFGE). Rates of MRSA among the companion animals of MRSA-infected patients were compared to rates of MRSA among companion animals of pet guardians attending a “veterinary wellness clinic” (controls). MRSA was isolated from at least one companion animal in 4/49 (8.2%) households of MRSA-infected outpatients vs. none of the pets of the 50 uninfected human controls. Using PFGE, patient-pets MRSA isolates were identical for three pairs and discordant for one pair (suggested MRSA inter-specie transmission p-value = 0.1175). These results suggest that companion animals of MRSA-infected patients can be culture-positive for MRSA, representing a potential source of infection or re-infection for humans. Further studies are required to better understand the epidemiology of MRSA human-animal inter-specie transmission.
doi:10.1371/journal.pone.0026978
PMCID: PMC3213111  PMID: 22102871
9.  The (1,3)β-d-Glucan Test as an Aid to Early Diagnosis of Invasive Fungal Infections following Lung Transplantation ▿  
Journal of Clinical Microbiology  2010;48(11):4083-4088.
The Fungitell assay for (1,3)β-d-glucan (BG) detection in serum has been evaluated in patients with invasive fungal infections (IFIs) and healthy controls and for the early diagnosis of IFI in cancer patients. We evaluated the BG assay for the detection of IFI in lung transplant recipients. Serial serum samples were prospectively collected from patients undergoing lung transplants at Duke Hospital. Fungal infections were classified according to revised European Organization for Research and Treatment of Cancer/Mycoses Study Group criteria. A receiver operator characteristic (ROC) curve was generated; possible causes for false-positive and false-negative tests were investigated by linear regression analysis. Seven hundred fifty-six serum specimens from 59 subjects without IFI and 41 specimens from 14 patients with proven or probable IFI were tested. The area under the ROC curve was 0.69. Based on a 60-pg/ml positive cutoff, per-patient sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 64%, 9%, 14%, and 50%, respectively; per-test estimates were 71%, 59%, 9%, and 97%, respectively. The majority (92%) of patients not diagnosed with an IFI had at least one BG level of ≥60 pg/ml, and 90% had at least one BG level of ≥80 pg/ml. Respiratory colonization with mold and hemodialysis significantly affected mean BG levels. In conclusion, the accuracy of the BG test is marginal and its utility as a tool for the early diagnosis of IFI is questionable in the lung transplant population. Although the NPV of the BG test is high, the low PPV limits its utility as a screening tool for early diagnosis of IFI.
doi:10.1128/JCM.01183-10
PMCID: PMC3020816  PMID: 20720025
10.  Potential Associations between Severity of Infection and the Presence of Virulence-Associated Genes in Clinical Strains of Staphylococcus aureus 
PLoS ONE  2011;6(4):e18673.
Background
The clinical spectrum of Staphylococcus aureus infection ranges from asymptomatic nasal carriage to osteomyelitis, infective endocarditis (IE) and death. In this study, we evaluate potential association between the presence of specific genes in a collection of prospectively characterized S. aureus clinical isolates and clinical outcome.
Methodology/Principal Findings
Two hundred thirty-nine S. aureus isolates (121 methicillin-resistant S. aureus [MRSA] and 118 methicillin-susceptible S. aureus [MSSA]) were screened by array comparative genomic hybridization (aCGH) to identify genes implicated in complicated infections. After adjustment for multiple tests, 226 genes were significantly associated with severity of infection. Of these 226 genes, 185 were not in the SCCmec element. Within the 185 non-SCCmec genes, 171 were less common and 14 more common in the complicated infection group. Among the 41 genes in the SCCmec element, 37 were more common and 4 were less common in the complicated group. A total of 51 of the 2014 sequences evaluated, 14 non-SCCmec and 37 SCCmec, were identified as genes of interest.
Conclusions/Significance
Of the 171 genes less common in complicated infections, 152 are of unknown function and may contribute to attenuation of virulence. The 14 non-SCCmec genes more common in complicated infections include bacteriophage-encoded genes such as regulatory factors and autolysins with potential roles in tissue adhesion or biofilm formation.
doi:10.1371/journal.pone.0018673
PMCID: PMC3082525  PMID: 21541311
11.  Dissemination of an Enterococcus Inc18-Like vanA Plasmid Associated with Vancomycin-Resistant Staphylococcus aureus▿  
Antimicrobial Agents and Chemotherapy  2010;54(10):4314-4320.
