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A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

The Human Microbiome Project used rigorous good clinical practice standards to complete comprehensive body site sampling in healthy 18- to 40-yr-old adults, creating an unparalleled reference set of microbiome specimens. To ensure that specimens represented minimally perturbed microbiomes, we first screened potential participants using exclusion criteria based on health history, including the presence of systemic diseases (e.g., hypertension, cancer, or immunodeficiency or autoimmune disorders), use of potential immunomodulators, and recent use of antibiotics or probiotics. Subsequent physical examinations excluded individuals based on body mass index (BMI), cutaneous lesions, and oral health. We screened 554 individuals to enroll 300 (149 men and 151 women, mean age 26 yr, mean BMI 24 kg/m2, 20.0% racial minority, and 10.7% Hispanic). We obtained specimens from the oral cavity, nares, skin, gastrointestinal tract, and vagina (15 specimens from men and 18 from women). The study evaluated longitudinal changes in an individual's microbiome by sampling 279 participants twice (mean 212 d after the first sampling; range 30-359 d) and 100 individuals 3 times (mean 72 d after the second sampling; range 30-224 d). This sampling strategy yielded 11,174 primary specimens, from which 12,479 DNA samples were submitted to 4 centers for metagenomic sequencing. Our clinical design and well-defined reference cohort has laid a foundation for microbiome research.—Aagaard, K., Petrosino, J., Keitel, W., Watson, M., Katancik, J., Garcia, N., Patel, S., Cutting, M., Madden, T., Hamilton, H., Harris, E., Gevers, D., Simone, G., McInnes, P., Versalovic, J. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters.

Varicella-zoster virus (VZV) is the causative agent of two diseases: varicella (chickenpox) and zoster (shingles). Although varicella generally is a mild disease in children, serious morbidity and mortality are common if infection occurs in neonates, pregnant women, adults, or immunocompromised patients. For this reason, the Centers for Disease Control and Prevention recommends that all the hospitals institute control measures. Healthcare workers should be screened for VZV immunity and, if susceptible, should receive the recently licensed Oka/Merck vaccine (unless contraindicated). This article reviews nosocomial outbreaks associated with VZV and provides detailed algorithms for preexposure immunization and postexposure management of healthcare workers exposed to VZV.

Men with genital ulcer disease (GUD) attending a clinic in Malawi were evaluated and treated with one of five drug regimens. Hemophilus ducreyi was isolated from 204 (26.2%) of 778 patients. Of 677 men 198 (29.2%) had treponemes detected in ulcer material by direct immunofluorescence or had rapid plasma reagin reactivity of > or = 1:8. Human immunodeficiency virus type 1 (HIV-1) seroprevalence was 58.9% overall and 75.8% among patients reporting a history of GUD (p < 0.001). By logistic regression analysis HIV-1 seropositivity was shown to impair ulcer healing (p = 0.003). Treatment failure rates for culture-proven chancroid were 19% for trimethoprim-sulfamethoxazole 12.9% and 7.4% respectively for low- and high-dose erythromycin regimens and 8.3% and 0 respectively for low- and high-dose ciprofloxacin regimens. Herpes antigen was detected by EIA in 6 (23.1%) of 26 nonhealing ulcers. In Malawi GUD should be managed as a syndrome to assure treatment of both syphilis and chancroid. (authors)

