Residents or Tourists: Is the Lactating Mammary Gland Colonized by Residential Microbiota?

The existence of the human milk microbiome has been widely recognized for almost two decades, with many studies examining its composition and relationship to maternal and infant health. However, the richness and viability of the human milk microbiota is surprisingly low. Given that the lactating mammary gland houses a warm and nutrient-rich environment and is in contact with the external environment, it may be expected that the lactating mammary gland would contain a high biomass microbiome. This discrepancy raises the question of whether the bacteria in milk come from true microbial colonization in the mammary gland ("residents") or are merely the result of constant influx from other bacterial sources ("tourists"). By drawing together data from animal, in vitro, and human studies, this review will examine the question of whether the lactating mammary gland is colonized by a residential microbiome.

Organisation of care for people receiving drug-resistant tuberculosis treatment in South Africa: a mixed methods study

OBJECTIVES

Treatment for multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB) is increasingly transitioning from hospital-centred to community-based care. A national policy for decentralised programmatic MDR/RR-TB care was adopted in South Africa in 2011. We explored variations in the implementation of care models in response to this change in policy, and the implications of these variations for people affected by MDR/RR-TB.

DESIGN

A mixed methods study was done of patient movements between healthcare facilities, reconstructed from laboratory records. Facility visits and staff interviews were used to determine reasons for movements.

PARTICIPANTS AND SETTING

People identified with MDR/RR-TB from 13 high-burden districts within South Africa.

OUTCOME MEASURES

Geospatial movement patterns were used to identify organisational models. Reasons for patient movement and implications of different organisational models for people affected by MDR/RR-TB and the health system were determined.

RESULTS

Among 191 participants, six dominant geospatial movement patterns were identified, which varied in average hospital stay (0-281 days), average patient distance travelled (12-198 km) and number of health facilities involved in care (1-5 facilities). More centralised models were associated with longer delays to treatment initiation and lengthy hospitalisation. Decentralised models facilitated family-centred care and were associated with reduced time to treatment and hospitalisation duration. Responsiveness to the needs of people affected by MDR/RR-TB and health system constraints was achieved through implementation of flexible models, or the implementation of multiple models in a district.

CONCLUSIONS

Understanding how models for organising care have evolved may assist policy implementers to tailor implementation to promote particular patterns of care organisation or encourage flexibility, based on patient needs and local health system resources. Our approach can contribute towards the development of a health systems typology for understanding how policy-driven models of service delivery are implemented in the context of variable resources.

Diagnostic performance of host protein signatures as a triage test for active pulmonary TB

The current four-symptom screen recommended by the World Health Organization (WHO) is widely used as screen to initiate diagnostic testing for active pulmonary tuberculosis (TB), yet the performance is poor especially when TB prevalence is low. In contrast, more sensitive molecular tests are less suitable for placement at primary care level in low-resource settings. In order to meet the WHO End TB targets, new diagnostic approaches are urgently needed to find the missing undiagnosed cases. Proteomics-derived blood host biomarkers have been explored because protein detection technologies are suitable for the point-of-care setting and could meet cost targets. This study aimed to find a biomarker signature that fulfills WHO's target product profile (TPP) for a TB screening. Twelve blood-based protein biomarkers from three sample populations (Vietnam, Peru, and South Africa) were analyzed individually and in combinations via advanced statistical methods and machine learning algorithms. The combination of I-309, SYWC and kallistatin showed the most promising results to discern active TB throughout the data sets meeting the TPP for a triage test in adults from two countries (Peru and South Africa). The top-performing individual markers identified at the global level (I-309 and SYWC) were also among the best-performing markers at country level in South Africa and Vietnam. This analysis clearly shows that a host protein biomarker assay is feasible in adults for certain geographical regions based on one or two biomarkers with a performance that meets minimal WHO TPP criteria.

A surge in human metapneumovirus paediatric respiratory admissions in Western Australia following the reduction of SARS-CoV-2 non-pharmaceutical interventions

AIM

Western Australian laboratory data demonstrated a decrease in human metapneumovirus (hMPV) detections through 2020 associated with SARS-CoV-2-related non-pharmaceutical interventions (NPIs), followed by a subsequent surge in metropolitan region in mid-2021. We aimed to assess the impact of the surge in hMPV on paediatric hospital admissions and the contribution of changes in testing.

METHODS

All respiratory-coded admissions of children aged <16 years at a tertiary paediatric centre between 2017 and 2021 were matched with respiratory virus testing data. Patients were grouped by age at presentation and by ICD-10 AM codes into bronchiolitis, other acute lower respiratory infection (OALRI), wheeze and upper respiratory tract infection (URTI). For analysis, 2017-2019 was utilised as a baseline period.

RESULTS

hMPV-positive admissions in 2021 were more than 2.8 times baseline. The largest increase in incidence was observed in the 1-4 years group (incidence rate ratio (IRR) 3.8; 95% confidence interval (CI): 2.5-5.9) and in OALRI clinical phenotype (IRR 2.8; 95% CI: 1.8-4.2). The proportion of respiratory-coded admissions tested for hMPV in 2021 doubled (32-66.2%, P < 0.001), with the greatest increase in wheeze (12-75% in 2021, P < 0.001). hMPV test percentage positivity in 2021 was higher than in the baseline period (7.6% vs. 10.1% in 2021, P = 0.004).

CONCLUSION

The absence and subsequent surge underline the susceptibility of hMPV to NPIs. Increased hMPV-positive admissions in 2021 can be partially attributable to testing, but test-positivity remained high, consistent with a genuine increase. Continued comprehensive testing will help ascertain true burden of hMPV respiratory diseases.

First CLAS12 Measurement of Deeply Virtual Compton Scattering Beam-Spin Asymmetries in the Extended Valence Region

Deeply virtual Compton scattering (DVCS) allows one to probe generalized parton distributions describing the 3D structure of the nucleon. We report the first measurement of the DVCS beam-spin asymmetry using the CLAS12 spectrometer with a 10.2 and 10.6 GeV electron beam scattering from unpolarized protons. The results greatly extend the Q^{2} and Bjorken-x phase space beyond the existing data in the valence region and provide 1600 new data points measured with unprecedented statistical uncertainty, setting new, tight constraints for future phenomenological studies.

First Measurement of Λ Electroproduction off Nuclei in the Current and Target Fragmentation Regions

We report results of Λ hyperon production in semi-inclusive deep-inelastic scattering off deuterium, carbon, iron, and lead targets obtained with the CLAS detector and the Continuous Electron Beam Accelerator Facility 5.014 GeV electron beam. These results represent the first measurements of the Λ multiplicity ratio and transverse momentum broadening as a function of the energy fraction (z) in the current and target fragmentation regions. The multiplicity ratio exhibits a strong suppression at high z and an enhancement at low z. The measured transverse momentum broadening is an order of magnitude greater than that seen for light mesons. This indicates that the propagating entity interacts very strongly with the nuclear medium, which suggests that propagation of diquark configurations in the nuclear medium takes place at least part of the time, even at high z. The trends of these results are qualitatively described by the Giessen Boltzmann-Uehling-Uhlenbeck transport model, particularly for the multiplicity ratios. These observations will potentially open a new era of studies of the structure of the nucleon as well as of strange baryons.

