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Sci Rep ; 12(1): 14372, 2022 08 23.
Article in English | MEDLINE | ID: covidwho-2016820


Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance (AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436 Escherichia coli were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype-phenotype associations. No significant differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations. The study also revealed limitations of in-silico technology on detecting resistance to certain antimicrobials due to lack of specific fine-tuning options in bioinformatics tool or a lack of representation of resistance mechanisms in reference databases. Lastly, we noted user friendliness of tools was also an important consideration. Therefore, our recommendations are timely for widespread standardisation of bioinformatics for genomic diagnostics and surveillance globally.

Anti-Bacterial Agents , Escherichia coli Infections , Anti-Bacterial Agents/pharmacology , Computational Biology/methods , Drug Resistance, Bacterial/genetics , Escherichia coli , Escherichia coli Infections/diagnosis , Escherichia coli Infections/epidemiology , Escherichia coli Infections/genetics , High-Throughput Nucleotide Sequencing , Humans , Microbial Sensitivity Tests
Am J Perinatol ; 38(7): 747-752, 2021 06.
Article in English | MEDLINE | ID: covidwho-1182901


OBJECTIVE: A majority of studies evaluating the risk of vertical transmission and adverse outcomes in pregnancies with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are mostly based on third-trimester infections. There is limited data available on pregnancy sequelae of maternal infection in the first or second trimester. STUDY DESIGN: We present a patient with monochorionic-diamniotic twins that develops coronavirus disease 2019 infection at 15 weeks of gestation. The pregnancy is further complicated by stage II twin-twin transfusion syndrome. She undergoes laser ablation, which is complicated by development of a subchorionic hematoma. The patient then develops Escherichia coli bacteremia, resulting in septic shock and preterm labor followed by previable delivery at 21 weeks of gestation. Amniotic fluid and placenta were negative for SARS-CoV-2 by real-time polymerase chain reaction. CONCLUSION: This case of SARS-CoV-2 argues against transplacental transmission after a second-trimester infection but brings attention to the possible downstream complications that may arise following early infection. KEY POINTS: · Vertical transmission of SARS-CoV-2 is not evident after a second-trimester infection.. · Antepartum coronavirus disease 2019 may cause vascular placental changes and placental insufficiency.. · SARS-CoV-2 is associated with a maternal hypercoagulable state with adverse perinatal outcomes..

COVID-19 , Escherichia coli Infections , Fetofetal Transfusion , Placenta , Pregnancy Complications, Infectious , Pregnancy Trimester, Second , Shock, Septic , Adult , COVID-19/complications , COVID-19/diagnosis , COVID-19/physiopathology , Escherichia coli Infections/complications , Escherichia coli Infections/diagnosis , Female , Fetofetal Transfusion/diagnosis , Fetofetal Transfusion/etiology , Humans , Infant, Newborn , Infectious Disease Transmission, Vertical/prevention & control , Placenta/diagnostic imaging , Placenta/physiopathology , Pregnancy , Pregnancy Complications, Infectious/physiopathology , Pregnancy Complications, Infectious/virology , Pregnancy Outcome , Pregnancy, Twin , Premature Birth/etiology , Premature Birth/virology , SARS-CoV-2 , Shock, Septic/diagnosis , Shock, Septic/etiology , Twins, Monozygotic , Ultrasonography, Prenatal/methods
Biosens Bioelectron ; 171: 112753, 2021 Jan 01.
Article in English | MEDLINE | ID: covidwho-885210


A polyethyleneimine (PEI)-assisted copper in-situ growth (CISG) strategy was proposed as a controlled signal amplification strategy to enhance the sensitivity of gold nanoparticle-based lateral flow sensors (AuNP-LFS). The controlled signal amplification is achieved by introducing PEI as a structure-directing agent to regulate the thermodynamics of anisotropic Cu nanoshell growth on the AuNP surface, thus controlling shape and size of the resultant AuNP@Cu core-shell nanostructures and confining free reduction and self-nucleation of Cu2+ for improved reproducibility and decreased false positives. The PEI-CISG-enhanced AuNP-LFS showed ultrahigh sensitivities with the detection limits of 50 fg mL-1 for HIV-1 capsid p24 antigen and 6 CFU mL-1 for Escherichia coli O157:H7. We further demonstrated its clinical diagnostic efficacy by configuring PEI-CISG into a commercial AuNP-LFS detection kit for SARS-CoV-2 antibody detection. Altogether, this work provides a reliable signal amplification platform to dramatically enhance the sensitivity of AuNP-LFS for rapid and accurate diagnostics of various infectious diseases.

Biosensing Techniques/methods , Copper/chemistry , Coronavirus Infections/diagnosis , Escherichia coli Infections/diagnosis , Gold/chemistry , HIV Infections/diagnosis , Pneumonia, Viral/diagnosis , Betacoronavirus/isolation & purification , Biosensing Techniques/instrumentation , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques , Equipment Design , Escherichia coli O157/isolation & purification , HIV Core Protein p24/analysis , HIV-1/isolation & purification , Humans , Limit of Detection , Metal Nanoparticles/chemistry , Metal Nanoparticles/ultrastructure , Oxidation-Reduction , Pandemics , Polyethyleneimine/chemistry , Reagent Strips/analysis , SARS-CoV-2