Fosfomycin for Non-Urinary Tract Infections: a systematic review.

Introduction: Although fosfomycin is currently approved for treating urinary tract infections, it is increasingly being used as salvage therapy for various infectious syndromes outside the urinary tract. This systematic review evaluates clinical and microbiological cure rates in patients with bacterial infections not restricted to the urinary tract where fosfomycin was used off-label. Materials and Methods: Articles from two databases (Pubmed and Scopus) were reviewed. The dosage, route, and duration of fosfomycin therapy along with the details of adjunctive antimicrobial agents were noted. The final outcomes captured were clinical or microbiological cures. Results: A total of 649 articles, not including duplicates, were selected for the title and abstract screening. After title and abstract screening, 102 articles were kept for full-text screening. Of the 102 articles, 23 studies (n=1227 patients) were kept in the final analysis. Of the 1227 patients, 301 (25%) received fosfomycin as monotherapy, and the remaining 926 75%) received fosfomycin in combination with at least one other antimicrobial agent. Most of the patients received intravenous fosfomycin (n=1046, 85%). Staphylococcus spp and Enterobacteriaceae were the most common organisms. The pooled clinical and microbiological cure rates were 75% and 84%, respectively. Conclusion: Fosfomycin has moderate clinical success in patients with non-urinary tract infections, especially when used with other antimicrobials. Due to the paucity of randomized controlled trials, fosfomycin's use should be limited to situations where no alternatives are supported by better clinical evidence.

Diagnostic capacities and treatment practices on implantation mycoses: Results from the 2022 WHO global online survey.

Between January and March 2022, WHO conducted a global online survey to collect data on diagnostic capacities and treatment practices in different settings for four implantation mycoses: eumycetoma, actinomycetoma, cutaneous sporotrichosis and chromoblastomycosis. The survey investigated the type of diagnostic methods available in countries at various health system levels (tertiary, secondary, primary level) and the medicines used to treat implantation mycoses, with a view to understanding the level of drug repurposing for treatment of these diseases. 142 respondents from 47 countries, including all continents, contributed data: 60% were from middle-income countries, with 59% working at the tertiary level of the health system and 30% at the secondary level. The results presented in this article provide information on the current diagnostic capacity and treatment trends for both pharmacological and non-pharmacological interventions. In addition, the survey provides insight on refractory case rates, as well as other challenges, such as availability and affordability of medicines, especially in middle-income countries. Although the study has limitations, the survey-collected data confirms that drug repurposing is occurring for all four surveyed implantation mycoses. The implementation of an openly accessible global and/or a national treatment registry for implantation mycoses could contribute to address the gaps in epidemiological information and collect valuable observational data to inform treatment guidelines and clinical research.

A Path to Real-World Evidence in Critical Care Using Open-Source Data Harmonization Tools.

COVID-19 highlighted the need for use of real-world data (RWD) in critical care as a near real-time resource for clinical, research, and policy efforts. Analysis of RWD is gaining momentum and can generate important evidence for policy makers and regulators. Extracting high quality RWD from electronic health records (EHRs) requires sophisticated infrastructure and dedicated resources. We sought to customize freely available public tools, supporting all phases of data harmonization, from data quality assessments to de-identification procedures, and generation of robust, data science ready RWD from EHRs. These data are made available to clinicians and researchers through CURE ID, a free platform which facilitates access to case reports of challenging clinical cases and repurposed treatments hosted by the National Center for Advancing Translational Sciences/National Institutes of Health in partnership with the Food and Drug Administration. This commentary describes the partnership, rationale, process, use case, impact in critical care, and future directions for this collaborative effort.

Efficacy of Cefoperazone Sulbactam in Patients with Acinetobacter Infections: A Systematic Review of the Literature.