Observation of Correlations between Spin and Transverse Momenta in Back-to-Back Dihadron Production at CLAS12

We report the first measurements of deep inelastic scattering spin-dependent azimuthal asymmetries in back-to-back dihadron electroproduction in the deep inelastic scattering process. In this reaction, two hadrons are produced in opposite hemispheres along the z axis in the virtual photon-target nucleon center-of-mass frame, with the first hadron produced in the current-fragmentation region and the second in the target-fragmentation region. The data were taken with longitudinally polarized electron beams of 10.2 and 10.6 GeV incident on an unpolarized liquid-hydrogen target using the CLAS12 spectrometer at Jefferson Lab. Observed nonzero sinΔϕ modulations in ep→e^{'}pπ^{+}X events, where Δϕ is the difference of the azimuthal angles of the proton and pion in the virtual photon and target nucleon center-of-mass frame, indicate that correlations between the spin and transverse momenta of hadrons produced in the target- and current-fragmentation regions may be significant. The measured beam-spin asymmetries provide a first access in dihadron production to a previously unexplored leading-twist spin- and transverse-momentum-dependent fracture function. The fracture functions describe the hadronization of the target remnant after the hard scattering of a virtual photon off a quark in the target particle and provide a new avenue for studying nucleonic structure and hadronization.

Impact of Sars COV2 infection on acute myocarditis: Observational study of patients admitted from 2019 to 2021

Introduction

Cases of acute myocarditis related to SARS COV2 infection and/or vaccines have been described but characteristics and complications require further research.

Objective

To analyze myocarditis directly related to SARS COV 2 infection and to compare with myocarditis before Covid as well as myocarditis related to Covid vaccines.

Method

Using PMSI coding, we included all patients hospitalized for myocarditis in 2 centers between 2019 and 2021 and analyzed clinical characteristics and early outcomes. The diagnosis had to be established by ESC guidelines including cardiac MRI and/or endomyocardial biopsy. We compared myocarditis related to COVID-19 infection with 2019 myocarditis (before Covid) and to Covid vaccination. Patients developing cardiogenic shock were also analyzed.

Results

Acute myocarditis related to COVID were diagnosed in 21 in-patients who had Covid symptoms several weeks before admission (post-Covid) or during hospitalization (per-Covid). Characteristics are shown in Table 1. Cardiogenic shock was observed in 7 patients and was associated with higher inflammation and more frequent myocardial necrosis in biopsy. As compared with 54 patients hospitalized in 2019 (before COVID), SarsCov2 related were more severe with more inflammation but had similar outcome.

Conclusion

Acute myocarditis related to COVID-19 are associated with severe systemic inflammation and relatively frequent heart failure as compared to others myocarditis, but all patients recovered whatever the cause in this cohort.

Machine-learning score using stress CMR for death prediction in patients with suspected or known CAD

Background

In patients with suspected or known coronary artery disease (CAD), traditional prognostic risk assessment is based upon a limited selection of clinical and imaging findings. Machine learning (ML) methods can take into account a greater number and complexity of variables.

Purpose

To investigate the feasibility and accuracy of ML using stress CMR and clinical data to predict 10-year all-cause mortality in patients with suspected or known CAD, and compared its performance to existing clinical or CMR scores.

Methods

Between 2008 and 2018, a retrospective cohort study with a median follow-up of 6.0 years (interquartile range: 5.0–8.0) included all consecutive patients referred for stress CMR. Twenty-three clinical and 11 stress CMR parameters were evaluated. Machine learning involved automated feature selection by random survival forest, model building with a multiple fractional polynomial algorithm, and 5 repetitions of 10-fold stratified cross-validation. The primary outcome was all-cause death based on the electronic National Death Registry. The external validation cohort of the ML score was performed in another center.

Results

Of 31,752 consecutive patients (mean age 63.7±12.1 years and 65.7% males), 2,679 (8.4%) died with 206,453 patient-years of follow-up. ML score (ranging 0 to 10 points) exhibited a higher area-under-the-curve compared with C-CMR-10-score, ESC-score, QRISK3-score, FRS and stress CMR data alone for prediction of 10-year all-cause mortality (ML: 0.76 vs. C-CMR-10-score: 0.68, ESC-score: 0.66, QRISK3-score: 0.64, FRS: 0.63, extent of inducible ischemia: 0.66, extent of LGE: 0.65, all p&lt;0.001). The ML score exhibited also a good area-under-the-curve in the external cohort (AUC: 0.75).

Conclusions

The ML score including clinical and stress CMR data exhibited a higher prognostic value to predict 10-year death compared with all traditional clinical or CMR scores.

Funding Acknowledgement

Type of funding sources: None.

Rifampicin resistance and mortality in patients hospitalised with HIV-associated tuberculosis

Background

Patients with HIV and drug-resistant tuberculosis (TB) are at high risk of death.

Objectives

We investigated the association between rifampicin-resistant TB (RR-TB) and mortality in a cohort of patients who were admitted to hospital at the time of TB diagnosis.

Method

Adults hospitalised at Khayelitsha Hospital and diagnosed with HIV-associated TB during admission, were enrolled between 2013 and 2016. Clinical, biochemical and microbiological data were prospectively collected and participants were followed up for 12 weeks.

Results

Participants with microbiologically confirmed TB (n = 482) were enrolled a median of two days (interquartile range [IQR]: 1-3 days) following admission. Fifty-three participants (11.0%) had RR-TB. Participants with rifampicin-susceptible TB (RS-TB) received appropriate treatment a median of one day (IQR: 1-2 days) following enrolment compared to three days (IQR: 1-9 days) in participants with RR-TB. Eight participants with RS-TB (1.9%) and six participants with RR-TB (11.3%) died prior to the initiation of appropriate treatment. Mortality at 12 weeks was 87/429 (20.3%) in the RS-TB group and 21/53 (39.6%) in the RR-TB group. RR-TB was a significant predictor of 12-week mortality (hazard ratio: 1.88; 95% confidence interval: 1.07-3.29; P = 0.03).

Conclusion

Mortality at 12 weeks in participants with RR-TB was high compared to participants with RS-TB. Delays in the initiation of appropriate treatment and poorer regimen efficacy are proposed as contributors to higher mortality in hospitalised patients with HIV and RR-TB.

