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Descriptions of the small intestinal microbiota are deficient and conflicting. We aimed to get a reliable description of the jejunal bacterial microbiota by investigating samples from two separate jejunal segments collected from the luminal mucosa during surgery. Sixty patients with morbid obesity selected for elective gastric bypass surgery were included in this survey. Samples collected by rubbing a swab against the mucosa of proximal and mid jejunal segments were characterized both quantitatively and qualitatively using a combination of microbial culture, a universal quantitative PCR and 16S deep sequencing. Within the inherent limitations of partial 16S sequencing, bacteria were assigned to the species level. By microbial culture, 53 patients (88.3%) had an estimated bacterial density of < 1600 cfu/ml in both segments whereof 31 (51.7%) were culture negative in both segments corresponding to a bacterial density below 160 cfu/ml. By quantitative PCR, 46 patients (76.7%) had less than 10 4 bacterial genomes/ml in both segments. The most abundant and frequently identified species by 16S deep sequencing were associated with the oral cavity, most often from the Streptococcus mitis group, the Streptococcus sanguinis group, Granulicatella adiacens/para-adiacens, the Schaalia odontolytica complex and Gemella haemolysans/taiwanensis . In general, few bacterial species were identified per sample and there was a low consistency both between the two investigated segments in each patient and between patients. The jejunal mucosa of fasting obese patients contains relatively few microorganisms and a core microbiota could not be established. The identified microbes are likely representatives of a transient microbiota and there is a high degree of overlap between the most frequently identified species in the jejunum and the recently described ileum core microbiota.

The small bowel is responsible for most of the body’s nutritional uptake and for the development of intestinal and systemic tolerance towards microbes. Nevertheless, the human small bowel microbiota has remained poorly characterized, mainly owing to sampling difficulties. Sample collection directly from the distal ileum was performed during radical cystectomy with urinary diversion. Material from the ileal mucosa were analysed using massive parallel sequencing of the 16S rRNA gene. Samples from 27 Caucasian patients were included. In total 280 unique Operational Taxonomic Units were identified, whereof 229 could be assigned to a species or a species group. The most frequently detected bacteria belonged to the genera Streptococcus , Granulicatella , Actinomyces , Solobacterium , Rothia , Gemella and TM7(G-1) . Among these, the most abundant species were typically streptococci within the mitis and sanguinis groups, Streptococcus salivarius , Rothia mucilaginosa and Actinomyces from the A . meyeri/odontolyticus group . The amounts of Proteobacteria and strict anaerobes were low. The microbiota of the distal part of the human ileum is oral-like and strikingly different from the colonic microbiota. Although our patient population is elderly and hospitalized with a high prevalence of chronic conditions, our results provide new and valuable insights into a lesser explored part of the human intestinal ecosystem.

There has been a gradual increase in 16S deep sequencing studies on infectious disease materials. Management of bacterial DNA contamination is a major challenge in such diagnostics, particularly in low biomass samples. In this article, we investigate patterns of microbial DNA contamination in targeted 16S rRNA amplicon sequencing (16S deep sequencing) and demonstrate how this can be used to filter background bacterial DNA in diagnostic microbiology. We also investigate the importance of sequencing depth. We first determined the patterns of contamination by performing repeat 16S deep sequencing of negative and positive extraction controls. This process identified a few bacterial species dominating across all replicates but also a high intersample variability among low abundance contaminant species in replicates split before PCR amplification. Replicates split after PCR amplification yielded almost identical sequencing results. On the basis of these observations, we suggest using the abundance of the most dominant contaminant species to define a threshold in each clinical sample from where identifications with lower abundances possibly represent contamination. We evaluated this approach by sequencing of a diluted, staggered mock community and of bile samples from 41 patients with acute cholangitis and noninfectious bile duct stenosis. All clinical samples were sequenced twice using different sequencing depths. We were able to demonstrate the following: (i) The high intersample variability between sequencing replicates is caused by events occurring before or during the PCR amplification step. (ii) Knowledge about the most dominant contaminant species can be used to establish sample-specific cutoffs for reliable identifications. (iii) Below the level of the most abundant contaminant, it rapidly becomes very demanding to reliably discriminate between background and true findings. (iv) Adequate sequencing depth can be claimed only when the analysis also picks up background contamination. IMPORTANCE There has been a gradual increase in 16S deep sequencing studies on infectious disease materials. Management of bacterial DNA contamination is a major challenge in such diagnostics, particularly in low biomass samples. Reporting a contaminant species as a relevant pathogen may cause unnecessary antibiotic treatment or even falsely classify a noninfectious condition as a bacterial infection. Yet, there are few studies on how to filter contamination in clinical microbiology. Here, we demonstrate that sequencing of extraction controls will not reveal the full spectrum of contaminants that could occur in the associated clinical samples. Only the most abundant contaminant species were consistently detected, and we present how this can be used to set sample specific thresholds for reliable identifications. We believe this work can facilitate the implementation of 16S deep sequencing in diagnostic laboratories. The new data we provide on the patterns of microbial DNA contamination is also important for microbiome research.

