Concordance of targeted and whole genome sequencing for Mycobacterium tuberculosis genotypic drug susceptibility testing

Targeted Next Generation Sequencing (tNGS) and Whole Genome Sequencing (WGS) are increasingly used for genotypic drug susceptibility testing (gDST) of Mycobacterium tuberculosis. Thirty-two multi-drugs resistant and 40 drug susceptible isolates from Madagascar were tested with Deeplex® Myc-TB and WGS using the Mykrobe analysis pipeline. Sixty-four of 72 (89 %) yielded concordant categorical gDST results for drugs tested by both assays. Mykrobe didn't detect pncA K96T, pncA Q141P, pncA H51P, pncA H82R, rrs C517T and rpsL K43R mutations, which were identified as minority variants in corresponding isolates by tNGS. One discrepancy (rrs C517T) was associated with insufficient sequencing depth on WGS. Deeplex® Myc-TB didn't detect inhA G-154A which isn't covered by the assay's amplification targets. Despite those targets being included in the Deeplex® Myc-TB assay, a pncA T47A and a deletion in gid were not identified in one isolate respectively. The evaluated WGS and tNGS gDST assays show high but imperfect concordance.

Solicited Cough Sound Analysis for Tuberculosis Triage Testing: The CODA TB DREAM Challenge Dataset

Cough is a common and commonly ignored symptom of lung disease. Cough is often perceived as difficult to quantify, frequently self-limiting, and non-specific. However, cough has a central role in the clinical detection of many lung diseases including tuberculosis (TB), which remains the leading infectious disease killer worldwide. TB screening currently relies on self-reported cough which fails to meet the World Health Organization (WHO) accuracy targets for a TB triage test. Artificial intelligence (AI) models based on cough sound have been developed for several respiratory conditions, with limited work being done in TB. To support the development of an accurate, point-of-care cough-based triage tool for TB, we have compiled a large multi-country database of cough sounds from individuals being evaluated for TB. The dataset includes more than 700,000 cough sounds from 2,143 individuals with detailed demographic, clinical and microbiologic diagnostic information. We aim to empower researchers in the development of cough sound analysis models to improve TB diagnosis, where innovative approaches are critically needed to end this long-standing pandemic.

Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis. However, molecular diagnostics to date have focused largely on first-line drugs and predicting susceptibilities in a binary manner (classifying strains as either susceptible or resistant). Here, we used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration (MIC) in 15,211 Mycobacterium tuberculosis clinical isolates from 23 countries across five continents. We identified 492 unique MIC-elevating variants across 13 drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.

Tuberculosis in Lemurs and a Fossa at National Zoo, Madagascar, 2022

We diagnosed Mycobacterium tuberculosis in captive lemurs and a fossa in Antananarivo, Madagascar. We noted clinical signs in the animals and found characteristic lesions during necropsy. The source of infection remains unknown. Our results illustrate the potential for reverse zoonotic infections and intraspecies transmission of tuberculosis in captive wildlife.

Improving measurement of tuberculosis care cascades to enhance people-centred care

Care cascades represent the proportion of people reaching milestones in care for a disease and are widely used to track progress towards global targets for HIV and other diseases. Despite recent progress in estimating care cascades for tuberculosis (TB) disease, they have not been routinely applied at national and subnational levels, representing a lost opportunity for public health impact. As researchers who have estimated TB care cascades in high-incidence countries (India, Madagascar, Nigeria, Peru, South Africa, and Zambia), we describe the utility of care cascades and identify measurement challenges, including the lack of population-based disease burden data and electronic data capture, the under-reporting of people with TB navigating fragmented and privatised health systems, the heterogeneity of TB tests, and the lack of post-treatment follow-up. We outline an agenda for rectifying these gaps and argue that improving care cascade measurement is crucial to enhancing people-centred care and achieving the End TB goals.

Performance evaluation of human cough annotators: optimal metrics and sex differences

INTRODUCTION

Despite its high prevalence and significance, there is still no widely available method to quantify cough. In order to demonstrate agreement with the current gold standard of human annotation, emerging automated techniques require a robust, reproducible approach to annotation. We describe the extent to which a human annotator of cough sounds (a) agrees with herself (intralabeller or intrarater agreement) and (b) agrees with other independent labellers (interlabeller or inter-rater agreement); we go on to describe significant sex differences in cough sound length and epochs size.

MATERIALS AND METHODS

24 participants wore an audiorecording smartwatch to capture 6-24 hours of continuous audio. A randomly selected sample of the whole audio was labelled twice by an expert annotator and a third time by six trained annotators. We collected 400 hours of audio and analysed 40 hours. The cough counts as well as cough seconds (any 1 s of time containing at least one cough) from different annotators were compared and summary statistics from linear and Bland-Altman analyses were used to quantify intraobserver and interobserver agreement.

RESULTS

There was excellent intralabeller (less than two disagreements per hour monitored, Pearson's correlation 0.98) and interlabeller agreement (Pearson's correlation 0.96), using cough seconds as the unit of analysis decreased annotator discrepancies by 50% in comparison to coughs. Within this data set, it was observed that the length of cough sounds and epoch size (number of coughs per bout or attach) differed between women and men.

CONCLUSION

Given the decreased interobserver variability in annotation when using cough seconds (vs just coughs) we propose their use for manually annotating cough when assessing of the performance of automatic cough monitoring systems. The differences in cough sound length and epochs size may have important implications for equality in the development of cough monitoring tools.

TRIAL REGISTRATION NUMBER

NCT05042063.

A social network analysis model approach to understand tuberculosis transmission in remote rural Madagascar

BACKGROUND

Quality surveillance data used to build tuberculosis (TB) transmission models are frequently unavailable and may overlook community intrinsic dynamics that impact TB transmission. Social network analysis (SNA) generates data on hyperlocal social-demographic structures that contribute to disease transmission.

METHODS

We collected social contact data in five villages and built SNA-informed village-specific stochastic TB transmission models in remote Madagascar. A name-generator approach was used to elicit individual contact networks. Recruitment included confirmed TB patients, followed by snowball sampling of named contacts. Egocentric network data were aggregated into village-level networks. Network- and individual-level characteristics determining contact formation and structure were identified by fitting an exponential random graph model (ERGM), which formed the basis of the contact structure and model dynamics. Models were calibrated and used to evaluate WHO-recommended interventions and community resiliency to foreign TB introduction.

RESULTS

Inter- and intra-village SNA showed variable degrees of interconnectivity, with transitivity (individual clustering) values of 0.16, 0.29, and 0.43. Active case finding and treatment yielded 67%-79% reduction in active TB disease prevalence and a 75% reduction in TB mortality in all village networks. Following hypothetical TB elimination and without specific interventions, networks A and B showed resilience to both active and latent TB reintroduction, while Network C, the village network with the highest transitivity, lacked resiliency to reintroduction and generated a TB prevalence of 2% and a TB mortality rate of 7.3% after introduction of one new contagious infection post hypothetical elimination.

CONCLUSION

In remote Madagascar, SNA-informed models suggest that WHO-recommended interventions reduce TB disease (active TB) prevalence and mortality while TB infection (latent TB) burden remains high. Communities' resiliency to TB introduction decreases as their interconnectivity increases. "Top down" population level TB models would most likely miss this difference between small communities. SNA bridges large-scale population-based and hyper focused community-level TB modeling.

