Low unspliced cell-associated HIV RNA in early treated adolescents living with HIV on long suppressive ART

Introduction

Initiation of antiretroviral treatment (ART) in patients early after HIV-infection and long-term suppression leads to low or undetectable levels of HIV RNA and cell-associated (CA) HIV DNA and RNA. Both CA-DNA and CA-RNA, overestimate the size of the HIV reservoir but CA-RNA as well as p24/cell-free viral RNA can be indicators of residual viral replication. This study describes HIV RNA amounts and levels of cytokines/soluble markers in 40 well-suppressed adolescents who initiated ART early in life and investigated which viral markers may be informative as endpoints in cure clinical trials within this population.

Methods

Forty adolescents perinatally infected with HIV on suppressive ART for >5 years were enrolled in the CARMA study. HIV DNA and total or unspliced CA-RNA in PBMCs were analyzed by qPCR/RT-qPCR and dPCR/RT-dPCR. Cell-free HIV was determined using an ultrasensitive viral load (US-VL) assay. Plasma markers and p24 were analyzed by digital ELISA and correlations between total and unspliced HIV RNA and clinical markers, including age at ART, Western Blot score, levels of cytokines/inflammation markers or HIV CA-DNA, were tested.

Results

CA-RNA was detected in two thirds of the participants and was comparable in RT-qPCR and RT-dPCR. Adolescents with undetectable CA-RNA showed significantly lower HIV DNA compared to individuals with detectable CA-RNA. Undetectable unspliced CA-RNA was positively associated with age at ART initiation and Western Blot score. We found that a higher concentration of TNF-α was predictive of higher CA-DNA and CA-RNA. Other clinical characteristics like US-VL, time to suppression, or percent CD4+ T-lymphocytes were not predictive of the CA-RNA in this cross-sectional study.

Conclusions

Low CA-DNA after long-term suppressive ART is associated with lower CA-RNA, in concordance with other reports. Patients with low CA-RNA levels in combination with low CA-DNA and low Western Blot scores should be further investigated to characterize candidates for treatment interruption trials. Unspliced CA-RNA warrants further investigation as a marker that can be prioritized in paediatric clinical trials where the sample volume can be a significant limitation.

Results of German external quality assessment schemes for SARS-CoV-2 antigen detection

The COVID-19 pandemic illustrated the important role of diagnostic tests, including lateral flow tests (LFTs), in identifying patients and their contacts to slow the spread of infections. INSTAND performed external quality assessments (EQA) for SARS-CoV-2 antigen detection with lyophilized and chemically inactivated cell culture supernatant of SARS-CoV-2 infected Vero cells. A pre-study demonstrated the suitability of the material. Participants reported qualitative and/or quantitative antigen results using either LFTs or automated immunoassays for five EQA samples per survey. 711 data sets were reported for LFT detection in three surveys in 2021. This evaluation focused on the analytical sensitivity of different LFTs and automated immunoassays. The inter-laboratory results showed at least 94% correct results for non-variant of concern (VOC) SARS-CoV-2 antigen detection for viral loads of ≥ 4.75 × 106 copies/mL and SARS-CoV-2 negative samples. Up to 85% had success for a non-VOC viral load of ~ 1.60 × 106 copies/mL. A viral load of ~ 1.42 × 107 copies/mL of the Delta VOC was reported positive in > 96% of results. A high specificity was found with almost 100% negative SARS-CoV-2 antigen results for HCoV 229E and HCoV NL63 positive samples. Quantitative results correlated with increasing SARS-CoV-2 viral load but showed a broad scatter. This study shows promising SARS-CoV-2 antigen test performance of the participating laboratories, but further investigations with the now predominant Omicron VOC are needed.

Pulmonary Hypertension in patients with Interstitial Lung Disease: a tool for early detection

Pulmonary hypertension (PH) complicates the treatment of interstitial lung disease (ILD) patients resulting in poor functional status and worse outcomes. Early recognition of PH in ILD is important for initiating therapy and considering lung transplantation. However, no standard exists regarding which patients to screen for PH‐ILD or the optimal method to do so. The aim of this study was to create a risk assessment tool that could reliably predict PH in ILD patients. We developed a PH‐ILD Detection tool that incorporated history, exam, 6‐min walk distance, diffusion capacity for carbon monoxide, chest imaging, and cardiac biomarkers to create an eight‐component score. This tool was analyzed retrospectively in 154 ILD patients where each patient was given a score ranging from 0 to 12. The sensitivity (SN) and specificity (SP) of the PH‐ILD Detection tool and an area‐under‐the‐curve (AUC) were calculated. In this cohort, 74 patients (48.1%) had PH‐ILD. A score of ≥6 on the PH‐ILD Detection tool was associated with a diagnosis of PH‐ILD (SN: 86.5%; SP: 86.3%; area‐under‐the‐curve: 0.920, p < 0.001). The PH‐ILD Detection tool provides high SN and SP for detecting PH in ILD patients. With confirmation in larger cohorts, this tool could improve the diagnosis of PH in ILD and may suggest further testing with right heart catheterization and earlier intervention with inhaled treprostinil and/or lung transplant evaluation.

Monkeypox: another test for PCR

Monkeypox was declared a public health emergency of international concern by the World Health Organization (WHO) on 23 July 2022. Between 1 January and 23 July 2022, 16,016 laboratory confirmed cases of monkeypox and five deaths were reported to WHO from 75 countries on all continents. Public health authorities are proactively identifying cases and tracing their contacts to contain its spread. As with COVID-19, PCR is the only method capable of being deployed at sufficient speed to provide timely feedback on any public health interventions. However, at this point, there is little information on how those PCR assays are being standardised between laboratories. A likely reason is that testing is still limited on a global scale and that detection, not quantification, of monkeypox virus DNA is the main clinical requirement. Yet we should not be complacent about PCR performance. As testing requirements increase rapidly and specimens become more diverse, it would be prudent to ensure PCR accuracy from the outset to support harmonisation and ease regulatory conformance. Lessons from COVID-19 should aid implementation with appropriate material, documentary and methodological standards offering dynamic mechanisms to ensure testing that most accurately guides public health decisions.

The Dangers of Using Cq to Quantify Nucleic Acid in Biological Samples: A Lesson From COVID-19

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA quantities, measured by reverse transcription quantitative PCR (RT-qPCR), have been proposed to stratify clinical risk or determine analytical performance targets. We investigated reproducibility and how setting diagnostic cutoffs altered the clinical sensitivity of coronavirus disease 2019 (COVID-19) testing.

METHODS

Quantitative SARS-CoV-2 RNA distributions [quantification cycle (Cq) and copies/mL] from more than 6000 patients from 3 clinical laboratories in United Kingdom, Belgium, and the Republic of Korea were analyzed. Impact of Cq cutoffs on clinical sensitivity was assessed. The June/July 2020 INSTAND external quality assessment scheme SARS-CoV-2 materials were used to estimate laboratory reported copies/mL and to estimate the variation in copies/mL for a given Cq.

RESULTS

When the WHO-suggested Cq cutoff of 25 was applied, the clinical sensitivity dropped to about 16%. Clinical sensitivity also dropped to about 27% when a simulated limit of detection of 106 copies/mL was applied. The interlaboratory variation for a given Cq value was >1000 fold in copies/mL (99% CI).

CONCLUSION

While RT-qPCR has been instrumental in the response to COVID-19, we recommend Cq (cycle threshold or crossing point) values not be used to set clinical cutoffs or diagnostic performance targets due to poor interlaboratory reproducibility; calibrated copy-based units (used elsewhere in virology) offer more reproducible alternatives. We also report a phenomenon where diagnostic performance may change relative to the effective reproduction number. Our findings indicate that the disparities between patient populations across time are an important consideration when evaluating or deploying diagnostic tests. This is especially relevant to the emergency situation of an evolving pandemic.

Association between coronary artery vitamin D receptor expression and select systemic risks factors for coronary artery atherosclerosis

OBJECTIVE

The aim of this study is to analyze the association between coronary artery vitamin D receptor (VDR) expression and systemic coronary artery atherosclerosis (CAA) risk factors.

