Cooperation in Microbial Populations: Theory and Experimental Model Systems

Cooperative behavior, the costly provision of benefits to others, is common across all domains of life. This review article discusses cooperative behavior in the microbial world, mediated by the exchange of extracellular products called public goods. We focus on model species for which the production of a public good and the related growth disadvantage for the producing cells are well described. To unveil the biological and ecological factors promoting the emergence and stability of cooperative traits we take an interdisciplinary perspective and review insights gained from both mathematical models and well-controlled experimental model systems. Ecologically, we include crucial aspects of the microbial life cycle into our analysis and particularly consider population structures where ensembles of local communities (subpopulations) continuously emerge, grow, and disappear again. Biologically, we explicitly consider the synthesis and regulation of public good production. The discussion of the theoretical approaches includes general evolutionary concepts, population dynamics, and evolutionary game theory. As a specific but generic biological example, we consider populations of Pseudomonas putida and its regulation and use of pyoverdines, iron scavenging molecules, as public goods. The review closes with an overview on cooperation in spatially extended systems and also provides a critical assessment of the insights gained from the experimental and theoretical studies discussed. Current challenges and important new research opportunities are discussed, including the biochemical regulation of public goods, more realistic ecological scenarios resembling native environments, cell-to-cell signaling, and multispecies communities.

A43 Translational research: NGS metagenomics into clinical diagnostics

As research next-generation sequencing (NGS) metagenomic pipelines transition to clinical diagnostics, the user-base changes from bioinformaticians to biologists, medical doctors, and lab-technicians. Besides the obvious need for benchmarking and assessment of diagnostic outcomes of the pipelines and tools, other focus points remain: reproducibility, data immutability, user-friendliness, portability/scalability, privacy, and a clear audit trail. We have a research metagenomics pipeline that takes raw fastq files and produces annotated contigs, but it is too complicated for non-bioinformaticians. Here, we present preliminary findings in adapting this pipeline for clinical diagnostics. We used information available on relevant fora (www.bioinfo-core.org) and experiences and publications from colleague bioinformaticians in other institutes (COMPARE, UBC, and LUMC). From this information, a robust and user-friendly storage and analysis workflow was designed for non-bioinformaticians in a clinical setting. Via Conda [https://conda.io] and Docker containers [http://www.docker.com], we made our disparate pipeline processes self-contained and reproducible. Furthermore, we moved all pipeline settings into a separate JSON file. After every analysis, the pipeline settings and virtual-environment recipes will be archived (immutably) under a persistent unique identifier. This allows long-term precise reproducibility. Likewise, after every run the raw data and final products will be automatically archived, complying with data retention laws/guidelines. All the disparate processes in the pipeline are parallelized and automated via Snakemake1 (i.e. end-users need no coding skills). In addition, interactive web-reports such as MultiQC [http://multiqc.info] and Krona2 are generated automatically. By combining Snakemake, Conda, and containers, our pipeline is highly portable and easily scaled up for outbreak situations, or scaled down to reduce costs. Since patient privacy is a concern, our pipeline automatically removes human genetic data. Moreover, all source code will be stored on an internal Gitlab server, and, combined with the archived data, ensures a clear audit trail. Nevertheless, challenges remain: (1) reproducible reference databases, e.g. being able to revert to an older version to reproduce old analyses. (2) A user-friendly GUI. (3) Connecting the pipeline and NGS data to in-house LIMS. (4) Efficient long-term storage, e.g. lossless compression algorithms. Nevertheless, this work represents a step forward in making user-friendly clinical diagnostic workflows.

Oral fluid: Non-invasive alternative for parvovirus B19 diagnosis?

BACKGROUND

Infections with parvovirus B19 (B19V) have been associated with a wide range of disease manifestations of which erythema infectiosum (fifth disease) in children is most common. Clinical signs following infection of children with B19V can be similar to measles and rubella. Laboratory detection of B19V infections is based on detection of B19V-specific IgM antibodies by enzyme immunoassay (IgM-EIA) and/or B19V DNA by quantitative PCR (qPCR) on blood samples. The need for invasive sampling can be a barrier for public health diagnostics.

