SeqSero, launched in 2015, is a software tool for
serotype determination from whole-genome sequencing (WGS) data. Despite its routine use in public health and food safety laboratories in the United ...States and other countries, the original SeqSero pipeline is relatively slow (minutes per genome using sequencing reads), is not optimized for draft genome assemblies, and may assign multiple serotypes for a strain. Here, we present SeqSero2 (github.com/denglab/SeqSero2; denglab.info/SeqSero2), an algorithmic transformation and functional update of the original SeqSero. Major improvements include (i) additional sequence markers for identification of
species and subspecies and certain serotypes, (ii) a k-mer based algorithm for rapid serotype prediction from raw reads (seconds per genome) and improved serotype prediction from assemblies, and (iii) a targeted assembly approach for specific retrieval of serotype determinants from WGS for serotype prediction, new allele discovery, and prediction troubleshooting. Evaluated using 5,794 genomes representing 364 common U.S. serotypes, including 2,280 human isolates of 117 serotypes from the National Antimicrobial Resistance Monitoring System, SeqSero2 is up to 50 times faster than the original SeqSero while maintaining equivalent accuracy for raw reads and substantially improving accuracy for assemblies. SeqSero2 further suggested that 3% of the tested genomes contained reads from multiple serotypes, indicating a use for contamination detection. In addition to short reads, SeqSero2 demonstrated potential for accurate and rapid serotype prediction directly from long nanopore reads despite base call errors. Testing of 40 nanopore-sequenced genomes of 17 serotypes yielded a single H antigen misidentification.
Serotyping is the basis of public health surveillance of
It remains a first-line subtyping method even as surveillance continues to be transformed by whole-genome sequencing. SeqSero allows the integration of
serotyping into a whole-genome-sequencing-based laboratory workflow while maintaining continuity with the classic serotyping scheme. SeqSero2, informed by extensive testing and application of SeqSero in the United States and other countries, incorporates important improvements and updates that further strengthen its application in routine and large-scale surveillance of
by whole-genome sequencing.
Little is known about the microbial communities found in distribution centers (DCs), especially in those storing and handling food. As many foodborne bacteria are known to establish residence in food ...facilities, it is reasonable to assume that DCs handling foods are also susceptible to pathogen colonization. To investigate the microbial communities within DCs, 16S amplicon sequencing was completed on 317 environmental surface sponge swabs collected in DCs (
= 18) across the United States. An additional 317 swabs were collected in parallel to determine if any viable
species were also present at each sampling site. There were significant differences in median diversity measures (observed, Shannon, and Chao1) across individual DCs, and top genera across all reads were
_A,
,
_E,
, and
based on taxonomic classifications using the Genome Taxonomy Database. Of the 39 16S samples containing
ASVs, four of these samples had corresponding
positive microbiological samples. Data indicated a predominance of ASVs identified as cold-tolerant bacteria in environmental samples collected in DCs. Differential abundance analysis identified
,
, and
present at a significantly greater abundance in
positive microbiological compared to those negative for
. Additionally, microbiome composition varied significantly across groupings within variables (e.g., DC, season, general sampling location).
For decades, quaternary ammonium compounds (QAC)-based sanitizers have been broadly used in food processing environments to control foodborne pathogens such as Listeria monocytogenes. Still, there is ...a lack of consensus on the likelihood and implication of reduced
susceptibility to benzalkonium chloride (BC) that may emerge due to sublethal exposure to the sanitizers in food processing environments. With a focus on fresh produce processing, we attempted to fill multiple data and evidence gaps surrounding the debate. We determined a strong correlation between tolerance phenotypes and known genetic determinants of BC tolerance with an extensive set of fresh produce isolates. We assessed BC selection on L. monocytogenes through a large-scale and source-structured genomic survey of 25,083 publicly available L. monocytogenes genomes from diverse sources in the United States. With the consideration of processing environment constraints, we monitored the temporal onset and duration of adaptive BC tolerance in both tolerant and sensitive isolates. Finally, we examined residual BC concentrations throughout a fresh produce processing facility at different time points during daily operation. While genomic evidence supports elevated BC selection and the recommendation for sanitizer rotation in the general context of food processing environments, it also suggests a marked variation in the occurrence and potential impact of the selection among different commodities and sectors. For the processing of fresh fruits and vegetables, we conclude that properly sanitized and cleaned facilities are less affected by BC selection and unlikely to provide conditions that are conducive for the emergence of adaptive BC tolerance in L. monocytogenes.