METHODS

Female cynomolgus monkeys (n = 39) consumed atherogenic diets containing the women's equivalent of 1000 IU/day of vitamin D₃. After 32 months consuming the diets, each monkey underwent surgical menopause. After 32 postmenopausal months, CAA and VDR expression were quantified in the left anterior descending coronary artery. Plasma 25OHD_3, lipid profiles and serum monocyte chemotactic protein-1 (MCP-1) were measured.

RESULTS

In postmenopausal monkeys receiving atherogenic diets, serum MCP-1 was significantly elevated compared with baseline (482.2 ± 174.2 pg/ml vs. 349.1 ± 163.2 pg/ml, respectively; p < 0.001; d = 0.79) and at the start of menopause (363.4 ± 117.2 pg/ml; p < 0.001; d = 0.80). Coronary VDR expression was inversely correlated with serum MCP-1 (p = 0.042). Additionally, the change of postmenopausal MCP-1 (from baseline to necropsy) was significantly reduced in the group with higher, compared to below the median, VDR expression (p = 0.038). The combination of plasma 25OHD₃ and total plasma cholesterol/high-density lipoprotein cholesterol was subsequently broken into low-risk, moderate-risk and high-risk groups; as the risk increased, the VDR quantity decreased (p = 0.04). CAA was not associated with various atherogenic diets.

CONCLUSION

Coronary artery VDR expression was inversely correlated with markers of CAA risk and inflammation, including MCP-1, suggesting that systemic and perhaps local inflammation in the artery may be associated with reduced arterial VDR expression.

Single base mutations in the nucleocapsid gene of SARS-CoV-2 affects amplification efficiency of sequence variants and may lead to assay failure

Reverse transcriptase quantitative PCR (RT-qPCR) is the main diagnostic assay used to detect SARS-CoV-2 RNA in respiratory samples. RT-qPCR is performed by specifically targeting the viral genome using complementary oligonucleotides called primers and probes. This approach relies on prior knowledge of the genetic sequence of the target. Viral genetic variants with changes to the primer/probe binding region may reduce the performance of PCR assays and have the potential to cause assay failure. In this work we demonstrate how two single nucleotide variants (SNVs) altered the amplification curve of a diagnostic PCR targeting the Nucleocapsid (N) gene and illustrate how threshold setting can lead to false-negative results even where the variant sequence is amplified. We also describe how in silico analysis of SARS-CoV-2 genome sequences available in the COVID-19 Genomics UK Consortium (COG-UK) and GISAID databases was performed to predict the impact of sequence variation on the performance of 22 published PCR assays. The vast majority of published primer and probe sequences contain sequence mismatches with at least one SARS-CoV-2 lineage. We recommend that visual observation of amplification curves is included as part of laboratory quality procedures, even in high throughput settings where thresholds are set automatically and that in silico analysis is used to monitor the potential impact of new variants on established assays. Ideally comprehensive in silico analysis should be applied to guide selection of highly conserved genomic regions to target with future SARS-CoV-2 PCR assays.

Digital PCR can augment the interpretation of RT-qPCR Cq values for SARS-CoV-2 diagnostics

Coronavirus disease 2019 (COVID-19) is an infectious, acute respiratory disease caused mainly by person-to-person transmission of the coronavirus SARS-CoV-2. Its emergence has caused a world-wide acute health crisis, intensified by the challenge of reliably identifying individuals likely to transmit the disease. Diagnosis is hampered by the many unknowns surrounding this disease, including those relating to infectious viral burden. This uncertainty is exacerbated by disagreement surrounding the clinical relevance of molecular testing using reverse transcription quantitative PCR (RT-qPCR) for the presence of viral RNA, most often based on the reporting of quantification cycles (Cq), which is also termed the cycle threshold (Ct) or crossing point (Cp). Despite it being common knowledge that Cqs are relative values varying according to a wide range of different parameters, there have been efforts to use them as though they were absolute units, with Cqs below an arbitrarily determined value, deemed to signify a positive result and those above, a negative one. Our results investigated the effects of a range of common variables on Cq values. These data include a detailed analysis of the effect of different carrier molecules on RNA extraction. The impact of sample matrix of buccal swabs and saliva on RNA extraction efficiency was demonstrated in RT-qPCR and the impact of potentially inhibiting compounds in urine along with bile salts were investigated in RT-digital PCR (RT-dPCR). The latter studies were performed such that the impact on the RT step could be separated from the PCR step. In this way, the RT was shown to be more susceptible to inhibitors than the PCR. Together, these studies demonstrate that the consequent variability of test results makes subjective Cq cut-off values unsuitable for the identification of infectious individuals. We also discuss the importance of using reliable control materials for accurate quantification and highlight the substantial role played by dPCR as a method for their development.

Comparison of SARS-CoV-2 N gene real-time RT-PCR targets and commercially available mastermixes

BACKGROUND

This study aimed to evaluate the impact of four different reverse transcription quantitative PCR (RT-qPCR) master mixes on the performance of SARS-CoV-2 diagnostic PCRs using three primer/probe assays targeting the N gene (A, B and C). The dynamic range and lowest detected quantity was determined using a SARS-CoV-2 partial N gene RNA transcript dilution series (100,000-1 copy/μl) and verified using 72 nose and throat swabs, 29 of which tested positive for SARS-CoV-2 RNA.

RESULTS

Assay C consistently detected the lowest quantity of partial N gene RNA transcript with all mastermixes. The Takara One Step PrimeScript™ III RT-PCR Kit mastermix enabled all primer pairs to detect the entire dynamic range evaluated, with the Qiagen Quantifast and Thermofisher TaqPath 1-Step kits also performing well. Sequences from all three primer/probe sets tested in this study (assay A, B and C) have 100 % homology to ≥97 % of the of SARS-CoV-2 sequences available up to 31st December 2020 (n = 291,483 sequences).

CONCLUSIONS

This work demonstrates that specific assays (in this case assay C) can perform well in terms of dynamic range and lowest detected quantity regardless of the mastermix used. However we also show that, by choosing the most appropriate mastermix, poorer performing primer pairs are also able to detect all of the template dilutions investigated. This work increases the potential options when choosing assays for SARS-CoV-2 diagnosis and provides solutions to enable them to work with optimal analytical sensitivity.

Detection of Mycobacterium tuberculosis complex DNA in CD34-positive peripheral blood mononuclear cells of asymptomatic tuberculosis contacts: an observational study

BACKGROUND

Haematopoietic stem cells expressing the CD34 surface marker have been posited as a niche for Mycobacterium tuberculosis complex bacilli during latent tuberculosis infection. Our aim was to determine whether M tuberculosis complex DNA is detectable in CD34-positive peripheral blood mononuclear cells (PBMCs) isolated from asymptomatic adults living in a setting with a high tuberculosis burden.

METHODS

We did a cross-sectional study in Ethiopia between Nov 22, 2017, and Jan 10, 2019. Digital PCR (dPCR) was used to determine whether M tuberculosis complex DNA was detectable in PBMCs isolated from 100 mL blood taken from asymptomatic adults with HIV infection or a history of recent household or occupational exposure to an index case of human or bovine tuberculosis. Participants were recruited from HIV clinics, tuberculosis clinics, and cattle farms in and around Addis Ababa. A nested prospective study was done in a subset of HIV-infected individuals to evaluate whether administration of isoniazid preventive therapy was effective in clearing M tuberculosis complex DNA from PBMCs. Follow-up was done between July 20, 2018, and Feb 13, 2019. QuantiFERON-TB Gold assays were also done on all baseline and follow-up samples.

