We report seven cases of Haemophilus haemolyticus invasive disease detected in the United States, which were previously misidentified as non-typeable Haemophilus influenzae (Hi). All cases had different symptoms and presentations. Our study suggests that a testing scheme that includes reliable PCR assays and standard microbiological methods should be used in order to improve H. haemolyticus identification.

Childhood acellular pertussis vaccines were licensed and implemented in the US in the 1990s following an effort to improve on the safety profile of whole-cell vaccines. However, waning of immunity from acellular vaccines may be driving the recent resurgence of pertussis, raising the need to consider new prevention strategies.

To investigate the potential herd immunity effect of MenAfriVac, a new conjugate vaccine against serogroup A Neisseria meningitidis, a multiple cross-sectional carriage study was conducted in three districts in Burkina Faso in 2009, yielding a total of 20 326 oropharyngeal samples. A major challenge was the harmonisation of operational procedures and ensuring the reliability of results. Here we describe the laboratory quality control (QC) system that was implemented. Laboratory analysis performed by three local laboratories included colony morphology assessment, oxidase test, Gram stain, β-galactosidase activity using o-nitrophenyl-β-galactopyranoside (ONPG), γ-glutamyl transferase (GGT) activity and slide agglutination serogrouping. Internal QC was performed on media, reagents, laboratory equipment and field conditions. Confirmation of results and molecular characterisation was performed at the Norwegian Institute of Public Health (Oslo, Norway). External QC was performed on 3% of specimens where no colonies morphologically resembling N. meningitidis had been identified and on 10% of non-ONPG-/GGT+ isolates. The QC system was a critical element: it identified logistical and operational problems in real time and ensured accuracy of the final data. The overall N. meningitidis carriage prevalence (3.98%) was probably slightly underestimated and the calculated true prevalence was 4.48%. The components of the presented QC system can easily be implemented in any other laboratory study.

In response to the 2007-2009 Haemophilus influenzae type b (Hib) vaccine shortage in the United States, we developed a flexible model of Hib transmission and disease for optimizing Hib vaccine programs in diverse populations and situations. The model classifies population members by age, colonization/disease status, and antibody levels, with movement across categories defined by differential equations. We implemented the model for the United States as a whole, England and Wales, and the Alaska Native population. This model accurately simulated Hib incidence in all 3 populations, including the increased incidence in England/Wales beginning in 1999 and the change in Hib incidence in Alaska Natives after switching Hib vaccines in 1996. The model suggests that a vaccine shortage requiring deferral of the booster dose could last 3 years in the United States before loss of herd immunity would result in increasing rates of invasive Hib disease in children <5 years of age.

BACKGROUND AND OBJECTIVES:We investigated a pertussis outbreak characterized by atypical cases, confirmed by polymerase chain reaction (PCR) alone at a single laboratory, which persisted despite high vaccine coverage and routine control measures. We aimed to determine whether Bordetella pertussis was the causative agent and advise on control interventions.METHODS:We conducted case ascertainment, confirmatory testing for pertussis and other pathogens, and an assessment for possible sources of specimen contamination, including a survey of clinic practices, sampling clinics for B pertussis DNA, and review of laboratory quality indicators.RESULTS:Between November 28, 2008, and September 4, 2009, 125 cases were reported, of which 92 (74%) were PCR positive. Cases occurring after April 2009 (n = 79; 63%) had fewer classic pertussis symptoms (63% vs 98%; P <.01), smaller amounts of B pertussis DNA (mean PCR cycle threshold value: 40.9 vs 33.1; P <.01), and a greater proportion of PCR-positive results (34% vs 6%; P <.01). Cultures and serology for B pertussis were negative. Other common respiratory pathogens were detected. We identified factors that likely resulted in specimen contamination at the point of collection: environmentally present B pertussis DNA in clinics from vaccine, clinic standard specimen collection practices, use of liquid transport medium, and lack of clinically relevant PCR cutoffs.CONCLUSIONS:A summer pertussis pseudo-outbreak, multifactorial in cause, likely occurred. Recommendations beyond standard practice were made to providers on specimen collection and environmental cleaning, and to laboratories on standardizing PCR protocols and reporting results, to minimize false-positive results from contaminated clinical specimens.

