Reproducible responses of geochemical and microbial successional patterns in the subsurface to carbon source amendment.

Carbon amendments designed to remediate environmental contamination lead to substantial perturbations when injected into the subsurface. For the remediation of uranium contamination, carbon amendments promote reducing conditions to allow microorganisms to reduce uranium to an insoluble, less mobile state. However, the reproducibility of these amendments and underlying microbial community assembly mechanisms have rarely been investigated in the field. In this study, two injections of emulsified vegetable oil were performed in 2009 and 2017 to immobilize uranium in the groundwater at Oak Ridge, TN, USA. Our objectives were to determine whether and how the injections resulted in similar abiotic and biotic responses and their underlying community assembly mechanisms. Both injections caused similar geochemical and microbial succession. Uranium, nitrate, and sulfate concentrations in the groundwater dropped following the injection, and specific microbial taxa responded at roughly the same time points in both injections, including Geobacter, Desulfovibrio, and members of the phylum Comamonadaceae, all of which are well established in uranium, nitrate, and sulfate reduction. Both injections induced a transition from relatively stochastic to more deterministic assembly of microbial taxonomic and phylogenetic community structures based on 16S rRNA gene analysis. We conclude that geochemical and microbial successions after biostimulation are reproducible, likely owing to the selection of similar phylogenetic groups in response to EVO injection.

Diluted Fecal Community Transplant Restores Clostridioides difficile Colonization Resistance to Antibiotic-Perturbed Murine Communities.

Fecal communities transplanted into individuals can eliminate recurrent Clostridioides difficile infection (CDI) with high efficacy. However, this treatment is only used once CDI becomes resistant to antibiotics or has recurred multiple times. We sought to investigate whether a fecal community transplant (FCT) pretreatment could be used to prevent CDI altogether. We treated male C57BL/6 mice with either clindamycin, cefoperazone, or streptomycin and then inoculated them with the microbial community from untreated mice before challenge with C. difficile. We measured colonization and sequenced the V4 region of the 16S rRNA gene to understand the dynamics of the murine fecal community in response to the FCT and C. difficile challenge. Clindamycin-treated mice became colonized with C. difficile but cleared it naturally and did not benefit from the FCT. Cefoperazone-treated mice became colonized by C. difficile, but the FCT enabled clearance of C. difficile. In streptomycin-treated mice, the FCT was able to prevent C. difficile from colonizing. We then diluted the FCT and repeated the experiments. Cefoperazone-treated mice no longer cleared C. difficile. However, streptomycin-treated mice colonized with 1:102 dilutions resisted C. difficile colonization. Streptomycin-treated mice that received an FCT diluted 1:103 became colonized with C. difficile but later cleared the infection. In streptomycin-treated mice, inhibition of C. difficile was associated with increased relative abundance of a group of bacteria related to Porphyromonadaceae and Lachnospiraceae. These data demonstrate that C. difficile colonization resistance can be restored to a susceptible community with an FCT as long as it complements the missing populations. IMPORTANCE Antibiotic use, ubiquitous with the health care environment, is a major risk factor for Clostridioides difficile infection (CDI), the most common nosocomial infection. When C. difficile becomes resistant to antibiotics, a fecal microbiota transplant from a healthy individual can effectively restore the gut bacterial community and eliminate the infection. While this relationship between the gut bacteria and CDI is well established, there are no therapies to treat a perturbed gut community to prevent CDI. This study explored the potential of restoring colonization resistance to antibiotic-induced susceptible gut communities. We described the effect that gut bacterial community variation has on the effectiveness of a fecal community transplant for inhibiting CDI. These data demonstrated that communities susceptible to CDI can be supplemented with fecal communities but that the effectiveness depended on the structure of the community following the perturbation. Thus, a reduced bacterial community may be able to recover colonization resistance in patients treated with antibiotics.

Response-adapted anti-PD-1-based salvage therapy for Hodgkin lymphoma with nivolumab alone or in combination with ICE.