Complexities and benefits of adopting next-generation sequencing-based tuberculosis diagnostics: a qualitative study among stakeholders in low and high-income countries

OBJECTIVES

To clarify perceived benefits, barriers and facilitators of Mycobacterium tuberculosis next-generation sequencing implementation in Madagascar and Canada, towards informing implementation of this diagnostic technology in public health agencies and clinical settings in and beyond these settings.

DESIGN

This qualitative study involved conducting semistructured interviews with key stakeholders engaged with next-generation sequencing implementation in Madagascar and Canada. Team-based descriptive analysis supported by Nvivo V.12.0 was used to identify key themes.

SETTING

The study was conducted with participants involved at the clinical, diagnostic and surveillance levels of tuberculosis (TB) management from Madagascar and Canada.

PARTICIPANTS

Eighteen participants were interviewed (nine Madagascar and nine Canada) and included individuals purposively sampled based on involvement with TB surveillance, laboratory diagnosis and clinical management.

RESULTS

The following five themes emerged in the analysis of Malagasy and Canadian interviews: (1) heterogeneity in experience with established TB diagnostics, (2) variable understanding of new sequencing-based diagnostics potential; (3) further evidence as being key to expand adoption; (4) ethical arguments and concerns; (5) operational and system-level considerations.

CONCLUSION

There persists important lack of familiarity with TB next-generation sequencing (TB NGS) applications among stakeholders in Canada and Madagascar. This translates into skepticism on the evidence underlying its use and its true potential value added within global public health systems. If deployed, TB NGS testing should be integrated with clinical and surveillance programmes. Although this is perceived as a priority, leadership and funding responsibilities for this integration to happen remains unclear to clinical, laboratory and public health stakeholders.

Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction

Universal access to drug susceptibility testing for newly diagnosed tuberculosis patients is recommended. Access to culture-based diagnostics remains limited, and targeted molecular assays are vulnerable to emerging resistance mutations. Improved protocols for direct-from-sputum Mycobacterium tuberculosis sequencing would accelerate access to comprehensive drug susceptibility testing and molecular typing. We assessed a thermo-protection buffer-based direct-from-sample M. tuberculosis whole-genome sequencing protocol. We prospectively analyzed 60 acid-fast bacilli smear-positive clinical sputum samples in India and Madagascar. A diversity of semiquantitative smear positivity-level samples were included. Sequencing was performed using Illumina and MinION (monoplex and multiplex) technologies. We measured the impact of bacterial inoculum and sequencing platforms on genomic read depth, drug susceptibility prediction performance, and typing accuracy. M. tuberculosis was identified by direct sputum sequencing in 45/51 samples using Illumina, 34/38 were identified using MinION-monoplex sequencing, and 20/24 were identified using MinION-multiplex sequencing. The fraction of M. tuberculosis reads from MinION sequencing was lower than from Illumina, but monoplexing grade 3+ samples on MinION produced higher read depth than Illumina (P < 0.05) and MinION multiplexing (P < 0.01). No significant differences in sensitivity and specificity of drug susceptibility predictions were seen across sequencing modalities or within each technology when stratified by smear grade. Illumina sequencing from sputum accurately identified 1/8 (rifampin) and 6/12 (isoniazid) resistant samples, compared to 2/3 (rifampin) and 3/6 (isoniazid) accurately identified with Nanopore monoplex. Lineage agreement levels between direct and culture-based sequencing were 85% (MinION-monoplex), 88% (Illumina), and 100% (MinION-multiplex). M. tuberculosis direct-from-sample whole-genome sequencing remains challenging. Improved and affordable sample treatment protocols are needed prior to clinical deployment.

Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis

BACKGROUND

Mycobacterium tuberculosis whole-genome sequencing (WGS) has been widely used for genotypic drug susceptibility testing (DST) and outbreak investigation. For both applications, Illumina technology is used by most public health laboratories; however, Nanopore technology developed by Oxford Nanopore Technologies has not been thoroughly evaluated. The aim of this study was to determine whether Nanopore sequencing data can provide equivalent information to Illumina for transmission clustering and genotypic DST for M tuberculosis.

METHODS

In this genomic analysis, we analysed 151 M tuberculosis isolates from Madagascar, South Africa, and England, which were collected between 2011 and 2018, using phenotypic DST and matched Illumina and Nanopore data. Illumina sequencing was done with the MiSeq, HiSeq 2500, or NextSeq500 platforms and Nanopore sequencing was done on the MinION or GridION platforms. Using highly reliable PacBio sequencing assemblies and pairwise distance correlation between Nanopore and Illumina data, we optimise Nanopore variant filters for detecting single-nucleotide polymorphisms (SNPs; using BCFtools software). We then used those SNPs to compare transmission clusters identified by Nanopore with the currently used UK Health Security Agency Illumina pipeline (COMPASS). We compared Illumina and Nanopore WGS-based DST predictions using the Mykrobe software and mutation catalogue.

FINDINGS

The Nanopore BCFtools pipeline identified SNPs with a median precision of 99·3% (IQR 99·1-99·6) and recall of 90·2% (88·1-94·2) compared with a precision of 99·6% (99·4-99·7) and recall of 91·9% (87·6-98·6) using the Illumina COMPASS pipeline. Using a threshold of 12 SNPs for putative transmission clusters, Illumina identified 98 isolates as unrelated and 53 as belonging to 19 distinct clusters (size range 2-7). Nanopore reproduced 15 out of 19 clusters perfectly; two clusters were merged into one cluster, one cluster had a single sample missing, and one cluster had an additional sample adjoined. Illumina-based clusters were also closely replicated using a five SNP threshold and clustering accuracy was maintained using mixed Illumina and Nanopore datasets. Genotyping resistance variants with Nanopore was highly concordant with Illumina, having zero discordant SNPs across more than 3000 SNPs and four insertions or deletions (indels), across 60 000 indels.

INTERPRETATION

Illumina and Nanopore technologies can be used independently or together by public health laboratories performing M tuberculosis genotypic DST and outbreak investigations. As a result, clinical and public health institutions making decisions on which sequencing technology to adopt for tuberculosis can base the choice on cost (which varies by country), batching, and turnaround time.

FUNDING

Academy for Medical Sciences, Oxford Wellcome Institutional Strategic Support Fund, and the Swiss South Africa Joint Research Award (Swiss National Science Foundation and South African National Research Foundation).

Digital cough monitoring - A potential predictive acoustic biomarker of clinical outcomes in hospitalized COVID-19 patients

PURPOSE

Recent developments in the field of artificial intelligence and acoustics have made it possible to objectively monitor cough in clinical and ambulatory settings. We hypothesized that time patterns of objectively measured cough in COVID-19 patients could predict clinical prognosis and help rapidly identify patients at high risk of intubation or death.

METHODS

One hundred and twenty-three patients hospitalized with COVID-19 were enrolled at University of Florida Health Shands and the Centre Hospitalier de l'Université de Montréal. Patients' cough was continuously monitored digitally along with clinical severity of disease until hospital discharge, intubation, or death. The natural history of cough in hospitalized COVID-19 disease was described and logistic models fitted on cough time patterns were used to predict clinical outcomes.