INTRODUCTION: Acinetobacter baumannii (AB) is a multidrug-resistant pathogen commonly associated with nosocomial infections. The resistance profile and ability to produce biofilm make it a complicated organism to treat effectively. Cefoperazone sulbactam (CS) is commonly used to treat AB, but the associated data are scarce. METHODS: We conducted a systematic review of articles downloaded from Cochrane, Embase, PubMed, Scopus, and Web of Science (through June 2022) to study the efficacy of CS in treating AB infections. Our review evaluated patients treated with CS alone and CS in combination with other antibiotics separately. The following outcomes were studied: clinical cure, microbiological cure, and mortality from any cause. RESULTS: We included 16 studies where CS was used for the treatment of AB infections. This included 11 studies where CS was used alone and 10 studies where CS was used in combination. The outcomes were similar in both groups. We found that the pooled clinical cure, microbiological cure, and mortality with CS alone for AB were 70%, 44%, and 20%, respectively. The pooled clinical cure, microbiological cure, and mortality when CS was used in combination with other antibiotics were 72%, 43%, and 21%, respectively. CONCLUSIONS: CS alone or in combination needs to be further explored for the treatment of AB infections. There is a need for randomized controlled trials with comparator drugs to evaluate the drug's effectiveness.

Role of tigecycline in the treatment of urinary tract infections: a systematic review of published case reports.

Introduction: The emergence of multi-drug resistance has forced clinicians to occasionally use drugs that are not approved to treat urinary tract infections (UTIs). This systematic review aimed to evaluate the utility of tigecycline in patients with UTIs. Methodology: A systematic review of case studies was used to retrieve articles between 1.1.1999 to 1.1.2021 from two databases, PubMed and Embase. The title-abstract screening was done for 198 articles, out of which 69 articles were included for full-text screening. A total of 18 articles with 27 cases were included for final analysis. Results: Of the 27 cases, there were 13 cases with complicated UTI and five had catheter-associated UTI. The most common organisms were Klebsiella pneumoniae (n=11), Acinetobacter baumannii (n=9), and Escherichia coli (n=6). Tigecycline was used as monotherapy in 19 patients and as a combination therapy in 8 patients. The median duration of tigecycline was 13 (10-15) days. A favourable clinical or microbiological response at varying intervals was seen in 24/27 (88.9%). Within three months of a favourable response, recurrence of symptoms was seen in four patients. Conclusion: In a small analysis of published case reports, tigecycline appeared to be a relatively effective treatment in patients with UTIs, caused by multidrug-resistant organisms. Where tigecycline is the only susceptible drug, it can be used for treatment. Further research, such as randomized controlled trials, is needed to fully assess the drug's efficacy in this context.

Biomarkers of Crohn's Disease to Support the Development of New Therapeutic Interventions.

BACKGROUND: Currently, 2 coprimary end points are used by health authorities to determine the effectiveness of therapeutic interventions in patients with Crohn's disease (CD): symptomatic remission (patient-reported outcome assessment) and endoscopic remission (ileocolonoscopy). However, there is lack of accepted biomarkers to facilitate regulatory decision-making in the development of novel therapeutics for the treatment of CD. METHODS: With support from the Helmsley Charitable Trust, Critical Path Institute formed the Crohn's Disease Biomarkers preconsortium (CDBpC) with members from the pharmaceutical industry, academia, and nonprofit organizations to evaluate the CD biomarker landscape. Biomarkers were evaluated based on biological relevance, availability of biomarker assays, and clinical validation data. RESULTS: The CDBpC identified the most critical need as pharmacodynamic/response biomarkers to monitor disease activity in response to therapeutic intervention. Fecal calprotectin (FC) and serum C-reactive protein (CRP) were identified as biomarkers ready for the regulatory qualification process. A number of exploratory biomarkers and potential panels of these biomarkers was also identified for additional development. Given the different factors involved in CD and disease progression, a combination of biomarkers, including inflammatory, tissue injury, genetic, and microbiome-associated biomarkers, will likely have the most utility. CONCLUSIONS: The primary focus of the Inflammatory Bowel Disease Regulatory Science Consortium will be development of exploratory biomarkers and the qualification of FC and CRP for IBD. The Inflammatory Bowel Disease Regulatory Science Consortium, focused on tools to support IBD drug development, will operate in the precompetitive space to share data, biological samples for biomarker testing, and assay information for novel biomarkers.

