Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls

The large number of blood-borne viruses, bacteria and parasites currently of concern, as well as many newly emerging pathogens, presents a daunting challenge to protection of the safety of blood for transfusion and diagnosing infectious diseases. Focusing on nucleic acid diagnostic tests, multiplex devices are coming into use with many more in various developmental stages that promise to offer solutions to the clinical need. The characteristics, advantages and disadvantages of platforms in clinical use and at the research and development stage are examined here. The presence of multiple assays and associated reagents operating simultaneously on one platform, implementation in traditional clinical laboratories and regulatory review will present special challenges. Fortunately, clinical laboratories have made dramatic technical progress in the last two decades and regulatory agencies have publicly expressed support for development of multiplex devices

Tracking ebolavirus genomic drift with a resequencing microarray.

Filoviruses are emerging pathogens that cause acute fever with high fatality rate and present a global public health threat. During the 2013-2016 Ebola virus outbreak, genome sequencing allowed the study of virus evolution, mutations affecting pathogenicity and infectivity, and tracing the viral spread. In 2018, early sequence identification of the Ebolavirus as EBOV in the Democratic Republic of the Congo supported the use of an Ebola virus vaccine. However, field-deployable sequencing methods are needed to enable a rapid public health response. Resequencing microarrays (RMA) are a targeted method to obtain genomic sequence on clinical specimens rapidly, and sensitively, overcoming the need for extensive bioinformatic analysis. This study presents the design and initial evaluation of an ebolavirus resequencing microarray (Ebolavirus-RMA) system for sequencing the major genomic regions of four Ebolaviruses that cause disease in humans. The design of the Ebolavirus-RMA system is described and evaluated by sequencing repository samples of three Ebolaviruses and two EBOV variants. The ability of the system to identify genetic drift in a replicating virus was achieved by sequencing the ebolavirus glycoprotein gene in a recombinant virus cultured under pressure from a neutralizing antibody. Comparison of the Ebolavirus-RMA results to the Genbank database sequence file with the accession number given for the source RNA and Ebolavirus-RMA results compared to Next Generation Sequence results of the same RNA samples showed up to 99% agreement

Original Article Analysis of Isoniazid, Streptomycin and Ethambutol resistance in

Background: Drug-resistant tuberculosis is a major problem worldwide. Based on the knowledge of specific mutations occurring in Mycobacterium tuberculosis genome, drug resistance can be detected earlier. The aim of this study was to determine the prevalence of the most common mutations associated with resistance to Isoniazid (INH), Streptomycin (SM) and Ethambutol (EMB) in Mycobacterium tuberculosis isolates from Morocco in order to select target mutations to develop tests for rapid detection of drug-resistant Mycobacterium tuberculosis Moroccan isolates. Methodology: A total of 199 M. tuberculosis isolates collected from the National Tuberculosis Reference Laboratory in Morocco were subject to katG, inhA, rrs, rpsL and emb mutation analysis by PCR probe-based assay. The genotypic results were then compared to drug susceptibility testing results for the corresponding drugs. Results: Among 66 phenotypically INH resistant isolates, 80.3 % (53/66) were found to be genotypically INH resistant from which 77.3% (51/66) and 3 % (2/66) had respective mutations in katG315 and inhp-15 codons. Of the 58 phenotypically SM resistant isolates, genotypic SM resistance was confirmed in 17.2 % (10/58) cases. Nucleotide mutations at codons 43 and 88 of rpsL gene and at codon 512 of rrs gene were found respectively in 12.1 % (7/58); 1.7 % (1/58) and 3.4 % (2/58) of the phenotypically SM resistant Mycobacterium tuberculosis isolates. Finally, mutations at codon 306 of embB gene were identified in 42.3 % (11/26) of Mycobacterium tuberculosis isolates phenotypically EMB resistant

Republished, corrected article.

Correction: Tracking ebolavirus genomic drift with a resequencing microarray</p

Originally published, uncorrected article.

Correction: Tracking ebolavirus genomic drift with a resequencing microarray</p