OBJECTIVES

To evaluate the use of a dual target B19V-qPCR directed against the NS1 and VP2 of B19V on oral fluid samples as a non-invasive alternative for laboratory diagnosis of B19V infections in children below 12 years of age with exanthema.

STUDY DESIGN

Oral fluid and serum samples were collected from 116 children with exanthema. All serum samples were tested by IgM-EIA/IgG-EIA, while all oral fluid and 56 serum samples were tested by B19V-qPCR.

RESULTS

B19V-specific IgM antibodies were detected in 25 of 116 children in the study. B19V DNA was detected in oral fluid in 17 of the 25 children who were IgM positive, as well as two children who were IgM-equivocal or negative. The child with the equivocal IgM had a high quantity of B19V DNA in oral fluid (7 log IU/ml), compatible with an acute B19V infection. The IgM-negative child was IgG-positive and 4 log IU/ml B19V DNA was detected in the oral fluid sample, suggesting an acute infection and a falsely negative IgM. Sample size calculations indicated that oral fluid samples for qPCR should be collected from 2 to 3 children during outbreaks of exanthema to achieve similar sensitivity as IgM-EIA for one child (≥0.9) to confirm or exclude B19V.

CONCLUSIONS

Results indicate that oral fluid samples are a suitable public health alternative for detection of B19V infections, potentially lowering the barriers for sampling.

Highly sensitive parechovirus CODEHOP PCR amplification of the complete VP1 gene for typing directly from clinical specimens and correct typing based on phylogenetic clustering

PURPOSE

Human parechoviruses (HPeVs), particularly type 3, can cause severe neurological disease and neonatal sepsis in infants. HPeV3 lacks the receptor-binding motif arginine-glycine aspartic acid (RGD), and is proposed to use a different receptor associated with severe disease. In contrast, HPeV1, which contains the RGD motif, is associated with mild disease. Rapid characterization of the presence/absence of this motif is essential for understanding their epidemiology and differential disease profiles. Current HPeV typing assays are based on partial capsid genes and often do not encompass the C-terminus where the RGD region is localized/absent. In addition, these assays lack sensitivity to enable characterization within low viral-load samples, such as cerebral spinal fluid.

METHODOLOGY

We developed a highly sensitive HPeV CODEHOP PCR, which enables typing of parechoviruses directly from clinical samples while generating a complete VP1 gene, including the C-terminus.

RESULTS

The assay was HPeV-specific and has a sensitivity of 6.3 TCID50 ml^-1 for HPeV1 and 0.63 TCID50 ml^-1 for HPeV3. Analysis of the complete VP1 gene in comparison to partial VP1 fragments generated by previously published PCRs showed homologous clustering for most types. However, phylogenetic analysis of partial VP1 fragments showed incongruent typing based on the 75  % homology classification rule. In particular, the strains designated as type 17 were found to be either type 3 or 4 when using the (near-) complete VP1 fragment.

CONCLUSION

While enabling sensitive characterization of HPeVs directly from clinical samples, the HPeV CODEHOP PCR enables the characterization of RGD and non-RGD strains and correct HPeV typing based on the complete VP1.