Vitamin D concentrations in infancy and the risk of tuberculosis in childhood: A prospective birth cohort in Cape Town, South Africa

INTRODUCTION

Low vitamin D may increase the risk of tuberculosis; however, previous observational cohort studies have had variable results. We investigated the relationship between vitamin D levels in infancy and subsequent development of tuberculosis throughout childhood.

METHODS

We enrolled pregnant women between 20-28 weeks' gestation attending antenatal care in a peri-urban South African setting in the Drakenstein Child Health Study. Serum 25(OH)D concentrations were measured in newborn infants between 6-10 weeks of age. Children were followed prospectively for tuberculosis infection and disease using annual tuberculin skin testing, radiographic examinations, and microbiological diagnosis with GeneXpert, culture, and smear testing. Univariable and multivariable Cox regression was performed and hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated.

RESULTS

Children were followed for tuberculosis for a median of 7.2 years (IQR, 6.2-7.9). Among 744 children (< 1% living with HIV, 21% HIV-exposed living without HIV), those who were vitamin D deficient in early infancy were not at increased risk of developing tuberculosis (AHR, 0.8; 95% CI, 0.4-1.6). Infants in the lowest vitamin D concentration tertile were at similar risk of tuberculosis compared to the highest tertile (AHR, 0.7; 95% CI, 0.4-1.4). Vitamin D deficiency was associated with tuberculin conversion ≤2 years of age at a <30nmol/l (AOR, 1.9; 95% CI, 1.2-3.2), but not <50nmol/l (AOR, 1.5; 95% CI, 0.8-2.9), cutoff.

CONCLUSION

In a setting with hyperendemic tuberculosis, vitamin D levels in infancy did not predict tuberculosis at any point in childhood. However, very low vitamin D levels were associated with tuberculin conversion in young children.

Drug-resistant tuberculosis patient care journeys in South Africa: a pilot study using routine laboratory data

SETTING: Thirteen districts in Eastern Cape (EC), KwaZulu-Natal (KZN) and Western Cape (WC) Provinces, South Africa.OBJECTIVE: To pilot a methodology for describing and visualising healthcare journeys among drug-resistant tuberculosis (DR-TB) patients using routine laboratory records.DESIGN: Laboratory records were obtained for 195 patients with laboratory-detected rifampicin-resistant TB (RR-TB) during July-September 2016. Health facility visits identified from these data were plotted to visualise patient healthcare journeys. Data were verified by facility visits.RESULTS: In the 9 months after the index RR-TB sample was collected, patients visited a mean of 2.3 health facilities (95% CI 2.1-2.6), with 9% visiting ≥4 facilities. The median distance travelled by patients from rural areas (116 km, interquartile range [IQR] 50-290) was greater than for urban patients (51 km, IQR 9-140). A median of 21% of patient's time was spent under the care of primary healthcare facilities: this was respectively 6%, 37% and 39% in KZN, EC and WC. Journey patterns were generally similar within districts. Some reflected a semi-centralised model of care where patients were referred to regional hospitals; other journeys showed greater involvement of primary care.CONCLUSION: Routine laboratory data can be used to explore DR-TB patient healthcare journeys and show how the use of healthcare services for DR-TB varies in different settings.

Markers of human endometrial hypoxia can be detected in vivo and ex vivo during physiological menstruation

STUDY QUESTION

Can markers of human endometrial hypoxia be detected at menstruation in vivo?

SUMMARY ANSWER

Our in vivo data support the presence of hypoxia in menstrual endometrium of women during physiological menstruation.

WHAT IS KNOWN ALREADY

Current evidence from animal models and human in vitro studies suggests endometrial hypoxia is present at menstruation and drives endometrial repair post menses. However, detection of human endometrial hypoxia in vivo remains elusive.

STUDY DESIGN, SIZE, DURATION

We performed a prospective case study of 16 women with normal menstrual bleeding.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Reproductively aged female participants with a regular menstrual cycle underwent objective measurement of their menstrual blood loss using the alkaline haematin method to confirm a loss of <80 ml per cycle. Exclusion criteria were exogenous hormone use, an intrauterine device, endometriosis or fibroids >3 cm. Participants attended for two MRI scans; during days 1-3 of menstruation and the early/mid-secretory phase of their cycle. The MRI protocol included dynamic contrast-enhanced MRI and T2* quantification. At each visit, an endometrial sample was also collected and hypoxia-regulated repair factor mRNA levels (ADM, VEGFA, CXCR4) were quantified by RT-qPCR.

MAIN RESULTS AND THE ROLE OF CHANCE

Women had reduced T2* during menstrual scans versus non-menstrual scans (P = 0.005), consistent with menstrual hypoxia. Plasma flow (Fp) was increased at menstruation compared to the non-menstrual phase (P = 0.0005). Laboratory findings revealed increased ADM, VEGF-A and CXCR4 at menstruation on examination of paired endometrial biopsies from the menstrual and non-menstrual phase (P = 0.008; P = 0.03; P = 0.009). There was a significant correlation between T2* and these ex vivo hypoxic markers (P < 0.05).

LIMITATIONS, REASONS FOR CAUTION

This study examined the in vivo detection of endometrial hypoxic markers at specific timepoints in the menstrual cycle in women with a menstrual blood loss <80 ml/cycle and without significant uterine structural abnormalities. Further research is required to determine the presence of endometrial hypoxia in those experiencing abnormal uterine bleeding with and without fibroids/adenomyosis.

WIDER IMPLICATIONS OF THE FINDINGS

Heavy menstrual bleeding (HMB) is a common, debilitating condition. Understanding menstrual physiology may improve therapeutics. To our knowledge, this is the first in vivo data supporting the presence of menstrual hypoxia in the endometrium of women with normal menstrual bleeding. If aberrant in those with HMB, these non-invasive tests may aid diagnosis and facilitate personalized treatments for HMB.

STUDY FUNDING/COMPETING INTEREST(S)

This work was funded by Wellbeing of Women grant RG1820, Wellcome Trust Fellowship 209589/Z/17/Z and undertaken in the MRC Centre for Reproductive Health, funded by grants G1002033 and MR/N022556/1. H.O.D.C. has clinical research support for laboratory consumables and staff from Bayer AG and provides consultancy advice (but with no personal remuneration) for Bayer AG, PregLem SA, Gedeon Richter, Vifor Pharma UK Ltd, AbbVie Inc; Myovant Sciences GmbH. H.O.D.C. receives royalties from UpToDate for articles on abnormal uterine bleeding.

TRIAL REGISTRATION NUMBER

N/A.

Etiology of Pulmonary Infections in Human Immunodeficiency Virus-infected Inpatients Using Sputum Multiplex Real-time Polymerase Chain Reaction

Background

There are limited data on the etiology of respiratory infections in human immunodeficiency virus (HIV)–infected patients in resource-limited settings.

