Rapid high-throughput processing of tissue samples for microbiological diagnosis of periprosthetic joint infections using bead-beating homogenization.

Enrichment of periprosthetic tissue samples in blood culture bottles (BCBs) for microbiological diagnosis of periprosthetic joint infections (PJI) is more reliable than the use of an enrichment broth. Nevertheless, the extremely time-consuming homogenization of the samples for BCB processing has so far limited its use, especially in high-throughput settings. We aimed to establish a highly scalable homogenization process of tissue samples for long-term incubation in BCBs. A protocol for homogenization of tissue samples using bead beating was established and validated. In a second step, the use of the homogenate for enrichment in BCBs was compared to the use of thioglycolate broth (TB) in terms of diagnostic accuracy using clinical tissue samples from 150 patients with suspected PJI. Among 150 analyzed samples, 35 samples met the microbiological criteria for PJI. Using BCB, 32 of 35 (91.4%) PJI were detected compared to 30 of 35 (85.7%) by TB. The use of BCB had a lower secondary contamination rate (2/115; 1.7% vs 4/115; 3.5%) but the trend was not significant due to low numbers of samples (P = 0.39). The time to process a batch of 12 samples using the established homogenization method was 23 ± 5 min (n = 10 batches). We established and validated a homogenization workflow that achieves the highest sensitivity in the microbiological diagnostic of PJI. The enrichment of the tissue homogenate in BCBs showed equally good results as the use of enrichment broth and allows semi-automated high-throughput processing while demonstrating lower contamination rates in our study.

Evidence of Bacterial Metabolism in Synovial Fluid of Patients With Graft Failure After Anterior Cruciate Ligament Reconstruction: A Microbiological Comparison of Primary Anterior Cruciate Ligament and Hamstring Tendon Autograft Ruptures.

PURPOSE: To investigate whether the bacterial presence in a primary ruptured native anterior cruciate ligament (ACL) differs from that in a ruptured hamstrings ACL autograft and whether low-grade infections cumulatively can be detected in the case of graft failure. METHODS: In a retrospective case-control study with prospectively collected data, synovial fluid aspirates and tissue samples of failed ACL grafts were examined for evidence of bacterial colonization and compared to samples of the native ACL in primary ACL reconstruction (ACLR) using microbiological culture, 16S rRNA-PCR and histopathological examination. Furthermore, synovial fluid aspiration was investigated for possible future biomarkers for a low-grade infection. RESULTS: A total of 112 consecutive patients undergoing primary ACLR without history of previous surgeries to the affected knee (n = 59) and revision ACLR after reconstruction with a hamstring tendon autograft (n = 53) were recruited from one center. No patient had a history or showed clinical signs of infection. A total of 389 samples were analyzed by culture. Bacteria were detected in 9.4% of patients with a graft rupture (n = 5/53) compared to 3.4% of patients with a primary ACL rupture (n = 2/59) showing no statistical difference (P = .192). One patient with a "true" low-grade infection was found in our study population, resulting in a prevalence of 1.9% (1/53) in the graft group. The percentage of polymorphonuclear leukocytes (PMN%) as a highly sensitive marker for joint infections was significantly higher in aspirated synovial fluid of graft ruptures (27% ± 3% vs 20% ± 4%; P = .032), as well as glucose levels were significantly lower (83 mg/dL ± 2 mg/dL vs 88 mg/dL ± 2 mg/dL; P = .042). CONCLUSIONS: Synovial fluid obtained before revision ACLR showed a higher percentage of polymorphonuclear leukocytes and lower glucose levels compared with primary ACLR, suggesting bacterial metabolism and demonstrating that the intra-articular milieu changes significantly after ACLR. Tissue samples of ACL grafts revealed a low-grade infection in one case, although overall cultivable bacterial presence did not differ significantly when compared to samples of a native ACL. LEVEL OF EVIDENCE: Level III, retrospective case-control study.

The tongue microbiome of young patients with chronic kidney disease and their healthy mothers.

