Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics

Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis

Improving sample efficiency and multi-agent communication in RL-based train rescheduling

We present preliminary results from our sixth placed entry to the Flatland international competition for train rescheduling, including two improvements for optimized reinforcement learning (RL) training efficiency, and two hypotheses with respect to the prospect of deep RL for complex real-world control tasks: first, that current state of the art policy gradient methods seem inappropriate in the domain of high-consequence environments; second, that learning explicit communication actions (an emerging machine-to-machine language, so to speak) might offer a remedy. These hypotheses need to be confirmed by future work. If confirmed, they hold promises with respect to optimizing highly efficient logistics ecosystems like the Swiss Federal Railways railway network

Campylobacter jejuni from Canine and Bovine Cases of Campylobacteriosis Express High antimicrobial Resistance Rates against (Fluoro)quinolones and Tetracyclines

Campylobacter (C.) spp. from poultry is the main source of foodborne human campylobacteriosis, but diseased pets and cattle shedding Campylobacter spp. may contribute sporadically as a source of human infection. As fluoroquinolones are one of the drugs of choice for the treatment of severe human campylobacteriosis, the resistance rates of C. jejuni and C. coli from poultry against antibiotics, including fluoroquinolones, are monitored within the European program on antimicrobial resistance (AMR) in livestock. However, much less is published on the AMR rates of C. jejuni and C. coli from pets and cattle. Therefore, C. jejuni and C. coli isolated from diseased animals were tested phenotypically for AMR, and associated AMR genes or mutations were identified by whole genome sequencing. High rates of resistance to (fluoro)quinolones (41%) and tetracyclines (61.1%) were found in C. jejuni (n = 29/66). (Fluoro)quinolone resistance was associated with the known point mutation in the quinolone resistance-determining region (QRDR) of gyrA, and tetracycline resistance was mostly caused by the tet(O) gene. These high rates of resistance, especially to critically important antibiotics in C. jejuni and C. coli, are worrisome not only in veterinary medicine. Efforts to preserve the effcacy of important antimicrobial treatment options in human and veterinary medicine have to be strengthened in the future

Dissociations of oral foci of infections with infectious complications and survival after haematopoietic stem cell transplantation

Introduction Haematopoietic stem cell transplantation (HSCT) recipients are at increased risk for severe infections. This study examined the associations of common oral infections with survival and infectious complications in HSCT recipients. Materials and methods All autologous and allogeneic HSCT recipients transplanted in the University Hospital of Basel, Switzerland, between 2008 and 2016 and referred to oral infection control pre-HSCT were included in this retrospective case-control study. All patients had a clinical and a panoramic radiological dental examination taken immediately prior to HSCT. Presence of acute or chronic oral foci of infections, decayed, missing or filled tooth index (DMFT) and radiological attachment loss (RAL) were examined. Survival and infections of the subjects were followed up for 6 months post-HSCT. Results Altogether 341 allogeneic and 125 autologous HSCT recipients were included in the study. Within 6 months post-HSCT, 47 (14%) of the allogeneic and 4 (3%) of the autologous recipients died. Oral foci of infections (acute or chronic), DMFT or periodontitis pre-HSCT were not associated with survival 6 months post-HSCT. Oral foci of infections were also not associated with hospital treated infectious diseases or blood culture positive bacteremia during the 6 month follow-up period. Untreated oral foci of infections were not associated with survival or severe infectious complications within 6 months post-HSCT. Conclusion The results of this study suggest that radical dental interventions to chronic oral infections could be postponed until post-HSCT.Peer reviewe

Aerococcus urinae - significance of detection in the paediatric urinary tract: a case series

Aerococcus urinae (A. urinae) is primarily recognized as a common pathogen in the geriatric population, causing urinary tract infection (UTI), sepsis, and endocarditis, predominantly in female patients. In the paediatric population, only a few case reports exist suggesting A. urinae causes malodorous urine in otherwise healthy boys. In this study, we investigated the spectrum of clinical and laboratory presentations of A. urinae detection in children. A retrospective, single-centre, case series including all patients with the detection of A. urinae during a 7-year study period. Patients with detection of A. urinae only in non-urogenital skin swabs were excluded. A total of 40 samples from 33 patients were identified of which 20 patients were included in the final analysis. The median (IQR) age was 6.8 (2.9-9.5) years; 18 (90%) patients were boys. Four patients were diagnosed with a UTI, six had malodorous urine without UTI, three were diagnosed with balanitis and seven showed A. urinae colonization in the urine culture. Urogenital disorders were present in 12 patients. Additional pathogens were detected in 13 patients. Recurrence of detection during our study period was observed in four (20%) patients. Conclusion: Beyond malodorous urine, A. urinae detection is associated with more severe presentations including UTI in the paediatric population. Pre-existing urogenital disorders were frequent, and therefore, a nephro-urological investigation should be considered in all cases of A. urinae detection in the paediatric population. What is Known: • Aerococcus urinae (A. urinae) is known to be a common pathogen in the geriatric population, causing urinary tract infection (UTI), sepsis, and endocarditis, predominantly in female patients. • In the paediatric population, A. urinae is mainly described as a low-grade pathogen. Some case reports describe A. urinae as the cause of extraordinary malodorous urine in otherwise healthy boys. What is New: • Beyond malodorous urine, A. urinae detection is associated with more severe presentations including UTI in the paediatric population. • A. urinae was mainly detected in boys with pre-existing urogenital disorders; therefore, a nephro-urological investigation should be considered in cases of A. urinae detection in the paediatric population. Keywords: CAKUT; Children; Malodorous; Pyelonephritis; Urinary tract infection; Urogenital disorder