FINDINGS

Valid dPCR data (ie, droplet counts >10 000 per well) were available for paired CD34-positive and CD34-negative PBMC fractions from 197 (70%) of 284 participants who contributed data to cross-sectional analyses. M tuberculosis complex DNA was detected in PBMCs of 156 of 197 participants with valid dPCR data (79%, 95% CI 74-85). It was more commonly present in CD34-positive than in CD34-negative fractions (154 [73%] of 197 vs 46 [23%] of 197; p<0·0001). Prevalence of dPCR-detected M tuberculosis complex DNA did not differ between QuantiFERON-negative and QuantiFERON-positive participants (77 [78%] of 99 vs 79 [81%] of 98; p=0·73), but it was higher in HIV-infected than in HIV-uninfected participants (67 [89%] of 75 vs 89 [73%] of 122, p=0·0065). By contrast, the proportion of QuantiFERON-positive participants was lower in HIV-infected than in HIV-uninfected participants (25 [33%] of 75 vs 73 [60%] of 122; p<0·0001). Administration of isoniazid preventive therapy reduced the prevalence of dPCR-detected M tuberculosis complex DNA from 41 (95%) of 43 HIV-infected individuals at baseline to 23 (53%) of 43 after treatment (p<0·0001), but it did not affect the prevalence of QuantiFERON positivity (17 [40%] of 43 at baseline vs 13 [30%] of 43 after treatment; p=0·13).

INTERPRETATION

We report a novel molecular microbiological biomarker of latent tuberculosis infection with properties that are distinct from those of a commercial interferon-γ release assay. Our findings implicate the bone marrow as a niche for M tuberculosis in latently infected individuals. Detection of M tuberculosis complex DNA in PBMCs has potential applications in the diagnosis of latent tuberculosis infection, in monitoring response to preventive therapy, and as an outcome measure in clinical trials of interventions to prevent or treat latent tuberculosis infection.

FUNDING

UK Medical Research Council.

Seroprevalence of SARS-CoV-2 antibodies, associated epidemiological factors and antibody kinetics among healthcare workers in Connecticut

BACKGROUND

Healthcare workers (HCWs) are at the front line of the ongoing coronavirus 2019 (COVID-19) pandemic. Comprehensive evaluation of the seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) among HCWs in a large healthcare system could help to identify the impact of epidemiological factors and the presence of symptoms on the immune response to the infection over time.

AIM

To determine the seroprevalence of SARS-CoV-2-specific antibodies among HCWs, identify associated epidemiological factors and study antibody kinetics.

METHODS

A longitudinal evaluation of the seroprevalence and epidemiology of SARS-CoV-2-specific antibodies was undertaken in approximately 30,000 HCWs in the largest healthcare system in Connecticut, USA.

FINDINGS

At baseline, the prevalence of SARS-CoV-2 antibody among 6863 HCWs was 6.3% [95% confidence interval (CI) 5.7-6.9%], and was highest among patient care support (16.7%), medical assistants (9.1%) and nurses (8.2%), and lower for physicians (3.8%) and advanced practice providers (4.5%). Seroprevalence was significantly higher among African Americans [odds ratio (OR) 3.26 compared with Caucasians, 95% CI 1.77-5.99], in participants with at least one symptom of COVID-19 (OR 3.00, 95% CI 1.92-4.68), and in those reporting prior quarantine (OR 3.83, 95% CI 2.57-5.70). No symptoms were reported in 24% of seropositive participants. Among the 47% of participants who returned for a follow-up serological test, the seroreversion rate was 39.5% and the seroconversion rate was 2.2%. The incidence of re-infection in the seropositive group was zero.

CONCLUSION

Although there is a decline in the immunoglobulin G antibody signal over time, 60.5% of seropositive HCWs had maintained their seroconversion status after a median of 5.5 months.

The performance of human cytomegalovirus digital PCR reference measurement procedure in seven external quality assessment schemes over four years

A candidate digital PCR (dPCR)-based reference measurement procedure for quantification of human cytomegalovirus (hCMV) was evaluated in 10 viral load comparison schemes (seven external quality assessment (EQA) and three additional training schemes) organized by INSTAND e.V. over four years (between September 2014 and March 2018). Four metrology institutes participated in these schemes using the same extraction method and dPCR measurement procedure for the hCMV specific target sequence of UL54 gene. The calibration independent reference measurement procedure results from the metrology institutes were compared to the results of the clinical diagnostic laboratories applying hCMV qPCR measurement procedures calibrated to reference materials. While the criteria for the acceptable deviation from the target value interval for INSTAND's EQA schemes is from -0.8 log₁₀ to +0.8 log₁₀, the majority of dPCR results were between -0.2 log₁₀ to +0.2 log₁₀. Only 4 out of 45 results exceeded this interval with the maximum deviation of -0.542 log₁₀. In the training schemes containing samples with lower hCMV concentrations, more than half of the results deviated less than ±0.2 log₁₀ from the target value, while more than 95% deviated less than ±0.4 log₁₀ from the target value. Evaluation of intra- and inter-laboratory variation of dPCR results confirmed high reproducibility and trueness of the method. This work demonstrates that dPCR has the potential to act as a calibration independent reference measurement procedure for the value assignment of hCMV calibration and reference materials to support qPCR calibration as well as ultimately for routine hCMV load testing.

An assessment of the reproducibility of reverse transcription digital PCR quantification of HIV-1

Viral load monitoring in human immunodeficiency virus type 1 (HIV-1) infection is often performed using reverse transcription quantitative PCR (RT-qPCR) to observe response to treatment and identify the development of resistance. Traceability is achieved using a calibration hierarchy traceable to the International Unit (IU). IU values are determined using consensus agreement derived from estimations by different laboratories. Such a consensus approach is necessary due to the fact that there are currently no reference measurement procedures available that can independently assign a reference value to viral reference materials for molecular in vitro diagnostic tests. Digital PCR (dPCR) is a technique that has the potential to be used for this purpose. In this paper, we investigate the ability of reverse transcriptase dPCR (RT-dPCR) to quantify HIV-1 genomic RNA without calibration. Criteria investigated included the performance of HIV-1 RNA extraction steps, choice of reverse transcription approach and selection of target gene with assays performed in both single and duplex format. We developed a protocol which was subsequently applied by two independent laboratories as part of an external quality assurance (EQA) scheme for HIV-1 genome detection. Our findings suggest that RT-dPCR could be used as reference measurement procedure to aid the value assignment of HIV-1 reference materials to support routine calibration of HIV-1 viral load testing by RT-qPCR.

STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies

The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study

Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results. Few published comparisons exist for the myriad analytical pipelines used for predicting AMR. To address this, we performed an inter-laboratory study providing sets of participating researchers with identical short-read WGS data from clinical isolates, allowing us to assess the reproducibility of the bioinformatic prediction of AMR between participants, and identify problem cases and factors that lead to discordant results. We produced ten WGS datasets of varying quality from cultured carbapenem-resistant organisms obtained from clinical samples sequenced on either an Illumina NextSeq or HiSeq instrument. Nine participating teams ('participants') were provided these sequence data without any other contextual information. Each participant used their choice of pipeline to determine the species, the presence of resistance-associated genes, and to predict susceptibility or resistance to amikacin, gentamicin, ciprofloxacin and cefotaxime. We found participants predicted different numbers of AMR-associated genes and different gene variants from the same clinical samples. The quality of the sequence data, choice of bioinformatic pipeline and interpretation of the results all contributed to discordance between participants. Although much of the inaccurate gene variant annotation did not affect genotypic resistance predictions, we observed low specificity when compared to phenotypic AST results, but this improved in samples with higher read depths. Had the results been used to predict AST and guide treatment, a different antibiotic would have been recommended for each isolate by at least one participant. These challenges, at the final analytical stage of using WGS to predict AMR, suggest the need for refinements when using this technology in clinical settings. Comprehensive public resistance sequence databases, full recommendations on sequence data quality and standardization in the comparisons between genotype and resistance phenotypes will all play a fundamental role in the successful implementation of AST prediction using WGS in clinical microbiology laboratories.

Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs

Background

Mycobacterium tuberculosis resistance to anti-tuberculosis drugs is a major threat to global public health. Whole genome sequencing (WGS) is rapidly gaining traction as a diagnostic tool for clinical tuberculosis settings. To support this informatically, previous work led to the development of the widely used TBProfiler webtool, which predicts resistance to 14 drugs from WGS data. However, for accurate and rapid high throughput of samples in clinical or epidemiological settings, there is a need for a stand-alone tool and the ability to analyse data across multiple WGS platforms, including Oxford Nanopore MinION.

