Host-Pathogen Interactions in Guillain-Barré Syndrome : the role of Campylobacter jejuni lipooligosaccharide sialylation

*Campylobacter jejuni* (*C. jejuni*) is a spiral, comma-shaped Gram-negative bacterium which is motile due to bipolar flagella. *C. jejuni* is frequently present in the intestines of poultry and birds, where it is considered to be part of the normal intestinal flora (1). During slaughter procedures, poultry meat products often become contaminated with fecal content containing *C. jejuni* (2, 3). As a consequence of the extensive consumption of chicken worldwide, the handling of raw chicken and ingestion of undercooked chicken meat are the main causes of *C. jejuni* infection in humans (3). Apart from poultry, other sources of *C. jejuni* infection include raw milk, (swimming) water and pets (4). Upon ingestion, *C. jejuni* can pass through the human gastrointestinal tract without clinical symptoms; however, infection with *C. jejuni* will often lead to a diarrheal illness (5). In the Netherlands, approximately 80,000 people per year (range, 30,000 – 160,000) are estimated to experience acute gastroenteritis caused by *Campylobacter* (6). The symptoms include fever, abdominal pain, and slimy or bloody diarrhea that lasts for several days (7). *C. jejuni* diarrhea is self-limiting, though complications such as bacteraemia, post-infectious reactive arthritis or Guillain-Barré syndrome (GBS) occasionally occur. In view of the broad spectrum of clinical disease presentations associated with *C. jejuni* infection, microbial as well as host factors are likely to contribute to *C. jejuni* pathogenesis

Genomic sequence of Campylobacter jejuni subsp. jejuni HS:19 Penner serotype reference strain RM3420

Campylobacter jejuni subsp. jejuni infections are a leading cause of foodborne gastroenteritis and the most prevalent antecedent to Guillain-Barré syndrome (GBS). Penner serotype HS:19 is among several capsular types shown to be markers for GBS. This study describes the genome of C. jejuni subsp. jejuni HS:19 Penner reference strain RM3420

Complete genomic sequence of Campylobacter jejuni subsp. jejuni HS: 19 strain RM1285 isolated from packaged chicken

Poultry products serve as the main source of Campylobacter jejuni subsp. jejuni infections in humans. C. jejuni subsp. jejuni infections are a leading cause of foodborne gastroenteritis and are a prevalent antecedent to Guillain-Barré syndrome. This study describes the genome of C. jejuni subsp. jejuni HS:19 strain RM1285, isolated from packaged chicken in California

Complete genome sequences of Campylobacter jejuni strains RM3196 (233.94) and RM3197 (308.95) isolated from patients with Guillain-Barré syndrome

Infections with Campylobacter jejuni subsp. jejuni are a leading cause of foodborne gastroenteritis and the most prevalent infection preceding Guillain-Barré syndrome (GBS). This study describes the genomes of C. jejuni subsp. jejuni HS:41 strains RM3196 (233.94) and RM3197 (308.95) that were isolated from patients with GBS in Cape Town, South Africa

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

Background: Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. As a result, long-read sequencing platforms are becoming more popular. In this respect, the Oxford Nanopore Technologies–based long-read sequencing “nanopore” platform is becoming a widely used tool with a broad range of applications and end-users. However, the need to explore and manipulate the complex data generated by long-read sequencing platforms necessitates accompanying specialized bioinformatics platforms and tools to process the long-read data correctly. Importantly, such tools should additionally help democratize bioinformatic

Comparison of illumina versus nanopore 16s rRNA gene sequencing of the human nasal microbiota

Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME (Oxford Nanopore Technologies—ONT, Oxford, UK) and an in-house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 (Oxford Nanopore Technologies—ONT, Oxford, UK) and R9.2 (Oxford Nanopore Technologies—ONT, Oxford, UK) were compared. In conclusion, the current study shows that the nanopore sequencing platform is comparable with the Illumina platform in detection bacterial genera of the nasal microbiota, but the nanopore platform does have problems in detecting bacteria within the genus Corynebacterium. Although advances are being made, thorough validation of the nanopore platform is still recommendable

WeFaceNano

Background: Bacterial plasmids often carry antibiotic resistance genes and are a significant factor in the spread of antibiotic resistance. The ability to completely assemble plasmid sequences would facilitate the localization of antibiotic resistance genes, the identification of genes that promote plasmid transmission and the accurate tracking of plasmid mobility. However, the complete assembly of plasmid sequences using the currently most widely used sequencing platform (Illumina-based sequencing) is restricted due to the generation of short sequence lengths. The long-read Oxford Nanopore Technologies (ONT) sequencing platform overcomes this limitation. Still, the assembly of plasmid sequence data remains challenging due to software incompatibility with long-reads and the error rate generated using ONT sequencing.