OBJECTIVES: Oral microbiome plays a crucial role in the incidence and development of oral diseases. An altered intestinal microbiome has been reported in adults with chronic kidney disease (CKD). This study aimed to characterize the tongue microbiome of young patients with CKD compared to their healthy mothers to identify the influence of CKD-associated factors on resilient tongue ecosystem. MATERIAL AND METHODS: Thirty patients with CKD (mean age, 14.2 years; 16 males and 14 females) and generalized gingivitis were included in the study. Swabs of the posterior tongue were collected from the patients and 21 mothers (mean age 40.8 years). Next-generation sequencing of 16S rDNA genes was employed to quantitatively characterize microbial communities. RESULTS: The bacterial communities were similar in terms of richness and diversity between patients and mothers (p > 0.05). In patients with CKD, 5 core phyla, 20 core genera, and 12 core species were identified. CONCLUSIONS: The tongue microbiome of the study participants showed no relevant CKD-associated differences compared to their mothers and appears to be a highly preserved niche in the oral cavity. Differences observed in the abundance of individual species in this study could be attributed to the age rather than CKD, even after a mean disease duration of 11 years. CLINICAL RELEVANCE: CKD and its associated metabolic changes appear to have no detectable impact on the resilient tongue microbiome observed in young patients.

Association of ward-level antibiotic consumption with healthcare-associated Clostridioides difficile infections: an ecological study in five German university hospitals, 2017-2019.

OBJECTIVES: To analyse the influence of antibiotic consumption on healthcare-associated healthcare onset (HAHO) Clostridioides difficile infection (CDI) in a German university hospital setting. METHODS: Monthly ward-level antibiotic consumption measured in DDD/100 patient days (pd) and CDI surveillance data from five university hospitals in the period 2017 through 2019 were analysed. Uni- and multivariable analyses were performed with generalized estimating equation models. RESULTS: A total of 225 wards with 7347 surveillance months and 4 036 602 pd participated. With 1184 HAHO-CDI cases, there was a median incidence density of 0.17/1000 pd (IQR 0.03-0.43) across all specialties, with substantial differences among specialties. Haematology-oncology wards showed the highest median incidence density (0.67/1000 pd, IQR 0.44-1.01), followed by medical ICUs (0.45/1000 pd, IQR 0.27-0.73) and medical general wards (0.32/1000 pd, IQR 0.18-0.53). Multivariable analysis revealed carbapenem (mostly meropenem) consumption to be the only antibiotic class associated with increased HAHO-CDI incidence density. Each carbapenem DDD/100 pd administered increased the HAHO-CDI incidence density by 1.3% [incidence rate ratio (IRR) 1.013; 95% CI 1.006-1.019]. Specialty-specific analyses showed this influence only to be valid for haematological-oncological wards. Overall, factors like ward specialty (e.g. haematology-oncology ward IRR 2.961, 95% CI 2.203-3.980) or other CDI cases on ward had a stronger influence on HAHO-CDI incidence density (e.g. community-associated CDI or unknown association case in same month IRR 1.476, 95% CI 1.242-1.755) than antibiotic consumption. CONCLUSIONS: In the German university hospital setting, monthly ward-level carbapenem consumption seems to increase the HAHO-CDI incidence density predominantly on haematological-oncological wards. Furthermore, other patient-specific factors seem to be equally important to control HAHO-CDI.

Antimicrobial resistance of clinical Enterobacterales isolates from urine samples, Germany, 2016 to 2021.

IntroductionEmpirical therapy for the treatment of urinary tract infections should be tailored to the current distribution and susceptibility of potential pathogens to ensure optimal treatment.AimWe aimed to provide an up-to-date overview of the epidemiology and susceptibility of Enterobacterales isolated from urine in Germany.MethodsWe retrospectively analysed antimicrobial susceptibility data from 201,152 urine specimens collected between January 2016 and June 2021 from in- and outpatients. Multiple logistic regression analysis was used to evaluate the association between year of investigation and antibiotic resistance, adjusted for age, sex and species subgroup. Subgroup analyses were performed for midstream urine samples obtained from (i) female outpatients aged 15 to 50 years, (ii) female outpatients older than 50 years and (iii) male outpatients.ResultsResistance rates of less than 20% were observed for nitroxoline (3.9%), fosfomycin (4.6%), nitrofurantoin (11.7%), cefuroxime (13.5%) and ciprofloxacin (14.2%). Resistance to trimethoprim/sulfamethoxazole (SXT) (20.1%), amoxicillin-clavulanic acid (20.5%), trimethoprim (24.2%), pivmecillinam (29.9%) and ampicillin (53.7%) was considerably higher. In the subgroup of outpatient women aged 15-50 years, resistance rates were generally lower. Resistance rates of all antibiotics decreased from 2016 to 2021. Multiple logistic regression revealed the lowest adjusted odds ratio (ORadj) of 0.838 (95% confidence interval (CI): 0.819-0.858; p < 0.001) for pivmecillinam and the highest ORadj of 0.989 (95% CI: 0.972-1.007; p = 0.226) for nitrofurantoin.ConclusionsResistance has generally decreased over the past years, independent of sex, age and causative pathogen. Our data provide an important basis for empirical antibiotic recommendations in various settings and patient collectives.

