Development and application of DETECTR-based rapid detection for pathogenic Bacillusanthracis

Bacillus anthracis (B. anthracis) is a gram-positive bacterium responsible for the acute disease anthrax. Rapid and reliable identification of pathogenic B. anthracis is important in the detection of natural infectious disease cases or bio-threats. Herein, a DNA endonuclease targeted CRISPR trans reporter (DETECTR) detection platform based on recombinase polymerase amplification (RPA) was studied. The DETECTR system targeted three sequences from B. anthracis (the BA_5345 chromosomal specific marker, the protective antigen gene pag A from pXO1 plasmid and the capsule-biosynthesis-related gene cap A from pXO2 plasmid). We developed a rapid (<40 min), easy-to-implement and accurate identification method for of B. anthracis nucleic acid with near two-copies sensitivity. The combination of tripartite primer sets is effective for the reliable identification of B. anthracis but also for fast screening of pathogenic strains. More importantly, DETECTR correctly detected simulated clinical blood samples and firstly detected positive samples collected from the location of world War-II site, preserved at north-east China (45°36'55.940″ N, 126°38'33.738″ E) with high sensitivity and specificity. Our study provides insight into the DETECTR-based detection of B. anthracis. We present a novel screening and diagnostic option for pathogenic B. anthracis that can be performed on a user-friendly portable device. Based on its proven reliability, sensitivity, specificity and simplicity, our proposed method can be readily adapted to detect pathogenic B. anthracis, anthrax and biothreats.

The role of mobile phones as a possible pathway for pathogen movement, a cross-sectional microbial analysis

INTRODUCTION

Mobile phones are used the world over, including in healthcare settings. This study aimed to investigate the viable microbial colonisation of mobile phones used by healthcare personnel.

METHODS

Swabs collected on the same day from 30 mobile phones belonging to healthcare workers from three separate paediatric wards of an Australian hospital were cultured on five types of agar plate, then colonies from each phone were pooled, extracted and sequenced by shotgun metagenomics. Questionnaires completed by staff whose phones were sampled assisted in the analysis and interpretation of results.

RESULTS AND DISCUSSION

All phones sampled cultured viable bacteria. Overall, 399 bacterial operational taxonomic units were identified from 30 phones, with 1432 cumulative hits. Among these were 58 recognised human pathogenic and commensal bacteria (37 Gram-negative, 21 Gram-positive). The total number of virulence factor genes detected was 347, with 1258 cumulative hits. Antibiotic resistance genes (ARGs) were detected on all sampled phones and overall, 133 ARGs were detected with 520 cumulative hits. The most important classes of ARGs detected encoded resistance to beta-lactam, aminoglycoside and macrolide antibiotics and efflux pump mediated resistance mechanisms.

CONCLUSION

Mobile phones carry viable bacterial pathogens and may act as fomites by contaminating the hands of their users and indirectly providing a transmission pathway for hospital-acquired infections and dissemination of antibiotic resistance. Further research is needed, but meanwhile adding touching mobile phones to the five moments of hand hygiene is a simple infection control strategy worth considering in hospital and community settings. Additionally, the implementation of practical and effective guidelines to decontaminate mobile phone devices would likely be beneficial to the hospital population and community at large.

Adult COVID-19 Patients Cared for in a Pediatric ICU Embedded in a Regional Biothreat Center: Disease Severity and Outcomes

The objective of this study was to describe the clinical characteristics and outcomes of adult coronavirus disease 2019 (COVID-19) patients admitted to a pediatric intensive care unit (PICU), with assessment of respiratory clinical severity and outcomes when cared for by pediatric intensivists utilizing specific care processes. We conducted a retrospective cohort study of adult patients admitted to the 14-bed PICU of a quaternary referral center during the COVID-19 surge in Boston between April and June 2020. A total of 37 adults were admitted: 28 tested COVID-19 positive and 9 tested COVID-19 negative. Of the COVID-19-positive patients, 21 (75%), were male and 12 (60.7%) identified as Hispanic/Latino. Comorbidities in the patients included diabetes mellitus (39.3%), hyperlipidemia (39.3%), and hypertension (32.1%). Twenty-four (85.7%) required mechanical ventilation, in whom the lowest median ratio of arterial oxygen partial pressure to fractional inspired pressure was 161.5 (141.0 to 184.5), the median peak positive end-expiratory pressure (PEEP) was 14 (12.0 to 15.8) cmH₂O and 15 (62.5%) underwent an optimal PEEP maneuver. Twelve (50%) patients were proned for a median of 3.0 (3.0 to 4.8) days. Of the 15 patients who were extubated, 3 (20%) required reintubation. Tracheostomy was performed in 10 patients: 3 after extubation failure and 7 for prolonged mechanical ventilation and weakness. Renal replacement therapy was required by 4 (14.3%) patients. There were 2 (7.1%) mortalities. We report detailed clinical outcomes of adult patients when cared for by intact pediatric critical care teams during the COVID-19 pandemic. Good clinical outcomes, when supported by adult critical care colleagues and dedicated operational processes are possible.

Monoclonal antibodies as anti-infective products: a promising future?

BACKGROUND

The paucity of licensed monoclonal antibodies (mAbs) in the infectious diseases arena strongly contrasts with the ready availability of these therapeutics for use in other conditions.

AIMS

This narrative review aims to assess the potential of monoclonal antibody-based interventions for infectious diseases.

SOURCES

A review of the literature via the Medline database was performed and complemented by published official documents on licensed anti-infective mAbs. In addition, ongoing trials were identified through a search of the clinical trial registration platform ClinicalTrials.gov.

CONTENT

We identified the few infections for which mAbs have been added to the therapeutic armamentarium and stressed their potential in representing a readily available protection tool against biothreats and newly emerging and reemerging infectious agents. In reviewing the historical context and main features of mAbs, we assert a potentially wider applicability and cite relevant examples of ongoing therapeutic developments. Factors hindering successful introduction of mAbs on a larger scale are outlined and thoughts are offered on how to possibly address some of these limitations.

IMPLICATIONS

mAbs may represent important tools in treating or preventing infections occurring with reasonably sufficient prevalence to justify demand and for which existing alternatives are not deemed fully adequate. Future initiatives need to address the prohibitive costs encountered in the development process. The feasibility of more large-scale administration of alternative modalities merits further exploration. In order to ensure optimal prospect of regulatory success, an early dialogue with competent authorities is encouraged.

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018

The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.

Biothreat Agents and Emerging Infectious Disease in the Emergency Department

The challenges faced by the emergency physician with recognizing and treating category A biothreat agents and emerging infectious disease are summarized and reviewed.