Of the 9 vancomycin-resistant Staphylococcus aureus (VRSA) cases reported to date in the literature, 7 occurred in Michigan. In 5 of the 7 Michigan VRSA cases, an Inc18-like vanA plasmid was identified in the VRSA isolate and/or an associated vancomycin-resistant Enterococcus (VRE) isolate from the same patient. This plasmid may play a critical role in the emergence of VRSA. We studied the geographical distribution of the plasmid by testing 1,641 VRE isolates from three separate collections by PCR for plasmid-specific genes traA, repR, and vanA. Isolates from one collection (phase 2) were recovered from surveillance cultures collected in 17 hospitals in 13 states. All VRE isolates from 2 Michigan institutions (n = 386) and between 60 and 70 VRE isolates (n = 883) from the other hospitals were tested. Fifteen VRE isolates (3.9%) from Michigan were positive for an Inc18-like vanA plasmid (9 E. faecalis [12.5%], 3 E. faecium [1.0%], 2 E. avium, and 1 E. raffinosus). Six VRE isolates (0.6%) from outside Michigan were positive (3 E. faecalis [2.7%] and 3 E. faecium [0.4%]). Of all E. faecalis isolates tested, 6.0% were positive for the plasmid, compared to 0.6% for E. faecium and 3.0% for other spp. Fourteen of the 15 plasmid-positive isolates from Michigan had the same Tn1546 insertion site location as the VRSA-associated Inc18-like plasmid, whereas 5 of 6 plasmid-positive isolates from outside Michigan differed in this characteristic. Most plasmid-positive E. faecalis isolates demonstrated diverse patterns by PFGE, with the exception of three pairs with indistinguishable patterns, suggesting that the plasmid is mobile in nature. Although VRE isolates with the VRSA-associated Inc18-like vanA plasmid were more common in Michigan, they remain rare. Periodic surveillance of VRE isolates for the plasmid may be useful in predicting the occurrence of VRSA.
doi:10.1128/AAC.00185-10
PMCID: PMC2944587  PMID: 20660665
12.  Multicenter Study To Determine Disk Diffusion and Broth Microdilution Criteria for Prediction of High- and Low-Level Mupirocin Resistance in Staphylococcus aureus▿  
Journal of Clinical Microbiology  2010;48(7):2469-2475.
Mupirocin susceptibility testing of Staphylococcus aureus has become more important as mupirocin is used more widely to suppress or eliminate S. aureus colonization and prevent subsequent health care- and community-associated infections. The present multicenter study evaluated two susceptibility testing screening methods to detect mupirocin high-level resistance (HLR), broth microdilution (BMD) MICs of ≥512 μg/ml, and a 6-mm zone diameter for a disk diffusion (DD) test with a 200-μg disk. Initial testing indicated that with Clinical and Laboratory Standards Institute methods for BMD and DD testing, the optimal conditions for the detection of mupirocin HLR were 24 h of incubation and reading of the DD zone diameters with transmitted light. Using the presence or absence of mupA as the “gold standard” for HLR, the sensitivity and specificity of a single-well 256 μg/ml BMD test were 97 and 99%, respectively, and those for the 200-μg disk test were 98 and 99%, respectively. Testing with two disks, 200 μg and 5 μg, was evaluated for its ability to distinguish HLR isolates (MICs ≥ 512 μg/ml), low-level-resistant (LLR) isolates (MICs = 8 to 256 μg/ml), and susceptible isolates (MICs ≤ 4 μg/ml). Using no zone with both disks as an indication of HLR and no zone with the 5-μg disk plus any zone with the 200-μg disk as LLR, only 3 of the 340 isolates were misclassified, with 3 susceptible isolates being classified as LLR. Use of standardized MIC or disk tests could enable the detection of emerging high- and low-level mupirocin resistance in S. aureus.
doi:10.1128/JCM.00340-10
PMCID: PMC2897470  PMID: 20444971
13.  Correlation of Cefoxitin MICs with the Presence of mecA in Staphylococcus spp.▿  
Journal of Clinical Microbiology  2009;47(6):1902-1905.