RESULTS

In both cohorts, higher early coughing rates were associated with more favorable clinical outcomes. The transitional cough rate, or maximum cough per hour rate predicting unfavorable outcomes, was 3·40 and the AUC for cough frequency as a predictor of unfavorable outcomes was 0·761. The initial 6 h (0·792) and 24 h (0·719) post-enrolment observation periods confirmed this association and showed similar predictive value.

INTERPRETATION

Digital cough monitoring could be used as a prognosis biomarker to predict unfavorable clinical outcomes in COVID-19 disease. With early sampling periods showing good predictive value, this digital biomarker could be combined with clinical and paraclinical evaluation and is well adapted for triaging patients in overwhelmed or resources-limited health programs.

On-demand, hospital-based, severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic epidemiology to support nosocomial outbreak investigations: A prospective molecular epidemiology study

Objectives

We evaluated the added value of infection control-guided, on demand, and locally performed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic sequencing to support outbreak investigation and control in acute-care settings.

Design and setting

This 18-month prospective molecular epidemiology study was conducted at a tertiary-care hospital in Montreal, Canada. When nosocomial transmission was suspected by local infection control, viral genomic sequencing was performed locally for all putative outbreak cases. Molecular and conventional epidemiology data were correlated on a just-in-time basis to improve understanding of coronavirus disease 2019 (COVID-19) transmission and reinforce or adapt control measures.

Results

Between April 2020 and October 2021, 6 outbreaks including 59 nosocomial infections (per the epidemiological definition) were investigated. Genomic data supported 7 distinct transmission clusters involving 6 patients and 26 healthcare workers. We identified multiple distinct modes of transmission, which led to reinforcement and adaptation of infection control measures. Molecular epidemiology data also refuted (n = 14) suspected transmission events in favor of community acquired but institutionally clustered cases.

Conclusion

SARS-CoV-2 genomic sequencing can refute or strengthen transmission hypotheses from conventional nosocomial epidemiological investigations, and guide implementation of setting-specific control strategies. Our study represents a template for prospective, on site, outbreak-focused SARS-CoV-2 sequencing. This approach may become increasingly relevant in a COVID-19 endemic state where systematic sequencing within centralized surveillance programs is not available.

Trial registration

clinicaltrials.gov identifier: NCT05411562.

High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region

Background

Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a serious health problem in India, also contributing to one-fourth of the global MDR tuberculosis (TB) burden. About 36% of the MDR MTBC strains are reported fluoroquinolone (FQ) resistant leading to high pre-extensively drug-resistant (pre-XDR) and XDR-TB (further resistance against bedaquiline and/or linezolid) rates. Still, factors driving the MDR/pre-XDR epidemic in India are not well defined.

Methods

In a retrospective study, we analyzed 1852 consecutive MTBC strains obtained from patients from a tertiary care hospital laboratory in Mumbai by whole genome sequencing (WGS). Univariate and multivariate statistics was used to investigate factors associated with pre-XDR. Core genome multi locus sequence typing, time scaled haplotypic density (THD) method and homoplasy analysis were used to analyze epidemiological success, and positive selection in different strain groups, respectively.

Results

In total, 1016 MTBC strains were MDR, out of which 703 (69.2%) were pre-XDR and 45 (4.4%) were XDR. Cluster rates were high among MDR (57.8%) and pre-XDR/XDR (79%) strains with three dominant L2 (Beijing) strain clusters (Cl 1–3) representing half of the pre-XDR and 40% of the XDR-TB cases. L2 strains were associated with pre-XDR/XDR-TB (P < 0.001) and, particularly Cl 1–3 strains, had high first-line and FQ resistance rates (81.6–90.6%). Epidemic success analysis using THD showed that L2 strains outperformed L1, L3, and L4 strains in short- and long-term time scales. More importantly, L2 MDR and MDR + strains had higher THD success indices than their not-MDR counterparts. Overall, compensatory mutation rates were highest in L2 strains and positive selection was detected in genes of L2 strains associated with drug tolerance (prpB and ppsA) and virulence (Rv2828c). Compensatory mutations in L2 strains were associated with a threefold increase of THD indices, suggesting improved transmissibility.

Conclusions

Our data indicate a drastic increase of FQ resistance, as well as emerging bedaquiline resistance which endangers the success of newly endorsed MDR-TB treatment regimens. Rapid changes in treatment and control strategies are required to contain transmission of highly successful pre-XDR L2 strains in the Mumbai Metropolitan region but presumably also India-wide.

Acoustic surveillance of cough for detecting respiratory disease using artificial intelligence

Research question

Can smartphones be used to detect individual and population-level changes in cough frequency that correlate with the incidence of coronavirus disease 2019 (COVID-19) and other respiratory infections?

Methods

This was a prospective cohort study carried out in Pamplona (Spain) between 2020 and 2021 using artificial intelligence cough detection software. Changes in cough frequency around the time of medical consultation were evaluated using a randomisation routine; significance was tested by comparing the distribution of cough frequencies to that obtained from a model of no difference. The correlation between changes of cough frequency and COVID-19 incidence was studied using an autoregressive moving average analysis, and its strength determined by calculating its autocorrelation function (ACF). Predictors for the regular use of the system were studied using a linear regression. Overall user experience was evaluated using a satisfaction questionnaire and through focused group discussions.

Results

We followed-up 616 participants and collected >62 000 coughs. Coughs per hour surged around the time cohort subjects sought medical care (difference +0.77 coughs·h−1; p=0.00001). There was a weak temporal correlation between aggregated coughs and the incidence of COVID-19 in the local population (ACF 0.43). Technical issues affected uptake and regular use of the system.

Interpretation

Artificial intelligence systems can detect changes in cough frequency that temporarily correlate with the onset of clinical disease at the individual level. A clearer correlation with population-level COVID-19 incidence, or other respiratory conditions, could be achieved with better penetration and compliance with cough monitoring.

Prevalence and factors associated with human Taenia solium taeniosis and cysticercosis in twelve remote villages of Ranomafana rainforest, Madagascar

Background

Infections with the tapeworm Taenia solium (taeniosis and cysticercosis) are Neglected Tropical Diseases (NTD) highly endemic in Madagascar. These infections are however underdiagnosed, underreported and their burden at the community level remains unknown especially in rural remote settings. This study aims at assessing the prevalence of T. solium infections and associated risk factors in twelve remote villages surrounding Ranomafana National Park (RNP), Ifanadiana District, Madagascar.

Methodology

A community based cross-sectional survey was conducted in June 2016. Stool and serum samples were collected from participants. Tapeworm carriers were identified by stool examination. Taenia species and T. solium genotypes were characterised by PCR and sequencing of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. Detection of specific anti-cysticercal antibodies (IgG) or circulating cysticercal antigens was performed by ELISA or EITB/Western blot assays.

Principal findings

Of the 459 participants with paired stool and blood samples included ten participants from seven distinct villages harbored Taenia spp. eggs in their stools samples DNA sequencing of the cox1 gene revealed a majority of T. solium Asian genotype (9/10) carriage. The overall seroprevalences of anti-cysticercal IgGs detected by ELISA and EITB were quite similar (27.5% and 29.8% respectively). A prevalence rate of 12.4% of circulating cysticercal antigens was observed reflecting cysticercosis with viable cysts. Open defecation (Odds Ratio, OR = 1.5, 95% CI: 1.0–2.3) and promiscuity with households of more than 4 people (OR = 1.9, 95% CI: 1.1–3.1) seem to be the main risk factors associated with anticysticercal antibodies detection. Being over 15 years of age would be a risk factor associated with an active cysticercosis (OR = 1.6, 95% CI: 1.0–2.7). Females (OR = 0.5, 95% CI: 0.3–0.9) and use of river as house water source (OR = 0.3, 95% CI: 0.1–1.5) were less likely to have cysticercosis with viable cysts.