We compared the ability of direct immunofluorescent staining (DFA) and the PCR to detect Treponema pallidum in specimens from patients with genital ulcer disease. Touch preparations from 156 patients with genital lesions were fixed in acetone and stained with a fluorescein-labeled monoclonal antibody specific for the 37-kDa antigen of T. pallidum. After microscopic examination, the smear was removed from the slide with a swab. DNA was extracted with phenol-chloroform and precipitated with isopropanol. Ten microliters of the extracted DNA was amplified by PCR using primers for the gene encoding the 47-kDa protein of T. pallidum and hybridized to an internal probe. Twenty-two of 156 specimens were positive for T. pallidum by DFA and PCR, while 127 were negative by both methods, yielding a concordance of 95.5% (kappa = 0.84). Four specimens were positive by PCR and negative by DFA, while three specimens were negative by PCR and positive by DFA. The DFA-negative, PCR-positive specimens may have resulted from the presence of large numbers of leukocytes on the slides, obscuring visualization of treponemes. The DFA-positive, PCR-negative results were not due to inhibition of the PCR since purified T. pallidum DNA was amplified when added to aliquots of these specimens. Negative results in these specimens were most likely due to inefficient recovery of their DNA. These data suggest that DFA and PCR are equivalent methods for detection of T. pallidum on touch preparations of genital lesions. Further refinements of the PCR assay are necessary for it to significantly improve the detection of T. pallidum in genital lesions.

Author Manuscript date: 2013 February 05., Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

Background and Objectives: The spread of sexually transmitted diseases (STDs), including gonorrhea, is affected by the duration of infection. Oral antibiotic therapy for gonococcal infection has been shown to be as effective as conventional intramuscular injection with ceftriaxone. Rapid cure would be expected to limit further spread of gonorrhea. However, the speed with which Neisseria gonorrhoeae is eliminated from the urogenital tract has not been evaluated. Goal of this Study: To determine the time required for elimination of Neisseria gonorrhoeae from the urine, mucosa, and semen in male subjects after treatment with ceftriaxone (250 mg intramuscularly), ciprofloxacin (500 mg by mouth, single dose) or cefixime (400 mg by mouth, single dose). Results: In 14 subjects, gonococci were eliminated from the urine within 4 hours of therapy and the mucosa within 24 hours after therapy. In 9 additional subjects, gonococci were eliminated from the semen by 24 hours after therapy. Conclusion: These results support the efficacy of single-dose oral therapy for gonorrhea and suggest that earlier follow-up for proof of cure in clinical trials of new antibiotics for gonorrhea may be acceptable. Rapid elimination of gonorrhea reduces the risk for continued transmission of the organism

OBJECTIVES--To evaluate gonococcal (GU) and nongonococcal urethritis (NGU), chlamydia antigen, and serostatus for syphilis and human immunodeficiency virus (HIV) among males attending a Malawian STD clinic with complaints of urethral discharge and/or dysuria. To collect demographic and behavioural data and to determine the effectiveness of five treatments for urethritis. METHODS--Urethritis was diagnosed using microscopy and culture for Neisseria gonorrhoeae. Sera were screened with rapid plasma reagin (RPR) and if reactive, with microhaemagglutination for Treponema pallidum (MHA-TP). HIV antibodies and chlamydia antigen were detected using enzyme immunoassay. Patients were randomised for treatment, cure was assessed 8-10 days later. RESULTS--At enrolment, GU was diagnosed in 415 (80.3%) and NGU in 59 (11.2%) of 517 males. Chlamydia antigen was found in 26 (5.2%) of 497 specimens tested. Syphilis seropositivity rate (RPR and MHA-TP reactive) was 10.7%. Overall HIV seroprevalence was 44.2%; 71.7% of men with reactive syphilis serology were HIV(+) compared with 40.9% of syphilis seronegatives (OR: 3.6, p < 0.001). Trimethoprim 320 mg/sulphamethoxazole 1600 mg by mouth for 2 days (TMPSMX), or the combination of amoxicillin 3 gm, probenicid 1 gm, and clavulanate 125 mg by mouth once (APC), failed to cure gonorrhoea effectively. Amoxicillin 3 gm, probenicid 1 gm, and clavulanate 125 mg, by mouth once with doxycycline 100 mg BID for 7 days (APC-D), gentamicin 240 mg IM once (GENT), ciprofloxacin 250 mg by mouth once (CIPRO) cured 92.9% to 95% of gonorrhoea. APC-D treatment did not generate less NGU at follow-up. HIV serostatus did not affect cure of urethritis. CONCLUSION--All patients presenting with urethritis should be treated syndromically using a simple algorithm and screened for syphilis seroreactivity for appropriate treatment and counselling.