Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000-year-old mammoth.

Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.

Increasing incidence of reported scabies infestations in the Netherlands, 2011-2021.

INTRODUCTION: Several Public Health Services and general practitioners in the Netherlands observed an increase in scabies in the Netherlands. Since individual cases of scabies are not notifiable in the Netherlands, the epidemiological situation is mostly unknown. To investigate the scabies incidence in the Netherlands, we described the epidemiology of scabies between 2011 and 2021. METHODS: Two national data sources were analysed descriptively. One data source obtained incidence data of scabies (per 1,000 persons) of persons consulting in primary care from 2011-2020. The other data source captured the number of prescribed scabicides in the Netherlands from 2011-2021. To describe the correlation between the incidence of diagnoses and the number of dispensations between 2011 and 2020, we calculated a correlation coefficient. RESULTS: The incidence of reported scabies has increased by more than threefold the last decade (2011-2020), mainly affecting adolescents and (young) adults. This was also clearly reflected in the fivefold increase in dispensations of scabicide medication during 2011-2021. The incidence and dispensations were at an all-time high in 2021. We found a strong correlation between the reported incidence and the number of dispensations between 2011 and 2020. CONCLUSIONS: More awareness on early diagnosis, proper treatment and treatment of close contacts is needed.

Short report: The potential of PCR on skin flakes from bed linens for diagnosis of scabies in an outbreak.

BACKGROUND: Scabies outbreaks are common in nursing homes in the Netherlands. In October 2018, a local public health service (PHS) in The Hague was notified of a new scabies outbreak in a nursing home in that region. The PHS initiated an outbreak investigation. Cases were defined as: possible (reported symptoms), probable (scabies-like lesions) and confirmed (PCR or microscopy in skin flakes). Head-to-toe examinations were performed of all residents and those staff members who reported symptoms suggestive of scabies. Skin scrapings of lesions were tested either with microscopy or by PCR. Experimentally for case finding, skin flakes from bed linens of residents who reported symptoms of itchiness but did not have primary lesions were sent for PCR testing. PRINCIPAL FINDINGS: All residents (41) and 37/44 staff were included in this outbreak investigation. We identified 30 possible, four probable and six confirmed cases. The overall attack rate for probable/confirmed cases was 10/78 (13%). Of the six confirmed cases, two were confirmed by PCR, three by microscopy, and one showed positive findings with both techniques. Two out of the three bed-linen specimens were PCR-positive. CONCLUSIONS: In this outbreak of scabies in a nursing home, PCR was used on skin flakes from bed linens, which led to the detection of two additional cases. This illustrates the potential of PCR during the investigation of scabies outbreaks.

Management of a hospital-wide vancomycin-resistant Enterococcus faecium outbreak in a Dutch general hospital, 2014-2017: successful control using a restrictive screening strategy.

BACKGROUND: The emergence of vancomycin resistant enterococci poses a major problem in healthcare settings. Here we describe a hospital-wide outbreak of vancomycin-resistant Enterococcus faecium in a general hospital in The Netherlands in the period December 2014-February 2017. Due to late detection of the outbreak, a large cohort of approximately 25,000 (discharged) patients was classified as 'VRE suspected'. Hereupon a mitigated screening and isolation policy, as compared with the national guideline, was implemented to control the outbreak. METHODS: After the outbreak was identified, a screening policy consisting of a single rectal swab culture (with enrichment broth) to discontinue isolation and removing 'VRE suspected' label in the electronic patient files for readmitted VRE suspected patients, was implemented. In addition to the on admission screening, periodic hospital-wide point prevalence screening, measures to improve compliance with standard infection control precautions and enhanced environmental cleaning were implemented to control the outbreak. RESULTS: Between September 2014 and February 2017, 140 patients were identified to be colonised by vanA mediated vancomycin-resistant Enterococcus faecium (VREfm). Two of these patients developed bacteraemia. AFLP typing showed that the outbreak was caused by a single clone. Extensive environmental contamination was found in multiple wards. Within nine months after the detection of the outbreak no new VRE cases were detected. CONCLUSION: We implemented a control strategy based on targeted screening and isolation in combination with implementation of general precautions and environmental cleaning. The strategy was less stringent than the Dutch national guideline for VRE control. This strategy successfully controlled the outbreak, while it was associated with a reduction in the number of isolation days and the number of cultures taken.

Accurate serology for SARS-CoV-2 and common human coronaviruses using a multiplex approach.

Serology is a crucial part of the public health response to the ongoing SARS-CoV-2 pandemic. Here, we describe the development, validation and clinical evaluation of a protein micro-array as a quantitative multiplex immunoassay that can identify S and N-directed SARS-CoV-2 IgG antibodies with high specificity and sensitivity and distinguish them from all currently circulating human coronaviruses. The method specificity was 100% for SARS-CoV-2 S1 and 96% for N antigen based on extensive syndromic (n=230 cases) and population panel (n=94) testing that also confirmed the high prevalence of seasonal human coronaviruses. To assess its potential role for both SARS-CoV-2 patient diagnostics and population studies, we evaluated a large heterogeneous COVID-19 cohort (n=330) and found an overall sensitivity of 89% (≥ 21 days post onset symptoms (dps)), ranging from 86% to 96% depending on severity of disease. For a subset of these patients longitudinal samples were provided up to 56 dps. Mild cases showed absent or delayed, and lower SARS-CoV-2 antibody responses. Overall, we present the development and extensive clinical validation of a multiplex coronavirus serological assay for syndromic testing, to answer research questions regarding to antibody responses, to support SARS-CoV-2 diagnostics and to evaluate epidemiological developments efficiently and with high-throughput.

Differences in Antibody Kinetics and Functionality Between Severe and Mild Severe Acute Respiratory Syndrome Coronavirus 2 Infections.

We determined and compared the humoral immune response in patients with severe (hospitalized) and mild (nonhospitalized) coronavirus disease 2019 (COVID-19). Patients with severe disease (n = 38) develop a robust antibody response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including immunoglobulin G and immunoglobulin A antibodies. The geometric mean 50% virus neutralization titer is 1:240. SARS-CoV-2 infection was found in hospital personnel (n = 24), who developed mild symptoms necessitating leave of absence and self-isolation, but not hospitalization; 75% developed antibodies, but with low/absent virus neutralization (60% with titers <1:20). While severe COVID-19 patients develop a strong antibody response, mild SARS-CoV-2 infections induce a modest antibody response. Long-term monitoring will show whether these responses predict protection against future infections.