Conclusions/Significance

This study indicates a high exposure of the investigated population to T. solium infections with a high prevalence of cysticercosis with viable cysts. These data can be useful to strengthen public health interventions in these remote settings.

Taenia solium infections in humans (taeniosis and neurocysticercosis) and in pigs (cysticercosis) are endemic in Madagascar presenting a significant public health burden. Neurocysticercosis with localization of the parasite in the Central Nervous System is the most severe and frequent form of parasitic brain diseases in humans and responsible of thousands of worldwide deaths per year. Madagascar is a T. solium endemic country where poor sanitation, free roaming pigs and outdoor defecation are common, and maintain the parasite transmission cycle. Little information is available regarding taeniosis/cysticercosis epidemiology in Madagascar. We carried out a community-based study to investigate the prevalence of human taeniosis/cysticercosis and associated risk factors in 12 rural remote villages of Ranomafana and Kelilalina townships (Ifanadiana district, Madagascar). Our results reveal that in 7/12 villages investigated, a high number of participants had teaniosis. Moreover, a high number of active cysticercosis cases were detected. Open defecation and promiscuity were seemed to be the main risk factors associated to T. solium infections. The results of this study will be useful to guide interventions in these remote settings surrounding the Ranomafana National Park.

Longitudinal Passive Cough Monitoring and Its Implications for Detecting Changes in Clinical Status

Research Question

What is the impact of the duration of cough monitoring on its accuracy in detecting changes in the cough frequency?

Materials and Methods

This is a statistical analysis of a prospective cohort study. Participants were recruited in the city of Pamplona (Northern Spain) and their cough frequency was passively monitored using smartphone-based acoustic artificial intelligence software. Differences in cough frequency were compared using a one-tailed Mann-Whitney U test and a randomisation routine to simulate 24-h monitoring.

Results

616 participants were monitored for an aggregated duration of over 9 person-years and registered 62 325 coughs. This empiric analysis found that an individual's cough patterns are stochastic, following a binomial distribution. When compared to continuous monitoring, limiting observation to 24 h can lead to inaccurate estimates of change in cough frequency, particularly in persons with low or small changes in rate.

Interpretation

Detecting changes in an individual's rate of coughing is complicated by significant stochastic variability within and between days. Assessing change based solely on intermittent sampling, including 24-h, can be misleading. This is particularly problematic in detecting small changes in individuals who have a low rate and/or high variance in cough pattern.

Voriconazole Sequestration During Extracorporeal Membrane Oxygenation for Invasive Lung Aspergillosis: A Case Report

The increasing use of extracorporeal membrane oxygenation (ECMO) in critical care introduces new challenges with medication dosing. Voriconazole, a commonly used antifungal and the first-choice agent for the treatment of invasive aspergillosis, is a poorly water-soluble and highly protein-bound drug. Significant sequestration in ECMO circuits can be expected; however, no specific dosing recommendations are available. We report on the therapeutic drug monitoring and clinical evolution of a patient treated with voriconazole for invasive pulmonary aspergillosis while receiving ECMO therapy. Voriconazole trough levels were persistently low (<1 µg/mL) after initiation of ECMO despite additional loading doses and dose increases. Voriconazole dose had to be increased to 6.5 mg/kg three times daily to obtain therapeutic trough levels. The inability to achieve therapeutic levels of voriconazole for a prolonged period (a minimum of 9 days) while undergoing ECMO therapy is believed to have been a significant contributing factor in the patient's fatal outcome. Therapeutic trough levels of voriconazole cannot be guaranteed with standard dosing in patients undergoing ECMO and much higher doses may be necessary. Empirical use of higher doses and/or combination therapy may be reasonable and frequent therapeutic drug monitoring is mandatory.

High-throughput digital cough recording on a university campus: A SARS-CoV-2-negative curated open database and operational template for acoustic screening of respiratory diseases

Objective

Respiratory illnesses have information-rich acoustic biomarkers, such as cough, that can potentially play an important role in screening populations for disease risk. To realize that potential, datasets of paired acoustic-clinical samples are needed for the development and validation of acoustic screening models, and protocols for collecting acoustic samples must be efficient and safe. We collected cough acoustic signatures at a high-throughput SARS-CoV-2 testing site on a college campus. Here, we share logistical details and the dataset of acoustic cough signatures paired with the gold standard in SARS-CoV-2 testing of SARS-CoV-2 genomic sequences using qRT-PCR.

Methods

Cough recordings were collected in winter-spring 2021 at a rural residential college (Sewanee, TN, USA), where approximately 2000 students were tested for SARS-CoV-2 on a weekly basis. Cough collection was managed by student volunteers using custom software.

Results

4302 coughs were recorded from 960 participants over 11 weeks. All coughs were COVID-19 negative. Approximately 30 s were required to check-in a participant and collect their cough.

Conclusion

The value of acoustic screening tools depends upon our ability to develop and implement them reliably and quickly. For that to happen, high-quality datasets and logistical insights must be collected and shared on an ongoing basis.

Clinical Evaluation of In-House-Produced 3D-Printed Nasopharyngeal Swabs for COVID-19 Testing

3D-printed alternatives to standard flocked swabs were rapidly developed to provide a response to the unprecedented and sudden need for an exponentially growing amount of diagnostic tools to fight the COVID-19 pandemic. In light of the anticipated shortage, a hospital-based 3D-printing platform was implemented in our institution for the production of swabs for nasopharyngeal and oropharyngeal sampling based on the freely available, open-source design provided to the community by University of South Florida's Health Radiology and Northwell Health System teams as a replacement for locally used commercial swabs. Validation of our 3D-printed swabs was performed with a head-to-head diagnostic accuracy study of the 3D-printed "Northwell model" with the cobas PCR Media® swab sample kit. We observed an excellent concordance (total agreement 96.8%, Kappa 0.936) in results obtained with the 3D-printed and flocked swabs, indicating that the in-house 3D-printed swab could be used reliably in the context of a shortage of flocked swabs. To our knowledge, this is the first study to report on autonomous hospital-based production and clinical validation of 3D-printed swabs.

Drug-Resistant Tuberculosis in Pet Ring-Tailed Lemur, Madagascar

We diagnosed tuberculosis in an illegally wild-captured pet ring-tailed lemur manifesting lethargy, anorexia, and cervical lymphadenopathy. Whole-genome sequencing confirmed the Mycobacterium tuberculosis isolate belonged to lineage 3 and harbored streptomycin resistance. We recommend reverse zoonosis prevention and determination of whether lemurs are able to maintain M. tuberculosis infection.

Digital acoustic surveillance for early detection of respiratory disease outbreaks in Spain: a protocol for an observational study

INTRODUCTION

Cough is a common symptom of COVID-19 and other respiratory illnesses. However, objectively measuring its frequency and evolution is hindered by the lack of reliable and scalable monitoring systems. This can be overcome by newly developed artificial intelligence models that exploit the portability of smartphones. In the context of the ongoing COVID-19 pandemic, cough detection for respiratory disease syndromic surveillance represents a simple means for early outbreak detection and disease surveillance. In this protocol, we evaluate the ability of population-based digital cough surveillance to predict the incidence of respiratory diseases at population level in Navarra, Spain, while assessing individual determinants of uptake of these platforms.