Methods

We performed quantitative multiplex real-time polymerase chain reaction (PCR) for Pneumocystis jirovecii and common bacterial and viral respiratory pathogens on sputum samples (spontaneous or induced) from a prospective cohort study of HIV-infected inpatients with World Health Organization danger signs and cough. Mycobacterial culture was done on 2 sputum samples, blood cultures, and relevant extrapulmonary samples.

Results

We enrolled 284 participants from 2 secondary-level hospitals in Cape Town, South Africa: median CD4 count was 97 cells/μL, 64% were women, and 38% were on antiretroviral therapy. One hundred forty-eight had culture-positive tuberculosis, 100 had community-acquired pneumonia (CAP), 26 had P. jirovecii pneumonia (PJP), and 64 had other diagnoses. Probable bacterial infection (>10⁵ copies/mL) was detected in 133 participants; the prevalence was highest in those with CAP (52%). Haemophilus influenzae and Streptococcus pneumoniae were the commonest bacterial pathogens detected; atypical bacteria were uncommon. Viruses were detected in 203 participants; the prevalence was highest in those with PJP (85%). Human metapneumovirus was the commonest virus detected. Multiple coinfections were commonly detected.

Conclusions

Sputum multiplex PCR could become a useful diagnostic tool for bacterial respiratory infections in HIV-infected inpatients, but its value is limited as quantitative cutoffs have only been established for a few bacterial pathogens and validation has not been done in this patient population. We found a high prevalence of respiratory viruses, but it is unclear whether these viruses were causing infection as there are no accepted quantitative PCR cutoffs for diagnosing respiratory viral infections.

High-sensitivity cardiac troponin T and NT-proBNP for ruling-in and ruling-out of cardiac amyloidosis

Background

Cardiac amyloidosis (CA) is caused by the extracellular deposition of misfolded proteins into insoluble amyloid fibrils, the 2 most common forms being transthyretin (ATTR) and immunoglobulin light chain (AL) amyloidosis. Chronic elevation of cardiac troponins and natriuretic peptides is common in CA and predicts worse outcome. The diagnostic yield of biomarkers of cardiac damage for CA has been less investigated.

Purpose

We aimed to evaluate the ruling-in/out values for the diagnosis of CA of high-sensitivity cardiac troponin T (hs-cTnT) and of N-terminal fraction of pro-B-type natriuretic peptide (NT-proBNP).

Methods

We studied 275 consecutive patients referred to two tertiary Centers in Italy (n=184) and France (n=91) with the clinical suspicion of CA due to the presence of a plasma cell dyscrasia or an unexplained left ventricular (pseudo)hypertrophy. CA was confirmed by the combination of suggestive features on imaging techniques (echocardiography, cardiac magnetic resonance, diphosphonate scintigraphy) and biopsy examination. All patients underwent a full baseline characterization including hs-cTnT and NT-proBNP. Biomarkers values corresponding to a negative likelihood ratio &lt;0.1 or a positive likelihood ratio &gt;10 were respectively chosen as rule-out and rule-in cut-offs for CA.

Results

CA was confirmed in 161 (59%) patients, who had either AL amyloidosis (n=96, 60%) or ATTR amyloidosis (n=65, 40%). At time of evaluation, 97 (35%) patients (34 CA vs. 63 controls, p=0.112) were hospitalized for decompensated heart failure. Patients with CA showed higher hs-cTnT (65 ng/L [44–122] vs. 31 [18–42], p&lt;0.001) and NT-proBNP (4260 ng/L [2006–8911] vs. 1199 [468–3357], p&lt;0.001) than those without CA. The area under the curve (AUC) values for hs-cTnT and NT-proBNP were 0.832 and 0.744 respectively (p=0.002 for the difference). The combination of the two biomarkers (AUC=0.836) improved discrimination over NT-proBNP (p=0.004), but not over hs-cTnT (p=0.423). A hs-cTnT value &lt;15 ng/L (sensitivity=100%, negative predictive value=100%, true negatives=13, false negatives=0) and a NT-proBNP &lt;550 ng/L (sensitivity=98%, negative predictive value=89%, true negatives=33, false negatives=4) were selected as rule-out cut-offs. A hs-cTnT level ≥80 ng/L (specificity=96%, positive predictive value=93%, true positives=71, false positives=5) was optimal for ruling in amyloidosis, while no rule-in cut-off could be selected for NT-proBNP. hs-cTnT values of either ≥80 or &lt;15 ng/dL could effectively rule-in/out 89 (32%) patients.

Conclusions

Plasma hs-cTnT and NT-proBNP have diagnostic value in patients with suspected CA. Stand-alone hs-cTnT levels &lt;15 or ≥80 ng/L may help to exclude or confirm the diagnosis of CA in up to one third of patients undergoing a diagnostic screening for the disease.

Figure 1

Funding Acknowledgement

Type of funding source: None

Two common echocardiographic variables to diagnose cardiac amyloidosis: the AMYLoidosis Index (AMYLI) score

Background

Early diagnosis of cardiac amyloidosis (CA) is warranted to initiate specific treatment and improve outcome. The amyloid light chain (AL) and inferior wall thickness (IWT) scores have been proposed to assess patients referred by hematologists or with unexplained left ventricular (LV) hypertrophy, respectively. These scores are composed of 4 or 5 variables, respectively, including strain data, and no decisional cut-offs were introduced.

Methods

Based on 2 variables common to the AL and IWT scores, we defined a simple score named AMYLoidosis Index (AMYLI) as the product of relative wall thickness (RWT) and E/e' ratio, and assessed its diagnostic performance. Optimal rule-out cut-offs were searched as those with negative likelihood ratio (LR−) &lt;0.1.

Results

In the derivation cohort (n=251), CA was ultimately diagnosed in 111 patients (44%). The 2.22 score value was selected as rule-out cut-off (LR- 0.0). In the hematology subset, AL CA was finally diagnosed in 32 patients (48%), with 2.36 as rule-out cut-off (LR− 0.0). In the hypertrophy subset, ATTR CA was diagnosed in 79 patients (43%), with 2.22 as best rule-out cut-off (LR− 0.0). In the validation cohort (n=691), where more patients were diagnosed with CA (94% and 68% in the hematology and in the hypertrophy subsets, respectively), the 2.22 rule-out cut-off had a LR− = ∞ (as no patient scoring &lt;2.22 had CA). In the hematology and hypertrophy subsets, the 2.36 and 2.22 cut-offs were effective for ruling-out CA, with both LR− = ∞ (as no patient scoring &lt;2.36 or 2.22, respectively, had CA).

Conclusions

The AMYLI score (RWT* E/e') is simpler than those proposed and similarly accurate. A 2.22 cut-off value excludes CA diagnosis in patients undergoing a diagnostic screening for CA, while a &lt;2.36 and a &lt;2.22 value may be better considered in the subsets with either blood dyscrasia or unexplained hypertrophy, respectively.

