Metagenomic next-generation sequencing as a diagnostic tool in the clinical routine of an infectious diseases department: a retrospective cohort study

BACKGROUND

Metagenomic next-generation sequencing (mNGS) of circulating cell-free DNA from plasma is a hypothesis-independent broadband diagnostic method for identification of potential pathogens. So far, it has only been investigated in special risk populations (e.g. patients with neutropenic fever).

PURPOSE

To investigate the extent to which mNGS (DISQVER® platform) can be used in routine clinical practice.

METHODS

We collected whole blood specimens for mNGS testing, blood cultures (BC), and pathogen-specific PCR diagnostics. Clinical data and pathogen diagnostics were retrospectively reviewed by an infectious disease expert panel regarding the adjustment of anti-infective therapy.

RESULTS

In 55 selected patients (median age 53 years, 67% male) with heterogeneous diagnoses, a total of 66 different microorganisms and viruses were detected using mNGS (51% viruses, 38% bacteria, 8% fungi, 3% parasites). The overall positivity rate of mNGS was 53% (29/55). Fifty-two out of 66 (79%) potential pathogens detected by mNGS were found in patients with primary or secondary immunodeficiency. The concordance rates of BC and pathogen-specific PCR diagnostics with mNGS testing were 14% (4/28) and 36% (10/28), respectively (p < 0.001). An additional bacterial pathogen (Streptococcus agalactiae) could only be detected by BC. Therapeutic consequences regarding anti-infective therapy were drawn from 23 pathogens (35% of detections), with 18 of these detections occurring in patients with immunodeficiency.

CONCLUSIONS

We conclude that mNGS is a useful diagnostic tool, but should only be performed selectively in addition to routine diagnostics of infectious diseases. The limited number of patients and the retrospective study design do not allow any further conclusions.

[Infectious Diseases - a new specialty for postgraduate training in Germany]

Medicine in Germany is currently facing major structural and economic challenges. Infectious Diseases, with the recent introduction of a new specialty in "Internal Medicine and Infectious Diseases" and with the existing additional training for almost all specializations, will make an important contribution to overcoming these challenges. Expertise in infectious diseases has to be very broad and requires high interdisciplinarity, which makes infectious diseases an attractive and demanding specialty. The complex fundamentals of infectious diseases must now be quickly conveyed to as many physicians as possible in a short period of time, as part of their specialization or as additional training. Until this is achieved, transitional solutions will be necessary for some time. The adaptation of the current billing and reimbursement system for infectious diseases services and improved intersectoral cooperation are of the utmost importance for the further development of the specialty.

Applying Machine Learning to Blood Count Data Predicts Sepsis with ICU Admission

BACKGROUND

Timely diagnosis is crucial for sepsis treatment. Current machine learning (ML) models suffer from high complexity and limited applicability. We therefore created an ML model using only complete blood count (CBC) diagnostics.

METHODS

We collected non-intensive care unit (non-ICU) data from a German tertiary care centre (January 2014 to December 2021). Using patient age, sex, and CBC parameters (haemoglobin, platelets, mean corpuscular volume, white and red blood cells), we trained a boosted random forest, which predicts sepsis with ICU admission. Two external validations were conducted using data from another German tertiary care centre and the Medical Information Mart for Intensive Care IV database (MIMIC-IV). Using the subset of laboratory orders also including procalcitonin (PCT), an analogous model was trained with PCT as an additional feature.

RESULTS

After exclusion, 1 381 358 laboratory requests (2016 from sepsis cases) were available. The CBC model shows an area under the receiver operating characteristic (AUROC) of 0.872 (95% CI, 0.857-0.887). External validations show AUROCs of 0.805 (95% CI, 0.787-0.824) for University Medicine Greifswald and 0.845 (95% CI, 0.837-0.852) for MIMIC-IV. The model including PCT revealed a significantly higher AUROC (0.857; 95% CI, 0.836-0.877) than PCT alone (0.790; 95% CI, 0.759-0.821; P < 0.001).

CONCLUSIONS

Our results demonstrate that routine CBC results could significantly improve diagnosis of sepsis when combined with ML. The CBC model can facilitate early sepsis prediction in non-ICU patients with high robustness in external validations. Its implementation in clinical decision support systems has strong potential to provide an essential time advantage and increase patient safety.

Presence of hypervirulence-associated determinants in Klebsiella pneumoniae from hospitalised patients in Germany

BACKGROUND

Klebsiella (K.) pneumoniae is a ubiquitous Gram-negative bacterium and a common coloniser of animals and humans. Today, K. pneumoniae is one of the most persistent nosocomial pathogens worldwide and poses a severe threat/burden to public health by causing urinary tract infections, pneumonia and bloodstream infections. Infections mainly affect immunocompromised individuals and hospitalised patients. In recent years, a new type of K. pneumoniae has emerged associated with community-acquired infections such as pyogenic liver abscess in otherwise healthy individuals and is therefore termed hypervirulent K. pneumoniae (hvKp). The aim of this study was the characterisation of K. pneumoniae isolates with properties of hypervirulence from Germany.

METHODS

A set of 62 potentially hypervirulent K. pneumoniae isolates from human patients was compiled. Inclusion criteria were the presence of at least one determinant that has been previously associated with hypervirulence: (I) clinical manifestation, (II) a positive string test as a marker for hypermucoviscosity, and (III) presence of virulence associated genes rmpA and/or rmpA2 and/or magA. Phenotypic characterisation of the isolates included antimicrobial resistance testing by broth microdilution. Whole genome sequencing (WGS) was performed using Illumina® MiSeq/NextSeq to investigate the genetic repertoire such as multi-locus sequence types (ST), capsule types (K), further virulence associated genes and resistance genes of the collected isolates. For selected isolates long-read sequencing was applied and plasmid sequences with resistance and virulence determinants were compared.