Results

We present a new command line version of the TBProfiler webserver, which includes hetero-resistance calling and will facilitate the batch processing of samples. The TBProfiler database has been expanded to incorporate 178 new markers across 16 anti-tuberculosis drugs. The predictive performance of the mutation library has been assessed using > 17,000 clinical isolates with WGS and laboratory-based drug susceptibility testing (DST) data. An integrated MinION analysis pipeline was assessed by performing WGS on 34 replicates across 3 multi-drug resistant isolates with known resistance mutations. TBProfiler accuracy varied by individual drug. Assuming DST as the gold standard, sensitivities for detecting multi-drug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) were 94% (95%CI 93–95%) and 83% (95%CI 79–87%) with specificities of 98% (95%CI 98–99%) and 96% (95%CI 95–97%) respectively. Using MinION data, only one resistance mutation was missed by TBProfiler, involving an insertion in the tlyA gene coding for capreomycin resistance. When compared to alternative platforms (e.g. Mykrobe predictor TB, the CRyPTIC library), TBProfiler demonstrated superior predictive performance across first- and second-line drugs.

Conclusions

The new version of TBProfiler can rapidly and accurately predict anti-TB drug resistance profiles across large numbers of samples with WGS data. The computing architecture allows for the ability to modify the core bioinformatic pipelines and outputs, including the analysis of WGS data sourced from portable technologies. TBProfiler has the potential to be integrated into the point of care and WGS diagnostic environments, including in resource-poor settings.

Electronic supplementary material

The online version of this article (10.1186/s13073-019-0650-x) contains supplementary material, which is available to authorized users.

Assessment of Digital PCR as a Primary Reference Measurement Procedure to Support Advances in Precision Medicine

BACKGROUND

Genetic testing of tumor tissue and circulating cell-free DNA for somatic variants guides patient treatment of many cancers. Such measurements will be fundamental in the future support of precision medicine. However, there are currently no primary reference measurement procedures available for nucleic acid quantification that would support translation of tests for circulating tumor DNA into routine use.

METHODS

We assessed the accuracy of digital PCR (dPCR) for copy number quantification of a frequently occurring single-nucleotide variant in colorectal cancer (KRAS c.35G>A, p.Gly12Asp, from hereon termed G12D) by evaluating potential sources of uncertainty that influence dPCR measurement.

RESULTS

Concentration values for samples of KRAS G12D and wild-type plasmid templates varied by <1.2-fold when measured using 5 different assays with varying detection chemistry (hydrolysis, scorpion probes, and intercalating dyes) and <1.3-fold with 4 commercial dPCR platforms. Measurement trueness of a selected dPCR assay and platform was validated by comparison with an orthogonal method (inductively coupled plasma mass spectrometry). The candidate dPCR reference measurement procedure showed linear quantification over a wide range of copies per reaction and high repeatability and interlaboratory reproducibility (CV, 2%-8% and 5%-10%, respectively).

CONCLUSIONS

This work validates dPCR as an SI-traceable reference measurement procedure based on enumeration and demonstrates how it can be applied for assignment of copy number concentration and fractional abundance values to DNA reference materials in an aqueous solution. High-accuracy measurements using dPCR will support the implementation and traceable standardization of molecular diagnostic procedures needed for advancements in precision medicine.

The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis

BACKGROUND

Real-time PCR (qPCR) based methods, such as the Xpert MTB/RIF, are increasingly being used to diagnose tuberculosis (TB). While qualitative methods are adequate for diagnosis, the therapeutic monitoring of TB patients requires quantitative methods currently performed using smear microscopy. The potential use of quantitative molecular measurements for therapeutic monitoring has been investigated but findings have been variable and inconclusive. The lack of an adequate reference method and reference materials is a barrier to understanding the source of such disagreement. Digital PCR (dPCR) offers the potential for an accurate method for quantification of specific DNA sequences in reference materials which can be used to evaluate quantitative molecular methods for TB treatment monitoring.

METHODS

To assess a novel approach for the development of quality assurance materials we used dPCR to quantify specific DNA sequences in a range of prototype reference materials and evaluated accuracy between different laboratories and instruments. The materials were then also used to evaluate the quantitative performance of qPCR and Xpert MTB/RIF in eight clinical testing laboratories.

RESULTS

dPCR was found to provide results in good agreement with the other methods tested and to be highly reproducible between laboratories without calibration even when using different instruments. When the reference materials were analysed with qPCR and Xpert MTB/RIF by clinical laboratories, all laboratories were able to correctly rank the reference materials according to concentration, however there was a marked difference in the measured magnitude.

CONCLUSIONS

TB is a disease where the quantification of the pathogen could lead to better patient management and qPCR methods offer the potential to rapidly perform such analysis. However, our findings suggest that when precisely characterised materials are used to evaluate qPCR methods, the measurement result variation is too high to determine whether molecular quantification of Mycobacterium tuberculosis would provide a clinically useful readout. The methods described in this study provide a means by which the technical performance of quantitative molecular methods can be evaluated independently of clinical variability to improve accuracy of measurement results. These will assist in ultimately increasing the likelihood that such approaches could be used to improve patient management of TB.

Development of sample clean up methods for the analysis of Mycobacterium tuberculosis methyl mycocerosate biomarkers in sputum extracts by gas chromatography-mass spectrometry

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We developed a sample clean-up method to detect tuberculosis from sputum by GC–MS.

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Biomarkers recovered: 64–70% (standards solution), and 36–68% (sputum extracts).

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Cholesterol removed: 93–98% (standards solution) and 62–92% (sputum extracts).

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Less cholesterol in the filtered extracts avoids overloading of the analytical system.

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Analyzing large sample batches will need fewer interruptions for system cleaning.

A proof of principle gas chromatography–mass spectrometry method is presented, in combination with clean up assays, aiming to improve the analysis of methyl mycocerosate tuberculosis biomarkers from sputum. Methyl mycocerosates are generated from the transesterification of phthiocerol dimycocerosates (PDIMs), extracted in petroleum ether from sputum of tuberculosis suspect patients. When a high matrix background is present in the sputum extracts, the identification of the chromatographic peaks corresponding to the methyl derivatives of PDIMs analytes may be hindered by the closely eluting methyl ether of cholesterol, usually an abundant matrix constituent frequently present in sputum samples. The purification procedures involving solid phase extraction (SPE) based methods with both commercial Isolute-Florisil cartridges, and purpose designed molecularly imprinted polymeric materials (MIPs), resulted in cleaner chromatograms, while the mycocerosates are still present. The clean-up performed on solutions of PDIMs and cholesterol standards in petroleum ether show that, depending on the solvent mix and on the type of SPE used, the recovery of PDIMs is between 64 and 70%, whilst most of the cholesterol is removed from the system. When applied to petroleum ether extracts from representative sputum samples, the clean-up procedures resulted in recoveries of 36–68% for PDIMs, allowing some superior detection of the target analytes.

Assessing the accuracy of quantitative molecular microbial profiling

The application of high-throughput sequencing in profiling microbial communities is providing an unprecedented ability to investigate microbiomes. Such studies typically apply one of two methods: amplicon sequencing using PCR to target a conserved orthologous sequence (typically the 16S ribosomal RNA gene) or whole (meta)genome sequencing (WGS). Both methods have been used to catalog the microbial taxa present in a sample and quantify their respective abundances. However, a comparison of the inherent precision or bias of the different sequencing approaches has not been performed. We previously developed a metagenomic control material (MCM) to investigate error when performing different sequencing strategies. Amplicon sequencing using four different primer strategies and two 16S rRNA regions was examined (Roche 454 Junior) and compared to WGS (Illumina HiSeq). All sequencing methods generally performed comparably and in good agreement with organism specific digital PCR (dPCR); WGS notably demonstrated very high precision. Where discrepancies between relative abundances occurred they tended to differ by less than twofold. Our findings suggest that when alternative sequencing approaches are used for microbial molecular profiling they can perform with good reproducibility, but care should be taken when comparing small differences between distinct methods. This work provides a foundation for future work comparing relative differences between samples and the impact of extraction methods. We also highlight the value of control materials when conducting microbial profiling studies to benchmark methods and set appropriate thresholds.