Funding Acknowledgement

Type of funding source: None

Differential RD-1-specific IFN-γ host responses to diverse Mycobacterium tuberculosis strains in HIV-uninfected persons may be explained by genotypic variation in the ESX-1 region

OBJECTIVES

Between-person variability in T-cell-specific interferon-gamma release assay (IGRA) responses and discordance between IGRA test formats are poorly understood.

METHODS

We evaluated the IFN-γ responses (QuantiFERON-TB Gold-In-Tube [QFT-GIT] and TSPOT-TB) stratified according to the Mycobacterium tuberculosis spoligotype of the culture isolate obtained from the same patients with confirmed active tuberculosis (n = 91). We further analysed differences within the RD-1-encoding ESX-1 region between the different strain types using whole genome sequencing.

RESULTS

In HIV-uninfected patients, TSPOT.TB and QFT-GIT IFN-γ responses were 5-fold (p < 0.01) and 2-fold higher (p < 0.05) for those infected with family 33 compared to the LAM strain (additionally, TSPOT.TB responses were 5.6-fold [p < 0.05] and 2.6-fold higher [p < 0.05] for the patients infected with the family 33 versus the X strain and Beijing versus the LAM strain, respectively). Multivariate analysis revealed that strain type (determined by spoligotyping) was independently associated with the magnitude of the IGRA response (varied by IGRA test type) and this is likely explained by variability in the ESX-1 region of Mycobacteriumtuberculosis (determined by next-generation sequencing).

CONCLUSIONS

These data have implications for the understanding of between-person heterogeneity in IGRA responses, Mycobateriumtuberculosis-specific host immunity, and the discordance between different IGRA test formats.

"A very humiliating illness": a qualitative study of patient-centered Care for Rifampicin-Resistant Tuberculosis in South Africa

BACKGROUND

Patient-centered care is pillar 1 of the "End TB" strategy, but little has been documented in the literature about what this means for people living with rifampicin-resistant (RR-TB). Optimizing care for such individuals requires a better understanding of the challenges they face and the support they need.

METHODS

A qualitative study was done among persons living with RR-TB and members of their support network. A purposive sample was selected from a larger study population and open-ended interviews were conducted using a semi-standard interview guide. Interviews were recorded and transcribed and the content analyzed using an iterative thematic analysis based in grounded theory.

RESULTS

16 participants were interviewed from three different provinces. Four distinct periods in which support was needed were identified: 1) pre-diagnosis; 2) pre-treatment; 3) treatment; and 4) post-treatment. Challenges common in all four periods included: socioeconomic issues, centralized care, and the need for better counseling at multiple levels.

CONCLUSIONS

Beyond being a "very humiliating illness", RR-TB robs people of their physical, social, economic, psychological, and emotional well-being far beyond the period when treatment is being administered. Efforts to tackle these issues are as important as new drugs and diagnostics in the fight against TB.

P2733Prognostic value of cardiac dysautonomia in AL amyloidosis

Introduction

Cardiac involvement is the major prognostic factor in patients with light chain amyloidosis (AL). Cardiac dysautonomia can occur early in amyloidosis and can be assess by Iodine-123-metaiodobenzylguanidine (123I-MIBG) scintigraphy. Its prognostic value has been shown in TTR amyloidosis but is unknown in AL amyloidosis. We aimed to evaluate the prognosis impact of cardiac dysautonomia in patients with AL amyloidosis.

Methods

We carried out a prospective study in consecutive patients with biopsy-proven AL amyloidosis. All patients underwent clinical examination, EKG, echocardiography, cardiac MRI and biological tests. The 2012 Mayo clinic prognostic classification was calculated by using blood levels of NT-proBNP, cardiac T troponin and the differential of free light chains as recommended. The sympathetic cardiac innervation was assessed by using 123I-MIBGscintigraphy and measurement of the heart-to-mediastinum uptake ratio (late H/M) in the anterior view of the chest. A cardiac denervation was defined by late H/M <1.8 4h after injection of 3 MBq/kg of 123I-MIBG. The primary end-point was all-cause mortality during follow-up.

Results

Fifty consecutive patients with AL amyloidosis were included. The median age was 68 years old [58–73]. By using both echocardiography and MRI, cardiac involvement was diagnosed in 33 patients (66%) and thirteen of these patients were NYHA class III or IV. By using Mayo clinic classification, patients were I, II, III and IV classes in 9 (18%), 14 (28%), 16 (32%) and 11 (22%) cases respectively. According to echocardiographic data, the median wall thickness of left ventricle was 13 mm [12–15]. The late H/M was 1.51 [1.33–1.67]. Cardiac denervation was found in 44 patients (88%). The 6 patients (12%) with a normal late H/M had no cardiac amyloidosis involvement.

During a median follow-up of 24 months, 9 patients (18%) died. The area under the ROC curve of late H/M for predicting death was 0.74 (CI 95% 0.58–0.86). According to this curve, the best threshold was 1.44 and 7 of the 9 patients who died had late H/M ≤1.44. The figure shows the 2 year-survival according to late H/M. Late H/M ≤1.44 predicted all-cause death irrespective of the Mayo clinic classification: HR 8.0 (CI 95% 2.1–63) after adjustment on the Mayo clinic score (p=0.005). In addition, unplanned hospitalization for heart failure occurred in 8 patients with late H/M ≤1.44 versus 3 patients with late H/M >1.44 (p=0.03).

Survival according to late H/M

Conclusion

Late H/M ≤1.44 is predictive of adverse outcomes in patients with AL amyloidosis, independently of the Mayo Clinic prognostic classification.

Integrating environmental health and genomics research in Africa: challenges and opportunities identified during a Human Heredity and Health in Africa (H3Africa) Consortium workshop

Individuals with African ancestry have extensive genomic diversity but have been underrepresented in genomic research. There is also extensive global diversity in the exposome (the totality of human environmental exposures from conception onwards) which should be considered for integrative genomic and environmental health research in Africa. To address current research gaps, we organized a workshop on environmental health research in Africa in conjunction with the H3Africa Consortium and the African Society of Human Genetics meetings in Kigali, Rwanda. The workshop was open to all researchers with an interest in environmental health in Africa and involved presentations from experts within and outside of the Consortium. This workshop highlighted innovative research occurring on the African continent related to environmental health and the interplay between the environment and the human genome. Stories of success, challenges, and collaborative opportunities were discussed through presentations, breakout sessions, poster presentations, and a panel discussion. The workshop informed participants about environmental risk factors that can be incorporated into current or future epidemiology studies and addressed research design considerations, biospecimen collection and storage, biomarkers for measuring chemical exposures, laboratory strategies, and statistical methodologies. Inclusion of environmental exposure measurements with genomic data, including but not limited to H3Africa projects, can offer a strong platform for building gene-environment (G x E) research in Africa. Opportunities to leverage existing resources and add environmental exposure data for ongoing and planned studies were discussed. Future directions include expanding the measurement of both genomic and exposomic risk factors and incorporating sophisticated statistical approaches for analyzing high dimensional G x E data. A better understanding of how environmental and genomic factors interact with nutrition and infection is also needed. Considering that the environment represents many modifiable risk factors, these research findings can inform intervention and prevention efforts towards improving global health.