Author Correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.

Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.

Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction.

BACKGROUND: The diagnosis of multidrug resistant and extensively drug resistant tuberculosis is a global health priority. Whole genome sequencing of clinical Mycobacterium tuberculosis isolates promises to circumvent the long wait times and limited scope of conventional phenotypic antimicrobial susceptibility, but gaps remain for predicting phenotype accurately from genotypic data especially for certain drugs. Our primary aim was to perform an exploration of statistical learning algorithms and genetic predictor sets using a rich dataset to build a high performing and fast predicting model to detect anti-tuberculosis drug resistance. METHODS: We collected targeted or whole genome sequencing and conventional drug resistance phenotyping data from 3601 Mycobacterium tuberculosis strains enriched for resistance to first- and second-line drugs, with 1228 multidrug resistant strains. We investigated the utility of (1) rare variants and variants known to be determinants of resistance for at least one drug and (2) machine and statistical learning architectures in predicting phenotypic drug resistance to 10 anti-tuberculosis drugs. Specifically, we investigated multitask and single task wide and deep neural networks, a multilayer perceptron, regularized logistic regression, and random forest classifiers. FINDINGS: The highest performing machine and statistical learning methods included both rare variants and those known to be causal of resistance for at least one drug. Both simpler L2 penalized regression and complex machine learning models had high predictive performance. The average AUCs for our highest performing model was 0.979 for first-line drugs and 0.936 for second-line drugs during repeated cross-validation. On an independent validation set, the highest performing model showed average AUCs, sensitivities, and specificities, respectively, of 0.937, 87.9%, and 92.7% for first-line drugs and 0.891, 82.0% and 90.1% for second-line drugs. Our method outperforms existing approaches based on direct association, with increased sum of sensitivity and specificity of 11.7% on first line drugs and 3.2% on second line drugs. Our method has higher predictive performance compared to previously reported machine learning models during cross-validation, with higher AUCs for 8 of 10 drugs. INTERPRETATION: Statistical models, especially those that are trained using both frequent and less frequent variants, significantly improve the accuracy of resistance prediction and hold promise in bringing sequencing technologies closer to the bedside.

Building the Framework for Standardized Clinical Laboratory Reporting of Next-generation Sequencing Data for Resistance-associated Mutations in Mycobacterium tuberculosis Complex.

Tuberculosis is the primary infectious disease killer worldwide, with a growing threat from multidrug-resistant cases. Unfortunately, classic growth-based phenotypic drug susceptibility testing (DST) remains difficult, costly, and time consuming, while current rapid molecular testing options are limited by the diversity of antimicrobial-resistant genotypes that can be detected at once. Next-generation sequencing (NGS) offers the opportunity for rapid, comprehensive DST without the time or cost burden of phenotypic tests and can provide useful information for global surveillance. As access to NGS expands, it will be important to ensure that results are communicated clearly, consistent, comparable between laboratories, and associated with clear guidance on clinical interpretation of results. In this viewpoint article, we summarize 2 expert workshops regarding a standardized report format, focusing on relevant variables, terminology, and required minimal elements for clinical and laboratory reports with a proposed standardized template for clinical reporting NGS results for Mycobacterium tuberculosis.

Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase.

Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) ( https://github.com/CPTR-ReSeqTB/UVP ) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified using Sanger sequencing and was 100% concordant with conventional methods of assigning lineage. We analyzed 4636 publicly available MTBC isolates in the ReSeqTB platform representing all seven major MTBC lineages. The variants detected have an above 94% accuracy of predicting drug based on the accompanying DST results in the platform. The aggregation of variants over time in the platform will establish confidence-graded mutations statistically associated with phenotypic drug resistance. These tools serve as critical reference standards for future molecular diagnostic assay developers, researchers, public health agencies and clinicians working towards the control of drug-resistant tuberculosis.

Mycobacterial biomaterials and resources for researchers.

There are many resources available to mycobacterial researchers, including culture collections around the world that distribute biomaterials to the general scientific community, genomic and clinical databases, and powerful bioinformatics tools. However, many of these resources may be unknown to the research community. This review article aims to summarize and publicize many of these resources, thus strengthening the quality and reproducibility of mycobacterial research by providing the scientific community access to authenticated and quality-controlled biomaterials and a wealth of information, analytical tools and research opportunities.

Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study.

BACKGROUND: In many countries, regular monitoring of the emergence of resistance to anti-tuberculosis drugs is hampered by the limitations of phenotypic testing for drug susceptibility. We therefore evaluated the use of genetic sequencing for surveillance of drug resistance in tuberculosis. METHODS: Population-level surveys were done in hospitals and clinics in seven countries (Azerbaijan, Bangladesh, Belarus, Pakistan, Philippines, South Africa, and Ukraine) to evaluate the use of genetic sequencing to estimate the resistance of Mycobacterium tuberculosis isolates to rifampicin, isoniazid, ofloxacin, moxifloxacin, pyrazinamide, kanamycin, amikacin, and capreomycin. For each drug, we assessed the accuracy of genetic sequencing by a comparison of the adjusted prevalence of resistance, measured by genetic sequencing, with the true prevalence of resistance, determined by phenotypic testing. FINDINGS: Isolates were taken from 7094 patients with tuberculosis who were enrolled in the study between November, 2009, and May, 2014. In all tuberculosis cases, the overall pooled sensitivity values for predicting resistance by genetic sequencing were 91% (95% CI 87-94) for rpoB (rifampicin resistance), 86% (74-93) for katG, inhA, and fabG promoter combined (isoniazid resistance), 54% (39-68) for pncA (pyrazinamide resistance), 85% (77-91) for gyrA and gyrB combined (ofloxacin resistance), and 88% (81-92) for gyrA and gyrB combined (moxifloxacin resistance). For nearly all drugs and in most settings, there was a large overlap in the estimated prevalence of drug resistance by genetic sequencing and the estimated prevalence by phenotypic testing. INTERPRETATION: Genetic sequencing can be a valuable tool for surveillance of drug resistance, providing new opportunities to monitor drug resistance in tuberculosis in resource-poor countries. Before its widespread adoption for surveillance purposes, there is a need to standardise DNA extraction methods, recording and reporting nomenclature, and data interpretation. FUNDING: Bill & Melinda Gates Foundation, United States Agency for International Development, Global Alliance for Tuberculosis Drug Development.

Enabling precision medicine via standard communication of HTS provenance, analysis, and results.

A personalized approach based on a patient's or pathogen's unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the "Open-Stand.org principles for collaborative open standards development." With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews.

A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis.