Semitendinosus tendons are commonly contaminated with skin flora during graft harvest for anterior cruciate ligament reconstruction.

PURPOSE: To investigate the rate of bacterial contamination of semitendinosus (ST) tendons during graft harvest in anterior cruciate ligament reconstruction (ACLR), in order to precisely specify the underlying pathogens and obtain data on their susceptibility to potential antibiotics. METHODS: In a prospective study, a total of 59 consecutive patients undergoing primary ACLR were recruited from one centre. No patient had history of previous surgery to the knee or showed clinical signs of infection. Four tissue samples of harvested ST tendons for anterior cruciate ligament (ACL) autografts (case group; ST) were examined for evidence of bacterial colonisation and compared to four tissue samples of the native ACL as negative controls (control group; ACL). Three of the respective samples were subjected to cultural microbiological examination and one to 16S rRNA-PCR. Antibiotic susceptibility testing was performed for each pathogen that was identified. RESULTS: A total of 342 samples were analysed by culture. Significantly more patients showed a positive culture of the ST (33.9%; n = 20/59) compared to 3.4% of patients (n = 2/59) with positive culturing of the ACL (p < 0.0001). Including 16S rRNA-PCR, in a total of 42.4% (25/59) of patients, bacteria were detected in at least one ST sample either by PCR and/or culture. All species found (n = 33) belong to the typical skin flora with Staphylococcus epidermidis (39.4%; n = 13/33) being the most common species, followed by Staphylococcus capitis (24.2%; n = 8/33). All tested isolates (n = 29) were susceptible to vancomycin (29/29, 100%), 69% (n = 20/29) to oxacillin and 65.5% (n = 19/29) to clindamycin. CONCLUSION: ST autografts for ACLR were commonly contaminated with skin commensal bacteria during harvest. One-third of the isolates showed resistance to typical perioperative intravenous antibiotics, whereas all isolates were sensitive to vancomycin. Therefore, routine prophylactic decontamination of all hamstring autografts before implantation should be recommended, preferably with topical vancomycin. LEVEL OF EVIDENCE: Level III.

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021.

BackgroundTracking person-to-person SARS-CoV-2 transmission in the population is important to understand the epidemiology of community transmission and may contribute to the containment of SARS-CoV-2. Neither contact tracing nor genomic surveillance alone, however, are typically sufficient to achieve this objective.AimWe demonstrate the successful application of the integrated genomic surveillance (IGS) system of the German city of Düsseldorf for tracing SARS-CoV-2 transmission chains in the population as well as detecting and investigating travel-associated SARS-CoV-2 infection clusters.MethodsGenomic surveillance, phylogenetic analysis, and structured case interviews were integrated to elucidate two genetically defined clusters of SARS-CoV-2 isolates detected by IGS in Düsseldorf in July 2021.ResultsCluster 1 (n = 67 Düsseldorf cases) and Cluster 2 (n = 36) were detected in a surveillance dataset of 518 high-quality SARS-CoV-2 genomes from Düsseldorf (53% of total cases, sampled mid-June to July 2021). Cluster 1 could be traced back to a complex pattern of transmission in nightlife venues following a putative importation by a SARS-CoV-2-infected return traveller (IP) in late June; 28 SARS-CoV-2 cases could be epidemiologically directly linked to IP. Supported by viral genome data from Spain, Cluster 2 was shown to represent multiple independent introduction events of a viral strain circulating in Catalonia and other European countries, followed by diffuse community transmission in Düsseldorf.ConclusionIGS enabled high-resolution tracing of SARS-CoV-2 transmission in an internationally connected city during community transmission and provided infection chain-level evidence of the downstream propagation of travel-imported SARS-CoV-2 cases.

Microbiota-associated Risk Factors for Clostridioides difficile Acquisition in Hospitalized Patients: A Prospective, Multicentric Study.

