Christian Brandt

Universitätsklinikum Jena · Institut für Infektionsmedizin und Krankenhaushygiene

The global spread and diversification of multidrug-resistant Gram-negative (MRGN) bacteria poses major challenges to healthcare. In particular, carbapenem-resistant Klebsiella pneumoniae strains have been frequently identified in infections and hospital-wide outbreaks. The most frequently underlying resistance gene (blaKPC) has been spreading over...

Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenomic sequencin...

Metagenomic sequencing is a promising tool for clinical applications to study microbial composition in relation to disease or patient outcome. Alterations of the vaginal microbiome are associated with adverse pregnancy outcomes, like preterm premature rupture of membranes and preterm birth. Methodologically these samples often have to deal with low...

Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we use real-time, on-devic...

In response to the SARS-CoV-2 pandemic, a highly increased sequencing effort has been established worldwide to track and trace ongoing viral evolution. Technologies such as nanopore sequencing via the ARTIC protocol are used to reliably generate genomes from raw sequencing data as a crucial base for molecular surveillance. However, for many labs th...

Background Lipid formation from glycerol was previously found to be activated in Rhodotorula toruloides when the yeast was cultivated in a mixture of crude glycerol (CG) and hemicellulose hydrolysate (CGHH) compared to CG as the only carbon source. RNA samples from R. toruloides CBS14 cell cultures grown on either CG or CGHH were collected at diffe...

Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we used real-time, on-devi...

Campylobacter fetus subsp. venerealis ( Cfv ) causes bovine genital campylobacteriosis (BGC), a World Organization for Animal Health (WOAH)-listed trade-relevant disease characterized by severe reproductive losses, such as infertility, early embryonic death and abortion in cattle. BGC has significant economic implications that have prompted several...

Metallo-β-lactamases (MBL) are a threat to public health, since they dramatically limit the use of β-lactams. We report the isolation of a multidrug-resistant Hafnia paralvei strain from urine and a rectal swab of a female patient after allogeneic hematopoietic stem cell transplantation for myelodysplastic syndrome. Antimicrobial susceptibility tes...

Background Lipid formation from glycerol was previously found to be activated in Rhodotorula toruloides when the yeast was cultivated in a mixture of crude glycerol (CG) and hemicellulose hydrolysate (CGHH) compared to CG as the only carbon source. RNA samples from R. toruloides CBS14 cell cultures grown on either CG or CGHH were collected at diffe...

Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, devel...

Streptobacillus moniliformis is the main cause of human streptobacillosis, also known as rat-bite or Haverhill fever. A correct diagnosis might be delayed due to scarcity, non-specific symptoms, and difficulties in cultivating this fastidious organism. We report on an 85-year-old man with periprosthetic streptobacillosis, which manifested itself in...

Brucellosis poses a significant burden to human and animal health worldwide. Robust and harmonized molecular epidemiological approaches and population studies that include routine disease screening are needed to efficiently track the origin and spread of Brucella strains.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease-19 (COVID-19) is still challenging healthcare systems and societies worldwide. While vaccines are available, therapeutic strategies are developing and need to be adapted to each patient. Many clinical approaches focus on the repurposing of approved ther...

The phylogenetic tree of the Staphylococcus aureus complex consists of several distinct clades and the majority of human and veterinary S. aureus isolates form one large clade. In addition, two divergent clades have recently been described as separate species. One was named Staphylococcus argenteus, due to the lack of the “golden” pigment staphylox...

Rapid susceptibility testing of bacterial isolates is crucial for anti-infective therapy, especially in critical cases such as bacteriaemia and sepsis. Nevertheless, empiric therapy is often initiated immediately and without testing because two days and more pass between a positive blood culture and a susceptibility profile, so in the meantime, the...

The genus Rhodotorula includes basidiomycetous oleaginous yeast species. Rhodotorula babjevae can produce compounds of biotechnological interest such as lipids, carotenoids, and bio- surfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal e...

Metagenomic sequencing is promising for clinical applications to study microbial composition concerning disease or patient outcomes. Alterations of the vaginal microbiome are associated with adverse pregnancy outcomes, like preterm premature rupture of membranes and preterm birth. Methodologically these samples often have to deal with low relative...

[This corrects the article DOI: 10.3389/fgene.2021.711437.].

Background Streptobacillus moniliformis is the main cause of human streptobacillosis, also known as rat-bite or Haverhill fever. Generally transferred by bites or scratches of rats and other rodents or by rat-excrement polluted water, symptoms commonly start to appear after < 10 days and are highly variable. Due to scarcity, non-specific symptoms,...