This report describes the results of an 11-laboratory study to determine if a cefoxitin broth microdilution MIC test could predict the presence of mecA in staphylococci. Using breakpoints of ≤4 μg/ml for mecA-negative and ≥6 or 8 μg/ml for mecA-positive isolates, sensitivity and specificity based on mecA or presumed mecA for Staphylococcus aureus at 18 h of incubation were 99.7 to 100% in three cation-adjusted Mueller-Hinton broths tested. For coagulase-negative strains at 24 h of incubation, breakpoints of ≤2 μg/ml for mecA-negative and ≥4 μg/ml for mecA-positive isolates gave sensitivity and specificity of 94 to 99% and 69 to 80%, respectively.
doi:10.1128/JCM.02304-08
PMCID: PMC2691132  PMID: 19357210
14.  Phylogenetic Analysis of Viridans Group Streptococci Causing Endocarditis ▿  
Journal of Clinical Microbiology  2008;46(9):3087-3090.
Identification of viridans group streptococci (VGS) to the species level is difficult because VGS exchange genetic material. We performed multilocus DNA target sequencing to assess phylogenetic concordance of VGS for a well-defined clinical syndrome. The hierarchy of sequence data was often discordant, underscoring the importance of establishing biological relevance for finer phylogenetic distinctions.
doi:10.1128/JCM.00920-08
PMCID: PMC2546745  PMID: 18650347
15.  Multicenter Evaluation of the New Vitek 2 Neisseria-Haemophilus Identification Card▿  
Journal of Clinical Microbiology  2008;46(8):2681-2685.
The new Neisseria-Haemophilus identification (NH) card for Vitek 2 was compared with 16S rRNA gene sequencing (16S) as the reference method for accurate identification of Neisseria spp., Haemophilus spp., and other fastidious gram-negative bacteria. Testing was performed on the Vitek 2 XL system with modified software at three clinical trial laboratories. Reproducibility was determined with nine ATCC quality control strains tested 20 times over a minimum of 10 days at all three sites. A challenge set of 30 strains with known identifications and 371 recent fresh and frozen clinical isolates were also tested. Expected positive and negative biochemical reactions were also evaluated for substrate reproducibility. All microorganisms were tested on the NH card, and all clinical and stock isolates were saved for 16S testing. All reproducibility tests yielded expected results within a 95% confidence interval. For challenge microorganisms, there was 98% overall correct identification, including 8% low discrimination, 2% incorrect identification, and 0% unidentified. For clinical strains, there was 96.5% overall correct identification, including 10.2% low discrimination, 2.7% incorrect identification, and 0.8% unidentified. The 2.7% (10/371) of clinical isolates that gave an incorrect identification consisted of 7 isolates correct to genus and 3 strains incorrect to genus. There were an additional 27 strains (primarily Neisseria species) for which the 16S identification result was different from the NH card result. These were all unclaimed species by the system. The new NH card met all performance criteria within a 95% confidence interval compared to identification of clinical isolates by 16S.
doi:10.1128/JCM.00449-08
PMCID: PMC2519493  PMID: 18579712
16.  Multicenter Evaluation of the Vitek 2 Anaerobe and Corynebacterium Identification Card▿  
Journal of Clinical Microbiology  2008;46(8):2646-2651.
The new anaerobe and Corynebacterium (ANC) identification card for Vitek 2 was compared with a 16S rRNA gene sequencing (16S) reference method for accuracy in the identification of corynebacteria and anaerobic species. Testing was performed on a Vitek 2 XL system with modified software at three clinical trial laboratories. Reproducibility was determined with nine ATCC quality control strains that were tested 20 times over a minimum of 10 days at all three sites. A challenge set of 50 well-characterized strains and 365 recent fresh and frozen clinical isolates were included in the study. The expected positive and negative biochemical well reactions were also evaluated for substrate reproducibility. All strains were tested with the ANC card, and clinical isolates were saved for 16S rRNA gene sequencing. All reproducibility tests yielded expected results within a 95% confidence interval, except for that with Corynebacterium striatum ATCC 6940, for which identification failed at one trial site. For the challenge isolates, there was 98% correct identification, 5% low discrimination, and 2% incorrect identification, and 0% were unidentified. For clinical strains, there was 95.1% correct identification, 4.9% low discrimination, and 4.6% incorrect identification, and 0.3% were unidentified. The 4.6% (17/365) of clinical isolates that were incorrectly identified consisted of 14 isolates that were correct at the genus level and three that were incorrect at the genus level. The new ANC card met all performance criteria within a 95% confidence interval compared to the identification performance by 16S rRNA gene sequencing.