METHODS AND ANALYSIS

Participants in the Cendea de Cizur, Zizur Mayor or attending the local University of Navarra (Pamplona) will be invited to monitor their night-time cough using the smartphone app Hyfe Cough Tracker. Detected coughs will be aggregated in time and space. Incidence of COVID-19 and other diagnosed respiratory diseases within the participants cohort, and the study area and population will be collected from local health facilities and used to carry out an autoregressive moving average analysis on those independent time series. In a mixed-methods design, we will explore barriers and facilitators of continuous digital cough monitoring by evaluating participation patterns and sociodemographic characteristics. Participants will fill an acceptability questionnaire and a subgroup will participate in focus group discussions.

ETHICS AND DISSEMINATION

Ethics approval was obtained from the ethics committee of the Centre Hospitalier de l'Université de Montréal, Canada and the Medical Research Ethics Committee of Navarre, Spain. Preliminary findings will be shared with civil and health authorities and reported to individual participants. Results will be submitted for publication in peer-reviewed scientific journals and international conferences.

TRIAL REGISTRATION NUMBER

NCT04762693.

Latent tuberculosis infection prevalence in rural Madagascar

BACKGROUND

Understanding latent Mycobacterium tuberculosis infection (LTBI) prevalence is crucial for the design of TB control strategies. There are no data on LTBI in rural Madagascar.

METHODS

Tuberculin skin tests were performed in 98 adults aged >15 y in five rural villages in the Ifanadiana district, Madagascar.

RESULTS

Of adults, 78.6% were positive for LTBI, ranging between 28.6% and 95.0% among villages. The majority (65.3%) showed an induration reaction of >15 mm.

CONCLUSIONS

LTBI prevalence is high in rural Madagascar. Long-term TB control strategies including LTBI testing and treatment must account for high and heterogeneous prevalence in remote, underdeveloped areas.

Pandoraea sp infection in a lung transplant patient and the critical role of MALDI-TOF in accurate bacterial identification

Diagnosis and clinical management of pulmonary infections in lung transplant patients are challenging. The increased diversity of bacterial species identified from clinical samples with novel proteomics-based systems can further complicate clinical decision making in this highly vulnerable population. Whether newly recognized organisms are colonizers or true pathogens often remains controversial since symptoms causality and impact on lung function is often unknown. We present the case of a 48-year-old female lung transplant patient with Pandoraea sp infection. We review and discuss the role of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for accurate bacterial identification. We report on therapeutic management and clinical outcome.

Isolated muscular cystic echinococcosis mimicking neoplasia

Musculoskeletal cystic echinococcosis can present as an isolated disease mimicking neoplasia. Along with albendazole therapy, complete excision avoiding cyst rupture is essential to prevent disease dissemination and hypersensitivity reactions. Conventional epidemiology and molecular typing can help differentiate between domestic and sylvatic strains of echinococcosis in the traveler and migrant population.

Drones and digital adherence monitoring for community-based tuberculosis control in remote Madagascar: A cost-effectiveness analysis

Background

Continuing tuberculosis control with current approaches is unlikely to reach the World Health Organization’s objective to eliminate TB by 2035. Innovative interventions such as unmanned aerial vehicles (or drones) and digital adherence monitoring technologies have the potential to enhance patient-centric quality tuberculosis care and help challenged National Tuberculosis Programs leapfrog over the impediments of conventional Directly Observed Therapy (DOTS) implementation. A bundle of innovative interventions referred to for its delivery technology as the Drone Observed Therapy System (DrOTS) was implemented in remote Madagascar. Given the potentially increased cost these interventions represent for health systems, a cost-effectiveness analysis was indicated.

Methods

A decision analysis model was created to calculate the incremental cost-effectiveness of the DrOTS strategy compared to DOTS, the standard of care, in a study population of 200,000 inhabitants in rural Madagascar with tuberculosis disease prevalence of 250/100,000. A mixed top-down and bottom-up costing approach was used to identify costs associated with both models, and net costs were calculated accounting for resulting TB treatment costs. Net cost per disability-adjusted life years averted was calculated. Sensitivity analyses were performed for key input variables to identify main drivers of health and cost outcomes, and cost-effectiveness.

Findings

Net cost per TB patient identified within DOTS and DrOTS were, respectively, $282 and $1,172. The incremental cost per additional TB patient diagnosed in DrOTS was $2,631 and the incremental cost-effectiveness ratio of DrOTS compared to DOTS was $177 per DALY averted. Analyses suggest that integrating drones with interventions ensuring highly sensitive laboratory testing and high treatment adherence optimizes cost-effectiveness.

Conclusion

Innovative technology packages including drones, digital adherence monitoring technologies, and molecular diagnostics for TB case finding and retention within the cascade of care can be cost effective. Their integration with other interventions within health systems may further lower costs and support access to universal health coverage.

Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe

Two billion people are infected with Mycobacterium tuberculosis, leading to 10 million new cases of active tuberculosis and 1.5 million deaths annually. Universal access to drug susceptibility testing (DST) has become a World Health Organization priority. We previously developed a software tool, Mykrobe predictor, which provided offline species identification and drug resistance predictions for M. tuberculosis from whole genome sequencing (WGS) data. Performance was insufficient to support the use of WGS as an alternative to conventional phenotype-based DST, due to mutation catalogue limitations.  Here we present a new tool, Mykrobe, which provides the same functionality based on a new software implementation. Improvements include i) an updated mutation catalogue giving greater sensitivity to detect pyrazinamide resistance, ii) support for user-defined resistance catalogues, iii) improved identification of non-tuberculous mycobacterial species, and iv) an updated statistical model for Oxford Nanopore Technologies sequencing data. Mykrobe is released under MIT license at https://github.com/mykrobe-tools/mykrobe. We incorporate mutation catalogues from the CRyPTIC consortium et al. (2018) and from Walker et al. (2015), and make improvements based on performance on an initial set of 3206 and an independent set of 5845 M. tuberculosis Illumina sequences. To give estimates of error rates, we use a prospectively collected dataset of 4362 M. tuberculosis isolates. Using culture based DST as the reference, we estimate Mykrobe to be 100%, 95%, 82%, 99% sensitive and 99%, 100%, 99%, 99% specific for rifampicin, isoniazid, pyrazinamide and ethambutol resistance prediction respectively. We benchmark against four other tools on 10207 (=5845+4362) samples, and also show that Mykrobe gives concordant results with nanopore data.  We measure the ability of Mykrobe-based DST to guide personalized therapeutic regimen design in the context of complex drug susceptibility profiles, showing 94% concordance of implied regimen with that driven by phenotypic DST, higher than all other benchmarked tools.

Kankanet: An artificial neural network-based object detection smartphone application and mobile microscope as a point-of-care diagnostic aid for soil-transmitted helminthiases

Background

Endemic areas for soil-transmitted helminthiases often lack the tools and trained personnel necessary for point-of-care diagnosis. This study pilots the use of smartphone microscopy and an artificial neural network-based (ANN) object detection application named Kankanet to address those two needs.