RESULTS

WGS analyses confirmed presence of several signature genes for hvKp. Among them, the most prevalent were the siderophore loci iuc and ybt and the capsule regulator genes rmpA and rmpA2. The most dominant ST among the hvKp isolates were ST395 capsule type K2 and ST395 capsule type K5; both have been described previously and were confirmed by our data as multidrug-resistant (MDR) isolates. ST23 capsule type K1 was the second most abundant ST in this study; this ST has been described as commonly associated with hypervirulence. In general, resistance to beta-lactams caused by the production of extended-spectrum beta-lactamases (ESBL) and carbapenemases was observed frequently in our isolates, confirming the threatening rise of MDR-hvKp strains.

CONCLUSIONS

Our study results show that K. pneumoniae strains that carry several determinants of hypervirulence are present for many years in Germany. The detection of carbapenemase genes and hypervirulence associated genes on the same plasmid is highly problematic and requires intensified screening and molecular surveillance. However, the non-uniform definition of hvKp complicates their detection. Testing for hypermucoviscosity alone is not specific enough to identify hvKp. Thus, we suggest that the classification of hvKp should be applied to isolates that not only fulfil phenotypical criteria (severe clinical manifestations, hypermucoviscosity) but also (I) the presence of at least two virulence loci e.g. iuc and ybt, and (II) the presence of rmpA and/or rmpA2.

Early-Outcome Differences between Acute and Chronic Periprosthetic Joint Infections-A Retrospective Single-Center Study

Periprosthetic joint infections (PJI) are serious complications after arthroplasty, associated with high morbidity, mortality, and complex treatment processes. The outcomes of different PJI entities are largely unknown. The aim of this study was to access the early outcomes of different PJI entities. A retrospective, single-center study was conducted. The characteristics and outcomes of patients with PJI treated between 2018 and 2019 were evaluated 12 months after the completion of treatment. Primary endpoints were mortality, relapse free survival (RFS) and postoperative complications (kidney failure, sepsis, admission to ICU). A total of 115 cases were included [19.1% early (EI), 33.0% acute late (ALI), and 47.8% chronic infections (CI)]. Patients with ALI were older (p = 0.023), had higher ASA scores (p = 0.031), preoperative CRP concentrations (p = 0.011), incidence of kidney failure (p = 0.002) and sepsis (p = 0.026). They also tended towards higher in-house mortality (ALI 21.1%, 13.6% EI, 5.5% CI) and admission to ICU (ALI 50.0%, 22.7% EI, 30.9% CI). At 12 months, 15.4% of patients with EI had a relapse, compared to 38.1% in ALI and 36.4% in CI. There are differences in patient characteristics and early outcomes between PJI entities. Patients with EI have better early clinical outcomes. Patients with ALI require special attention during follow-up because they have higher occurrences of relapses and postoperative complications than patients with EI and CI.

[Exposures to fruit plants in Germany from 2010-2019 : Analysis of the Erfurt joint poison information center database]

BACKGROUND

Inquiries about fruit plants are a frequent reason for consultation with poison information centers, although it should be emphasized that there are no large systematic studies on toxicity based on exposure data. The aim of this work is to determine the risk of poisoning by fruit plants in Germany.

METHODS

Retrospective study of data from the Erfurt Joint Poison Information Center on poisoning inquiries regarding fruit plants (2010-2019) with a detailed presentation of interim results, a tabular handout, plant photos as identification aids, and trend analyses.

RESULTS

From 16,088 plant exposures with 16,700 plants, 214 different fruit plant species were identified. Forty-five fruit plant species (21%) turned out to be relevant (≥ 30 inquiries) and of these, 6 (2.8%) turned out to be highly relevant (≥ 300 inquiries). All relevant plants were assigned a defined risk category (RC): RC 0 (2; 4.4%), RC 1 (26; 57.8%), RC 2 (12; 26.7%), and RC 3 (5; 11.1%). Regarding the inquiries, 6% (459/7607) were related to RC 0; 47.9% (3645/7607) to RC 1; 39.3% to RC 2 (2986/7607); and 6.8% (517/7607) to RC 3. Of the inquiries, 69.5% (5284/7607) were related to young children (1 to < 6 years). Exposure outcomes for all age groups were asymptomatic in 82%, mild in 14.7%, moderate in 3%, and severe in 0.3%, with severe poisoning caused by seven plant species. Interventions were initiated in 66.8% (5079) of the inquiries. Inquiries were most frequently related to Taxus baccata, Ligustrum vulgare, Physalis alkekengi, Prunus laurocerasus, Convallaria majalis, Mahonia spec., Sambucus spec., Lonicera spec., Sorbus aucuparia, Thuja spec., Hedera helix, and Cotoneaster spec.

DISCUSSION

Poisoning by fruit plants in Germany is rare. However, there is a great need for information and education.

COVID-19 treatment strategies with drugs centrally procured by the German Federal Ministry of Health in a representative tertiary care hospital: a temporal analysis

Introduction

To ensure the fastest and earliest possible treatment, the German Federal Ministry of Health (BMG) initiated central procurement and nationwide distribution of new drugs against COVID-19. A single centre was used for a retrospective temporal analysis of this procedure.

Methods

A descriptive analysis of hospitalization and treatment of COVID-19 patients with drugs centrally procured by the BMG at St. Georg Hospital, Leipzig, Germany, for the period from 1 March 2020 to 28 February 2023 was employed considering the approval status, evolving guidelines and recommendations of medical societies.