Lower respiratory tract (LRT) infections, including community-acquired pneumonia (CAP), are a leading cause of hospital admissions and mortality. Molecular tests have the potential to optimize treatment decisions and management of CAP, but limited evidence exists to support their routine use. To determine whether the judicious use of a syndromic polymerase chain reaction (PCR)-based panel for rapid testing of CAP in the emergency department (ED) leads to faster, more accurate microbiological test result-based treatment. This parallel-arm, single-blinded, single-center, randomized clinical superiority trial was conducted between September 25, 2020, and June 21, 2022, in the ED of Haukeland University Hospital, a large tertiary care hospital in Bergen, Norway. Adult patients who presented to the ED with suspected CAP were recruited. Participants were randomized 1:1 to either the intervention arm or standard-of-care arm. The primary outcomes were analyzed according to the intention-to-treat principle. Patients randomized to the intervention arm received rapid syndromic PCR testing (BioFire FilmArray Pneumonia plus Panel; bioMérieux) of LRT samples and standard of care. Patients randomized to the standard-of-care arm received standard microbiological diagnostics alone. The 2 primary outcomes were the provision of pathogen-directed treatment based on a microbiological test result and the time to provision of pathogen-directed treatment (within 48 hours after randomization). There were 374 patients (221 males [59.1%]; median (IQR) age, 72 [60-79] years) included in the trial, with 187 in each treatment arm. Analysis of primary outcomes showed that 66 patients (35.3%) in the intervention arm and 25 (13.4%) in the standard-of-care arm received pathogen-directed treatment, corresponding to a reduction in absolute risk of 21.9 (95% CI, 13.5-30.3) percentage points and an odds ratio for the intervention arm of 3.53 (95% CI, 2.13-6.02; P < .001). The median (IQR) time to provision of pathogen-directed treatment within 48 hours was 34.5 (31.6-37.3) hours in the intervention arm and 43.8 (42.0-45.6) hours in the standard-of-care arm (mean difference, -9.4 hours; 95% CI, -12.7 to -6.0 hours; P < .001). The corresponding hazard ratio for intervention compared with standard of care was 3.08 (95% CI, 1.95-4.89). Findings remained significant after adjustment for season. Results of this randomized clinical trial indicated that routine deployment of PCR testing for LRT pathogens led to faster and more targeted microbial treatment for patients with suspected CAP. Rapid molecular testing could complement or replace selected standard, time-consuming, laboratory-based diagnostics. ClinicalTrials.gov Identifier: NCT04660084.

Purpose To perform an extensive investigation of the clinical features and long-term complications among the n  = 134 adults and children with nucleic acid amplification test (NAAT) verified SARS-CoV-2-infection in the immunologically naïve population of Ulvik, Norway, during the single variant B.1.1.7 outbreak in late January through February 2021. Methods Every infected person regardless of whether symptoms of COVID-19 were present was invited to answer a web-based questionnaire at two- and seven months after testing positive. The period from initial infection to the first questionnaire was assessed retrospectively, and the time points at two- and seven months were assessed prospectively. Results A total of 87 of 134 (65%) NAAT-positive persons answered the first questionnaire, of which 35/87 (40%) were children, and 74 of 87 (85%) answered the second questionnaire. Children experienced symptoms less often than adults during the acute phase of infection (51% (18/35) versus 81% (42/52) ( p  = .004)). At two-months follow-up 88% (53/60) of participants with symptoms during the acute phase, including all children, reported no longer having symptoms. Among those with persisting symptoms at seven months, fatigue (18/25) and insomnia (16/24) were common. Conclusion In an immunologically naïve population infected with the SARS-CoV-2 B.1.1.7 variant, the clinical features of acute phase symptoms were similar to previous studies. Children underwent asymptomatic infection more often than adults, and adults more often experienced persisting symptoms. Insomnia and fatigue were common complaints among those with persisting symptoms seven months after infection.