The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this stu...

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 metagen...

The genus Rhodotorula includes basidiomycetous oleaginous yeast species. R. babjevae can produce compounds of biotechnological interest such as lipids, carotenoids and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and...

Newly sequenced genomes are often not noticed by potential stakeholders because submission to public databases is delayed, and search options are limited. However, the discovery of genomes can be vital: in pathogen outbreaks, fast updates are essential to coordinate containment efforts and prevent further spread. Here we introduce DarkQ, a message...

Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in Rhodosporidium toruloides and to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft of R. toruloides CBS 14, using a hybrid assembly approach, consi...

In response to the SARS-CoV-2 pandemic, a highly increased sequencing effort has been established worldwide to track and trace ongoing viral evolution. Technologies, such as nanopore sequencing via the ARTIC protocol are used to reliably generate genomes from raw sequencing data as a crucial base for molecular surveillance. However, for many labs t...

Background Acinetobacter baumannii ability to develop and acquire resistance makes it one of the most critical nosocomial pathogens globally. Whole-genome sequencing (WGS) was applied to identify the acquired or mutational variants of antimicrobial resistance (AMR) genes in 85 German A. baumannii strains utilizing Illumina technology. Additionally,...

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 more than ten thousand genomes, 500 thousa...

Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in R. toruloides and to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft of R. toruloides CBS 14, using a hybrid assembly approach, consisting of sho...

Infections with severe acute respiratory syndrome coronavirus 2 (SARSCoV- 2) can be asymptomatic, but they can also be accompanied by a variety of symptoms that result in mild to severe coronavirus disease-19 (COVID-19) and are sometimes associated with systemic symptoms. Although the viral infection originates in the respiratory system, it is uncl...

Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analys...

Background: After a year of the global SARS-CoV-2 pandemic, a highly dynamic genetic diversity is surfacing. Among nearly 1000 reported virus lineages, dominant lineages such as B.1.1.7 or B.1.351 attract media attention with questions regarding vaccine efficiency and transmission potential. In response to the pandemic, the Jena University Hospital...

Motivation Newly sequenced genomes are often not noticed by potential stakeholders because submission to public databases is delayed, and search options are limited. However, the discovery of genomes can be vital: In pathogen outbreaks, fast updates are essential to coordinate containment efforts and prevent spread. Results Here we introduce DarkQ...

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need...

Infections with SARS-CoV-2 lead to mild to severe coronavirus disease-19 (COVID-19) with systemic symptoms. Although the viral infection originates in the respiratory system, it is unclear how the virus can overcome the alveolar barrier, which is observed in severe COVID-19 disease courses. To elucidate the viral effects on the barrier integrity an...

Phages are among the most abundant and diverse biological entities on earth. Identification from sequence data is a crucial first step to understand their impact on the environment. A variety of bacteriophage identification tools have been developed over the years. They differ in algorithmic approach, results and ease of use. We, therefore, develop...

General: This is an optimized DNA isolation protocol adapted to the properties of bacteria isolated from biogas substrate and digestate, using NucleoBond® AXG Columns and NucleoBond® Buffer Set. The protocol reliably retrieves DNA of sufficient quality, length and yield. The performance has been validated on seven bacterial isolates from one biogas...

Background: Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenom...

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need...

Effective public health response to viral outbreaks such as SARS-CoV-2 is often informed by real-time PCR screening of large populations. Pooling samples can increase screening capacity. However, when a traditional pool is tested positive, all samples in the pool need individual retesting, which becomes ineffective at a higher proportion of positiv...

The SHV β-lactamases (BLs) have undergone strong allele diversification that changed their substrate specificities. Based on 147 NCBI entries for SHV alleles, in silico mathematical models predicted five positions as relevant for the β-lactamase inhibitor (BLI) resistant (2br) phenotype, 12 as relevant for the extended-spectrum BL (ESBL) (2be) phen...

Acinetobacter (A.) baumannii has gained global notoriety as a significant nosocomial pathogen because it is frequently associated with multi-drug resistance and hospital-based outbreaks. There is a substantial difference in the incidence of A. baumannii infections between different countries and within Germany. However, its continuous spread within...

Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analys...

Many recent microbial genome collections curate hundreds of thousands of genomes. This volume complicates many genomic analyses such as taxon assignment because the associated computational burden is substantial. However, the number of representatives of each species is highly skewed towards human pathogens and model organisms. Thus many genomes co...