Development and evaluation of a novel taekwondo chest protector to improve mobility when performing axe kicks

The axe kick, in Olympic style taekwondo, has been identified as the most popular scoring technique aimed to the head during full contact competition. The first purpose of this study was to identify and investigate design issues with the current World Taekwondo Federation approved chest protector. A secondary purpose was to develop a novel chest protector addressing the identified design issues and to conduct a biomechanical analysis. Fifteen male elite Taekwondo players were selected to perform three different styles of the axe kick, i.e., front, in-out, and out-in axe kick five times each for a total of 45 kicks. Two-way repeated measures ANOVA showed significant differences between the novel and existing chest protector conditions for vertical height of the toe, downward kicking foot speed, hip flexion angle and ipsilateral shoulder flexion extension range of motion (ROM) (p < 0.05). There were no significant differences between the control condition (no chest protector) and the novel chest protector condition for these variables (p > 0.05). These results indicate that the novel chest protector interferes less with both the lower and upper limbs during the performance of the axe kick and provides a more natural, free-moving alternative to the current equipment used.

Development and optimization of a gas chromatography/mass spectrometry method for the analysis of thermochemolytic degradation products of phthiocerol dimycocerosate waxes found in Mycobacterium tuberculosis

RATIONALE

The phthiocerol dimycocerosates (PDIMs) are certain stable and hydrophobic waxes found in the cell membrane of Mycobacterium tuberculosis, bacteria that cause an infectious disease of growing concern worldwide. Previous studies report the analysis of derivatives of the hydrolysed PDIMs from biological samples, following complex extraction and offline derivatization of PDIMs biomarkers, prior to their analysis by gas chromatography/mass spectrometry (GC/MS).

METHODS

We developed and optimized a GC/MS method based on selected ion monitoring (SIM) to detect the derivatives produced via the thermally assisted hydrolysis and methylation (THM) of the PDIMs from the cell membrane of M. tuberculosis. The extraction of PDIMs from culture is simple, and their thermochemolysis is carried out automatically online, thus avoiding the time-consuming derivatization steps of hydrolysis and esterification, usually performed offline.

RESULTS

For standard PDIMs in petroleum ether, our optimized method gave an excellent linearity (R(2) = 0.99) at concentrations between 0.172 and 27.5 ng/mL, a good precision (RSD = 11.42%), and a limit of detection (LOD) of 100 pg/mL. For the PDIMs extracted from dilutions of M. tuberculosis culture, the method gave good linearity (R(2) = 0.9685) and an estimated LOD of 400 CFU/mL (CFU = colony forming units) in sterile distilled water.

CONCLUSIONS

A GC/MS(SIM) method is presented for the rapid and quantitative detection of M. tuberculosis, based on the online thermochemolysis of lipidic biomarkers extracted from the bacterial culture. The method has the potential to be applied in human and veterinary clinical laboratories for the rapid diagnosis of tuberculosis in infected biological samples.

Detection of Mycobacterium tuberculosis in sputum by gas chromatography-mass spectrometry of methyl mycocerosates released by thermochemolysis

Tuberculosis requires rapid diagnosis to prevent further transmission and allow prompt administration of treatment. Current methods for diagnosing pulmonary tuberculosis lack sensitivity are expensive or are extremely slow. The identification of lipids using gas chromatography- electron impact mass spectrometry (GC-EI/MS) could provide an alternative solution. We have studied mycocerosic acid components of the phthiocerol dimycocerosate (PDIM) family of lipids using thermochemolysis GC-EI/MS. To facilitate use of the technology in a routine diagnostic laboratory a simple extraction procedure was employed where PDIMs were extracted from sputum using petroleum ether, a solvent of low polarity. We also investigated a method using methanolic tetramethylammonium hydroxide, which facilitates direct transesterification of acidic components to methyl esters in the inlet of the GC-MS system. This eliminates conventional chemical manipulations allowing rapid and convenient analysis of samples. When applied to an initial set of 40 sputum samples, interpretable results were obtained for 35 samples with a sensitivity relative to culture of 94% (95%CI: 69.2,100) and a specificity of 100% (95%CI: 78.1,100). However, blinded testing of a larger set of 395 sputum samples found the assay to have a sensitivity of 61.3% (95%CI: 54.9,67.3) and a specificity of 70.6% (95%CI: 62.3,77.8) when compared to culture. Using the results obtained we developed an improved set of classification criteria, which when applied in a blinded re-analysis increased the sensitivity and specificity of the assay to 64.9% (95%CI: 58.6,70.8) and 76.2% (95%CI: 68.2,82.8) respectively. Highly variable levels of background signal were observed from individual sputum samples that inhibited interpretation of the data. The diagnostic potential of using thermochemolytic GC-EI/MS of PDIM biomarkers for diagnosis of tuberculosis in sputum has been established; however, further refinements in sample processing are required to enhance the sensitivity and robustness of the test.

PD03-07: Breast Cancer Heterogeneity and Treatment Resistance: Clues from Metaplastic Tumors

At late stage, nearly all breast cancers are heterogeneous and refractory to treatment, like metaplastic breast cancer is at an early stage. These rare carcinomas are highly aggressive and de-differentiated. They are enriched for mesenchymal and stem cell features and essentially fail current therapies. As metaplastic tumors provide a time-compressed picture of breast cancer progression early on, understanding these tumors will yield insight into mechanisms that drive breast cancer into advanced stages and treatment resistance.

To investigate a genetic basis for heterogeneity in metaplastic breast cancer, we established a progression model comprising three cell lines. The cell lines were derived from a primary tumor, a local recurrence and a pleural effusion of a 40-year old patient. The primary tumor was a stage III invasive metaplastic, triple negative, inflammatory breast cancer, resected after neoadjuvant chemotherapy (capecitabine and taxotere, then adriamycin and one cycle of bevacizumab). The local recurrence, biopsied seven months post mastectomy, developed after the patient received adjuvant carboplatin and gemcitabine for 3 cycles and then radiation to the chest wall. At this time, the patient had lung metastases and was treated with taxol and bevacizumab yielding a mixed response. Local invasive growth continued and a malignant pleural effusion developed four months later. Analyzing the genetic and molecular characteristics of this progression model in vitro, its tumorigenicity and metastasis in vivo, and interrogating lead findings in a growing collection of metaplastic tumors helps us to dissect the genetic heterogeneity in breast cancer, and potentially to identify the cell types that drive disease progression and treatment resistance. Our gene expression analyses and genomic evaluations identified epithelial to mesenchymal transition (EMT) as a key characteristic in the progression and treatment resistance of this cancer. Major changes in cytoskeletal genes, chemokines and their receptors, amplification of drug transporter proteins, metalloproteinases and matrix proteins seen with increasing motility and invasiveness along with recruitment of host inflammatory responses in the in vivo model, loss of chromosomal regions harboring known and putative tumor suppressors, and deletions of genes encoding proteins for metabolic inactivation of sex hormones in the breast tissue, along with specific loss of clusters of desmosomal genes are guiding our understanding of metaplastic breast cancer progression. The results provide insight into the development, the extremely invasive nature, and treatment resistance of these tumors. Our collaborative network of clinicians, pathologists, translational genomic researchers and bioinformatics specialists will enable us to identify and prioritize genetic events as disease drivers, prognostic biomarkers of disease progression, and determinants of treatment resistance. Our goal is to identify molecular and functional targets for effective therapy and evaluate them in the clinic. Lessons learned from metaplastic breast cancer will improve our understanding of breast cancer progression in general, and could translate into effective treatments for advanced breast cancer where current standard of care is failing.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr PD03-07.