In outbreak investigations, obtaining a full overview of infected individuals within a population is seldom achieved. We here present an example where a single introduction of B1.1.7 SARS-CoV-2 within a rural community allowed for tracing of the virus from an introductor via dissemination through larger gatherings into households. The outbreak occurred before widespread vaccination, allowing for a “natural” outbreak development with community lockdown. We show through sequencing that the virus can infect up to five consecutive persons without gaining mutations, thereby showing that contact tracing seems more important than sequencing for local outbreak investigations in settings with few alternative introductory transmission pathways. We also show how larger households where a child introduced transmission appeared more likely to promote further spread of the virus compared to households with an adult as the primary introductor.

Background Community-acquired pneumonia (CAP) causes a large burden of disease. Due to difficulties in obtaining representative respiratory samples and insensitive standard microbiological methods, the microbiological aetiology of CAP is difficult to ascertain. With a few exceptions, standard-of-care diagnostics are too slow to influence initial decisions on antimicrobial therapy. The management of CAP is therefore largely based on empirical treatment guidelines. Empiric antimicrobial therapy is often initiated in the primary care setting, affecting diagnostic tests based on conventional bacterial culture in hospitalized patients. Implementing rapid molecular testing may improve both the proportion of positive tests and the time it takes to obtain test results. Both measures are important for initiation of pathogen-targeted antibiotics, involving rapid de-escalation or escalation of treatment, which may improve antimicrobial stewardship and potentially patient outcome. Methods Patients presenting to the emergency department of Haukeland University Hospital (HUH) in Bergen, Norway, will be screened for inclusion into a pragmatic randomised controlled trial (RCT). Eligible patients with a suspicion of CAP will be included and randomised to receive either standard-of-care methods (standard microbiological testing) or standard-of-care methods in addition to testing by the rapid and comprehensive real-time multiplex PCR panel, the BioFire® FilmArray® Pneumonia Panel plus (FAP plus ) (bioMérieux S.A., Marcy-l’Etoile, France). The results of the FAP plus will be communicated directly to the treating staff within ~2 h of sampling. Discussion We will examine if rapid use of FAP plus panel in hospitalized patients with suspected CAP can improve both the time to and the proportion of patients receiving pathogen-directed treatment, thereby shortening the exposure to unnecessary antibiotics and the length of hospital admission, compared to the standard-of-care arm. The pragmatic design together with broad inclusion criteria and a straightforward intervention could make our results generalizable to other similar centres. Trial registration ClinicalTrials.gov NCT04660084 . Registered on December 9, 2020