doi:10.1128/JCM.00450-08
PMCID: PMC2519455  PMID: 18562580
17.  Association between 16S-23S Internal Transcribed Spacer Sequence Groups of Mycobacterium avium Complex and Pulmonary Disease▿ †  
Journal of Clinical Microbiology  2008;46(8):2790-2793.
Organisms within the Mycobacterium avium complex (MAC) may have differential virulence. We compared 33 subjects with MAC pulmonary disease to 75 subjects with a single positive culture without disease. M. avium isolates were significantly more likely to be associated with MAC pulmonary disease (odds ratio = 5.14, 95% confidence interval = 1.25 to 22.73) than M. intracellulare.
doi:10.1128/JCM.00719-08
PMCID: PMC2519484  PMID: 18550734
18.  Effect of Trimethoprim-Sulfamethoxazole Prophylaxis on Antimicrobial Resistance of Fecal Escherichia coli in HIV-Infected Patients in Tanzania 
Background
Trimethoprim-sulfamethoxazole (SXT) reduces morbidity and mortality among HIV-infected persons in Africa, but its impact on antimicrobial resistance is of concern.
Methods
HIV-uninfected (group A), HIV-infected but not requiring SXT (group B), and HIV-infected and eligible for SXT (group C) adults were recruited into a prospective observational cohort study in Moshi, Tanzania. Stool was examined for Escherichia coli nonsusceptible to SXT at baseline and at weeks 1, 2, 4, and 24. General estimating equation models were used to assess differences in susceptibility over time and cross-resistance to other antimicrobials.
Results
Of 181 subjects, 118 (65.1%) were female and the median (range) age was 36 (20 to 72) years. At baseline, E. coli nonsusceptible to SXT was isolated from 23 (53.5%) of 43 patients in group A, 25 (67.6%) of 37 patients in group B, and 37 (64.9%) of 57 patients in group C. The odds ratios (P value) for SXT nonsusceptibility in group C at weeks 1, 2, 4, and 24 compared with baseline were 3.4 (0.013), 3.0 (0.019), 2.9 (0.030), and 1.5 (0.515), respectively. SXT nonsusceptibility was associated with nonsusceptibility to ampicillin, chloramphenicol, ciprofloxacin, and nalidixic acid (P ≤ 0.006).
Conclusion
In Tanzania, carriage of fecal E. coli nonsusceptible to SXT is common before SXT prophylaxis. Initiation of SXT leads to further loss of susceptibility to SXT and to other antimicrobials.
doi:10.1097/QAI.0b013e31816856db
PMCID: PMC2586846  PMID: 18285712
antibiotic prophylaxis; Escherichia coli; feces; HIV; Tanzania; trimethoprim-sulfamethoxazole combination
19.  Murine Typhus and Febrile Illness, Nepal 
Emerging Infectious Diseases  2008;14(10):1656-1659.
Murine typhus was diagnosed by PCR in 50 (7%) of 756 adults with febrile illness seeking treatment at Patan Hospital in Kathmandu, Nepal. Of patients with murine typhus, 64% were women, 86% were residents of Kathmandu, and 90% were unwell during the winter. No characteristics clearly distinguished typhus patients from those with blood culture–positive enteric fever.
doi:10.3201/eid1410.080236
PMCID: PMC2609894  PMID: 18826840
Murine typhus; Rickettsia typhi; PCR; Nepal; typhoid; dispatch
20.  Genotypic Diversity of Coagulase-Negative Staphylococci Causing Endocarditis: a Global Perspective▿  
Journal of Clinical Microbiology  2008;46(5):1780-1784.