Association between proton pump inhibitors and spontaneous bacterial peritonitis in cirrhotic patients - a systematic review and meta-analysis

Acid suppressive therapy, in the form of proton pump inhibitor (PPI), is widely used in cirrhotic patients, often in indications which are not clearly justified. PPI facilitates enteric bacterial colonisation, overgrowth and translocation, which might predispose to spontaneous bacterial peritonitis. However, observational studies evaluating the association of PPI and SBP in cirrhotic patients have yielded inconsistent results. We therefore conducted a meta-analysis of relevant clinical studies to determine the nature of this association. Observational studies assessing the association between SBP and PPI in cirrhosis, conducted in adult population and published in all languages, were identified through systematic search in the MEDLINE, EMBASE and manual reviews of all major gastroenterology meeting proceedings up to May 2010. The relevant studies were pooled using traditional meta-analytic techniques with a random-effects model. Four studies were identified and included in the meta-analysis. The pooled analysis, involving a total of 772 patients, found a significant association between the use of PPI and the development of SBP (OR 2.77, 95% CI 1.82-4.23). There was very little degree of heterogeneity as reflected by an I(2) value of 22% and the visual inspection of the funnel plot. There is a potential association between use of PPI and development of SBP. Therefore, PPIs should be used judiciously and only when clearly indicated in cirrhotics. Further studies are essential to clarify this relationship and elucidate the underlying mechanisms.

Real-time PCR methods to study expression of genes related to hypermutability

Pathogenic bacteria can have sub-populations of hypermutable bacteria. This sub-population has a higher spontaneous mutation rate than the majority of the population which can be attributed to defects in proofreading and repair mechanisms. This leads to the evolution of drug-resistant strains of bacteria through genetic change. It is important to study the expression of genes involved in, for example, mismatch repair and the SOS system by real-time PCR to determine hypermutability and therefore provide an indicator of the mutagenic ability of certain strains of pathogenic bacteria.

Enhanced heterogeneity of rpoB in Mycobacterium tuberculosis found at low pH

OBJECTIVES

The aim of this study was to gain an insight into the molecular mechanisms of the evolution of rifampicin resistance in response to controlled changes in the environment.

METHODS

We determined the proportion of rpoB mutants in the chemostat culture and characterized the sequence of mutations found in the rifampicin resistance-determining region of rpoB in a steady-state chemostat at pH 7.0 and 6.2.

RESULTS

The overall proportion of rpoB mutants of strain H37Rv remained constant for 37 days at pH 7.0, ranging between 3.6 x 10(-8) and 8.9 x 10(-8); however, the spectrum of mutations varied. The most commonly detected mutation, serine to leucine mutation at codon 531 (S531L), increased from 40% to 89%, while other mutations (S531W, H526Y, H526D, H526R, S522L and D516V) decreased over the 37 day sampling period. Changing the pH from 7.0 to 6.2 did not significantly alter the overall proportion of mutants, but resulted in a decrease in the percentage of strains harbouring S531L (from 89% to 50%) accompanied by an increase in the range of different mutations from 4 to 12.

CONCLUSIONS

The data confirm that the fitness of strains with the S531L mutation is greater than that of strains containing other mutations. We also conclude that at low pH the environment is permissive for a wider spectrum of mutations, which may provide opportunities for a successful mutant to survive.

Mycobacterium tuberculosis DNA repair in response to subinhibitory concentrations of ciprofloxacin

OBJECTIVES

To investigate how the SOS response, an error-prone DNA repair pathway, is expressed following subinhibitory quinolone treatment of Mycobacterium tuberculosis.

METHODS

Genome-wide expression profiling followed by quantitative RT (qRT)-PCR was used to study the effect of ciprofloxacin on M. tuberculosis gene expression.

RESULTS

Microarray analysis showed that 16/110 genes involved in DNA protection, repair and recombination were up-regulated. There appeared to be a lack of downstream genes involved in the SOS response. qRT-PCR detected an induction of lexA and recA after 4 h and of dnaE2 after 24 h of subinhibitory treatment.

CONCLUSIONS

The pattern of gene expression observed following subinhibitory quinolone treatment differed from that induced after other DNA-damaging agents (e.g. mitomycin C). The expression of the DnaE2 polymerase response was significantly delayed following subinhibitory quinolone exposure.

Evaluation of liquid culture for quantitation of Mycobacterium tuberculosis in murine models

Quantitation of bacterial load in tissues is essential for experimental investigation of Mycobacterium tuberculosis infection and immunity. We have used an automated liquid culture system to determine the number of colony forming units (CFU) in murine tissues and compared the results to those obtained by conventional plating on Middlebrook agar. There is an overall good correlation between results obtained by the two methods. Although less consistency and more contamination was observed in the automated liquid culture, the method is more sensitive, less labour intensive and allows the processing of large numbers of samples.

Effect of subinhibitory concentrations of ciprofloxacin on Mycobacterium fortuitum mutation rates

OBJECTIVES

Fluoroquinolones have found a place in the management of mycobacterial diseases including tuberculosis. It has been previously shown that subinhibitory concentrations of quinolones increase the mutation rate in Escherichia coli and staphylococci. The purpose of this study is to extend this observation to mycobacteria and to quantify mutation rates.

METHODS

The mutation rate in Mycobacterium fortuitum to ciprofloxacin, levofloxacin, moxifloxacin, rifampicin, erythromycin and gentamicin resistance was determined when grown with and without various sub-MIC concentrations of ciprofloxacin.

RESULTS

M. fortuitum exposed to 1/2 MIC ciprofloxacin had an increase in the mutation rate of between 72- and 120-fold when selected on quinolones or other antimycobacterial antibiotics. Smaller, but significant increases in mutation rate were seen when the organism was exposed to lower concentrations (1/4 MIC and 1/8 MIC).

CONCLUSIONS

These data show that sub-MIC concentrations of fluoroquinolone significantly increase mutation rates and these data suggest that care must be taken to ensure that bacteria are not exposed to subinhibitory concentrations when adding quinolones to a regimen used to treat mycobacterial infection.

Analysis of rpoB and pncA mutations in the published literature: an insight into the role of oxidative stress in Mycobacterium tuberculosis evolution?

INTRODUCTION

It is perceived wisdom that within the host macrophage, Mycobacterium tuberculosis frequently encounters oxidative stress. Exposure of bacteria to reactive oxygen intermediates can have a mutagenic effect on the DNA. Various mutations are thought to arise as a consequence, including the oxidation of guanine residues, leading to G?C-->T?A substitution, and oxidation of cytosine resulting in a G?C-->A?T substitution.

METHODS

We measured the relative contribution of oxidative stress by recording the percentage of single nucleotide substitutions reported in the genes rpoB and pncA that confer resistance to the antimicrobials rifampicin and pyrazinamide, respectively, and determined whether there is an excess of G?C-->T?A or G?C-->A?T substitutions.

RESULTS

Out of 840 clinical isolates reported with single nucleotide mutations in the rpoB gene, 67% were G?C-->A?T changes, and 3% were G?C-->T?A substitutions. These figures were compared to the pncA gene, where out of 114 isolates, 30% of the single nucleotide mutations were G?C-->A?T transitions and 9% were G?C-->T?A changes.

CONCLUSIONS

While there is an excess of G?C-->A?T changes in the rpoB gene, this was not the case in the pncA gene. Fifty-three percent of mutations within the rpoB gene were C-->T mutations of the type S531L. Although this mutation gives a fitness disadvantage, it is less than other common mutations, so it is more likely that that fitness is the determinant of surviving mutation rather than oxidative stress because of the small numbers of other C-->T and G-->A mutations at other sites (12%). There was no evidence of oxygen free radicals damaging the guanine bases in either gene.

Technique for cloning and sequencing the ends of bacterial artificial chromosome inserts

Bacterial artificial chromosome (BAC) libraries are an important tool for positional cloning, gene analysis and physical mapping. During studies using BAC clones, it is often necessary to organize them into contiguous sequences (contigs). To finalize, join and extend the contigs, both cloning and sequencing of the ends of the inserts are required. Here, we describe a low-cost, accessible, fast and powerful method for the routine isolation of BAC ends. This method allows the isolation of 20 BAC clone ends in one day. The analysis of the ends reveals fragment sizes compatible with sequencing, and the structure of these clones allows the sequencing of both ends using the same plasmid. Moreover, long end fragments can be sequenced in both directions.

Salivary mutans streptococci and caries development in the primary and mixed dentitions of children

OBJECTIVES

For more than 25 years, both cross-sectional and longitudinal studies of dental caries have focused on the role of salivary mutans streptococci (SMS) as a predictor of caries risk. This study examined the relationship between SMS and longitudinal caries development in the primary and mixed dentitions.