OBJECTIVE: To evaluate the impact of the adolescent Tdap vaccination (tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis vaccine) program on pertussis trends in the United States. DESIGN: Retrospective analysis of nationally reported pertussis cases, January 1, 1990, through December 31, 2009. SETTING: United States. PARTICIPANTS: Confirmed and probable pertussis cases. Intervention  The US Tdap vaccination program. Main Outcome Measure  Rate ratios of reported pertussis incidence (defined as incidence among 11- to 18-year-olds divided by the combined incidence in all other age groups) modeled through segmented regression analysis and age-specific trends in reported pertussis incidence over time. RESULTS: A total of 200 401 pertussis cases were reported in the United States from 1990 to 2009. Overall incidence ranged from 1.0 to 8.8 per 100 000 persons (1991 and 2004, respectively). Slope coefficients (estimated annual rate of change in rate ratios) from segmented regression showed a steady increase in pertussis incidence among adolescents 11 to 18 years old compared with all other age groups before Tdap introduction (slope = 0.22; P < .001), and a steep decreasing trend postintroduction (slope = -0.48; P < .001) suggesting a direct impact of vaccination among adolescents. Indirect effects of adolescent vaccination were not observed among infants younger than 1 year. CONCLUSIONS: Changes in pertussis incidence in the United States from 2005 to 2009 revealed a divergence between 11- to 18-year-olds and other age groups, suggesting that targeted use of Tdap among adolescents reduced disease preferentially in this age group. Increased Tdap coverage in adolescents and adults is needed to realize the full direct and indirect benefits of vaccination.

ABSTRACT: Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time (SMRT) DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications.

DNA methylation is the most common form of DNA modification in prokaryotic and eukaryotic genomes. We have applied the method of single-molecule, real-time (SMRT®) DNA sequencing that is capable of direct detection of modified bases at single-nucleotide resolution to characterize the specificity of several bacterial DNA methyltransferases (MTases). In addition to previously described SMRT sequencing of N6-methyladenine and 5-methylcytosine, we show that N4-methylcytosine also has a specific kinetic signature and is therefore identifiable using this approach. We demonstrate for all three prokaryotic methylation types that SMRT sequencing confirms the identity and position of the methylated base in cases where the MTase specificity was previously established by other methods. We then applied the method to determine the sequence context and methylated base identity for three MTases with unknown specificities. In addition, we also find evidence of unanticipated MTase promiscuity with some enzymes apparently also modifying sequences that are related, but not identical, to the cognate site.

Vanadium can induce potent hypoglycemic effects in type 1 and type 2 diabetes mellitus animals, but toxic adverse effects have inhibited the translation of these findings. Administration of vanadate in a black tea decoction has shown impressive hypoglycemic effects without evidence of toxicity in short-term studies. The purpose of this study was to investigate the hypoglycemic action and the toxic adverse effects of a tea/vanadate (T/V) decoction in diabetic rats over a 14-month treatment period. Streptozotocin-induced type 1 diabetes mellitus rats were orally gavaged with 40 mg sodium vanadate in a black tea decoction only when blood glucose levels were greater than 10 mmol/L. Glycemic status and liver and kidney function were monitored over 14 months. All of the diabetic rats in this treatment group (n = 25) required treatment with the T/V decoction at the start of the study to reduce blood glucose levels to less than 10 mmol/L. Diarrhea was uncommon among the T/V-treated animals during the first week of T/V treatment and was absent thereafter. There was no evidence of liver or kidney dysfunction or injury. From 2 to 6 months, fewer animals required the T/V treatment to maintain their blood glucose levels. After 9 months of treatment, none of the diabetic animals required any T/V to maintain their blood glucose levels at less than 10 mmol/L. Oral administration of a T/V decoction provides safe, long-acting hypoglycemic effects in type 1 diabetes mellitus rats. The typical glycemic signs of diabetes were absent for the last 5 months of the study.

We describe strand-specific, base-resolution detection of 5-hydroxymethylcytosine (5-hmC) in genomic DNA with single-molecule sensitivity, combining a bioorthogonal, selective chemical labeling method of 5-hmC with single-molecule, real-time (SMRT) DNA sequencing. The chemical labeling not only allows affinity enrichment of 5-hmC-containing DNA fragments but also enhances the kinetic signal of 5-hmC during SMRT sequencing. We applied the approach to sequence 5-hmC in a genomic DNA sample with high confidence.