Results

In total, 3,412 patients ≥18 years (54.9% men) with PCR-confirmed SARS-CoV-2 infection were admitted. The mean age was 64 years during the reporting period and 66.1/70.6 years during the first and second COVID-19 waves, respectively. 964 patients (28.2%) received COVID-19 therapy with drugs procured centrally by the BMG. Remdesivir was the most commonly used (63%). SARS-CoV-2 neutralizing monoclonal antibodies represented 23% of the therapies. Peroral antivirals (nirmatrelvir/ritonavir and molnupiravir) were used in 14% of COVID-19 patients, with molnupiravir being insignificant (five prescriptions).

Conclusions

Specific therapeutic approaches were mainly based on antiviral therapy in the early phase of COVID-19 to prevent severe disease progression in vulnerable patient groups. Most drugs had not been approved at the time of central procurement; therefore, prescriptions were given on a case-by-case basis after careful risk-benefit assessments. All available neutralizing monoclonal SARS-CoV-2 antibodies lost efficacy during the pandemic due to different circulating immune escape variants. Remdesivir and nirmatrelvir/ritonavir remained effective therapies in the early phase of COVID-19.

A case for routine microbial diagnostics: Results from antimicrobial susceptibility testing in post-traumatic wound infections at a Ugandan tertiary care hospital

The global spread of antimicrobial resistance (AMR) poses an increasing challenge for clinicians in Uganda, where microbiological diagnostics are not routinely available or accessible. The aim of this study was to determine pathogen prevalence and antibiotic resistance patterns in patients with wound infections following trauma at a national referral hospital in Kampala, Uganda. In addition, the suitability of currently used empirical treatment options in this setting was evaluated. This prospective, observational study analysed antimicrobial prescriptions, culture results and antimicrobial sensitivity testing (AST) of wound swabs and blood samples from patients with clinical signs of wound infections on the trauma ward. A total of 124 patients (n = 99, 79.8% male) with a median age of 30 years (IQR 23-39) were enrolled between October 2021 and January 2022. Wound infections were classified as nosocomial in 69% of the cases. Pathogens were isolated from 122 wound swabs, yielding 238 bacterial isolates. The most prevalent pathogens were gram-negative bacteria including Escherichia coli (n = 48, 20.2%) and Acinetobacter spp. (n = 43, 18.1%). Empiric treatment consisted of ceftriaxone and gentamicin which was administered to 67.2% (n = 78) and 62.1% (n = 72) of patients, respectively. High rates of antimicrobial resistance could be demonstrated across gram-negative and gram-positive species towards the most common empiric antibiotics. Following the AST results, over 95% (n = 111) of patients required a change of treatment. Our findings demonstrate that current empiric treatment for wound infections is missing its target in hospitalized patients in Kampala. To address the growing problem of AMR in Uganda, there is a pressing need to enhance diagnostic capacity and implement structured antimicrobial stewardship programs.

Individuals at risk for severe COVID-19 in whom ritonavir-containing therapies are contraindicated or may lead to interactions with concomitant medications: a retrospective analysis of German health insurance claims data

Background

Nirmatrelvir/ritonavir is authorized for the treatment of COVID-19 but has several contraindications and potential drug-drug interactions (pDDIs) due to ritonavir-induced irreversible inhibition of cytochrome P450 3A4. We aimed to assess the prevalence of individuals with one or more risk factors for severe COVID-19 along with contraindications and pDDIs due to ritonavir-containing COVID-19 therapy.

Methods

Retrospective observational study of individuals with one or more risk factors according to Robert Koch Institute criteria for severe COVID-19 according to German statutory health insurance (SHI) claims data from the pre-pandemic years 2018-2019 based on the German Analysis Database for Evaluation and Health Services Research. Prevalence was extrapolated to the entire SHI population using age-adjusted and sex-adjusted multiplication factors.

Results

Nearly 2.5 million fully insured adults, representing 61 million people in the German SHI population, were included in the analysis. In 2019, prevalence of individuals that would have been at risk of severe COVID-19 was 56.4%. Amongst them, the prevalence of contraindications for treatment with ritonavir-containing COVID-19 therapy was approximately 2% according to presence of somatic comorbidities (severe liver or kidney disease). Prevalence of intake of medicines contraindicated for their potential interactions with ritonavir-containing COVID-19 therapy was 16.5% according to Summary of Product Characteristics and 31.8% according to previously published data. The prevalence of individuals at risk of pDDIs during ritonavir-containing COVID-19 therapy without adjustment of their concomitant therapy was 56.0% and 44.3%, respectively. Prevalence data for 2018 were similar.

Conclusion

Administering ritonavir-containing COVID-19 therapy can be challenging as thorough medical record review and close monitoring are required. In some cases, ritonavir-containing treatment may not be appropriate due to contraindications, risk of pDDIs, or both. For those individuals, an alternative ritonavir-free treatment should be considered.

[Clostridioides difficile - New Insights and Therapy Recommendations]

After an increase in Clostridioides difficile infections (CDI) until 2013 due to epidemic ribotypes such as 027 and 078, CDI incidence in Germany is now declining, as confirmed by recent epidemiological data. Despite this success through antimicrobial stewardship and hospital hygiene, the burden of disease remains high, especially in older patients (>65 years) with comorbidities. The main risk factor for CDI is the use of broad-spectrum antibiotics, which disrupt the gut microbiota, allowing C. difficile colonization. Coinfection with other intestinal pathogens such as enterococci can further increase the virulence of C. difficile. The updated 2021 ESCMID guidelines recommend fidaxomicin instead of vancomycin as the antibiotic of choice for the treatment of CDI because of its lower recurrence rate. Vancomycin remains a good alternative; however, metronidazole should only be used if neither antibiotic is available. In the future, ridinilazole may be available as another therapeutic option that has a narrow spectrum of activity and low intestinal absorption. For the treatment of recurrent CDI, the new guidelines also include the use of the monoclonal antibody bezlotoxumab. In addition, a new oral microbiome therapy, SER-109 (capsules containing purified Firmicutes spores), which showed promising results in a phase 3 study, may provide an easy-to-administer alternative to fecal microbiota transplantation. Hopes for a well-performing toxoid vaccine for primary and secondary prevention of CDI have unfortunately not been fulfilled in the CLOVER trial.