Genetic Analysis of mcr-1-Carrying Plasmids From Gram-Negative Bacteria in a Dutch Tertiary Care Hospital

The role of plasmids in the complex pandemic of antimicrobial resistance is increasingly being recognized. In this respect, multiple mobile colistin resistance (mcr) gene-carrying plasmids have been described. However, the characteristics and epidemiology of these plasmids within local healthcare settings are largely unknown. We retrospectively characterized the genetic composition and epidemiology of plasmids from mcr-1-positive bacterial isolates identified from patients from a large academic hospital in the Netherlands. Clinical Gram-negative bacteria with an MIC &gt; 2 μg/mL for colistin, obtained from patients hospitalized at the Erasmus MC University Medical Center Rotterdam during the years 2010–2018, were screened for presence of the mcr-1 gene. Extracted plasmids from mcr-1-positive isolates were sequenced using a combination of short- and long-read sequencing platforms, characterized by incompatibility type and genetic composition and compared to publicly available mcr-1-carrying plasmid sequences. In 21 isolates from 14 patients, mcr-1 was located on a plasmid. These plasmids were of diverse genetic background involving Inc types IncX4, IncI2(delta), IncHI2, as well as double Inc types IncHI2/IncN and IncHI2/IncQ. mcr-1-carrying plasmids were found in Escherichia coli, Klebsiella pneumoniae, and Kluyvera georgiana, and within the chromosome of an ST147 K. pneumoniae isolate. In depth analysis indicated intrapatient, interpatient, and interspecies transmission events of mcr-1-carrying plasmids. In addition, our results show that the mcr-1 gene resides in a rich environment full of other (mcr-1 negative) plasmids and of many different Inc types, enabling interplasmidal transfer events and facilitating widespread dissemination of the mcr-1 gene. Multiple mcr-1-carrying plasmid transmission events had likely occurred among isolates from hospitalized patients. Recognition and identification of plasmid transmission events within hospitals is necessary in order to design and implement effective infection control measures.</p

Enhanced, sialoadhesin-dependent uptake of guillain-barré syndrome-associated Campylobacter jejuni strains by human macrophages

Molecular mimicry between Campylobacter jejuni sialylated lipooligosaccharides (LOS) and human nerve gangliosides can trigger the production of cross-reactive antibodies which induce Guillain-Barré syndrome (GBS). To better understand the immune events leading to GBS, it is essential to know how sialylated LOS are recognized by the immune system. Here, we show that GBSassociated C. jejuni strains bind to human sialoadhesin (hSn), a conserved, mainly macrophage-restricted I-type lectin. Using hSn-transduced THP-1 cells, we observed that C. jejuni strains with α(2,3)-sialylated LOS, including strains expressing GM1aand GD1a-like epitopes, bind to hSn. This observation is of importance, as these epitopes are frequently the targets of the crossreactive antibodies detected in GBS patients. Interestingly, the Sn binding domains were not constitutively exposed on the surface of C. jejuni. Heat inactivation and the environmental conditions which food-borne C. jejuni encounters during its passage through the intestinal tract, such as low pH and contact with bile constituents, exposed LOS and facilitated Sn binding. Sn binding enhanced bacterial uptake and increased the production of interleukin-6 (IL-6) by primary human Sn-expressing monocytederived macrophages compared to control conditions, where Sn was blocked using neutralizing antibodies or when nonsialylated C. jejuni was used. Sn-mediated uptake has been reported to enhance humoral immune responses. As C. jejuni strains expressing ganglioside mimics GD1a and GM1a are closely associated with GBS, Sn binding may be a determining event in the production of cross-reactive antibodies and the development of GBS