BACKGROUND: Asymptomatic C. difficile colonization is believed to predispose to subsequent C. difficile infection (CDI). While emerging insights into the role of the commensal microbiota in mediating colonization resistance against C. difficile have associated CDI with specific microbial components, corresponding prospectively collected data on colonization with C. difficile are largely unavailable. METHODS: C. difficile status was assessed by GDH EIA and real-time PCR targeting the toxin A (tcdA) and B (tcdB) genes. 16S V3 and V4 gene sequencing results from fecal samples of patients tested positive for C. difficile were analyzed by assessing alpha and beta diversity, LefSe, and the Piphillin functional inference approach to estimate functional capacity. RESULTS: 1506 patients were recruited into a prospective observational study (DRKS00005335) upon admission into one of five academic hospitals. 936 of them provided fecal samples on admission and at discharge and were thus available for longitudinal analysis. Upon hospital admission, 5.5% (83/1506) and 3.7% (56/1506) of patients were colonized with toxigenic (TCD) and non-toxigenic C. difficile (NTCD), respectively. During hospitalization, 1.7% (16/936) acquired TCD. Risk factors for acquisition of TCD included pre-existing lung diseases, lower GI endoscopy and antibiotics. Species protecting against hospital-related C. difficile acquisition included Gemmiger spp., Odoribacter splanchnicus, Ruminococcus bromii and other Ruminococcus spp. Metagenomic pathway analysis identified steroid biosynthesis as the most underrepresented metabolic pathway in patients who later acquire C. difficile colonization. CONCLUSIONS: Gemmiger spp., Odoribacter splanchnicus, Ruminococcus bromii and other Ruminococci were associated with a decreased risk of C. difficile acquisition. CLINICAL TRIALS REGISTRATION: DRKS00005335.

Comparison of stool samples and rectal swabs with and without pre-enrichment for the detection of third-generation cephalosporin-resistant Enterobacterales (3GCREB).

To establish the optimal detection of third-generation cephalosporin-resistant Enterobacterales (3GCREB), the performance of four different screening methods has been investigated: stool samples without (A) and with (B) pre-enrichment and rectal swabs without (C) and with (D) pre-enrichment were contrasted. Pre-enrichment approaches (B and D) increased the detection of 3GCREB carriers by 29.4% (20/68 3GCREB carriers only found using pre-enrichment, p < 0.0001) compared to direct plating approaches (A and C). Moreover, the study demonstrates a minor advantage of stool samples in contrast to rectal swabs in both cases (with and without pre-enrichment). Registration number: DRKS00022520, 24 July 2020.

Clinical Impact of Rapid Species Identification From Positive Blood Cultures With Same-day Phenotypic Antimicrobial Susceptibility Testing on the Management and Outcome of Bloodstream Infections.

BACKGROUND: Timely availability of microbiological results from positive blood cultures is essential to enable early pathogen-directed therapy. The Accelerate Pheno system (ADX) is a novel technology using fluorescence in situ hybridization for rapid species identification (ID) and morphokinetic bacterial analysis for phenotypic antimicrobial susceptibility testing (AST), with promising results. Yet the impact of this technology on clinical management and patient outcome remains unclear. METHODS: We conducted a quasiexperimental before-and-after observational study and analyzed 3 groups with different diagnostic and therapeutic pathways following recent integration of ADX: conventional microbiological diagnostics with and without antimicrobial stewardship program (ASP) intervention, and rapid diagnostics (ADX in addition to conventional standard) with ASP intervention. Primary endpoints were time to adequate, to optimal and to step-down antimicrobial therapy. Secondary endpoints were antimicrobial consumption, in-hospital mortality, length of stay (LOS), and the incidence of Clostridioidesdifficile infection (CDI). RESULTS: Two hundred four patients (conventional diagnostics, n = 64; conventional diagnostics + ASP, n = 68; rapid diagnostics + ASP; n = 72) were evaluated. The use of ADX significantly decreased time from Gram stain to ID (median, 23 vs 2.2 hours, P < .001) and AST (median, 23 vs 7.4 hours, P < .001), from Gram stain to optimal therapy (median, 11 vs 7 hours, P = .024) and to step-down antimicrobial therapy (median, 27.8 vs 12 hours, P = .019). However, groups did not differ in antimicrobial consumption, duration of antimicrobial therapy, mortality, LOS, or incidence of CDI. CONCLUSIONS: Use of ADX significantly reduced time to ID and AST as well as time to optimal antimicrobial therapy but did not affect antimicrobial consumption and clinical outcome.