Carbapenemase-producing Gram-negative bacteria in hospital wastewater, wastewater treatment plants and surface waters in a metropolitan area in Germany, 2020

Carbapenemase-producing bacteria (CPB) such as Klebsiella pneumoniae and Escherichia coli are causing hospital outbreaks worldwide. An important transfer route into the aquatic environment is the urban water cycle. We aimed to determine the presence of CPB in hospital wastewater, wastewater treatment plants (WWTPs) and surface waters in a German metropolitan area and to characterise these bacteria by whole-genome comparisons. During two periods in 2020, 366 samples were collected and cultivated on chromogenic screening media. Bacterial colonies were selected for species identification and PCR-based carbapenemase gene screening. Genomes of all detected CPB were sequenced and analysed for resistance gene content, followed by multilocus sequence typing (MLST) and core genome MLST (cgMLST) for K. pneumoniae and E. coli isolates. Carbapenemase genes were detected in 243 isolates, most of which belonged to genera/species Citrobacter spp. (n = 70), Klebsiella spp. (n = 57), Enterobacter spp. (n = 52) and E. coli (n = 42). Genes encoding KPC-2 carbapenemase were detected in 124 of 243 isolates. K. pneumoniae produced mainly KPC-2 and OXA-232 whereas E. coli harboured various enzymes (KPC-2, VIM-1, OXA-48, NDM-5, KPC-2 + OXA-232, GES-5, GES-5 + VIM-1, IMP-8 + OXA-48). Eight and twelve sequence types (STs) were identified for K. pneumoniae and E. coli, respectively, forming different clusters. The detection of numerous CPB species in hospital wastewater, WWTPs and river water is of concern. Genome data highlight a hospital-specific presence of distinct carbapenemase-producing K. pneumoniae and E. coli strains belonging to "global epidemic clones" in wastewater samples representing local epidemiology. The various detected CPB species including E. coli ST635, which is not known to cause human infections, could serve as reservoirs/vectors for the spread of carbapenemase genes in the environment. Therefore, effective pretreatment of hospital wastewater prior to discharge into the municipal wastewater system may be required, although swimming lakes do not appear to be a relevant risk factor for CPB ingestion and infection.

SARS-CoV-2 Vaccine Breakthrough Infections of Omicron and Delta Variants in Healthcare Workers

Understanding SARS-CoV-2 breakthrough infections in vaccinated healthcare workers is of key importance in mitigating the effects of the COVID-19 pandemic in healthcare facilities. An observational prospective cohort study was conducted in vaccinated employees with acute SARS-CoV-2 infection between October 2021 and February 2022. Serological and molecular testing was performed to determine SARS-CoV-2 viral load, lineage, antibody levels, and neutralizing antibody titers. A total of 571 (9.7%) employees experienced SARS-CoV-2 breakthrough infections during the enrolment period, of which 81 were included. The majority (n = 79, 97.5%) were symptomatic and most (n = 75, 92.6%) showed Ct values < 30 in RT-PCR assays. Twenty-four (30%) remained PCR-positive for > 15 days. Neutralizing antibody titers were strongest for the wildtype, intermediate for Delta, and lowest for Omicron variants. Omicron infections occurred at higher anti-RBD-IgG serum levels (p = 0.00001) and showed a trend for higher viral loads (p = 0.14, median Ct difference 4.3, 95% CI [-2.5-10.5]). For both variants, viral loads were significantly higher in participants with lower anti-RBD-IgG serum levels (p = 0.02). In conclusion, while the clinical course of infection with both the Omicron and Delta variants was predominantly mild to moderate in our study population, waning immune response over time and prolonged viral shedding were observed.

Chylothorax due to hepatic alveolar echinococcosis with infiltration of diaphragm and left pleura: a case report

BACKGROUND

Alveolar echinococcosis (AE) is an endemic parasitic zoonosis in Germany. In most cases, the liver is the primary organ affected.

CASE PRESENTATION

A 59-year old female patient presented with increasing exertional dyspnea and unintentional weight loss. A computed tomography (CT) scan showed a left-sided chylous pleural effusion and multiple intrahepatic masses with infiltration of the diaphragm and the pleura. The findings were initially misinterpreted as hepatocellular carcinoma (HCC) with infiltrating growth. Liver biopsy of one of the masses showed no evidence of malignancy, but an amorphous necrosis of unclear origin. HCC was further ruled out by magnetic resonance imaging (MRI). However, MRI findings were highly suspicious for hepatothoracic dissemination and complications due to AE. Typical histologic findings in a repeated and more specific examination of the liver tissue and a positive serology for echinococcosis confirmed the diagnosis of AE. As the hepatic and pulmonary manifestations were considered inoperable in a curative matter, an anti-parasitic treatment with albendazole was initiated. A video-assisted thoracoscopic surgery (VATS) with removal of the chylous effusion as well as a talc pleurodesis was performed to relieve the patient from dyspnea. Two months later, the patient was asymptomatic and a positron emission tomography (PET)-CT-scan with [18 F] fluoro-2-deoxy-d-glucose (FDG) showed a remarkable diminution of the hepatic manifestation.