A clear understanding of the genetic basis of antibiotic resistance in Mycobacterium tuberculosis is required to accelerate the development of rapid drug susceptibility testing methods based on genetic sequence.Raw genotype-phenotype correlation data were extracted as part of a comprehensive systematic review to develop a standardised analytical approach for interpreting resistance associated mutations for rifampicin, isoniazid, ofloxacin/levofloxacin, moxifloxacin, amikacin, kanamycin, capreomycin, streptomycin, ethionamide/prothionamide and pyrazinamide. Mutation frequencies in resistant and susceptible isolates were calculated, together with novel statistical measures to classify mutations as high, moderate, minimal or indeterminate confidence for predicting resistance.We identified 286 confidence-graded mutations associated with resistance. Compared to phenotypic methods, sensitivity (95% CI) for rifampicin was 90.3% (89.6-90.9%), while for isoniazid it was 78.2% (77.4-79.0%) and their specificities were 96.3% (95.7-96.8%) and 94.4% (93.1-95.5%), respectively. For second-line drugs, sensitivity varied from 67.4% (64.1-70.6%) for capreomycin to 88.2% (85.1-90.9%) for moxifloxacin, with specificity ranging from 90.0% (87.1-92.5%) for moxifloxacin to 99.5% (99.0-99.8%) for amikacin.This study provides a standardised and comprehensive approach for the interpretation of mutations as predictors of M. tuberculosis drug-resistant phenotypes. These data have implications for the clinical interpretation of molecular diagnostics and next-generation sequencing as well as efficient individualised therapy for patients with drug-resistant tuberculosis.

Performance of the SAMBA I and II HIV-1 Semi-Q Tests for viral load monitoring at the point-of-care.

Although access to antiretroviral therapy for HIV infection is increasing in resource-poor countries, viral load testing for monitoring of treatment efficacy remains limited, expensive, and confined to centralized laboratories. The SAMBA HIV-1 Semi-Q Test is a nucleic acid-based amplification assay developed for viral load monitoring performed on either the semi-automated SAMBA I system for laboratory use or the fully automated SAMBA II system for point-of care use. We have assessed the performance characteristics of the SAMBA HIV-1 Semi-Q Test on SAMBA I and SAMBA II systems according to the Common Technical Specifications of the European Community's 98/79 In Vitro Diagnostic Medical Devices Directive. The sensitivity, specificity, reproducibility, and viral subtype coverage of the test were similar on the SAMBA I and SAMBA II platforms. The clinical performance on the SAMBA I system was compared with the Roche CAP/CTM assay and evaluated in-house with 130 patient specimens from London as well as in the field with 390 specimens in Kenya and Zimbabwe. The overall concordance between the SAMBA and CAP/CTM assays was 98.1%. The clinical performance of the test on the SAMBA II platform in comparison with the Abbott HIV-1 RealTime Assay was evaluated in-house with 150 specimens from Ukraine, yielding a concordance of 98.0%. The results thus show that the SAMBA HIV-1 Semi-Q Test performs equivalently on SAMBA I and SAMBA II, and they suggest that the test is suitable for implementation at the point-of-care in resource-poor regions where viral load testing is desperately needed but often unavailable.

Tuberculosis eradication versus control.

According to the World Health Organization (WHO), 10.4 million people died of tuberculosis (TB) in 2015, and the disease is now the number one cause of death from a preventable infectious disease worldwide. A bold vision is needed from global leaders to end the TB epidemic and plans to this end have been proposed. However enthusiasm must be matched by tangible and achievable goals based on the science and available funding. In order to reach the target and goals set by the WHO End TB Strategy, the challenges for TB eradication need to be addressed. In order to achieve the targets, several areas need to be bolstered, including the requirement to better identify and treat existing drug-susceptible cases and diagnose all the drug-resistant forms of the disease. Although treatment is available for most TB patients, stock-outs and other delays are problematic in some settings, resulting in ongoing transmission, especially for the drug-resistant forms of the disease. Despite the fact that a majority of multidrug-resistant cases are linked to treatment, the cure rate is only 50%, which highlights the need for safer, shorter, and more efficacious drug regimens that are more tolerable to patients. Prospects for a more efficacious vaccine are limited, with no correlates of protection identified; thus the availability of a vaccine by 2025 is highly improbable. Support for instituting infection control methods should be prioritized to subvert transmission while patients seek treatment and care. Finally, more adequate financial mechanisms should be instituted to reduce patient expenditures and support national TB programs. Moreover, funding to support basic science, drug development, clinical trials, vaccine development, diagnostics, and implementation research needs to be secured in order to reduce global TB incidence in the future.