This phase 2 trial evaluated PET-adapted nivolumab alone or in combination with ifosfamide, carboplatin, and etoposide (NICE) as first salvage therapy and bridge to autologous hematopoietic cell transplantation (AHCT) in relapsed/refractory (RR) classical Hodgkin lymphoma (cHL). Patients with RR cHL received 240 mg nivolumab every 2 weeks for up to 6 cycles (C). Patients in complete response (CR) after C6 proceeded to AHCT, whereas patients with progressive disease at any point or not in CR after C6 received NICE for 2 cycles. The primary endpoint was CR rate per the 2014 Lugano classification at completion of protocol therapy. Forty-three patients were evaluable for toxicity; 42 were evaluable for response. Thirty-four patients received nivolumab alone, and 9 patients received nivolumab+NICE. No unexpected toxicities were observed after nivolumab or NICE. After nivolumab, the overall response rate (ORR) was 81%, and the CR rate was 71%. Among 9 patients who received NICE, all responded, with 8 (89%) achieving CR. At the end of protocol therapy, the ORR and CR rates were 93% and 91%. Thirty-three patients were bridged directly to AHCT, including 26 after Nivo alone. The 2-year progression-free survival (PFS) and overall survival in all treated patients (n = 43) were 72% and 95%, respectively. Among 33 patients who bridged directly to AHCT, the 2-year PFS was 94% (95% CI: 78-98). PET-adapted sequential salvage therapy with nivolumab/nivolumab+NICE was well tolerated and effective, resulting in a high CR rate and bridging most patients to AHCT without chemotherapy. This trial was registered at www.clinicaltrials.gov #NCT03016871.

An Osmotic Laxative Renders Mice Susceptible to Prolonged Clostridioides difficile Colonization and Hinders Clearance.

Antibiotics are a major risk factor for Clostridioides difficile infections (CDIs) because of their impact on the microbiota. However, nonantibiotic medications such as the ubiquitous osmotic laxative polyethylene glycol 3350 (PEG 3350) also alter the microbiota. Clinicians also hypothesize that PEG helps clear C. difficile. But whether PEG impacts CDI susceptibility and clearance is unclear. To examine how PEG impacts susceptibility, we treated C57BL/6 mice with 5-day and 1-day doses of 15% PEG in the drinking water and then challenged the mice with C. difficile 630. We used clindamycin-treated mice as a control because they consistently clear C. difficile within 10 days postchallenge. PEG treatment alone was sufficient to render mice susceptible, and 5-day PEG-treated mice remained colonized for up to 30 days postchallenge. In contrast, 1-day PEG-treated mice were transiently colonized, clearing C. difficile within 7 days postchallenge. To examine how PEG treatment impacts clearance, we administered a 1-day PEG treatment to clindamycin-treated, C. difficile-challenged mice. Administering PEG to mice after C. difficile challenge prolonged colonization up to 30 days postchallenge. When we trained a random forest model with community data from 5 days postchallenge, we were able to predict which mice would exhibit prolonged colonization (area under the receiver operating characteristic curve [AUROC] = 0.90). Examining the dynamics of these bacterial populations during the postchallenge period revealed patterns in the relative abundances of Bacteroides, Enterobacteriaceae, Porphyromonadaceae, Lachnospiraceae, and Akkermansia that were associated with prolonged C. difficile colonization in PEG-treated mice. Thus, the osmotic laxative PEG rendered mice susceptible to C. difficile colonization and hindered clearance. IMPORTANCE Diarrheal samples from patients taking laxatives are typically rejected for Clostridioides difficile testing. However, there are similarities between the bacterial communities from people with diarrhea and those with C. difficile infections (CDIs), including lower diversity than the communities from healthy patients. This observation led us to hypothesize that diarrhea may be an indicator of C. difficile susceptibility. We explored how osmotic laxatives disrupt the microbiota's colonization resistance to C. difficile by administering a laxative to mice either before or after C. difficile challenge. Our findings suggest that osmotic laxatives disrupt colonization resistance to C. difficile and prevent clearance among mice already colonized with C. difficile. Considering that most hospitals recommend not performing C. difficile testing on patients taking laxatives, and laxatives are prescribed prior to administering fecal microbiota transplants via colonoscopy to patients with recurrent CDIs, further studies are needed to evaluate if laxatives impact microbiota colonization resistance in humans.

Test and vaccinate or remove: Methodology and preliminary results from a badger intervention research project.