CONCLUSIONS

This case demonstrates a rare presentation of alveolar echinococcosis with a focus on pulmonary symptoms, emphasizing the importance of evaluation for pulmonary involvement in patients with AE and respiratory symptoms.

Diagnostic Specificity of Two Dengue Virus IgG ELISAs after Yellow Fever and Japanese Encephalitis Virus Vaccination

Dengue virus (DENV) antibody assays frequently cross-react with sera from individuals who have been infected with or vaccinated against related flaviviruses. The goal of this study was to determine the specificity of two DENV ELISAs with sera from individuals vaccinated against yellow fever virus (YFV) and Japanese encephalitis virus (JEV). The Panbio and the Novatec Dengue IgG ELISAs were tested with sera obtained 3-4 weeks or 0.5-6 years after YFV or JEV vaccination and the diagnostic specificity of the assays was determined. As controls, the sera were tested using DENV, YFV, JEV, Zika and West Nile virus neutralization assays. The diagnostic specificity of the Panbio and the Novatec ELISA with sera from YFV-vaccinated subjects was 98.2% and 88.2%, respectively. Cross-reactions were rare in the first 4 weeks despite high YFV-neutralizing antibody titers and were mostly found later. The specificity of the Panbio and Novatec assays with sera from JEV-vaccinated individuals was 100% and 92.9%. Cross-reactions occurred in the early time period after vaccination. The measurement values of the two ELISAs correlated strongly. Thus, the Panbio ELISA showed higher diagnostic specificity and may be suitable for seroprevalence studies in areas with high disease prevalence.

Evaluation of the systemic and mucosal immune response induced by COVID-19 and the BNT162b2 mRNA vaccine for SARS-CoV-2

BACKGROUND

The currently used SARS-CoV-2 mRNA vaccines have proven to induce a strong and protective immune response. However, functional relevance of vaccine-generated antibodies and their temporal progression are still poorly understood. Thus, the central aim of this study is to gain a better understanding of systemic and mucosal humoral immune response after mRNA vaccination with BNT162b2.

METHODS

We compared antibody production against the S1 subunit and the RBD of the SARS-CoV-2 spike protein in sera of BNT162b2 vaccinees, heterologous ChAdOx1-S/BNT162b2 vaccinees and COVID-19 patients. We monitored the neutralizing humoral response against SARS-CoV-2 wildtype strain and three VOCs over a period of up to eight months after second and after a subsequent third vaccination.

RESULTS

In comparison to COVID-19 patients, vaccinees showed higher or similar amounts of S1- and RBD-binding antibodies but similar or lower virus neutralizing titers. Antibodies peaked two weeks after the second dose, followed by a decrease three and eight months later. Neutralizing antibodies (nAbs) poorly correlated with S1-IgG levels but strongly with RBD-IgGAM titers. After second vaccination we observed a reduced vaccine-induced neutralizing capacity against VOCs, especially against the Omicron variant. Compared to the nAb levels after the second vaccination, the neutralizing capacity against wildtype strain and VOCs was significantly enhanced after third vaccination. In saliva samples, relevant levels of RBD antibodies were detected in convalescent samples but not in vaccinees.

CONCLUSIONS

Our data demonstrate that BNT162b2 vaccinated individuals generate relevant nAbs titers, which begin to decrease within three months after immunization and show lower neutralizing potential against VOCs as compared to the wildtype strain. Large proportion of vaccine-induced S1-IgG might be non-neutralizing whereas RBD-IgGAM appears to be a good surrogate marker to estimate nAb levels. A third vaccination increases the nAb response. Furthermore, the systemic vaccine does not seem to elicit readily detectable mucosal immunity.

Predictive performance and clinical application of COV50, a urinary proteomic biomarker in early COVID-19 infection: a prospective multicentre cohort study

Background

The SARS-CoV-2 pandemic is a worldwide challenge. The CRIT-CoV-U pilot study generated a urinary proteomic biomarker consisting of 50 peptides (COV50), which predicted death and disease progression from SARS-CoV-2. After the interim analysis presented for the German Government, here, we aimed to analyse the full dataset to consolidate the findings and propose potential clinical applications of this biomarker.

Methods

CRIT-CoV-U was a prospective multicentre cohort study. In eight European countries (Austria, France, Germany, Greece, North Macedonia, Poland, Spain, and Sweden), 1012 adults with PCR-confirmed COVID-19 were followed up for death and progression along the 8-point WHO scale. Capillary electrophoresis coupled with mass spectrometry was used for urinary proteomic profiling. Statistical methods included logistic regression and receiver operating characteristic curve analysis with a comparison of the area under curve (AUC) between nested models. Hospitalisation costs were derived from the care facility corresponding with the Markov chain probability of reaching WHO scores ranging from 3 to 8 and flat-rate hospitalisation costs adjusted for the gross per capita domestic product of each country.