Methodology/Principal findings

A smartphone was equipped with a USB Video Class (UVC) microscope attachment and Kankanet, which was trained to recognize eggs of Ascaris lumbricoides, Trichuris trichiura, and hookworm using a dataset of 2,078 images. It was evaluated for interpretive accuracy based on 185 new images. Fecal samples were processed using Kato-Katz (KK), spontaneous sedimentation technique in tube (SSTT), and Merthiolate-Iodine-Formaldehyde (MIF) techniques. UVC imaging and ANN interpretation of these slides was compared to parasitologist interpretation of standard microscopy.Relative to a gold standard defined as any positive result from parasitologist reading of KK, SSTT, and MIF preparations through standard microscopy, parasitologists reading UVC imaging of SSTT achieved a comparable sensitivity (82.9%) and specificity (97.1%) in A. lumbricoides to standard KK interpretation (97.0% sensitivity, 96.0% specificity). The UVC could not accurately image T. trichiura or hookworm. Though Kankanet interpretation was not quite as sensitive as parasitologist interpretation, it still achieved high sensitivity for A. lumbricoides and hookworm (69.6% and 71.4%, respectively). Kankanet showed high sensitivity for T. trichiura in microscope images (100.0%), but low in UVC images (50.0%).

Conclusions/Significance

The UVC achieved comparable sensitivity to standard microscopy with only A. lumbricoides. With further improvement of image resolution and magnification, UVC shows promise as a point-of-care imaging tool. In addition to smartphone microscopy, ANN-based object detection can be developed as a diagnostic aid. Though trained with a limited dataset, Kankanet accurately interprets both standard microscope and low-quality UVC images. Kankanet may achieve sensitivity comparable to parasitologists with continued expansion of the image database and improvement of machine learning technology.

For rainforest-enshrouded rural villages of Madagascar, soil-transmitted helminthiases are more the rule than the exception. However, the microscopy equipment and lab technicians needed for diagnosis are a distance of several days’ hike away. We piloted a solution for these communities by leveraging resources the villages already had: a traveling team of local health care workers, and their personal Android smartphones. We demonstrated that an inexpensive, commercially available microscope attachment for smartphones could rival the sensitivity and specificity of a regular microscope using standard field fecal sample processing techniques. We also developed an artificial neural network-based object detection Android application, called Kankanet, based on open-source programming libraries. Kankanet was used to detect eggs of the three most common soil-transmitted helminths: Ascaris lumbricoides, Trichuris trichiura, and hookworm. We found Kankanet to be moderately sensitive and highly specific for both standard microscope images and low-quality smartphone microscope images. This proof-of-concept study demonstrates the diagnostic capabilities of artificial neural network-based object detection systems. Since the programming frameworks used were all open-source and user-friendly even for computer science laymen, artificial neural network-based object detection shows strong potential for development of low-cost, high-impact diagnostic aids essential to health care and field research in resource-limited communities.

Bi-directional drones to strengthen healthcare provision: experiences and lessons from Madagascar, Malawi and Senegal

Drones are increasingly being used globally for the support of healthcare programmes. Madagascar, Malawi and Senegal are among a group of early adopters piloting the use of bi-directional transport drones for health systems in sub-Saharan Africa. This article presents the experiences as well as the strengths, weaknesses, opportunities and threats (SWOT analysis) of these country projects. Methods for addressing regulatory, feasibility, acceptability, and monitoring and evaluation issues are presented to guide future implementations. Main recommendations for governments, implementers, drone providers and funders include (1) developing more reliable technologies, (2) thorough vetting of drone providers' capabilities during the selection process, (3) using and strengthening local capacity, (4) building in-country markets and businesses to maintain drone operations locally, (5) coordinating efforts among all stakeholders under government leadership, (6) implementing and identifying funding for long-term projects beyond pilots, and (7) evaluating impacts via standardised indicators. Sharing experiences and evidence from ongoing projects is needed to advance the use of drones for healthcare.

Performance and impact of GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® assays on tuberculosis case detection in Madagascar

Background

Tuberculosis rapid molecular assays, including GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit®, are highly sensitive and specific. Such performance does not automatically translate in improved disease control and highly depends on their use, local epidemiology and the diagnostic algorithms they’re implemented within. We evaluate the performance of both assays and assess their impact on additional cases notification when implemented within WHO recommended tuberculosis diagnostic algorithms in Madagascar.

Methods

Five hundred forty eight presumptive pulmonary tuberculosis patients were prospectively recruited between November 2013 and December 2014 in Antananarivo, Madagascar, a high TB incidence sub-Saharan African urban setting. Both molecular assays were evaluated as first line or add-on testing following negative smear microscopy. Based on locally defined assay performance characteristics we measure the impact of both assays and WHO-recommended diagnostic algorithms on additional tuberculosis case notifications.

Results

High sensitivity and specificity was confirmed for both GeneXpert MTB/RIF® (86.6% (95% CI 81.1–90.7%) and 97.4% (95% CI 94.9–98.8%)) and Loopamp MTBC Detection Kit® (84.6% (95% CI 78.9–89.0%) and 98.4% (95% CI 96.2–99.4%)). Implementation of GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® increased tuberculosis diagnostic algorithms sensitivity from 73.6% (95% CI 67.1–79.3%) up to 88.1% (95% CI 82.8–91.9%). This increase was highest when molecular assays were used as add-on testing following negative smear microscopy. As add-on testing, GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® respectively improved case detection by 23.8 and 21.2% (p < 0.05).

Conclusion

Including GeneXpert MTB/RIF® or Loopamp MTBC Detection Kit® molecular assays for TB detection on sputum samples from presumptive TB cases can significantly increase case notification in TB diagnostic centers. The TB case detection rate is further increased when those tests are use as second-line follow-on testing following negative smear microscopy results. A country wide scale-up and digital integration of molecular-based TB diagnosis assays shows promises for TB control in Madagascar.

Perceptions of drones, digital adherence monitoring technologies and educational videos for tuberculosis control in remote Madagascar: a mixed-method study protocol

INTRODUCTION

Poor road and communication infrastructure pose major challenges to tuberculosis (TB) control in many regions of the world. TB surveillance and patient support often fall to community health workers (CHWs) who may lack the time or knowledge needed for this work. To meet the End TB Strategy goal of reducing TB incidence by 90% by 2035, the WHO calls for intensified research and innovation including the rapid uptake of new tools, interventions and strategies. Technologies that 'leapfrog' infrastructure challenges and support CHWs in TB control responsibilities have the potential to dramatically change TB outcomes in remote regions. Such technologies may strengthen TB control activities within challenged national tuberculosis treatment and control programmes (NTPs), and be adapted to address other public health challenges. The deployment of innovative technologies needs to be differentially adapted to context-specific factors. The Drone Observed Therapy System (DrOTS) project was launched in Madagascar in 2017 and integrates a bundle of innovative technologies including drones, digital adherence monitoring technology and mobile device-based educational videos to support TB control.

METHODS AND ANALYSIS

This mixed-methods study gathers and analyses cultural perceptions of the DrOTS project among key stakeholders: patients, community members, CHWs, village chiefs and NTP-DrOTS mobile health teams. Data from questionnaires, semistructured interviews, focus group discussions (FGD) and ethnographic observation gathered from June 2018 to June 2019 are thematically analysed and compared to identify patterns and singularities in how DrOTS stakeholders perceive and interact with DrOTS technologies, its enrolment processes, objectives and team.

