Quality of MALDI-TOF mass spectra in routine diagnostics: results from an international external quality assessment including 36 laboratories from 12 countries using 47 challenging bacterial strains.

OBJECTIVES: Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a widely used method for bacterial species identification. Incomplete databases and mass spectral quality (MSQ) still represent major challenges. Important proxies for MSQ are the number of detected marker masses, reproducibility, and measurement precision. We aimed to assess MSQs across diagnostic laboratories and the potential of simple workflow adaptations to improve it. METHODS: For baseline MSQ assessment, 47 diverse bacterial strains, which are challenging to identify by MALDI-TOF MS, were routinely measured in 36 laboratories from 12 countries, and well-defined MSQ features were used. After an intervention consisting of detailed reported feedback and instructions on how to acquire MALDI-TOF mass spectra, measurements were repeated and MSQs were compared. RESULTS: At baseline, we observed heterogeneous MSQ between the devices, considering the median number of marker masses detected (range = [2-25]), reproducibility between technical replicates (range = [55%-86%]), and measurement error (range = [147 parts per million (ppm)-588 ppm]). As a general trend, the spectral quality was improved after the intervention for devices, which yielded low MSQs in the baseline assessment as follows: for four out of five devices with a high measurement error, the measurement precision was improved (p-values <0.001, paired Wilcoxon test); for six out of ten devices, which detected a low number of marker masses, the number of detected marker masses increased (p-values <0.001, paired Wilcoxon test). DISCUSSION: We have identified simple workflow adaptations, which, to some extent, improve MSQ of poorly performing devices and should be considered by laboratories yielding a low MSQ. Improving MALDI-TOF MSQ in routine diagnostics is essential for increasing the resolution of bacterial identification by MALDI-TOF MS, which is dependent on the reproducible detection of marker masses. The heterogeneity identified in this external quality assessment (EQA) requires further study.

External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories.

This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.

COVID-19 new diagnostics development: novel detection methods for SARS-CoV-2 infection and considerations for their translation to routine use.

PURPOSE OF REVIEW: COVID-19 has put the in-vitro-diagnostic community under an unprecedented spotlight, with a global requirement for accurate SARS-CoV-2 tests. This review will outline technological responses to this need and the analytical considerations required for their translation to routine use. RECENT FINDINGS: SARS-CoV-2 diagnostic solutions directly detect the virus or measure host-derived surrogate markers of infection. With pressure upon supply chains for the 'traditional' molecular approaches, a wide variety of analytical tools spanning the molecular, serology, imaging and chemistry space are being developed, including high throughput solutions and simplified near-patient formats. SUMMARY: The unique genetic nature of SARS-CoV-2 means high analytical specificity is achievable by most diagnostic formats. However, clinical sensitivity assessment is complicated by wide discrepancies in analytical range and challenges associated with standardising these differences. When coupled with the acute nature of SARS-CoV-2 infection, reported precise metrics of test performance must be questioned. The response to SARS-CoV-2 has delivered considerable diagnostic innovation, but for a technology to be maximised, it must be demonstrably reproducible and fit for purpose. If novel diagnostic solutions for SARS-CoV-2 are to succeed, equally innovative mechanisms are needed to ensure widespread clinical and surveillance application, enabling agreed standards and metrics to ensure comparability.

Cyber security threats in the microbial genomics era: implications for public health.

Next generation sequencing (NGS) is becoming the new gold standard in public health microbiology. Like any disruptive technology, its growing popularity inevitably attracts cyber security actors, for whom the health sector is attractive because it combines mission-critical infrastructure and high-value data with cybersecurity vulnerabilities. In this Perspective, we explore cyber security aspects of microbial NGS. We discuss the motivations and objectives for such attack, its feasibility and implications, and highlight policy considerations aimed at threat mitigation. Particular focus is placed on the attack vectors, where the entire process of NGS, from sample to result, could be vulnerable, and a risk assessment based on probability and impact for representative attack vectors is presented. Cyber attacks on microbial NGS could result in loss of confidentiality (leakage of personal or institutional data), integrity (misdetection of pathogens) and availability (denial of sequencing services). NGS platforms are also at risk of being used as propagation vectors, compromising an entire system or network. Owing to the rapid evolution of microbial NGS and its applications, and in light of the dynamics of the cyber security domain, frequent risk assessments should be carried out in order to identify new threats and underpin constantly updated public health policies.

Outbreak of human leptospirosis linked to contaminated water bodies in Northern Israel, June to August 2018.

We report preliminary findings of a large outbreak of human leptospirosis with 36 confirmed/probable and 583 suspected cases from June-August 2018, linked to contaminated water bodies in Northern Israel. There was a travel-associated case in Germany; additional cases are being investigated in other countries. The presumed chain of transmission, implicating wild boar and cattle, raises multiple challenges for risk assessment, risk management and risk communication currently being addressed by a public health response team.