Findings

From June 30 to Nov 19, 2020, 228 participants were recruited, and from April 30, 2020, to April 14, 2021, 784 participants were recruited, resulting in a total of 1012 participants. The entry WHO scores were 1–3 in 445 (44%) participants, 4–5 in 529 (52%) participants, and 6 in 38 (4%) participants; and of all participants, 119 died and 271 had disease progression. The odds ratio (OR) associated with COV50 in all 1012 participants for death was 2·44 (95% CI 2·05–2·92) unadjusted and 1·67 (1·34–2·07) when adjusted for sex, age, BMI, comorbidities, and baseline WHO score; and for disease progression, the OR was 1·79 (1·60–2·01) when unadjusted and 1·63 (1·41–1·91) when adjusted (p<0·0001 for all). The predictive accuracy of the optimised COV50 thresholds was 74·4% (71·6–77·1%) for mortality (threshold 0·47) and 67·4% (64·4–70·3%) for disease progression (threshold 0·04). When adjusted for covariables and the baseline WHO score, these thresholds improved AUCs from 0·835 to 0·853 (p=0·033) for death and from 0·697 to 0·730 (p=0·0008) for progression. Of 196 participants who received ambulatory care, 194 (99%) did not reach the 0·04 threshold. The cost reductions associated with 1 day less hospitalisation per 1000 participants were million Euro (M€) 0·887 (5–95% percentile interval 0·730–1·039) in participants at a low risk (COV50 <0·04) and M€2·098 (1·839-2·365) in participants at a high risk (COV50 ≥0·04).

Interpretation

The urinary proteomic COV50 marker might be predictive of adverse COVID-19 outcomes. Even in people with mild-to-moderate PCR-confirmed infections (WHO scores 1–4), the 0·04 COV50 threshold justifies earlier drug treatment, thereby potentially reducing the number of days in hospital and associated costs.

Funding

German Federal Ministry of Health.

Recurrent bacteremia with a hypermucoviscous Escherichia coli isolated from a patient with perihilar cholangiocarcinoma: insights from a comprehensive genome-based analysis

Background

Escherichia coli (E. coli) is a common human pathogen, responsible for a broad spectrum of infections. Sites of infection can vary, but the hepato-biliary system is of particular concern due to the infection-associated formation of gallstones and the spread of pathogens from the bile ducts into the bloodstream.

Case presentation

The presented case is striking, as the detected isolate showed a positive string test. This hypermucoviscous phenotype is atypical for E. coli and a particular feature of hypervirulent Klebsiella pneumoniae (K. pneumoniae) variants.

Objectives

To provide new insights into the genomic background of an E. coli strain with an unusual hypermucoviscous phenotype using hybrid short- and long-read sequencing approaches.

Results

Complete hybrid assemblies of the E. coli genome and plasmids were done and used for genome based typing. Isolate 537–20 was assigned to the multilocus sequence type ST88 and serotype O8:H4. The strain showed a close relationship to avian pathogenic strains. Analysis of the chromosome and plasmids revealed the presence of several virulence factors, such as the Conserved Virulence Plasmidic (CVP) region on plasmid 537-20_1, including several iron acquisition genes (sitABCD, iroABCDEN, iucABCD, hbd) and the iutA gene encoding the receptor of the siderophore aerobactin. The hypermucoviscous phenotype could be caused by encapsulation of putative K. pneumoniae origin.

Conclusions

Hybrid sequencing enabled detailed genomic characterization of the hypermucoviscous E. coli strain, revealing virulence factors that have their putative origin in K. pneumoniae.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00521-7.

Fever in the Returning Traveler

BACKGROUND

It is predicted that approximately two billion tourist trips to foreign countries will be taken worldwide each year by 2030. Germany has long been among the most active countries in tourism. The frequency of illness among persons returning from developing and newly industrialized countries is 43-79%. The appropriate diagnosis of fever in returning travelers is a clinically important matter, as it can be a sign of a life-threatening illness.

METHODS

This review is based on publications (2001-2022) retrieved by a selective search in PubMed for studies on the epidemiology, diagnosis, and treatment of febrile illnesses in returning travelers, or on specific tropical diseases.

RESULTS

Diarrhea, fever, and skin changes are the most common manifestations of disease after travel to tropical and sub - tropical areas. The diagnostic evaluation should be performed in a series of steps, beginning with a precise travel history and the identification of specific risk factors. Among travelers returning from sub-Saharan Africa, Plasmodium falciparum malaria is the most common cause of fever on presentation to centers for infectious diseases and tropical medicine, affecting approximately 50 per 1000 travelers. Among persons returning from travel to Southeast Asia, dengue fever is the most common infectious disease, affecting 50-160 per 1000 travelers. Further potentially dangerous diseases include chikungunya and zika fever, typhoid and paratyphoid fever, amoebic liver abscess, visceral leishmaniasis (kala-azar), leptospirosis, and, very rarely, imported cases of viral hemorrhagic fever. COVID-19 and influenza are important differential diagnoses.

CONCLUSION

The differential diagnosis can be narrowed by thorough history-taking with particular attention to the patient's travel route, combined with a good knowledge of the geographic spread and incubation times of the main tropical diseases. Algorithms help clinicians to focus the diagnostic work-up and select the appropriate further laboratory tests and diagnostic procedures.

Poisoning by Plants

BACKGROUND

Questions on poisoning by plants are a common reason for inquiries to poison information centers (PIC). Over the years 2011-2020, plant poisoning was the subject of 15% of all inquiries to the joint poison information center in Erfurt, Germany (Gemeinsames Giftinformationszentrum Erfurt, GGIZ) that concerned poisoning in children (2.3% in adults). In this patient collective, plant poisoning occupied third place after medical drugs (32%) and chemical substances (24%), and was a more common subject of inquiry than mushroom poisoning (1.5%).

METHODS

This review is based on pertinent publications retrieved by a selective literature search in PubMed/TOXLINE on plant poisoning and on 12 epidemiologically and toxicologically relevant domestic species of poisonous plants in risk categories 2 and 3 (up to 2021).