Our study demonstrates an integrative approach to improve food safety assessment and control strategies in food processing environments through the collective leveraging of genomic surveys, laboratory assays, and processing facility sampling. In the example of assessing reduced
susceptibility to a widely used sanitizer, this approach yielded multifaceted evidence that incorporates population genetic signals, experimental findings, and real-world constraints to help address a lasting debate of policy and practical importance.
Abstract
Background
Following relocation to our current institution we observed a 40% reduction in the incidence of T cell-induced colitis in our well-established mouse model of IBD. The objectives ...of this study were to: a) quantify and compare the colonic microbiota in healthy and colitic mice obtained from our current (TTUHSC) and former insitution (LSUHSC), and b) determine whether colonization of healthy mice housed at our current institution with feces from healthy or colitic mice from LSUHSC alters the incidence and/or severity of colitis.
Methods
DNA from frozen feces was isolated using standard protocols and 16S rRNA sequencing was performed using the Illumina MiSeq platform. For some studies, RAG1−/−mice were colonized (via gastric gavage) with 40 mg donor feces 1 week prior to adoptive transfer of naïve (CD4+CD45RBhigh) T-cells.
Results
Intestinal microbial populations are markedly different between the two institutions in healthy and colitic animals. Transplant of fecal microbiota from LSUHSC mice with chronic colitis into healthy RAG−/− recipients accelerates the onset, increases the incidence (>95%) and enhances the severity of chronic colitis following T cell transfer. However, colonization of healthy WT or RAG−/− mice (in the absence of T cell transfer) with colitic feces did not induce disease over the 8 week observation period.
Conclusion
We conclude that colonization of healthy RAG−/− mice with dysbiotic but nonpathogenic microbiota obtained from colitic mice markedly increases the incidence and severity of chronic colitis in the T cell transfer model.
Colorectal cancer is diagnosed progressively in employed patients due to screening programs and increasing retirement age. The objective of this study was to identify prognostic factors for return to ...work and work disability in patients with colorectal cancer.
The research protocol was published at PROSPERO with registration number CRD42017049757. A systematic review of cohort and case-control studies in colorectal cancer patients above 18 years, who were employed when diagnosed, and who had a surgical resection with curative intent were included. The primary outcome was return to work or work disability. Potentially prognostic factors were included in the analysis if they were measured in at least three studies. Risk of bias was assessed according to the QUality In Prognosis Studies tool. A qualitative synthesis analysis was performed due to heterogeneity between studies. Quality of evidence was evaluated according to Grading of Recommendation Assessment, Development and Evaluation.
Eight studies were included with a follow-up period of 26 up to 520 weeks. (Neo)adjuvant therapy, higher age, and more comorbidities had a significant negative influence on return to work. A previous period of unemployment, extensive surgical resection and postoperative complications significantly increased the risk of work disability. The quality of evidence for these prognostic factors was considered very low to moderate.
Health care professionals need to be aware of these prognostic factors to select patients eligible for timely intensified rehabilitation in order to optimize the return to work process and prevent work disability.
Patients with autoimmune hepatitis (AIH) almost invariably require lifelong immunosuppressive treatment. There is genuine concern about the efficacy and tolerability of the current standard ...combination therapy of prednisolone and azathioprine. Mycophenolate mofetil (MMF) has emerged as an alternative option. The aim of this study was to compare MMF to azathioprine as induction therapy for AIH.
In this 24-week, prospective, randomised, open-label, multicentre superiority trial, 70 patients with treatment-naive AIH received either MMF or azathioprine, both in combination with prednisolone. The primary endpoint was biochemical remission defined as normalisation of serum levels of alanine aminotransferase and IgG after 24 weeks of treatment. Secondary endpoints included safety and tolerability.
Seventy patients (mean 57.9 years SD 14.0; 72.9% female) were randomly assigned to the MMF plus prednisolone (n = 39) or azathioprine plus prednisolone (n = 31) group. The primary endpoint was met in 56.4% and 29.0% of patients assigned to the MMF group and the azathioprine group, respectively (difference, 27.4 percentage points; 95% CI 4.0 to 46.7; p = 0.022). The MMF group exhibited higher complete biochemical response rates at 6 months (72.2% vs. 32.3%; p = 0.004). No serious adverse events occurred in patients who received MMF (0%) but serious adverse events were reported in four patients who received azathioprine (12.9%) (p = 0.034). Two patients in the MMF group (5.1%) and eight patients in the azathioprine group (25.8%) discontinued treatment owing to adverse events or serious adverse events (p = 0.018).
