Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria.

There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitoring antimicrobial resistance (AMR) and protecting the safety of people and animals. With the availability of smaller and more affordable sequencing platforms coupled with well-defined bioinformatic protocols, the technological capability to incorporate this technique for real-time surveillance and genomic epidemiology has greatly expanded. There is a need, however, to ensure that data are of high quality. The goal of this study was to assess the utility of a small benchtop sequencing platform using a multi-laboratory verification approach. Thirteen laboratories were provided the same equipment, reagents, protocols and bacterial reference strains. The Illumina DNA Prep and Nextera XT library preparation kits were compared, and 2×150 bp iSeq i100 chemistry was used for sequencing. Analyses comparing the sequences produced from this study with closed genomes from the provided strains were performed using open-source programs. A detailed, step-by-step protocol is publicly available via protocols.io (https://www.protocols.io/view/iseq-bacterial-wgs-protocol-bij8kcrw). The throughput for this method is approximately 4-6 bacterial isolates per sequencing run (20-26 Mb total load). The Illumina DNA Prep library preparation kit produced high-quality assemblies and nearly complete AMR gene annotations. The Prep method produced more consistent coverage compared to XT, and when coverage benchmarks were met, nearly all AMR, virulence and subtyping gene targets were correctly identified. Because it reduces the technical and financial barriers to generating WGS data, the iSeq platform is a viable option for small laboratories interested in genomic surveillance of microbial pathogens.

Physiological concentrations of retinoic acid favor myeloid dendritic cell development over granulocyte development in cultures of bone marrow cells from mice.

Differentiation of hematopoietic progenitors to dendritic cells (DCs) is a complex, poorly understood process regulated by cytokines, colony-stimulating factors, growth factor receptors, and transcription factors. However, nutritional factors may play an important role. Vitamin A is essential for proper immune function and is implicated in the development of myeloid lineage cells, especially granulocytes. We investigated the role of vitamin A in the differentiation of myeloid DCs. Cultures of bone marrow cells from mice stimulated with granulocyte-macrophage colony-stimulating factor (GM-CSF) in medium with reduced serum retinol demonstrated significantly decreased DC development compared with control cultures containing retinol. Surprisingly, granulocytes predominated in cultures stimulated with GM-CSF when retinol was depleted. The addition of all-trans or 9-cis retinoic acid to cultures depleted of retinol significantly restored DCs and inhibited granulocyte development. The DC-promoting effect of vitamin A was specific to myeloid lineage development stimulated by GM-CSF because vitamin A significantly inhibited DC development stimulated by flt-3 ligand. Vitamin A also affected DC major histocompatibility complex (MHC) class II and costimulatory molecule expression. In response to increasing concentrations of vitamin A, the expression of MHC class II decreased on the DC, whereas the expression of costimulatory molecules increased, especially CD86. Our data suggest that vitamin A favors the differentiation of myeloid progenitors to immature myeloid DC instead of granulocytes when dietary vitamin A is adequate, and that vitamin A deficiency may compromise adaptive immune responses that depend on myeloid DC antigen presentation.