Background: Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenom...

General: This is an DNA isolation protocol adapted to the properties of sludge samples from biogas and wastewater treatment plants. The protocol reliably retrieves metagenomic DNA of sufficient quality, length and yield. The performance has been validated on 20 different reactor plants. Observed Performance on 20 ONT runs using this protocol: It do...

MALDI-TOF mass spectrometry (MS) may be used as a rapid typing method for nosocomial pathogens. Here, we evaluated MALDI-TOF MS for discrimination of hospital outbreak-related clusters of Serratia marcescens and carbapenemase-producing Citrobacter freundii. Thirty-three S. marcescens isolates collected from neonatal intensive care unit (NICU) patie...

General: This is an DNA isolation protocol adapted to the properties of sludge samples from biogas and wastewater treatment plants. The protocol reliably retrieves metagenomic DNA of sufficient quality, length and yield. The performance has been validated on 20 different reactor plants. Observed Performance on 20 ONT runs using this protocol: It do...

A prospective cohort study (German Clinical Trial Registry, No. 00005273) was performed to determine pre-admission colonization rates, hospital acquisition risk factors, subsequent infection rates and colonization persistence including the respective molecular epidemiology and transmission rates of extended-spectrum β-lactamase (ESBL)-producing Ent...

Supporting tables and figures to the manuscript. (PDF)

Details of the isolates. (CSV)

Phylogeny of the E. coli isolates based on the ERIC-PCR band pattern. Analysis was performed applying the Dice similarity coefficient (0.5% optimization, 1% tolerance) using BioNumerics 7.6 software (Applied Math NV, Sint-Martens-Latem, Belgium). Tree construction was performed using the unweighted pair group method with arithmetic means (UPGMA). (...

Background: A foodborne outbreak of VIM carbapenemase-expressing Citrobacter freundii (CPC) occurred between February and June 2016 at a major university hospital in Germany. Methods: An explosive increase of CPC isolated from rectal swabs of patients during weekly routine screening led to the declaration of an outbreak. A hospital-wide prevalen...

Background: Healthcare-associated infections (HAI) are one of the leading complications in hospitalized patients and are associated with increased morbidity and mortality. There is no agreement about the frequency of HAIs caused by multidrug resistant organisms (MDROs) in Germany. The aim of this study was to analyse MIC distribution of all isolate...

The secretion of antimicrobial compounds is an ancient mechanism with clear survival benefits for microbes competing with other microorganisms. Consequently, mechanisms that confer resistance are also ancient and may represent an underestimated reservoir in environmental bacteria. In this context, β-lactamases (BLs) are of great interest due to the...

Streptococcus pneumoniae is a major pathogen that causes different invasive pneumococcal diseases (IPD). The pneumococcal polysaccharide capsule is a main virulence factor. More than 94 capsule types have been described, but only a limited number of capsule types accounted for the majority of IPD cases before the introduction of pneumococcal vaccin...

Aim: To countermeasure the global spread of β-lactamases, we developed a rapid molecular test for the highly variable OXA-β-lactamases that allows minimizing the time to effective treatment. Methods: OXA-mRNA was specifically enriched from total RNA using group-specific biotinylated DNA probes and streptavidin-coated magnetic beads. Phylogenetic...

Spurred by the latest EUCAST and CLSI recommendation to adjust antibiotic therapy on the basis of MICs instead of resistance mechanisms, we aimed to investigate the ability of CTX-M-1 and CTX-M-14 to achieve ceftazidime resistance under selective conditions. We exposed Escherichia coli transconjugants bearing natural plasmids that express CTX-M-1,...

Monitoring the rapid global spread of antimicrobial resistance requires an over-regional and fast surveillance tool. Data from major surveillance studies based on aggregated results of selected sentinel laboratories or retrospective strain collections are not available for the whole scientific community and are limited by time and region. Thus, we...

The current global spread of multi-resistant Gram-negatives, particularly extended spectrum β-lactamases expressing bacteria, increases the likelihood of inappropriate empiric treatment of critically ill patients with subsequently increased mortality. From a clinical perspective, fast detection of resistant pathogens would allow a pre-emptive corre...

Introduction: Monitoring global antimicrobial resistance trends is an essential basis for anticipating research strategies aiming to counter the threat of spreading antibiotic resistance. Surveillance systems provide accurate data but are restricted to limited time frames and regions and may therefore be not representative for global trends. Pubmed...