BACKGROUND: In the British Isles, it is generally accepted that the Eurasian badger (Meles meles) plays a role in the maintenance of bovine tuberculosis (bTB) in cattle. Non-selective culling is the main intervention method deployed in controlling bTB in badgers along with smaller scale Bacillus Calmette-Guérin (BCG) vaccination areas. This paper describes the use of selective badger culling combined with vaccination in a research intervention trial. METHODS: In Northern Ireland, a 100 km2 area was subjected to a test and vaccinate or remove (TVR) badger intervention over a 5-year period. Badgers were individually identified and tested on an annual basis. Physical characteristics and clinical samples were obtained from each unique badger capture event. RESULTS: A total of 824 badgers were trapped with 1520 capture/sampling events. There were no cage-related injuries to the majority of badgers (97%). A low level of badger removal was required (4.1%-16.4% annually), while 1412 BCG vaccinations were administered. A statistically significant downward trend in the proportion of test positive badgers was observed. CONCLUSION: This is the first project to clearly demonstrate the feasibility of cage side testing of badgers. The results provide valuable data on the logistics and resources required to undertake a TVR approach to control Mycobacterium bovis in badgers.

Quantifying intraherd cattle movement metrics: Implications for disease transmission risk.

There are a paucity of data quantifying on-farm management practices such as the frequency of intraherd cattle movements, use of consolidated or spatially fragmented grazing pastures, and duration of time cattle spend at grass with respect to biosecurity and disease transmission. Such movement dynamics are important when attempting to understand the maintenance of chronic infectious disease, such as bovine tuberculosis (bTB). We captured empirical data on daily cattle movements for a sample of eighteen farms throughout one complete grazing season (n = 18,988 grazing days) and assessed these attributes in relation to herd bTB risk. Dairy herds were stocked at significantly higher densities compared to beef production systems (6.6 animals/ha, 95 % confidence intervals (CI) 6.5-6.7 and 4.1 animals/ha, 95 %CI 4.1 - 4.1 respectively, p < 0.001). Most notably milking cows, were grazed at higher densities than other life stages (e.g. calves, heifers and bullocks) (p < 0.001) and experienced four times the number of movements between pastures. Beef cattle were more likely to be grazed across multiple (rather than single) fields (p < 0.001), with greater time spent on fragmented land away from the main/home farm (p < 0.001). None of the farm or herd attributes analysed (e.g. stocking density, frequency of movement, movement distances or land fragmentation) were associated with herd bovine tuberculosis (bTB) breakdowns during this study. However, there was a weak positive association between bTB breakdowns during the 3 years prior to the study and cattle movement distances (p = 0.05) and time spent on fragmented land (p = 0.08). After a bTB breakdown occurs, restrictions on animals moving out of these herds are implemented to control disease spread, yet we argue that more attention is needed on the role of intraherd grazing patterns in modelling disease transmission risk between herds.

Grazing cattle exposure to neighbouring herds and badgers in relation to bovine tuberculosis risk.

Bovine tuberculosis (bTB) can be spread between and among cattle and wildlife hosts e.g. European badger (Meles meles). The majority of cattle in the UK and Ireland are grazed during the summer, potentially exposing them to Mycobacterium bovis. 18 farms were surveyed (39% dairy, 61% beef; fields n = 697) for one grazing season (May-November 2016, n = 148,461 field days) to quantify the co-occurrence of cattle with badger setts and latrines and adjacency to neighbouring cattle herds. 3% (n = 24) of the fields had a badger sett or latrine recorded, dairy cattle were significantly more likely to co-occur with badger setts and latrines than beef cattle. Most farms (89%) grazed cattle adjacent to a neighbouring herd, which accounted for 18% of the grazing season. Potential exposure to neighbouring herds did not differ between production systems but did vary between life stages. A significant positive association between the proportion of time cattle spent grazing fields with setts present and the historic 1-, 3- and 5- year bTB status (p = 0.007, p = 0.013 and p = 0.013 respectively) was found. However, when cattle were grazed in fields with latrines, a significant negative association was found between the proportion of time cattle spent grazing fields with latrines present and the historic 3- and 5- year bTB status (p = 0.033 and p = 0.012 respectively). Historic bTB status and percentage of days spent beside a neighbouring herd was unrelated. Idiosyncrasies at farm-level and between risk factors indicated that individual farm assessments would be beneficial to understand potential exposure risk.

Interspecific visitation of cattle and badgers to fomites: A transmission risk for bovine tuberculosis?