Patient-Specific Three-Dimensional Composite Bone Models for Teaching and Operation Planning

Background: Orthopedic trauma care relies on two-dimensional radiograms both before and during the operation. Understanding the three-dimensional nature of complex fractures on plain radiograms is challenging. Modern fluoroscopes can acquire three-dimensional volume datasets even during an operation, but the device limitations constrain the acquired volume to a cube of only 12-cm edge. However, viewing the surrounding intact structures is important to comprehend the fracture in its context. We suggest merging a fluoroscope's volume scan into a generic bone model to form a composite full-length 3D bone model. Methods: Materials consisted of one cadaver bone and 20 three-dimensional surface models of human femora. Radiograms and computed tomography scans were taken before and after applying a controlled fracture to the bone. A 3D scan of the fracture was acquired using a mobile fluoroscope (Siemens Siremobil). The fracture was fitted into the generic bone models by rigid registration using a modified least-squares algorithm. Registration precision was determined and a clinical appraisal of the composite models obtained. Results: Twenty composite bone models were generated. Average registration precision was 2.0mm (range 1.6 to 2.6). Average processing time on a laptop computer was 35s (range 20 to 55). Comparing synthesized radiograms with the actual radiograms of the fractured bone yielded clinically satisfactory results. Conclusion: A three-dimensional full-length representation of a fractured bone can reliably be synthesized from a short scan of the patient's fracture and a generic bone model. This patient-specific model can subsequently be used for teaching, surgical operation planning, and intraoperative visualization purpose

Draft Genome Sequences of Enterococcus mundtii Strains Isolated from Beef Slaughterhouses in Kenya

We present here draft genome sequences of Enterococcus mundtii strains K7-EM, P2-EM, C11-EM, and H18-EM, which were isolated from slaughterhouse equipment, carcasses, and personnel of small- and medium-sized beef slaughterhouses in Kenya

Changing Face of Vaccination in Immunocompromised Hosts

Infection prevention is a key component of care and an important determinant of clinical outcomes in a diverse population of immunocompromised hosts. Vaccination remains a fundamental preventative strategy, and clear guidelines exist for the vaccination of immunocompromised individuals and close contacts. Unfortunately, adherence to such guidelines is frequently suboptimal, with consequent missed opportunities to prevent infection. Additionally, vaccination of immunocompromised individuals is known to produce responses inferior to those observed in immunocompetent hosts. Multiple factors contribute to this finding, and developing improved vaccination strategies for those at high risk of infectious complications remains a priority of care providers. Herein, we review potential factors contributing to vaccine outcomes, focusing on host immune responses, and propose a means for applying modern, innovative systems biology technology to model critical determinants of vaccination success. With influenza vaccine in solid organ transplants used as a case in point, novel means for stratifying individuals using a host "immunophenotype” are explored, and strategies for individualizing vaccine approaches tailored to safely optimize vaccine responses in those most at risk are discussed

Rapid Bacteria Detection from Patients' Blood Bypassing Classical Bacterial Culturing

Sepsis is a life-threatening condition mostly caused by a bacterial infection resulting in inflammatory reaction and organ dysfunction if not treated effectively. Rapid identification of the causing bacterial pathogen already in the early stage of bacteremia is therefore vital. Current technologies still rely on time-consuming procedures including bacterial culturing up to 72 h. Our approach is based on ultra-rapid and highly sensitive nanomechanical sensor arrays. In measurements we observe two clearly distinguishable distributions consisting of samples with bacteria and without bacteria respectively. Compressive surface stress indicates the presence of bacteria. For this proof-of-concept, we extracted total RNA from EDTA whole blood samples from patients with blood-culture-confirmed bacteremia, which is the reference standard in diagnostics. We determined the presence or absence of bacterial RNA in the sample through 16S-rRNA hybridization and species-specific probes using nanomechanical sensor arrays. Via both probes, we identified two clinically highly-relevant bacterial species i.e., Escherichia coli and Staphylococcus aureus down to an equivalent of 20 CFU per milliliter EDTA whole blood. The dynamic range of three orders of magnitude covers most clinical cases. We correctly identified all patient samples regarding the presence or absence of bacteria. We envision our technology as an important contribution to early and sensitive sepsis diagnosis directly from blood without requirement for cultivation. This would be a game changer in diagnostics, as no commercial PCR or POCT device currently exists who can do this