RESULTS

Medical personnel should have basic toxicological knowledge of the following highly poisonous plants: wolfsbane (aconitum), belladonna, angel's trumpet, cowbane (cicuta virosa), autumn crocus, hemlock, jimson weed, henbane, castor bean (ricinus), false hellebore, foxglove (digitalis), and European yew. The intoxication is evaluated on the basis of a structured history (the "w" questions) and the clinical manifestations (e.g., toxidromes). Special analysis is generally not readily available and often expensive and time-consuming. In case of poisoning, a poison information center should be contacted for plant identification, risk assessment, and treatment recommendations. Specimens of plant components and vomit should be obtained, if possible, for further testing. Measures for the elimination of the poisonous substance may be indicated after a risk-benefit analysis. Specific antidotes are available for only a few types of plant poisoning, e.g., physostigmine for tropane alkaloid poisoning or digitalis antibodies for foxglove poisoning. The treatment is usually symptomatic and only rarely evidence-based. Individualized medical surveillance is recommended after the ingestion of large or unknown quantities of poisonous plant components.

CONCLUSION

The clinician should be able to recognize dangerous domestic species of poisonous plants, take appropriate initial measures, and avoid overdiagnosis and overtreatment. To improve patient care, systematic epidemiological and clinical studies are needed.

Bacterial contamination of the smartphones of healthcare workers in a German tertiary-care hospital before and during the COVID-19 pandemic

Background

Assuming that hygiene measures have improved significantly due to COVID-19, we aimed to investigate bacterial colonization on smartphones (SPs) owned by healthcare workers (HCWs) before and during the pandemic.

Methods

Employing a before-and-after study design, randomly selected HCWs were included. Devices underwent sampling under real-life conditions, without prior manipulation. Swabs were collected in 2012 (pre-pandemic) and 2021 to determine microbial colonization. Isolates were identified by MALDI-TOF mass spectrometry and underwent microbiological susceptibility testing.

Results

The final analysis included 295 HCWs (67% female, mean age 34 years) from 26 wards. Bacterial contamination was present on 293 of 295 SP screens (99.3%). The proportion of clinically relevant bacterial pathogens (eg Staphylococcus aureus, enterococci, Enterobacterales, non-fermenting bacteria) ranged from 21.2% in 2012 to 39.8% in 2021. Resistance profiles revealed a proportion of multidrug-resistant bacteria such as MRSA and VRE of less than 2%. The comparison of before-and-after sampling showed a significant increase in smartphone use during work from 2012 to 2021 with a simultaneous increase in cleaning intensity, probably as a result of the COVID-19 pandemic.

Conclusions

Bacterial contamination of SPs within the hospital is of concern and can serve as a source of cross-contamination. Hence, in addition to excellent hand hygiene, SPs must be carefully disinfected after handling in healthcare. Behavioral changes related to the COVID-19 pandemic could have a significant impact if implemented sustainably in everyday clinical practice.

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carbapenemase-carrying Klebsiella pneumoniae strain in Germany and show the value of contextual data. By screening about 10 000 genomes, over 400 000 metagenomes and two culture collections using in silico and in vitro methods, we identify a total of 415 closely related genomes reported in 28 studies. We identify the relationship between the two outbreaks through time-dated phylogeny, including their respective origin. One of the outbreaks presents extensive hidden transmission, with descendant isolates only identified in other studies. We then leverage the genome collection from this meta-analysis to identify genes under positive selection. We thereby identify an inner membrane transporter (ynjC) with a putative role in colistin resistance. Contextual data from other sources can thus enhance local genomic surveillance at multiple levels and should be integrated by default when available.

[Vaccinations]

Vaccination is considered one of the most important achievements of modern medicine and has saved millions of lives. As a result, the age-old fear of severe or fatal infectious diseases has largely been forgotten in society; however, the pandemic triggered by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shows how quickly this fear can return. Also, many people have reservations about medical measures, especially if they are directed against vague dangers. Paradoxically, the success of vaccinations jeopardizes the acceptance. To counteract this development, this article provides information on basic vaccination principles, legal frameworks and components of vaccines. It explains the most important categories, goals, core elements of vaccination programs and the most important recommendations of the Standing Committee on Vaccination at the Robert Koch Institute (STIKO). It explains the current state of knowledge with respect to required resources, assessment of vaccine reactions, complication management and possible vaccine damage.

Correlation of humoral immune responses to different SARS-CoV-2 antigens with virus neutralizing antibodies and symptomatic severity in a German COVID-19 cohort

Monitoring the humoral protective immune response and its durability after SARS-CoV-2 infections is essential for risk assessment of reinfections, the improvement of diagnostic methods and the evaluation of vaccine trials. We have analyzed neutralizing antibodies and IgG responses specific to different antigens, including the inactivated whole-virion of SARS-CoV-2, the spike subunit 1 protein and its receptor binding domain, as well as the nucleocapsid protein. We show the dynamic developments of the responses from the early convalescent stages up to 9 months post symptoms onset in follow-up samples from 57 COVID-19 patients with varying clinical severity. By correlating antibody signals to neutralizing titres, valid diagnostic markers for the estimation of neutralizing protection could be identified.