Clinical, microbiologic, and immunologic determinants of mortality in hospitalized patients with HIV-associated tuberculosis: A prospective cohort study

BACKGROUND

In high-burden settings, case fatality rates are reported to be between 11% and 32% in hospitalized patients with HIV-associated tuberculosis, yet the underlying causes of mortality remain poorly characterized. Understanding causes of mortality could inform the development of novel management strategies to improve survival. We aimed to assess clinical and microbiologic determinants of mortality and to characterize the pathophysiological processes underlying death by evaluating host soluble inflammatory mediators and determined the relationship between these mediators and death as well as biomarkers of disseminated tuberculosis.

METHODS AND FINDINGS

Adult patients with HIV hospitalized with a new diagnosis of HIV-associated tuberculosis were enrolled in Cape Town between 2014 and 2016. Detailed tuberculosis diagnostic testing was performed. Biomarkers of tuberculosis dissemination and host soluble inflammatory mediators at baseline were assessed. Of 682 enrolled participants, 576 with tuberculosis (487/576, 84.5% microbiologically confirmed) were included in analyses. The median age was 37 years (IQR = 31-43), 51.2% were female, and the patients had advanced HIV with a median cluster of differentiation 4 (CD4) count of 58 cells/L (IQR = 21-120) and a median HIV viral load of 5.1 log10 copies/mL (IQR = 3.3-5.7). Antituberculosis therapy was initiated in 566/576 (98.3%) and 487/576 (84.5%) started therapy within 48 hours of enrolment. Twelve-week mortality was 124/576 (21.5%), with 46/124 (37.1%) deaths occurring within 7 days of enrolment. Clinical and microbiologic determinants of mortality included disseminated tuberculosis (positive urine lipoarabinomannan [LAM], urine Xpert MTB/RIF, or tuberculosis blood culture in 79.6% of deaths versus 60.7% of survivors, p = 0.001), sepsis syndrome (high lactate in 50.8% of deaths versus 28.9% of survivors, p < 0.001), and rifampicin-resistant tuberculosis (16.9% of deaths versus 7.2% of survivors, p = 0.002). Using non-supervised two-way hierarchical cluster and principal components analyses, we describe an immune profile dominated by mediators of the innate immune system and chemotactic signaling (interleukin-1 receptor antagonist [IL-1Ra], IL-6, IL-8, macrophage inflammatory protein-1 beta [MIP-1β]/C-C motif chemokine ligand 4 [CCL4], interferon gamma-induced protein-10 [IP-10]/C-X-C motif chemokine ligand 10 [CXCL10], MIP-1 alpha [MIP-1α]/CCL3), which segregated participants who died from those who survived. This immune profile was associated with mortality in a Cox proportional hazards model (adjusted hazard ratio [aHR] = 2.2, 95%CI = 1.9-2.7, p < 0.001) and with detection of biomarkers of disseminated tuberculosis. Clinicians attributing causes of death identified tuberculosis as a cause or one of the major causes of death in 89.5% of cases. We did not perform longitudinal sampling and did not have autopsy-confirmed causes of death.

CONCLUSIONS

In this study, we did not identify a major contribution from coinfections to these deaths. Disseminated tuberculosis, sepsis syndrome, and rifampicin resistance were associated with mortality. An immune profile dominated by mediators of the innate immune system and chemotactic signaling was associated with both tuberculosis dissemination and mortality. These findings provide pathophysiologic insights into underlying causes of mortality and could be used to inform the development of novel treatment strategies and to develop methods to risk stratify patients to appropriately target novel interventions. Causal relationships cannot be established from this study.

Human Breast Milk Bacteriome in Health and Disease

It is well-known that, beyond nutritional components, human breast milk (HBM) contains a wide variety of non-nutritive bio-factors perfectly suited for the growing infant. In the pre-2000 era, HBM was considered sterile and devoid of micro-organisms. Though HBM was not included as part of the human microbiome project launched in 2007, great strides have been made in studying the bacterial diversity of HBM in both a healthy state and diseased state, and in understanding their role in infant health. HBM provides a vast array of beneficial micro-organisms that play a key role in colonizing the infant’s mucosal system, including that of the gut. They also have a role in priming the infant’s immune system and supporting its maturation. In this review, we provide an in-depth and updated insight into the immunomodulatory, metabolic, and anti-infective role of HBM bacteriome (bacterial community) and its effect on infant health. We also provide key information from the literature by exploring the possible origin of microbial communities in HBM, the bacterial diversity in this niche and the determinants influencing the HBM bacteriome. Lastly, we investigate the role of the HBM bacteriome in maternal infectious disease (human immunodeficiency virus (HIV) and mastitis)), and cancer. Key gaps in HBM bacterial research are also identified.

Gene expression in cord blood links genetic risk for neurodevelopmental disorders with maternal psychological distress and adverse childhood outcomes

Prenatal exposure to maternal stress and depression has been identified as a risk factor for adverse behavioral and neurodevelopmental outcomes in early childhood. However, the molecular mechanisms through which maternal psychopathology shapes offspring development remain poorly understood. We applied transcriptome-wide screens to 149 umbilical cord blood samples from neonates born to mothers with posttraumatic stress disorder (PTSD; n = 20), depression (n = 31) and PTSD with comorbid depression (n = 13), compared to carefully matched trauma exposed controls (n = 23) and healthy mothers (n = 62). Analyses by maternal diagnoses revealed a clear pattern of gene expression signatures distinguishing neonates born to mothers with a history of psychopathology from those without. Co-expression network analysis identified distinct gene expression perturbations across maternal diagnoses, including two depression-related modules implicated in axon-guidance and mRNA stability, as well as two PTSD-related modules implicated in TNF signaling and cellular response to stress. Notably, these disease-related modules were enriched with brain-expressed genes and genetic risk loci for autism spectrum disorder and schizophrenia, which may imply a causal role for impaired developmental outcomes. These molecular alterations preceded changes in clinical measures at twenty-four months, including reductions in cognitive and socio-emotional outcomes in affected infants. Collectively, these findings indicate that prenatal exposure to maternal psychological distress induces neuronal, immunological and behavioral abnormalities in affected offspring and support the search for early biomarkers of exposures to adverse in utero environments and the classification of children at risk for impaired development.