Clostridioides difficile infections in the intensive care unit: a monocentric cohort study.

INTRODUCTION: Patient-level data from Clostridioides difficile infections (CDI) treated in an intensive care setting is limited, despite the growing medical and financial burden of CDI. METHODS: We retrospectively analyzed data from 100 medical intensive care unit patients at the University Hospital Cologne with respect to demography, diagnostics, severity scores, treatment, and outcome. To analyze factors influencing response to treatment and death, a backward-stepwise multiple logistic regression model was applied. RESULTS: Patients had significant comorbidities including 26% being immunocompromised. The mean Charlson Comorbidity Index was 6.3 (10-year survival rate of 2.25%). At the time of diagnosis, the APACHE II was 17.4±6.3 (predicted mortality rate of 25%), and the ATLAS score was 5.2±1.9 (predicted cure rate of 75%). Overall, 47% of CDI cases were severe, 35% were complicated, and 23% were both. At least one concomitant antibiotic was given to 74% of patients. The cure rate after 10 and 90 days was 56% and 51%, respectively. Each unit increment in APACHE II score was associated with poorer treatment response (OR 0.931; 95% CI 0.872-0.995; p = 0.034). Age above 65 years was associated with death (OR 2.533; 95% CI 1.031-6.221; p = 0.043), and overall mortality at 90 days was 56%. CONCLUSIONS: CDI affects a high-risk population, in whom predictive scoring tools are not accurate, and outcomes are poor despite intensive treatment. Further research in this field is warranted to improve prediction scoring and patient outcomes.

Diagnostic challenges in infective endocarditis: is PET/CT the solution?

PURPOSE: Despite developments in both imaging and microbiological techniques, the final diagnosis of IE often remains challenging. In this single-center cohort study, we aimed to identify the specific indications for request of 18F-FDG-PET/CT in clinical practice and to evaluate the diagnostic benefit of this nuclear imaging technique. METHODS: A total of 235 patients with possible (n = 43) or definite (n = 192) IE according to the revised Duke criteria were prospectively studied from July 2013 until December 2016. Echocardiography was generally used as the primary cardiac imaging technique. All patients were treated by a multidisciplinary Endocarditis Team. Diagnostics with 18F-FDG-PET/CT were undertaken on request by at least one member of the multidisciplinary team when overall diagnostics were inconclusive. RESULTS: In 20 patients, 18F-FDG-PET/CT scan was performed for additional diagnostic evaluation. Hereof, 15 patients had a history of implanted cardiac prosthetic material. In six patients with definite IE, the use of 18F-FDG-PET/CT was helpful for further clarification of the diagnosis. In one patient with possible IE, the diagnosis could be reclassified to definite IE. In addition, one case of vertebral osteomyelitis as well as upper and lower leg abscesses and knee empyema were detectable as extracardiac foci. Furthermore, 18F-FDG-PET/CT leads to a modification of the management in five patients. CONCLUSION: Our findings support the utility of 18F-FDG-PET/CT as an adjunctive diagnostic tool especially in the evaluation of prosthetic valve-/cardiac device-related IE and for the detection of extracardiac foci in some cases. However, due to remaining limitations also of this imaging technique, a multidisciplinary clinical evaluation still remains the essential basis for the diagnostic assessment.

Use of an Enrichment Broth Improves Detection of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae in Clinical Stool Samples.

This study evaluated the impact of preenrichment on the detection of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) in clinical stool samples. ESBL-E were detected in 41 of 343 patients (12.0%). As 31.7% of the ESBL-E carriers were identified by preenrichment, only this additional diagnostic step significantly improved the detection of ESBL-E.

Evaluation of the Qiagen artus C. difficile QS-RGQ Kit for Detection of Clostridium difficile Toxins A and B in Clinical Stool Specimens.

We compared the Qiagen artus C. difficile QS-RGQ kit, a new nucleic acid amplification test for the detection of Clostridium difficile toxins in stool specimens, with the Cepheid Xpert C. difficile test. The sensitivity, specificity, positive predictive value, and negative predictive value for the Qiagen artus C. difficile QS-RGQ test were 100%, 89.5%, 60.9%, and 100%, and those for the Cepheid Xpert C. difficile test were 100%, 90%, 62.2%, and 100%, respectively.

Occurrence and trends of Clostridioides difficile infections in hospitalized patients: a prospective multicentre cohort study in six German university hospitals, 2016-2020.