Clinical Relevance of Elevated Soluble ST2, HSP27 and 20S Proteasome at Hospital Admission in Patients with COVID-19

Although, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) represents one of the biggest challenges in the world today, the exact immunopathogenic mechanism that leads to severe or critical Coronavirus Disease 2019 (COVID-19) has remained incompletely understood. Several studies have indicated that high systemic plasma levels of inflammatory cytokines result in the so-called "cytokine storm", with subsequent development of microthrombosis, disseminated intravascular coagulation, and multiorgan-failure. Therefore, we reasoned those elevated inflammatory molecules might act as prognostic factors. Here, we analyzed 245 serum samples of patients with COVID-19, collected at hospital admission. We assessed the levels of heat shock protein 27 (HSP27), soluble suppressor of tumorigenicity-2 (sST2) and 20S proteasome at hospital admission and explored their associations with overall-, 30-, 60-, 90-day- and in-hospital mortality. Moreover, we investigated their association with the risk of ventilation. We demonstrated that increased serum sST2 was uni- and multivariably associated with all endpoints. Furthermore, we also identified 20S proteasome as independent prognostic factor for in-hospital mortality (sST2, AUC = 0.73; HSP27, AUC = 0.59; 20S proteasome = 0.67). Elevated sST2, HSP27, and 20S proteasome levels at hospital admission were univariably associated with higher risk of invasive ventilation (OR = 1.8; p < 0.001; OR = 1.1; p = 0.04; OR = 1.03, p = 0.03, respectively). These findings could help to identify high-risk patients early in the course of COVID-19.

Changes in antibiotic consumption, AMR and Clostridioides difficile infections in a large tertiary-care center following the implementation of institution-specific guidelines for antimicrobial therapy: A nine-year interrupted time series study

BACKGROUND

Institution-specific guidelines (ISGs) within the framework of antimicrobial stewardship programs offer locally tailored decision support taking into account local pathogen and resistance epidemiology as well as national and international guidelines.

OBJECTIVES

To assess the impact of ISGs for antimicrobial therapy on antibiotic consumption and subsequent changes in resistance rates and Clostridioides difficile infections (CDIs).

METHODS

The study was conducted at the Leipzig University Hospital, a 1,451-bed tertiary-care medical center, and covered the years 2012 to 2020. Since 2014, ISGs were provided to optimize empirical therapies, appropriate diagnostics, and antimicrobial prophylaxis. We used interrupted time series analysis (ITSA) and simple linear regression to analyze changes in antimicrobial consumption, resistance and CDIs.

RESULTS

Over the study period, 1,672,200 defined daily doses (DDD) of antibiotics were dispensed, and 85,645 bacterial isolates as well as 2,576 positive C. difficile cultures were collected. Total antimicrobial consumption decreased by 14% from 2012 to 2020, without clear impact of the deployment of ISGs. However, implementation of ISGs was associated with significant decreases in the use of substances that were rarely recommended (e.g., fluoroquinolones). Over the whole study period, we observed declining resistance rates to most antibiotic classes of up to 25% in Enterobacterales, staphylococci, and Pseudomonas aeruginosa. Switching from ceftriaxone to cefotaxime was associated with reduced resistance to third-generation cephalosporins. The number of CDI cases fell by 65%, from 501 in 2012 to 174 in 2020.

CONCLUSIONS

Well-implemented ISGs can have a significant, immediate, and lasting impact on the prescription behavior. ISGs might thereby contribute to reduce resistance rates and CDI incidences in the hospital setting.

Unhappy Triad: Infection with Leptospira spp. Escherichia coli and Bacteroides uniformis Associated with an Unusual Manifestation of Portal Vein Thrombosis

Portal vein thrombosis (PVT) is a rare disease with an incidence of 0.7/100,000 inhabitants per year. Septic PVT (pylephlebitis) usually occurs secondary to infection in the anatomic region drained by the portal venous system. We report on a 76-year-old German male who was admitted with a history of recurrent fever and acute renal failure. Blood cultures taken on admission showed Escherichia coli, as well as Bacteroides uniformis after an extended incubation period of 90 h. In addition, infection with Leptospira spp. was diagnosed serologically. Computerized tomography of the abdomen revealed an extensive PVT along with signs of colonic diverticulitis. Symptoms resolved under prolonged antimicrobial therapy with beta-lactams and adequate heparinization. A myeloproliferative disorder could be excluded. There was no evidence of an underlying coagulation disorder. Imaging controls showed an almost complete resolution of the PVT after 6 months of anticoagulation therapy. To the best of our knowledge, this is the first report of such an “unhappy triad,” which includes atypical manifestations of leptospirosis and involvement of other intestinal bacteria.

[Traveler's Diarrhea]

Travelers' diarrhea is the most common infectious disease in travel medicine. This article deals with epidemiology, diagnostics, prophylaxis and therapy. The causative pathogens, important differential diagnoses and indications for extended diagnostic measures are discussed in detail. Furthermore, aspects of travel medicine advice as well as the possibilities and limits of infection prevention are presented.

Medical Advice for Travelers

BACKGROUND

In 2019, 1.5 billion international tourist trips were counted worldwide. Germany, with 70.8 million vacations lasting ≥ 5 days, was one of the populations most willing to travel. These days, even elderly and multimorbid persons regularly travel long-distance, which can be associated with significant health risks. By advising travelers and implementing preventive measures, the risk of illness can be reduced significantly.

METHODS

A selective survey of PubMed was performed to identify publications on medical advice for travelers between 2000 and 2020. We included guidelines, studies, and recommendations that mainly deal with the preventive aspects of travel medicine and have a high level of practical relevance and the highest possible level of evidence. Previously published guidelines (based on the GRADE criteria) were adopted, and recommendations not based on the results of scientific studies were characterized as Good Clinical Practice (GCP).

RESULTS

Many medical recommendations for travelers still rely on individualized, experience-based, or consensus-based assessments. Apart from a review of medical history and vaccination status, a risk analysis is performed, travel fitness is evaluated individually, and a prevention plan is designed. Particular attention is devoted to malaria prophylaxis, vector protection, and traveler's diarrhea. Medical advice before travel is especially important for the elderly, children, pregnant women, the chronically ill, long-term and adventure travelers as well as migrants from malaria-endemic areas who are returning home.

CONCLUSION

The health risks associated with travel can be minimized by specialist medical advice. Many recommendations are empirical in nature and require further research.