Development of a clinical prediction rule to diagnose Pneumocystis jirovecii pneumonia in the World Health Organization's algorithm for seriously ill HIV-infected patients

Background

The World Health Organization (WHO) algorithm for the diagnosis of tuberculosis in seriously ill HIV-infected patients recommends that treatment for Pneumocystis jirovecii pneumonia (PJP) should be considered without giving clear guidance on selecting patients for empiric PJP therapy. PJP is a common cause of hospitalisation in HIV-infected patients in resource-poor settings where diagnostic facilities are limited.

Methods

We developed clinical prediction rules for PJP in a prospective cohort of HIV-infected inpatients with WHO danger signs and cough of any duration. The reference standard for PJP was > 1000 copies/mL of P. jirovecii DNA on real-time sputum polymerase chain reaction (PCR). Four potentially predictive variables were selected for regression models: dyspnoea, chest X-ray, haemoglobin and oxygen saturation. Respiratory rate was explored as a replacement for oxygen saturation as pulse oximetry is not always available in resource-poor settings.

Results

We enrolled 500 participants. After imputation for missing values, there were 56 PJP outcome events. Dyspnoea was not independently associated with PJP. Oxygen saturation and respiratory rate were inversely correlated. Two clinical prediction rules were developed: chest X-ray possible/likely PJP, haemoglobin ≥ 9 g/dL and either oxygen saturation < 94% or respiratory rate. The area under the receiver operating characteristic curve of the clinical prediction rule models was 0.761 (95% CI 0.683–0.840) for the respiratory rate model and 0.797 (95% CI 0.725–0.868) for the oxygen saturation model. Both models had zero probability for PJP for scores of zero, and positive likelihood ratios exceeded 10 for high scores.

Conclusion

We developed simple clinical prediction rules for PJP, which, if externally validated, could assist decision-making in the WHO seriously ill algorithm.

Hypermetabolism is a deleterious prognostic factor in patients with amyotrophic lateral sclerosis

BACKGROUND AND PURPOSE

The aim of this study was to investigate patients with amyotrophic lateral sclerosis in order to determine their nutritional, neurological and respiratory parameters, and survival according to metabolic level.

METHODS

Nutritional assessment included resting energy expenditure (REE) measured by indirect calorimetry [hypermetabolism if REE variation (ΔREE) > 10%] and fat mass (FM) using impedancemetry. Neurological assessment included the Amyotrophic Lateral Sclerosis Functional Rating Scale-Revised score. Survival analysis used the Kaplan-Meier method and multivariate Cox model.

RESULTS

A total of 315 patients were analysed. Median age at diagnosis was 65.9 years and 55.2% of patients were hypermetabolic. With regard to the metabolic level (ΔREE: < 10%, 10-20% and >20%), patients with ΔREE > 20% initially had a lower FM(29.7% vs. 32.1% in those with ΔREE ≤10%; P = 0.0054). During follow-up, the median slope of Amyotrophic Lateral Sclerosis Functional Rating Scale-Revised tended to worsen more in patients with ΔREE > 20% (-1.4 vs. -1.0 points/month in those with ΔREE ≤10%; P = 0.07). Overall median survival since diagnosis was 18.4 months. ΔREE > 20% tended to increase the risk of dying compared with ΔREE ≤10% (hazard ratio, 1.33; P = 0.055). In multivariate analysis, an increased REE:FM ratio was independently associated with death (hazard ratio, 1.005; P = 0.001).

CONCLUSIONS

Hypermetabolism is present in more than half of patients with amyotrophic lateral sclerosis. It modifies the body composition at diagnosis, and patients with hypermetabolism >20% have a worse prognosis than those without hypermetabolism.

Fluctuating asymmetry of the normal facial skeleton

The purpose of this study was to produce reliable estimations of fluctuating facial asymmetry in a normal population. Fifty-four computed tomography (CT) facial models of average-looking and symmetrical Chinese subjects with a class I occlusion were used in this study. Eleven midline landmarks and 12 pairs of bilateral landmarks were digitized. The repeatability of the landmark digitization was first evaluated. A Procrustes analysis was then used to measure the fluctuating asymmetry of each CT model, after all of the models had been scaled to the average face size of the study sample. A principal component analysis was finally used to establish the direction of the fluctuating asymmetries. The results showed that there was excellent absolute agreement among the three repeated measurements. The mean fluctuating asymmetry of the average-size face varied at each anthropometric landmark site, ranging from 1.0mm to 2.8mm. At the 95% upper limit, the asymmetries ranged from 2.2mm to 5.7mm. Most of the asymmetry of the midline structures was mediolateral, while the asymmetry of the bilateral landmarks was more equally distributed. These values are for the average face. People with larger faces will have higher values, while subjects with smaller faces will have lower values.

The Influence of HIV on the Evolution of Mycobacterium tuberculosis

HIV significantly affects the immunological environment during tuberculosis coinfection, and therefore may influence the selective landscape upon which M. tuberculosis evolves. To test this hypothesis whole genome sequences were determined for 169 South African M. tuberculosis strains from HIV-1 coinfected and uninfected individuals and analyzed using two Bayesian codon-model based selection analysis approaches: FUBAR which was used to detect persistent positive and negative selection (selection respectively favoring and disfavoring nonsynonymous substitutions); and MEDS which was used to detect episodic directional selection specifically favoring nonsynonymous substitutions within HIV-1 infected individuals. Among the 25,251 polymorphic codon sites analyzed, FUBAR revealed that 189-fold more were detectably evolving under persistent negative selection than were evolving under persistent positive selection. Three specific codon sites within the genes celA2b, katG, and cyp138 were identified by MEDS as displaying significant evidence of evolving under directional selection influenced by HIV-1 coinfection. All three genes encode proteins that may indirectly interact with human proteins that, in turn, interact functionally with HIV proteins. Unexpectedly, epitope encoding regions were enriched for sites displaying weak evidence of directional selection influenced by HIV-1. Although the low degree of genetic diversity observed in our M. tuberculosis data set means that these results should be interpreted carefully, the effects of HIV-1 on epitope evolution in M. tuberculosis may have implications for the design of M. tuberculosis vaccines that are intended for use in populations with high HIV-1 infection rates.

Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagar™STEC media

Shiga-toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) are key diarrhoea-causing foodborne pathogens. We used proteomics to characterize the virulence and antimicrobial resistance protein profiles of three clinical pathogenic E. coli isolates (two EPEC [one resistant to ciprofloxacin] and one STEC) cultured on CHROMagar™STEC solid media after minimal laboratory passage. We identified 4767 unique peptides from 1630 protein group across all three clinical E. coli strains. Label-free proteomic analysis allowed the identification of virulence and drug resistance proteins that were unique to each of the clinical isolates compared in this study. The B subunit of Shiga toxin, ToxB, was uniquely detected in the STEC strain while several other virulence factors including SheA, OmpF, OmpC and OmpX were significantly more abundant in the STEC strain. The ciprofloxacin resistant EPEC isolate possessed reduced levels of key virulence proteins compared to the ciprofloxacin susceptible EPEC and STEC strains. Parallel reaction monitoring assays validated the presence of biologically relevant proteins across biologically-replicated cultures. Propagation of clinical isolates on a relevant solid medium followed by mass spectrometry analysis represents a convenient means to quantify virulence factors and drug resistance determinants that might otherwise be lost through extensive in vitro passage in enteropathogenic bacteria.