METHODS

Eighty-five children, initial mean age 3.8 years, were examined for dental caries at baseline and once annually for 6 years. Children's SMS were sampled with a tongue blade, which was impressed onto plates containing a medium selective for SMS. After incubation, colony forming units of SMS were determined semi-quantitatively and categorized as low, moderate or high.

RESULTS

Children classified as high caries risk at baseline had significantly greater (P<0.05) dmfs scores for all teeth, and in the primary molars, than children classified as moderate or low caries risk at every age but 9 (P<0.10). Children classified as high risk at age 3 had the greatest DMFS increment through age 8. Based on annual examinations, there was a trend towards increasing mean dmfs/DMFS scores among children classified as high risk in every year.

CONCLUSIONS

The current study is among the first to report on the ability of annual measurements of SMS to identify long-term caries risk in both the primary and the mixed dentitions. Despite limitations in predicting caries risk using microbiological methods, this longitudinal study supports the overall benefits of this type of testing.

Failure of intense preventive efforts to arrest early childhood and rampant caries: three case reports

This report presents the first three children who developed dental caries despite being enrolled in a randomized, control trial to test methods to prevent early childhood caries. The children's caretakers received education on decreasing frequent and prolonged feeding with a nursing bottle and other sugar containing foods, as well as brushing the children's teeth daily with 0.4% SnF2 gel. One of the child's caretaker additionally received training sessions to improve confidence in eliminating the child's nursing bottle habit and in performing daily tooth brushing. The two other children received monthly topical fluoride treatments with 2% NaF. Despite these intensive preventive efforts, these three children developed dental caries. Two of the children had mutans streptococci colonization at the time of initial visit, (12 and 14 months of age, respectively). All had high mutans streptococci levels at the time that caries was detected. Incorrigible, high-frequency sugar consumption from a bottle or from solid foods was suggested in all three cases. In one case, dental caries was associated with defects of the tooth enamel. Conceivably, the cariogenic challenge and harmful behaviors in certain children may be so extreme that they can overwhelm even extraordinary preventive efforts.

Colonization of mutans streptococci in 8- to 15-month-old children

OBJECTIVE

The age at which a child becomes colonized with mutans streptococci (MS) is important for understanding early childhood caries. The aim of this study was to explore the relationship of age with MS colonization in infants.

METHODS

Inner-city children (n = 149) between the ages of 8 months and 15 months, inclusive, who reportedly were still using a baby bottle, were sampled for MS.

RESULTS

Evidence of MS colonization was seen as early at 10 months of age. For children 12 months old or younger (n = 80), 25 percent had detectable levels of MS; in the 15-month age group, 60 percent were colonized.

CONCLUSION

This study suggests that prevention of MS colonization in some populations may need to be initiated prior to the child's first birthday.

The relationship between bottle usage/content, age, and number of teeth with mutans streptococci colonization in 6-24-month-old children

OBJECTIVES

Mutans streptococci (MS) are the primary pathogens involved in the development of early childhood caries. However, factors that may affect their acquisition in the mouths of young children are not well understood, and the period of initial colonization remains controversial. This study investigated the relationship of age, number of teeth, and bottle usage/content with regard to the isolation of MS in 6-24-month-old children.

METHODS

A total of 122 children from low-income families attending a nutritional supplement program, and their mothers, participated in this study. Children were examined for dental caries and number of erupted teeth and were sampled for MS. Mothers were administered a questionnaire to obtain details of baby bottle use, including what food items were put in the bottle during the last week.

RESULTS

MS was detected in more than one-third of the 6-24-month-olds. Unlike some studies that suggest a later period of infectivity, approximately 20% of children under 14 months of age, including 4 of 22 infants aged 6-9 months, were colonized with MS. When examined separately, age, number of teeth, and bottle usage/content were each found to be related to the presence of MS. Mutans streptococci colonization was more likely with increasing age and number of teeth, and children whose bottles contained sweetened beverages were more likely to be colonized than children whose bottles contained milk. Logistic regression models that controlled for both age and number of teeth indicated that children who consumed sweetened beverages in their baby bottle had a statistically significant, four-fold increase in the odds of colonization by MS relative to children who consumed milk.

CONCLUSIONS

The finding that approximately 20% of the children under 14 months of age were infected with MS indicates that colonization in this sample of low-income preschool children may begin earlier than suggested by some investigations. Additionally, the risk of MS colonization appears lower among infants who consume milk rather than sweetened beverages in the bottle.

Early childhood caries: overview and recent findings

Early childhood caries is of epidemic proportions in some U.S. minority populations and in developing countries, yet a review of the literature reveals numerous conflicting reports and unanswered questions regarding the etiology and prevention of the disease. Better knowledge of the cause of early childhood caries and effective strategies to reduce its risk should produce enormous reductions in initial and long-term dental treatment costs, as well as the pain and suffering of affected children.

Dental caries prevalence and treatment levels in Arizona preschool children

OBJECTIVES

To assess the prevalence of dental caries in a large group of preschool children, to determine the extent to which the children received dental treatment, to examine the association between demographic and socioeconomic factors and the prevalence of caries, and to compare these findings with those from previous studies of preschool populations in the United States.

METHODS

Dental caries exams were performed on 5171 children ages 5 months through 4 years, and a parent or other caregiver was asked to complete a questionnaire giving information about the child and her or his household. The children were recruited from Head Start programs; Women, Infants, and Children (WIC) nutrition programs; health fairs; and day care centers in a representative sample of Arizona communities with populations of more than 1000 people.

RESULTS

Of the 994 one-year-old children examined, 6.4% had caries, with a mean dmft (decayed, missing [extracted due to caries], and filled teeth) score of 0.18. Nearly 20% of the 2-year-olds had caries, with a mean dmft of 0.70. Thirty-five percent of the 3-year-olds had caries, with a mean dmft of 1.35, and 49% of the 4-year-olds had caries, with a mean dmft of 2.36. Children whose caregivers fell into the lowest education category had a mean dmft score three times higher than those with caregivers in the highest education category. Children with caregivers in the lowest income category had a mean dmft score four times higher than those with caregivers in the highest category. Children younger than age 3 had little evidence of dental treatment, and most of the children with caries in each age group had no filled or extracted teeth.

CONCLUSIONS

The data show that dental caries is highly prevalent in this preschool population, with little of the disease being treated. Timing of diagnostic examinations and prevention strategies for preschool children need to be reconsidered, especially for children identified as having a high risk of caries.

Caries experience and mutans streptococci as indicators of caries incidence

Studies indicate that previous caries experience can influence future caries development; however, caries-free individuals also may develop caries. The aim of this study was to examine the relationship between baseline caries experience and salivary mutans streptococci (SMS) levels as an indicator for predicting caries incidence in pre-school children. One hundred forty-eight preschool children (mean baseline age, 3-8 years) of low socioeconomic status were examined for dental caries and SMS levels at baseline and annually for 2 years. All children were identified at baseline as either caries free or caries positive. The 2-year delta dmfs scores for both groups were evaluated as 0, 1-2, 3-4, or > 4. The children's baseline SMS levels were categorized as low (0 CFU), moderate (1-50 CFU), or high (> 50 CFU), and were recoded to assigned ranges of 1, 2, and 3, respectively, in each year for longitudinal analysis. Both the caries-free and caries-positive groups had high SMS levels associated with the greatest delta dmfs, and when SMS ranges were added for the three examination years (minimum = 3, maximum = 9), the mean second-year dmfs scores varied directly as the sum of the ranges. Results from this study suggest that SMS levels may be useful in identifying and predicting future caries in preschool children, independent of baseline caries experience.

Temporal changes in dental caries levels and patterns in a Native American preschool population

OBJECTIVES

The purposes of this study were to assess current dental caries experience and levels of mutans streptococci in Apache children in 1993 and to determine how caries levels and patterns were different from 15 years before.

METHODS

Four-year-old Head Start children (n = 127) were examined for dental caries and sampled for salivary mutans streptococci in 1993. Dental caries information on 113 4-year-old children from the same location was obtained from a chart audit of the 1978-79 Head Start dental examinations.