Coagulase-negative staphylococci (CNS) are important causes of infective endocarditis (IE), but their microbiological profiles are poorly described. We performed DNA target sequencing and susceptibility testing for 91 patients with definite CNS IE who were identified from the International Collaboration on Endocarditis—Microbiology, a large, multicenter, multinational consortium. A hierarchy of gene sequences demonstrated great genetic diversity within CNS from patients with definite endocarditis that represented diverse geographic regions. In particular, rpoB sequence data demonstrated unique genetic signatures with the potential to serve as an important tool for global surveillance.
doi:10.1128/JCM.02405-07
PMCID: PMC2395089  PMID: 18367572
21.  Genotypic Diversity of Anaerobic Isolates from Bloodstream Infections▿  
Journal of Clinical Microbiology  2008;46(5):1596-1601.
Accurate species determination for anaerobes from blood culture bottles has become increasingly important with the reemergence of anaerobic bacteremia and prevalence of multiple-drug-resistant microorganisms. Our knowledge of the taxonomical diversity of anaerobes that cause bloodstream infections is extremely limited, because identification historically has relied on conventional methods. Over a 5-year period, we profiled anaerobic bacteremia at a large tertiary care hospital with 16S rRNA gene sequencing to gain a better understanding of the taxonomical diversity of the bacteria. Of 316 isolates, 16S rRNA gene sequencing and phylogenetic analysis identified 316 (100%) to the genus or taxonomical group level and 289 (91%) to the species level. Conventional methods identified 279 (88%) to the genus level and 208 (66%) to the species level; 75 (24%) were misidentified at the species level, and 33 (10%) results were inconclusive. High intragenus variability was observed for Bacteroides and Clostridium species, and high intraspecies variability was observed for Bacteroides thetaiotaomicron and Fusobacterium nucleatum. Sequence-based identification has potential benefits in comparison to conventional methods, because it more accurately characterizes anaerobes within taxonomically related clusters and thereby may enable better correlation with specific clinical syndromes and antibiotic resistance patterns.
doi:10.1128/JCM.02469-07
PMCID: PMC2395081  PMID: 18322067
22.  Detection of Inducible Clindamycin Resistance in Staphylococci by Broth Microdilution Using Erythromycin-Clindamycin Combination Wells▿  
Journal of Clinical Microbiology  2007;45(12):3954-3957.
A study conducted by 11 laboratories investigated the ability of four combinations of erythromycin (ERY) and clindamycin (CC) (ERY and CC at 4 and 0.5, 6 and 1, 8 and 1.5, and 0.5 and 2 μg/ml) in a single well of a broth microdilution panel to predict the presence of inducible CC resistance. Each laboratory tested approximately 30 Staphylococcus aureus isolates and 20 coagulase-negative staphylococcus (CoNS) isolates in a panel using cation-adjusted Mueller-Hinton broth from three different manufacturers. Only the strains resistant to ERY and those susceptible or intermediate to CC were included in the analysis (S. aureus, n = 333; CoNS, n = 97). Results of the D-zone test were used as the gold standard. After an 18-h incubation, the combination of 4 μg/ml ERY and 0.5 μg/ml CC performed the best, with 98 to 100% sensitivity and 100% specificity for both organism groups. After a 24-h incubation, the ERY-CC combinations of 4 and 0.5, 6 and 1, and 8 and 1.5 μg/ml correlated well with the D-zone test.
doi:10.1128/JCM.01501-07
PMCID: PMC2168576  PMID: 17942655
23.  Detection of Bloodstream Infections in Adults: How Many Blood Cultures Are Needed?▿  
Journal of Clinical Microbiology  2007;45(11):3546-3548.