In patients with treatment-naive AIH, MMF with prednisolone led to a significantly higher rate of biochemical remission at 24 weeks compared to azathioprine combined with prednisolone. Azathioprine use was associated with more (serious) adverse events leading to cessation of treatment, suggesting superior tolerability of MMF.
This randomised-controlled trial directly compares azathioprine and mycophenolate mofetil, both in combination with prednisolone, for the induction of biochemical remission in treatment-naive patients with autoimmune hepatitis. Achieving complete remission is desirable to prevent disease progression. Patients assigned to the mycophenolate mofetil group reached biochemical remission more often and experienced fewer adverse events. The findings in this trial may contribute to the re-evaluation of international guidelines for the standard of care in treatment-naive patients with autoimmune hepatitis.
#NCT02900443.
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•Limited efficacy and tolerability of standard prednisolone and azathioprine combination therapy in autoimmune hepatitis.•Mycophenolate mofetil combined with prednisolone is effective as first-line therapy for achieving biochemical remission.•Mycophenolate mofetil has a more favourable tolerability profile than azathioprine.
Despite the adoption of minimally invasive techniques, recovery after abdominal surgery takes a long time. Electronic health (eHealth) modalities can provide guidance to patients, facilitating early ...return to normal activities. We aimed to assess the impact of a personalised eHealth programme on patients' return to normal activities after major abdominal surgery.
This single-blind, randomised, placebo-controlled trial was done at 11 teaching hospitals in the Netherlands. Eligible participants were aged 18–75 years who underwent a laparoscopic or open colectomy or hysterectomy. An independent researcher randomly allocated participants (in a 1:1 ratio) to either the intervention or control group by use of computer-based randomisation lists, with stratification by sex, type of surgery, and hospital. Participants in the intervention group had access to a perioperative, personalised eHealth programme consisting of both standard face-to-face care and eHealth, that comprised interactive tools offering goal attainment and a personalised outcome measurement, which managed recovery expectations and provided postoperative guidance tailored to each patient. Patients were provided with an activity tracker and had access to a website and mobile app with an electronic consultation (eConsult) functionality. The control group received standard care and access to a placebo website containing recovery advice provided by the hospital. The primary outcome was the number of days between surgery and personalised return to normal activities, assessed with Kaplan-Meier curves. Intention-to-treat and per-protocol analyses were done with a Cox regression model. This trial is registered with the Netherlands National Trial Register (NTR5686).
Between Feb 11, 2016, and Aug 9, 2017, 355 participants were randomly assigned to the intervention (n=178) or control (n=177) groups. 342 participants were included in the intention-to-treat analysis. The median time until return to normal activities was 52 days (IQR 33–111) in the intervention group, and 65 days (39–152) in the control group (adjusted hazard ratio 1·30 95% CI 1·03–1·64; p=0·027). The frequency of postoperative complications did not differ between groups.
This eHealth programme, delivering personalised care based on goal attainment scaling, enabled patients to return to their normal activities 13 days earlier than those who received standard care.
ZonMw.
Autoimmune hepatitis (AIH) is a rare, chronic inflammatory disease of the liver. The treatment goal is reaching complete biochemical response (CR), defined as the normalisation of aspartate and ...alanine aminotransferases and immunoglobulin gamma. Ongoing AIH activity can lead to fibrosis and (decompensated) cirrhosis. Incomplete biochemical response is the most important risk factor for liver transplantation or liver-related mortality. First-line treatment consists of a combination of azathioprine and prednisolone. If CR is not reached, tacrolimus (TAC) or mycophenolate mofetil (MMF) can be used as second-line therapy. Both products are registered for the prevention of graft rejection in solid organ transplant recipients. The aim of this study is to compare the effectiveness and safety of TAC and MMF as second-line treatment for AIH.