BACKGROUND: For Clostridioides difficile infections (CDI) in Germany no longitudinal multicentre studies with standardized protocols for diagnosing CDI are available. Recent evaluations of general surveillance databases in Germany indicate a downward trend in CDI rates. We aimed to describe the actual burden and trends of CDI in German university hospitals from 2016 to 2020. METHODS: Our study is a prospective multicentre study covering six German university hospitals. We report the data in total, stratified by year, by medical specialty as well as by CDI severity. Multivariable regression analyses were performed to assess risk factors for severe CDI. RESULTS: We registered 3,780 CDI cases among 1,436,352 patients. The median length of stay (LOS) of CDI cases was 20 days (IQR 11-37) compared with a general LOS of 4.2 days. In-hospital all-cause mortality in CDI patients was 11.7% (n=444/3780), while mortality attributed to CDI was 0.4% (n=16/3761). CDI recurrence rate was comparatively low at 7.2%. The incidence density of severe healthcare-associated healthcare onset (HAHO)-CDI showed a significant decrease from 2.25/10,000 patient days (pd) in 2016 to 1.49/10,000 pd in 2020 (trend calculation p = 0.032). CONCLUSIONS: Compared with a European point-prevalence study in 2013/2014, where overall CDI incidence density was 11.2 cases/10,000 pd in Germany (EUCLID), we see in our study halved overall CDI rates of 5.6 cases/10,000 pd in 2020. Our study shows current data on the distribution of CDI cases in German university hospitals and thus provides international comparative data on the key indicators of CDI.

Parenting and caregiving duties as career challenges among clinical microbiologists: a cross-sectional survey.

Aim: To estimate the burden of parenting and caregiving duties among clinical microbiologists in Germany and to identify workplace-related support systems and barriers to engaging in career-relevant activities. Methods: A cross-sectional web-based survey was conducted. Participants were asked to answer 37 questions, of which 24 specifically addressed parenting and caregiving duties. Results: Only few workplace-related support systems are currently available, and experiences of job-related disadvantages were frequently reported (27 of 47; 57.4%). Main barriers were a lack of flexible working hours and reliable childcare. Sociocultural norms and a lack of role models were perceived as detrimental. Conclusion: More support systems and a credible culture of family friendliness are needed to prevent jeopardizing the academic potential of young parents.

Longitudinal variability in the urinary microbiota of healthy premenopausal women and the relation to neighboring microbial communities: A pilot study.

BACKGROUND: The understanding of longitudinal changes in the urinary microbiota of healthy women and its relation to intestinal microbiota is limited. METHODS: From a cohort of 15 premenopausal women without known urogenital disease or current symptoms, we collected catheter urine (CU), vaginal and periurethral swabs, and fecal samples on four visits over six months. Additionally, ten participants provided CU and midstream urine (MU) to assess comparability. Urine was subjected to expanded culture. 16S rRNA gene sequencing was performed on all urine, fecal, and selected vaginal and periurethral samples. Sequence reads were processed (DADA2 pipeline) and analyzed using QIIME 2 and R. RESULTS: Relative abundances of urinary microbiota were variable over 6-18 months. The degree of intraindividual variability of urinary microbiota was higher than that found in fecal samples. Still, nearly half of the observed beta diversity of all urine samples could be attributed to differences between volunteers (R2 = 0.48, p = 0.001). After stratification by volunteer, time since last sexual intercourse was shown to be a factor significantly contributing to beta diversity (R2 = 0.14, p = 0.001). We observed a close relatedness of urogenital microbial habitats and a clear distinction from intestinal microbiota in the overall betadiversity analysis. Microbiota compositions derived from MU differed only slightly from CU compositions. Within this analysis of low-biomass samples, we identified contaminating sequences potentially stemming from sequencing reagents. CONCLUSIONS: Results from our longitudinal cohort study confirmed the presence of a rather variable individual urinary microbiota in premenopausal women. These findings from catheter urine complement previous observations on temporal dynamics in voided urine. The higher intraindividual variability of urinary microbiota as compared to fecal microbiota will be a challenge for future studies investigating associations with urogenital diseases and aiming at identifying pathogenic microbiota signatures.

SARS-CoV-2 Infection in Fully Vaccinated Individuals of Old Age Strongly Boosts the Humoral Immune Response.