Although several reports have shown that two to three 20-ml blood cultures are adequate for the detection of bacteremia and fungemia in adults, a recent study (F. R. Cockerill et al., Clin. Infect. Dis. 38:1724-1730, 2004) found that two blood cultures detected only 80% of bloodstream infections and that three blood cultures detected 96% of episodes. We reviewed data at two university hospitals to determine whether the recent observations by Cockerill et al. are applicable more widely. We assessed all blood cultures obtained from adult inpatients from 1 January 2004 through 31 December 2005 at Robert Wood Johnson University Hospital and Duke University Medical Center. All instances in which ≥3 blood cultures per patient were obtained during a 24-h period were included. The medical records of patients who met the inclusion criteria were reviewed retrospectively to determine the clinical significance of the positive blood culture (true infection versus contamination). Data were analyzed to determine the cumulative sensitivity of blood cultures obtained sequentially during the 24-h time period. Of 629 unimicrobial episodes with ≥3 blood cultures obtained during the 24-h period, 460 (73.1%) were detected with the first blood culture, 564 (89.7%) were detected with the first two blood cultures, 618 (98.2%) were detected with the first three blood cultures, and 628 (99.8%) were detected with the first four blood cultures. Of 351 unimicrobial episodes with ≥4 blood cultures obtained during the 24-h period, 257 (73.2%) were detected with the first blood culture, 308 (93.9%) were detected with the first two blood cultures, 340 (96.9%) were detected with the first three blood cultures, and 350 (99.7%) were detected with the first four blood cultures. Among unimicrobial episodes, Staphylococcus aureus was more likely to be detected with the first blood culture (approximately 90% detected with the first blood culture). There were 58 polymicrobial episodes in which ≥3 blood cultures were obtained. Forty-seven (81.0%) were detected with the first blood culture, 54 (93.1%) were detected with the first two blood cultures, and 58 (100%) were detected with the first three blood cultures. The results of this study indicate that two blood cultures in a 24-h period will detect approximately 90% of bloodstream infections in adults. To achieve a detection rate of >99%, as many as four blood cultures may be needed. The previously held axiom that virtually all bloodstream infections can be detected with two to three blood cultures may no longer be valid but may also depend on the definition of the “first” blood culture obtained (see Materials and Methods and Discussion in the text).
doi:10.1128/JCM.01555-07
PMCID: PMC2168497  PMID: 17881544
24.  Comparison of the Digene Hybrid Capture System Cytomegalovirus (CMV) DNA (Version 2.0), Roche CMV UL54 Analyte-Specific Reagent, and QIAGEN RealArt CMV LightCycler PCR Reagent Tests Using AcroMetrix OptiQuant CMV DNA Quantification Panels and Specimens from Allogeneic-Stem-Cell Transplant Recipients▿  
Journal of Clinical Microbiology  2007;45(6):1972-1973.
The Digene Hybrid Capture system cytomegalovirus (CMV) DNA (version 2.0), Roche CMV UL54 analyte-specific reagent, and QIAGEN RealArt CMV LightCycler PCR reagent tests were compared using whole-virus standards and plasma specimens collected from allogeneic-stem-cell transplant recipients. PCR assays showed better speed, sensitivity, and specificity.
doi:10.1128/JCM.02515-06
PMCID: PMC1933098  PMID: 17314226
25.  Reevaluation of Clinical and Laboratory Standards Institute Disk Diffusion Breakpoints for Tetracyclines for Testing Enterobacteriaceae▿  
Journal of Clinical Microbiology  2007;45(5):1640-1643.
We reevaluated Enterobacteriaceae disk diffusion breakpoints for the tetracyclines published in the Clinical and Laboratory Standards Institute (CLSI) document M100-S16, which were (susceptible/resistant) ≥19 mm/≤14 mm for tetracycline, ≥16 mm/≤12 mm for doxycycline, and ≥19 mm/≤14 mm for minocycline. A collection of 504 recent clinical isolates of Enterobacteriaceae were tested against these tetracycline compounds by disk diffusion and broth microdilution methods according to CLSI guidelines. Regression line and scattergram plot analyses determined intermethod accuracy for current disk diffusion breakpoints and showed excellent r values of 0.91 to 0.95. However, error rates (minor/major [false-resistant]/very major [false-susceptible]) were 14.9/0.8/0.0% for tetracycline, 11.5/0.4/0.0% for doxycycline, and 30.6/0.7/0.0% for minocycline and only 4.4/0.0/0.0% for tetracycline, 5.6/0.0/0.2% for doxycycline, and 8.3/0.0/0.3% for minocycline when proposed breakpoints were modified to (susceptible/resistant) ≥15 mm/≤11 mm for tetracycline, ≥14 mm/≤10 mm for doxycycline, and ≥16 mm/≤12 mm for minocycline. Listed modifications were recently approved by the CLSI (M100-S17).
doi:10.1128/JCM.00143-07
PMCID: PMC1865907  PMID: 17360844

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