Background The COVID-19 pandemic was met with strict containment measures. We hypothesized that societal infection control measures would impact the number of hospital admissions for respiratory tract infections, as well as, the spectrum of pathogens detected in patients with suspected community acquired pneumonia (CAP). Methods This study is based on aggregated surveillance data from electronic health records of patients admitted to the hospitals in Bergen Hospital Trust from January 2017 through June 2021, as well as, two prospective studies of patients with suspected CAP conducted prior to and during the COVID-19 pandemic (pre-COVID cohort versus COVID cohort, respectively). In the prospective cohorts, microbiological detections were ascertained by comprehensive PCR-testing in lower respiratory tract specimens. Mann–Whitney’s U test was used to analyse continuous variables. Fisher’s exact test was used for analysing categorical data. The number of admissions before and during the outbreak of SARS-CoV-2 was compared using two-sample t-tests on logarithmic transformed values. Results Admissions for respiratory tract infections declined after the outbreak of SARS-CoV-2 (p < 0.001). The pre-COVID and the COVID cohorts comprised 96 and 80 patients, respectively. The proportion of viruses detected in the COVID cohort was significantly lower compared with the pre-COVID cohort [21% vs 36%, difference of 14%, 95% CI 4% to 26%; p = 0.012], and the proportion of bacterial- and viral co-detections was less than half in the COVID cohort compared with the pre-COVID cohort (19% vs 45%, difference of 26%, 95% CI 13% to 41%; p < 0.001). The proportion of bacteria detected was similar (p = 0.162), however, a difference in the bacterial spectrum was observed in the two cohorts. Haemophilus influenzae was the most frequent bacterial detection in both cohorts, followed by Streptococcus pneumoniae in the pre-COVID and Staphylococcus aureus in the COVID cohort. Conclusion During the first year of the COVID-19 pandemic, the number of admissions with pneumonia and the microbiological detections in patients with suspected CAP, differed from the preceding year. This suggests that infection control measures related to COVID-19 restrictions have an overall and specific impact on respiratory tract infections, beyond reducing the spread of SARS-CoV-2.

Background There is controversy about chronic health consequences of tick-borne infections, especially Lyme borreliosis. This study aims to assess whether general function, physical fitness and subjective health complaints are associated with tick bites or antibodies to Borrelia burgdorferi sensu lato in blood donors. Methods Sera from 1,213 blood donors at four different blood banks in Sogn and Fjordane county in western Norway were obtained during January to June 2010, and analysed for specific IgG and IgM antibodies. A questionnaire including questions on tick bites, subjective health complaints, general function and physical fitness was completed. Results Tick bites had been experienced by 65.7 % of the study population. 78 (6.4 %) were positive for IgG (9.7 % in men, 2.4 % in women), and 69 (5.7 %) for IgM (6.1 % in men, 5.1 % in women), verified by immunoblot. No association between number of experienced tick bites or seropositivity for Borrelia antibodies and subjective health complaints, reduced general function or reduced physical fitness was found. Conclusion The results do not support any association between tick bites or Borrelia antibodies and subjective health complaints in blood donors in an endemic area for Lyme borreliosis.

Background Antimicrobial resistance (AMR) is a global health threat with millions of deaths annually attributable to bacterial resistance. Effective antimicrobial stewardship programs are crucial for optimizing antibiotic use. This study aims to identify factors contributing to deviations from antibiotic treatment guidelines in hospitalized adults with suspected community-acquired pneumonia (CAP). Methods We conducted a prospective study at Haukeland University Hospital's Emergency Department in Bergen, Norway, from September 2020 to April 2023. Patients were selected from two cohorts, with data on clinical and microbiologic test results collected. We analysed adherence of antibiotic therapy to guidelines for the choice of empirical treatment and therapy duration using multivariate regression models to identify predictors of non-adherence. Results Of the 523 patients studied, 479 (91.6%) received empirical antibiotic therapy within 48 h of admission, with 382 (79.7%) adhering to guidelines. However, among the 341 patients included in the analysis of treatment duration adherence, only 69 (20.2%) received therapy durations that were consistent with guideline recommendations. Key predictors of longer-than-recommended therapy duration included a C-reactive protein (CRP) level exceeding 100 mg/L (RR 1.37, 95% CI 1.18–1.59) and a hospital stay longer than two days (RR 1.22, 95% CI 1.04–1.43). The primary factor contributing to extended antibiotic therapy duration was planned post-discharge treatment. No significant temporal trends in adherence to treatment duration guidelines were observed following the publication of the updated guidelines. Conclusion While adherence to guidelines for the choice of empirical antibiotic therapy was relatively high, adherence to guidelines for therapy duration was significantly lower, largely due to extended post-discharge antibiotic treatment. Our findings suggest that publishing updated guidelines alone is insufficient to change clinical practice. Targeted stewardship interventions, particularly those addressing discharge practices, are essential. Future research should compare adherence rates across institutions to identify factors contributing to higher adherence and develop standardized benchmarks for optimal antibiotic stewardship. Trial registration NCT04660084.