RESULTS

Neither the caries prevalence (95%) nor the prevalence of caries patterns differed between the 1978-79 and 1993 cohorts. However, the level of treatment received in 1993 was greater than that in 1978-79. Children with nursing caries (64%) had a greater severity of fissure caries and a greater prevalence of posterior proximal caries compared with caries-positive children without nursing caries. The mean dmfs and dmft on the children categorized in the high mutans streptococci range were greater than those of children categorized in the moderate range.

CONCLUSIONS

The caries prevalence found in these preschool Native Americans is among the highest reported for this age group and does not differ from that found at this location 15 years before. It appears that children with nursing caries in this population are at greater risk for posterior caries patterns.

Salivary mutans streptococci and dental caries patterns in pre-school children

Recent studies have suggested that the identification of caries as discrete patterns may be valuable in describing and predicting caries experience on an individual basis. The purpose of this study was to assess the association between levels of salivary mutans streptococci and the prevalence, incidence and distribution of caries patterns in the primary dentition. A cohort of pre-school children (n = 146, mean age 3.8 yr) were examined for dental caries and sampled for salivary mutans streptococci (SMS) at baseline and once annually for 2 yr. Children's tooth surfaces were categorized into four patterns: pit/fissure, maxillary anterior, posterior proximal, and buccal/lingual smooth surface. Salivary mutans streptococci were enumerated using a tongue blade technique, and were categorized as low (0 CFU), moderate (1-50 CFU) and high (> 50 CFU). At year 2, children with high baseline SMS had the 1) highest prevalence of caries (87%) and the highest dmfs (9.15); 2) highest prevalence of each pattern, and 3) greatest number of patterns. Among children with the pit/fissure pattern, those with high baseline SMS had the greatest pit/fissure dmfs after 2 yr. Results show that baseline SMS levels were associated with both cross-sectional and longitudinal caries experience, numbers of caries patterns, and the prevalence and severity of those patterns.

The association of early dental caries patterns with caries incidence in preschool children

OBJECTIVES

This study assessed the development of caries in preschool children over two years according to baseline caries pattern.

METHODS

Connecticut Head Start children (n = 142, mean age = 3.8 years) were examined for dental caries at baseline (spring 1991) and once annually for two years. Children were categorized at baseline as caries-free, having pit and fissure (PF) caries, or having maxillary anterior (MA) caries.

RESULTS

After two years, children who presented at baseline with MA or PF caries had a mean posterior dmfs of greater than seven and four times, respectively, that of children who were caries-free at baseline. When dental caries of the primary dentition was categorized by specific posterior patterns (i.e., posterior proximal [PP] and buccal/lingual [BL]), change in dmfs for the PP and BL patterns in the group that presented with pit/fissure caries at baseline were nearly four and three times greater, respectively, than for those in the caries-free group. The group that presented with maxillary anterior caries at baseline had PP and BL caries increments eight times those of children who began caries-free.

CONCLUSION

Dental caries presentation in 3- to 4-year-old children can identify those children and tooth surfaces that will be at the greatest risk for future caries development.

Salivary mutans streptococci and incidence of caries in preschool children

The aim of this study was to assess the relationship between salivary mutans streptococcus (SMS) levels and the prevalence and incidence of dental caries in 148 children (mean baseline age 3.8 years) of low socioeconomic status. Caries data (dmfs) and semiquantitative SMS counts were obtained at baseline and annually for 2 years. The children were classified during each of the 3 years as low (0 colony-forming units; CFU), moderate (1-50 CFU), or high (> 50 CFU) caries risk based on total SMS counts. The results indicated that the prevalence of dental caries increased with SMS levels at baseline and generally in both assessment years. At baseline the mean dmfs of the children classified as low, moderate, or high caries risk was 0.15, 1.44, and 3.36, respectively, while the mean dmfs of the same children at year 2 was 1.18, 3.10, and 7.87, respectively. The mean dmfs of the high-caries-risk group increased by 79% between baseline and year 1 and by 30% between year 1 and year 2. At year 2, 50% of the children in the low- and 47% in the moderate-caries-risk groups were caries free as compared with 11% in the high-caries-risk group. Thirty-three percent of the children examined remained in the same caries risk category from baseline to year 2; the incidence (delta dmfs) of dental caries in those children designated as low, moderate, and high caries risk during this period was 1.44, 3.36, and 10.07, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Dental caries prevalence and treatment among Navajo preschool children

OBJECTIVES

The purpose of this study was to assess the dental health of Navajo preschool children, a population about whom little dental information is published.

METHODS

Caries data were collected and analyzed for 2,003 Navajo children aged 3-5 years in the Head Start program, and for a convenience sample of 115 children younger than three years old from the Women, Infants and Children (WIC) program.

RESULTS

Each age group had an extremely high mean dmfs; however, as much as 70 percent of this index comprised treated surfaces. Maxillary anterior caries was observed in the WIC children under two years of age and posterior proximal caries was observed as early as two years of age. The prevalence of maxillary anterior caries reached a maximum of 68 percent in the three-year-old Head Start children, and may be associated with the high level of posterior caries in this population.

CONCLUSIONS

Most children in this population may be considered at risk for developing caries. This Navajo preschool population has perhaps the earliest caries onset, among the highest caries prevalence, and among the highest level of treatment of any reported population.

Maxillary anterior caries associated with increased caries risk in other primary teeth

It has been suggested that children with caries of maxillary anterior primary teeth may have increased caries incidence in other teeth. This study aimed to quantify the extent of posterior dental caries in those children who initially presented with maxillary anterior caries compared with that of those who did not. Data were collected for 217 Head Start children participating in a one-year study to determine caries risk factors. Tooth surfaces were recorded as carious, restored, or extracted (missing due to caries). Caries was then categorized into the following pattern(s): maxillary anterior (MA), pit/fissure (PF), posterior proximal (PP), and posterior buccal/lingual smooth surface (BL). Compared with children who did not initially present with the maxillary anterior pattern, those with the maxillary anterior pattern had 2.5 times (p < 0.01) the mean number of posterior decayed, missing, and filled surfaces (dmfs) and approximately 3 times the prevalence (p < 0.01) of the PP and BL patterns. The positive predictive value of the MA pattern was 86.8% for children who developed the PF pattern, and the negative predictive values were greater than 91% for children who did not develop the PP and BL patterns. The prevalence of maxillary anterior caries among children in this study is associated with a significantly greater caries incidence in posterior teeth.

Mutans streptococci and caries prevalence in preschool children

Numerous studies have reported a correlation between mutants streptococci levels and dental caries. The aim of this study was to assess the relationship between salivary mutans streptococci levels and caries in preschool children of low socioeconomic status. A total of 462 Head Start children, mean age 3.8 yr (range 2.0-5.3 yr), were examined by the modified method of Radike. Saliva samples from 458 of these children were collected with tongue blades and impressed onto mutants streptococci selective agar. Children's mutants streptococci levels were categorized as low (0 CFU), moderate (1-50 CFU) or high (> 50 CFU), and the mean dmfs was 0.40, 1.92 and 4.88, respectively. All study groups (Black, Hispanic and White) had infection rates of approximately 83%; however, 39.1% of Black children had high mutans streptococci levels compared with 28.4% of White children. Pit/fissure caries was the most prevalent disease type in children with moderate or high mutants streptococci levels, although White children in the high group had significantly less of this pattern than Blacks and Hispanics. Sensitivity, specificity, and positive and negative predictive values for the high mutants streptococci group were 91.3%, 57.5%, 69.3% and 86.3%. Results from this study indicate that differences between Black, Hispanic and White preschool children may influence caries activity within populations that have similar mutants streptococci infection levels and socioeconomic backgrounds.

Staurosporine advances interblastomeric flattening of the mouse embryo

Staurosporine, an inhibitor of protein kinase activity, causes premature intercellular flattening of blastomeres but does not induce their premature polarisation. The flattening induced is calcium dependent, is reversed transiently at mitosis and requires the continuing presence of the drug. Staurosporine also blocks the decompacting effect of phorbol ester on 8-cell embryos.