ETHICS AND DISSEMINATION

Ethics approval was obtained from the National Bioethics Research Committee of Madagascar and Stony Brook University institutional review board. Study results will be submitted for peer-reviewed publication. In Madagascar, results will be presented in person to Ministry and other Malagasy decision-makers through the Institut Pasteur de Madagascar.

PATIENT AND PUBLIC INVOLVEMENT

This study is designed to foreground the voices of patients and potential patients in the DrOTS programme. CHW participants in this study also supported the design of study information sessions and recruitment strategies. One member of the mobile health team provided detailed input on the wording and content of FGD and interview guides. Study findings will be presented via a report in French and Malagasy to CHW, mobile health team and other village-level participants who have email/internet access.

Epidemiology of soil transmitted helminth and Strongyloides stercoralis infections in remote rural villages of Ranomafana National Park, Madagascar

Soil-transmitted helminth (STH) infections carry the highest number of disability adjusted life years among all neglected tropical diseases, disproportionately affecting low-income countries such as Madagascar.  This study describes the epidemiology of STH and S. stercoralis infections in twelve remote villages surrounding Ranomafana National Park (RNP), Ifanadiana, Madagascar. Questionnaires and stool samples were collected from 574 subjects from random households. The Kato-Katz method and spontaneous sedimentation technique were used to examine stool samples for evidence of infection. Infection prevalence rates were 71.4% for Ascaris lumbricoides (95% CI: 67.7-75.1), 74.7% for Trichuris trichiura (95% CI: 71.1-78.2), 33.1% for hookworm (95% CI: 29.2-36.9), and 3.3% for Strongyloides stercoralis (95% CI: 1.84-4.77). Participants who were older in age (OR = 0.96; 95% CI: 0.95-0.99) and who had a high school education (OR = 0.17; 95% CI: 0.04-0.77) were less likely to be infected with a STH. Females were less likely to be infected with A. lumbricoides (OR = 0.52; 95% CI: 0.33-0.82). Participants living in villages further from the main road were more likely to be infected with a STH (F = 4.00, p = 0.02). Overall, this study found that 92.5% (95% CI: 90.3-94.6) of the people living in rural regions near RNP have at least one STH infection. This calls into question the current preventative chemotherapy (PC) program in place and suggests that further medical, socioeconomic, and infrastructural deveopments are needed to reduce STH prevalence rates among this underserved population.

Evaluation of the Abbott ARCHITECT™ cytomegalovirus IgM/IgG, rubella IgM/IgG, and syphilis treponemal antibodies enzyme immunoassays in a mother and child health center population

This study evaluated the concordance of Architect™ chemiluminescent microparticle immunoassays with Captia™ ELISA for cytomegalovirus (CMV) IgM and IgG, with Enzygnost™ and Captia™ ELISA for rubella IgM and IgG and with Trep-Sure™ ELISA for syphilis treponemal antibodies in a mixed pediatric and obstetrical population. Total agreement between assays and Kappa statistic value were 82.5% (95% CI: 75.6-87.7) and 0.65 (95% CI: 0.54-0.77) for CMV IgM, 82.8% (95% CI: 76.7-87.6) and 0.65 (95% CI: 0.55-0.75) for CMV IgG, 89.2% (95% CI: 82.9-93.4) and 0.56 (95% CI: 0.36-0.75) for rubella IgM, 88.6% (95% CI: 82.9-92.6) and 0.74 (95% CI: 0.63-0.84) for rubella IgG, and 97.9% (95% CI: 94.5-99.4) and 0.89 (95% CI: 0.79-1.00) for syphilis treponemal antibodies. This study demonstrates that the Architect™ chemiluminescent microparticle immunoassays correlate well with other FDA-approved ELISA assays in this specific population.

rpoB Targeted Loop-Mediated Isothermal Amplification (LAMP) Assay for Consensus Detection of Mycobacteria Associated With Pulmonary Infections

Loop-mediated isothermal amplification (LAMP) is a nucleic acid method which has been used to identify mycobacteria including Mycobacterium tuberculosis in clinical microbiology laboratory and point of care settings. Previously published LAMP protocols for detection of mycobacterial species used conventional specific primer and targeted the 16S rRNA, gyrB, and insertion sequence genes. We developed and evaluated a LAMP assay targeting a mycobacterial rpoB gene conserved sequence and incorporating degenerate primers. This assay allowed consensus detection of mycobacterial species from pure culture, clinical respiratory tract samples, and mycobacteria growth indicator tube (MGIT) liquid-based culture medium. A panel of twenty mycobacterial species were successfully detected at detection thresholds of 102 CFU/mL and 103 CFU/mL when respectively performed on pure culture suspension or sputum and MGIT broth. The inclusion of degenerate bases in LAMP primers increased the diversity of mycobacterial species identified by the assay without negatively affecting analytical sensitivity. LAMP-based consensus detection of multiple pathogens can be achieved with degenerate primers therefore allowing the design of rapid multi-disease screening assays. Despite high analytical sensitivity, species specificity and the advantageous operational characteristics of LAMP over PCR, challenges such as potential ambiguity in visual interpretation of results and occasional non-specific amplification precludes the implementation of novel LAMP assay in routine diagnostics both in centralized and point-of-care laboratory.

2001. Susceptibility of Aerococcus urinae to Fluoroquinolones: Broth Microdilution and Gradient Diffusion

Background

Aerococcus urinae is an emerging urinary pathogen frequently identified by MALDI-TOF. It is generally susceptible to β-lactams, however, its susceptibility pattern to fluoroquinolones (FQ) remains variable. The goals of this study were (i) to evaluate the performance of the gradient diffusion method (Etest^®) to determine FQ resistance compared with broth microdilution (BMD) and (ii) to estimate the resistance rate of A. urinae toward FQ in Quebec hospitals.

Methods

Two hundred seven consecutive isolates of A. urinae from urinary tract specimens originating from five hospitals in Quebec and Montreal were identified by MALDI-TOF (Vitek-MS and Bruker). All isolates were tested with the BMD and gradient diffusion methods. BMD was carried out in triplicate and was conducted in accordance with CLSI guidelines (M45-A3). Isolates with insufficient growth at 24 hours were reincubated and evaluated at 48 hours. The gradient diffusion method was carried out using Etest^® strips on MH agar with 5% sheep blood.

Results

Of the 207 isolates of A. urinae, 52 (25%) gave uninterpretable results using the BMD method (insufficient growth = 20; trailing = 32). We obtained the following results for the remaining 155 isolates:

BMD readings were often complicated by noticeably poor growth. The categorical agreement of the Etest^® was 83% for ciprofloxacin and 95% for levofloxacin. Four very major errors were identified in a preliminary manner on 11% (4/35) of the ciprofloxacin-resistant isolates and 11%(4/35) of the levofloxacin-resistant isolates. Agar dilution will be done to confirm these results.

Conclusion

In our experience, the method recommended by the CLSI for A. urinae susceptibility testing of FQ presented several problems, including insufficient growth and difficult reading. The Etest^® appears to be a promising method for susceptibility testing of FQ for urinary tract isolates, but will first require a further comparison with agar dilution methods. In our study, the rate of FQ non-susceptibility of A. urinae was 27% for levofloxacin and 33% for ciprofloxacin. Therefore, FQ cannot be empirically recommended for the treatment of urinary tract infections caused by A. urinae.