The TAILOR study is a phase IIIB, multicentre, open-label, parallel-group, randomised (1:1) controlled trial performed in large teaching and university hospitals in the Netherlands. We will enrol 86 patients with AIH who have not reached CR after at least 6 months of treatment with first-line therapy. Patients are randomised to TAC (0.07 mg/kg/day initially and adjusted by trough levels) or MMF (max 2000 mg/day), stratified by the presence of cirrhosis at inclusion. The primary endpoint is the difference in the proportion of patients reaching CR after 12 months. Secondary endpoints include the difference in the proportion of patients reaching CR after 6 months, adverse effects, difference in fibrogenesis, quality of life and cost-effectiveness.
This is the first randomised controlled trial comparing two second-line therapies for AIH. Currently, second-line treatment is based on retrospective cohort studies. The rarity of AIH is the main issue in clinical research for alternative treatment options. The results of this trial can be implemented in existing international clinical guidelines.
ClinicalTrials.gov NCT05221411 . Retrospectively registered on 3 February 2022; EudraCT number 2021-003420-33. Prospectively registered on 16 June 2021.
Currently, the standard therapy for autoimmune hepatitis (AIH) consists of a combination of prednisolone and azathioprine. However, 15% of patients are intolerant to azathioprine which necessitates ...cessation of azathioprine or changes in therapy. In addition, not all patients achieve complete biochemical response (CR). Uncontrolled data indicate that mycophenolate mofetil (MMF) can induce CR in a majority of patients. Better understanding of first-line treatment and robust evidence from randomised clinical trials are needed. The aim of this study was to explore the potential benefits of MMF as compared to azathioprine, both combined with prednisolone, as induction therapy in a randomised controlled trial in patients with treatment-naive AIH.
CAMARO is a randomised (1:1), open-label, parallel-group, multicentre superiority trial. All patients with AIH are screened for eligibility. Seventy adult patients with AIH from fourteen centres in the Netherlands and Belgium will be randomised to receive MMF or azathioprine. Both treatment arms will start with prednisolone as induction therapy. The primary outcome is biochemical remission, defined as serum levels of alanine aminotransferase and immunoglobulin G below the upper limit of normal. Secondary outcomes include safety and tolerability of MMF and azathioprine, time to remission, changes in Model For End-Stage Liver Disease (MELD)-score, adverse events, and aspects of quality of life. The study period will last for 24 weeks.
The CAMARO trial investigates whether treatment with MMF and prednisolone increases the proportion of patients in remission compared with azathioprine and prednisolone as the current standard treatment strategy. In addition, we reflect on the challenges of conducting a randomized trial in rare diseases.
EudraCT 2016-001038-91 . Prospectively registered on 18 April 2016.
Support for guiding and monitoring postoperative recovery and resumption of activities is usually not provided to patients after discharge from the hospital. Therefore, a perioperative electronic ...health (eHealth) intervention ("ikherstel" intervention or "I recover" intervention) was developed to empower gynecological patients during the perioperative period. This eHealth intervention requires a need for further development for patients who will undergo various types of general surgical and gynecological procedures.
This study aimed to further develop the "ikherstel" eHealth intervention using Intervention Mapping (IM) to fit a broader patient population.
The IM protocol was used to guide further development of the "ikherstel" intervention. First, patients' needs were identified using (1) the information of a process evaluation of the earlier performed "ikherstel" study, (2) a review of the literature, (3) a survey study, and (4) focus group discussions (FGDs) among stakeholders. Next, program outcomes and change objectives were defined. Third, behavior change theories and practical tools were selected for the intervention program. Finally, an implementation and evaluation plan was developed.
The outcome for an eHealth intervention tool for patients recovering from abdominal general surgical and gynecological procedures was redefined as "achieving earlier recovery including return to normal activities and work." The Attitude-Social Influence-Self-Efficacy model was used as a theoretical framework to transform personal and external determinants into change objectives of personal behavior. The knowledge gathered by needs assessment and using the theoretical framework in the preparatory steps of the IM protocol resulted in additional tools. A mobile app, an activity tracker, and an electronic consultation (eConsult) will be incorporated in the further developed eHealth intervention. This intervention will be evaluated in a multicenter, single-blinded randomized controlled trial with 18 departments in 11 participating hospitals in the Netherlands.
The intervention is extended to patients undergoing general surgical procedures and for malignant indications. New intervention tools such as a mobile app, an activity tracker, and an eConsult were developed.
Netherlands Trial Registry NTR5686; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=5686.
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