Prophylactic vaccination against SARS-CoV-2 is one of the most important measures to contain the COVID-19 pandemic. Recently, break-through infections following vaccination against this virus have been reported. Here, we describe the humoral immune response of break-through infections in fully vaccinated individuals of old age from an outbreak in a nursing home. In cooperation with the local health authority, blood samples from fully vaccinated and infected as well as fully vaccinated and uninfected residents of the nursing home were collected 4 weeks after the onset of the outbreak. The humoral immune response was determined in a neutralisation assay with replication-competent virus isolates and by a quantitative ELISA. In this outbreak a total of 23 residents and four health care workers were tested positive for SARS-CoV-2. Four residents were unvaccinated, including one with a severe course of disease who later severe disease course who later succumbed to infection. Despite their old age, all vaccinated residents showed no or only mild disease. Comparison of the humoral immune response revealed significantly higher antibody levels in fully vaccinated infected individuals compared to fully vaccinated uninfected individuals (p < 0.001). Notably, although only a minority of the vaccinated uninfected group showed neutralisation capacity against SARS-CoV-2, all vaccinated and infected individuals showed high-titre neutralisation of SARS-CoV-2 including the alpha and beta variant. Large SARS-CoV-2 outbreaks can occur in fully vaccinated populations, but seem to associate with mild disease. SARS-CoV-2 infection in fully vaccinated individuals is a strong booster of the humoral immune response providing enhanced neutralisation capacity against immune evasion variants.

Association between the dietary regimen and infection-related complications in neutropenic high-risk patients with cancer.

BACKGROUND: Many haematology/oncology departments still provide a germ-free diet for neutropenic patients (neutropenic diet, ND) to minimise pathogen exposure, even though evidence on benefits is missing. We analysed the effects of a standard diet (SD) in neutropenic high-risk patients with cancer while focussing on infection-related outcomes. PATIENTS AND METHODS: Based on the Cologne Cohort of Neutropenic Patients, we conducted a propensity score-matched case-control study in haematological/oncological patients with a period of neutropenia longer than five days treated at our department between January 2004 and December 2012 (implementation of SD in January 2008). We assessed the association between an SD and selected infection-related end-points in an adjusted multivariable regression model and time-to-event analysis. RESULTS: In total, 2086 neutropenic episodes (1043 per diet group) were included into analysis. The median days of neutropenia were 9 (interquartile range 7-16). The adjusted multivariable model revealed no association between the SD and severity and persistence of fever, death within 28 days, antibiotic treatment and weight loss >3 kg and a non-significant adjusted association between SD and duration of antibiotic treatment and blood stream infections. There was a significant association between SD and incidence of diarrhoea (odds ratio [OR], 0.55; 95% confidence interval [CI], 0.45-0.68; P < 0.001), nausea (OR, 0.53; 95% CI, 0.43-0.66; P < 0.001) and weight loss >1 kg (OR, 0.93; 95% CI, 0.89-0.98; P = 0.002) with fewer events in SD than in the ND group. The hazard ratios of SD for the analysed end-points were non-significant. CONCLUSION: In our study, the implementation of an SD for high-risk neutropenic patients with cancer was safe regarding infection-related end-points.

Incidence and predictive biomarkers of Clostridioides difficile infection in hospitalized patients receiving broad-spectrum antibiotics.

Trial enrichment using gut microbiota derived biomarkers by high-risk individuals can improve the feasibility of randomized controlled trials for prevention of Clostridioides difficile infection (CDI). Here, we report in a prospective observational cohort study the incidence of CDI and assess potential clinical characteristics and biomarkers to predict CDI in 1,007 patients ≥ 50 years receiving newly initiated antibiotic treatment with penicillins plus a beta-lactamase inhibitor, 3rd/4th generation cephalosporins, carbapenems, fluoroquinolones or clindamycin from 34 European hospitals. The estimated 90-day cumulative incidences of a first CDI episode is 1.9% (95% CI 1.1-3.0). Carbapenem treatment (Hazard Ratio (95% CI): 5.3 (1.7-16.6)), toxigenic C. difficile rectal carriage (10.3 (3.2-33.1)), high intestinal abundance of Enterococcus spp. relative to Ruminococcus spp. (5.4 (2.1-18.7)), and low Shannon alpha diversity index as determined by 16 S rRNA gene profiling (9.7 (3.2-29.7)), but not normalized urinary 3-indoxyl sulfate levels, predicts an increased CDI risk.