Optimizing molecular surveillance of mumps genotype G viruses

Mumps viruses continue to cause sporadic cases and outbreaks in countries with a high vaccination coverage for mumps. Molecular surveillance of mumps viruses can be supportive to elucidate the origin and transmission routes of mumps virus in case of an outbreak. Currently, molecular surveillance is worldwide primarily focused on sequencing of the small hydrophobic (SH) gene. However, few studies have already shown that additional genes or regions contribute to the resolution of the sequence data in such a way that mumps cases that seem to be linked to the same source on basis of the SH sequence, appear to be linked to another source or chain of transmission. Notably, this sequence information was recently extracted from the hemagglutinin-neuraminidase (HN) and fusion (F) genes (total 3364 nucleotides), or from the sum of the three non-coding regions (NCRs; total 1954 nt) between the nucleocapsid protein, phosphoprotein, matrix protein and F protein, but also from the complete genome. Here, sequence data from NCRs were compared with that of the HN and F gene, using mumps genotype G viruses detected in the Netherlands between 2010 and 2018. Results of this study indicate that NCRs sequence data provided similar or slightly better sequence resolution compared to the HN and F genes for most viruses. For molecular surveillance of currently circulating mumps genotype G viruses is sequencing of SH in combination with NCRs currently a useful approach.

Genetic variation of hepatitis B surface antigen among acute and chronic hepatitis B virus infections in The Netherlands

Genetic variation within hepatitis B surface antigen (HBsAg), in particular within the major hydrophobic region (MHR), is related to immune/vaccine and test failures and can have a significant impact on the vaccination and diagnosis of acute infection. This study shows, for the first time, variation among acute cases and compares the amino acid variation within the HBsAg between acute and chronic infections. We analyzed the virus isolated from 1231 acute and 585 chronic cases reported to an anonymized public health surveillance database between 2004 and 2014 in The Netherlands. HBsAg analysis revealed the circulation of 6 genotypes (Gt); GtA was the dominant genotype followed by GtD among both acute (68.2% and 17.4%, respectively) and chronic (34.9% and 34.2%, respectively) cases. Variation was the highest among chronic strains compared to that among acute strains. Both acute and chronic GtD showed the highest variation compared to that of other genotypes (P < .01). Substitutions within the MHR were found in 8.5% of the acute strains and 18.6% of the chronic strains. Specific MHR substitutions described to have an impact on vaccine/immune escape and/or HBsAg test failure were found among 4.1% of the acute strains and 7.0% of the chronic strains. In conclusion, we show a high variation of HBsAg among acute and chronic hepatitis B virus–infected cases in The Netherlands, in particular among those infected with GtD, and compare, for the first time, variation in frequencies between acute and chronic cases. Additional studies on the impact of these variations on vaccination and test failure need to be conducted, as well as whether HBsAg false–negative variants have been missed.

Extracorporeal Membrane Oxygenation (Ecmo): Extended Indications for Artificial Support of Both Heart and Lungs

Extracorporeal membrane oxygenation (ECMO) was used to achieve temporary artificial support in cardiac and pulmonary function in 22 patients from 1987 to September 1990. Standard indications were postcardiotomy cardiogenic shock (n=4), neonatal (n=1) and adult respiratory distress syndrome (n=4). ECMO was also used for extended indications, such as graft failure following heart (n=11) or lung transplantation (n=2). In six of these cases ECMO was instituted as a bridge device to subsequent retransplantation of either the heart (n=4) or one lung (n=2). One out of nine patients supported by ECMO for standard indications, and two out of 13 patients supported for extended indications are long-term survivors. This series illustrates the results with ECMO in emergency situations, in patients under immunosuppressive protocols, or in patients with advanced lung failure requiring almost complete artificial gas exchange. In such complex situations, ECMO does provide stabilization until additional therapeutic measures are in effect. ECMO cannot be recommended for postoperative cardiogenic shock but short-term ECMO support is an accepted method in most cases with graft failure or pulmonary failure or other origin.

Szintigraphischer Nachweis einer stillen Aspiration nach beidseitiger Lungentransplantation

Vorgestellt wird der Fall einer 25jährigen Patientin nach beidseitiger Lungentransplantation und rezidivierenden Pneumonien. Klinisch bestand der Verdacht auf eine stille Aspiration. Szintigraphisch gelang sowohl der Aspirationsnachweis als auch eine Differenzierung hinsichtlich der Genese: direkte oro-pulmonale Aspiration versus Aspiration nach gastro-öspohagealem Reflux.