Disclosures

J. M. Leduc, Biomérieux: Investigator, Research grant.

Case: Eosinophilic cystitis presenting as a bladder mass in an 11-year-old girl

We report the case of an 11-year-old girl who presented with acute urinary retention and microscopic hematuria. Pelvic imaging revealed a bladder mass for which sarcoma was initially suspected. Surgical biopsies revealed a massive eosinophilic infiltration of the submucosa confirming a diagnosis of eosinophilic cystitis. Clinical evolution was favourable without treatment. Eosinophilic cystitis prognosis is usually benign, but rare severe complications, such as complete bladder fibrosis requiring bladder augmentation or cystectomy, may occur.

Cystic fibrosis respiratory tract salt concentration: An Exploratory Cohort Study

In cystic fibrosis patients, electrolytic and osmolality imbalance secondary to cystic fibrosis transmembrane conductance regulator mutations may impact on mucoid secretion accumulation and secondary colonization by opportunistic pathogens such as nontuberculous mycobacteria.We performed a noninvasive exploratory prospective controlled clinical study comparing sputum salinity and acid-base characteristics of cystic fibrosis and noncystic fibrosis control patients. A total of 57 patients and 62 controls were included.Sputum salt concentrations were 10.5 g/L (95% CI: 7.7-13.3) in patients and 7.4 g/L (95% CI: 5.9-8.9) in aged-matched controls, a difference that was found to be statistically significant (P < .05). No difference in pH was observed between patients and controls.These differences in respiratory secretions salt concentrations could influence host-pathogen interactions in the context of cystic fibrosis respiratory infections. We propose to include respiratory secretion salt measurement as a routine analysis on cystic fibrosis patients' sputum submitted for bacterial culture.

A concordance study of the Altona RealStar Varicella-Zoster virus real-time quantitative PCR and in-house conventional qualitative PCR

This study compared the Altona RealStar™ VZV Kit 1.0 real time quantitative VZV PCR with in-house qualitative conventional VZV PCR on cerebrospinal fluid, mucocutaneous, and other uncommon clinical specimens. Overall, positive and negative agreement percentages were respectively 97.9% (95%CI: 93.8-99.6), 100.0% (95%CI: 93.1-100.0), and 96.3% (95%CI: 89.4-99.2) while Cohen's kappa statistic value was 0.96 (95%CI: 0.91-1.00). RealStar™ VZV quantitative PCR assay reported average quantitative viral loads of 4.4 × 10⁵ and 1.1 × 10⁷  copies/mL in cerebrospinal fluid and cutaneous specimens, respectively (P < 0.01). RealStar™ VZV PCR assay showed excellent agreement with in house conventional assay for various clinical specimens.

Multifocal ulceronecrotic skin lesions-A stigmatizing case

Mycobacterium chelonae is a rapidly growing nontuberculous mycobacteria, ubiquitous in the environment and mostly involved in skin, soft tissue and bone infections. An atypical, severe and multifocal dermatological manifestation of Mycobacterium chelonae infection in an immunocompetent patient is described here. The lesions completely resolved using a multidisciplinary approach. This case emphasizes the important aspects of diagnosis, antimicrobial and surgical management.

Mycobacterium malmoense pulmonary infection in France: a case report

BACKGROUND

Mycobacterium malmoense infections have frequently been reported in northern Europe since the late 1970s. Factors accounting for this geographically localized epidemiology remain poorly understood.

CASE PRESENTATION

We report the case of a 54-year old man concomitantly diagnosed with non-small cell lung carcinoma and M. malmoense pulmonary infection. We present detailed clinical, microbiological and radiological elements strongly arguing for M. malmoense true pathogenicity. Since M. malmoense infection has rarely been reported in France, we also provide elements of the epidemiological investigation and a literature review of potential acquisition and transmission pathways of M. malmoense. We detail therapeutic interventions and subsequent favorable evolution.

CONCLUSION

Mycobacterium malmoense is a recognized respiratory pathogen for which routes of infection need to be better investigated.

Mycobacterium iranicum bacteremia and hemophagocytic lymphohistiocytosis: a case report

BACKGROUND

Mycobacterium iranicum has recently been recognised as an opportunistic human pathogen. Although infectious conditions represent frequent triggers for hemophagocytic lymphohistiocytosis, non-tuberculous mycobacterial infections are rarely associated with this entity. To this date, M. iranicum infection has never been reported in France, has never been associated with hemophagocytic lymphohistiocytosis and has never been found to be multi-resistant on standardized antimicrobial susceptibility testing.

CASE PRESENTATION

We report a case of a French Caucasian man with secondary hemophagocytic lymphohistiocytosis in the context of M. iranicum bacteraemia and Hodgkin's disease. We review available data concerning M. iranicum antimycobacterial susceptibility testing and treatment outcomes. We also review the association between hemophagocytic lymphohistiocytosis and non-tuberculous mycobacterial infections.

CONCLUSION

Interpretation of M. iranicum positive cultures remains a clinical challenge and non-tuberculous mycobacterial infections need to be considered in secondary hemophagocytic lymphohistiocytosis differential diagnosis.

Mycobacterium abscessus Lung Infection: A Case Report

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Evaluation of the abbot Architect(™) epstein-barr virus viral capsid antigen IgM, viral capsid antigen IgG and nuclear antigen IgG assays in a pediatric and adult population

BACKGROUND

The detection of antibodies against Epstein-Barr viral capsid (VCA) and nuclear (EBNA) antigens is routinely performed with different commercially available immunoassays.

OBJECTIVES

In this study, we evaluated the concordance and performance of the Architect(™) chemiluminescent microparticle immunoassays (CMIAs) using Captia(™) enzyme linked immunosorbent assays (ELISA) for VCA IgM, and standard immunofluorescence (IF) assays for VCA IgG and EBNA IgG as comparative techniques.

STUDY DESIGN

Sera were selected from a heterogeneous population including pediatric and adult patients.

RESULTS

Concordance between CMIAs and comparative assays was high with total agreement percentages of 84,1% (95% CI: 77.8-88.9) for VCA IgM, 90,6% (95% CI: 84.2-94.7) for EBNA IgG and 98,0% (95% CI: 93.9-99.6) for VCA IgG. Moreover, kappa statistic values showed good to excellent correlation with values of 0.68 (95% CI: 0.57-0.79) for VCA IgM, 0.73 (95% CI: 0.58-0.87) for EBNA IgG and 0.95 (95% CI: 0.89-1.00) for VCA IgG. A correlation was observed between positivity levels on CMIAs and semi-quantitative fluorescence intensity on IF for VCA IgG and EBNA IgG assays. With regard to an accepted gold standard IF assays, CMIA was 98,1% (95% CI: 93.3-99.8) sensitive and 97,4% (95% CI: 86.5-99.9) specific for the detection of VCA IgG. For the detection of EBNA IgG, it was 92,2% (95% CI: 85.1-96.6) sensitive and 84,6% (95% CI: 65.1-95.6) specific.

CONCLUSION

In summary, we demonstrated that the CMIA EBV antibody detection panel has high performance and high concordance with other commercially available immunoassays.