SIGNIFICANCE

Through the use of quantitative proteomics, we have characterized the virulence and antimicrobial resistance attributes of three clinically isolated, pathogenic E. coli strains cultured on solid media. Our results provide new, quantitative data on the expressed proteomes of these tellurite-resistant, diarrhoeagenic E. coli strains and reveal a subset of antimicrobial resistance and virulence proteins that are differentially abundant between these clinical strains. Our quantitative proteomics-based approach should thus have applicability in microbiological diagnostic labs for the identification of pathogenic/drug resistant E. coli in the future.

Regulatory T Cells and Pro-inflammatory Responses Predominate in Children with Tuberculosis

Background

Following infection with Mycobacterium tuberculosis (M.tb), children are more susceptible to develop disease particularly extrapulmonary disease than adults. The exact mechanisms required for containment of M.tb are not known, but would be important to identify correlates of protection.

Objective

To comprehensively analyze key immune responses to mycobacteria between HIV-negative children with extrapulmonary TB (EPTB) compared to children with pulmonary TB (PTB) or healthy controls.

Methods

Whole blood was stimulated in vitro with mycobacteria for 24 h or 6 days to induce effector and memory responses. CD4, CD8, γδ, regulatory T cells, and their related cytokines were measured. Samples of children with tuberculosis (TB) disease were analyzed both at time of diagnosis and at the end of TB treatment to determine if any differences were due to TB disease or an underlying host phenotype.

Results

Seventy-six children with TB disease (48 with PTB and 28 with EPTB) and 83 healthy controls were recruited to the study. The frequency of CD4⁺CD25⁺CD39⁺FOXP3⁺ regulatory T cells and secreted IL10 were significantly higher in children with TB compared to healthy controls. IFNγ-, IL17-, and IL22-producing γδ T cells, IL22-producing CD4⁺ T cells and secreted pro-inflammatory cytokines (IFNγ, IL1β, and TNFα) were significantly lower in children with TB disease compared to healthy controls. IFNγ-producing CD4⁺ T cells and Ki67⁺-proliferating CD4⁺ T cells, however, were present in equal numbers in both groups. Following treatment, these immune parameters recovered to “healthy” levels or greater in children with PTB, but not those with extrapulmonary TB.

Conclusion

In children with TB disease, a predominantly immune regulatory state is present. These immune findings do not distinguish between children with PTB and EPTB at the time of diagnosis. Following treatment, these inflammatory responses recover in PTB, suggesting that the effect is disease specific rather than due to an underlying host defect.

Diagnostic accuracy of two multiplex real-time polymerase chain reaction assays for the diagnosis of meningitis in children in a resource-limited setting

INTRODUCTION

Accurate etiological diagnosis of meningitis is important, but difficult in resource-limited settings due to prior administration of antibiotics and lack of viral diagnostics. We aimed to develop and validate 2 real-time multiplex PCR (RT-PCR) assays for the detection of common causes of community-acquired bacterial and viral meningitis in South African children.

METHODS

We developed 2 multiplex RT- PCRs for detection of S. pneumoniae, N. meningitidis, H. influenzae, enteroviruses, mumps virus and herpes simplex virus. We tested residual CSF samples from children presenting to a local paediatric hospital over a one-year period, whose CSF showed an abnormal cell count. Results were compared with routine diagnostic tests and the final discharge diagnosis. We calculated accuracy of the bacterial RT-PCR assay compared to CSF culture and using World Health Organisation definitions of laboratory-confirmed bacterial meningitis.

RESULTS

From 292 samples, bacterial DNA was detected in 12 (4.1%) and viral nucleic acids in 94 (32%). Compared to CSF culture, the sensitivity and specificity of the bacterial RT-PCR was 100% and 97.2% with complete agreement in organism identification. None of the cases positive by viral RT-PCR had a bacterial cause confirmed on CSF culture. Only 9/90 (10%) of patients diagnosed clinically as bacterial meningitis or partially treated bacterial meningitis tested positive with the bacterial RT-PCR.

DISCUSSION

In this population the use of 2 multiplex RT-PCRs targeting 6 common pathogens gave promising results. If introduced into routine diagnostic testing, these multiplex RT-PCR assays would supplement other diagnostic tests, and have the potential to limit unnecessary antibiotic therapy and hospitalisation.

Improved method for collection of sputum for tuberculosis testing to ensure adequate sample volumes for molecular diagnostic testing

The quality and quantity of sputum collected has an important impact on the laboratory diagnosis of pulmonary TB. We conducted a pilot study to assess a new collection cups for the collection of sputum for the diagnosis of pulmonary tuberculosis. The pilot study utilized the standard collection cup in South Africa demonstrating a mean collection volume of 2.86±2.36SDml for 198 samples; 19% of the specimens contained <1ml and 12% contained >5ml. We designed and tested two novel sputum cups with a narrow bottom section and clear minimum and maximum markings to allow patients and clinicians to know whether sufficient sputum volume has been produced. The cups differed in their shape and manufacturing approach. The two options also support different mixing approaches being considered for a highly sensitive companion TB-screening assay being developed at Northwestern University (XtracTB assay). Sputum was collected from 102 patients at Nolungile Youth Centre, Khayelitsha, Cape Town, South Africa for a total of 204 samples. The mean volumes collected from the two cups were 2.70±0.88SDml and 2.88±0.89SDml. While the mean volumes of current and novel cups are similar, the volume ranges collected with the novel cups were narrower, and 98% of the specimen volumes were within the target range. Only 4 samples contained >5ml, but none were >6ml, and none of the specimens contained <1ml. The number of coughs that produced the samples, patient HIV and TB status plus qualitative descriptions of the sputum specimens were also evaluated.

Algorithm for planning a double-jaw orthognathic surgery using a computer-aided surgical simulation (CASS) protocol. Part 2: three-dimensional cephalometry

Three-dimensional (3D) cephalometry is not as simple as just adding a 'third' dimension to a traditional two-dimensional cephalometric analysis. There are more complex issues in 3D analysis. These include how reference frames are created, how size, position, orientation and shape are measured, and how symmetry is assessed. The main purpose of this article is to present the geometric principles of 3D cephalometry. In addition, the Gateno-Xia cephalometric analysis is presented; this is the first 3D cephalometric analysis to observe these principles.