In Great Britain and Ireland, badgers (Meles meles) are a wildlife reservoir of Mycobacterium bovis and implicated in bovine tuberculosis transmission to domestic cattle. The route of disease transmission is unknown with direct, so-called "nose-to-nose," contact between hosts being extremely rare. Camera traps were deployed for 64,464 hr on 34 farms to quantify cattle and badger visitation rates in space and time at six farm locations. Badger presence never coincided with cattle presence at the same time, with badger and cattle detection at the same location but at different times being negatively correlated. Badgers were never recorded within farmyards during the present study. Badgers utilized cattle water troughs in fields, but detections were infrequent (equivalent to one badger observed drinking every 87 days). Cattle presence at badger-associated locations, for example, setts and latrines, were three times more frequent than badger presence at cattle-associated locations, for example, water troughs. Preventing cattle access to badger setts and latrines and restricting badger access to cattle water troughs may potentially reduce interspecific bTB transmission through reduced indirect contact.

Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm.

Thalassospira sp. strain KO164 was isolated from eastern Mediterranean seawater and sediment laboratory microcosms enriched on insoluble organosolv lignin under oxic conditions. The near-complete genome sequence presented here will facilitate analyses into this deep-ocean bacterium's ability to degrade recalcitrant organics such as lignin.

Evaluation of a new disposable "tampon like" electrostimulation technology (Pelviva®) for the treatment of urinary incontinence in women: a 12-week single blind randomized controlled trial.

AIMS: To test the null hypothesis that a novel disposable "tampon like" electrostimulation device (Pelviva(®)) is no better than unsupervised pelvic floor muscle exercise for treatment of urinary incontinence in women. METHODS: Pre/post-intervention assessor blinded, single center RCT. A total of 123 community dwelling self referred women with symptoms of stress, urge, or mixed incontinence were randomly assigned to one of two 12-week duration treatments: Pelviva(®) used for 30 min a day plus unsupervised pelvic floor muscle exercise or unsupervised exercises alone. Outcome measures included ICIQ-UI (primary), ICIQ FLUTSex and global impression of severity and improvement (secondary) completed at recruitment, after 4 weeks of unsupervised exercise and immediately post-treatment. Diary of exercise frequency/type, overall impression, and usage of device was completed mid- and post-treatment. RESULTS: Pelviva(®) plus exercise produced significantly better outcome than unsupervised exercise alone: 5 points (45%) versus 1 point (10%) for ICIQ-UI (P = 0.014); 67% versus 33% for leak frequency (P = 0.005); 40% versus 20% for leak interference with life (P = 0.018). Incontinence was less bothersome during sex to a greater extent in the Pelviva(®) group (P = 0.026). Women were enthusiastic about the device, found it comfortable/easy to use and experienced no adverse events. CONCLUSIONS: The Pelviva(®) device plus unsupervised exercise is more successful than unsupervised pelvic floor muscle exercise alone in treating urinary incontinence. The device is easy/comfortable to use, there are no apparent adverse incidents, and women can manage their incontinence in the privacy of their own home. The product will be launched 2013.

Quantitative analysis of minimal residual disease predicts relapse in children with B-lineage acute lymphoblastic leukemia in DFCI ALL Consortium Protocol 95-01.

In a prospective trial in 284 children with B-lineage acute lymphoblastic leukemia (ALL), we assessed the clinical utility of real-time quantitative polymerase chain reaction analysis of antigen receptor gene rearrangements for detection of minimal residual disease (MRD) to identify children at high risk of relapse. At the end of induction therapy, the 5-year risk of relapse was 5% in 176 children with no detectable MRD and 44% in 108 children with detectable MRD (P < .001), with a linear association of the level of MRD and subsequent relapse. Recursive partitioning and clinical characteristics identified that the optimal cutoff level of MRD to predict outcome was 10(-3). The 5-year risk of relapse was 12% for children with MRD less than one leukemia cell per 10(3) normal cells (low MRD) but 72% for children with MRD levels greater than this level (high MRD) (P < .001) and children with high MRD had a 10.5-fold greater risk of relapse. Based upon these results we have altered our treatment regimen for children with B-lineage ALL and children with MRD levels greater than or equal to 10(-3) at the end of 4 weeks of multiagent induction chemotherapy now receive intensified treatment to attempt to decrease their risk of subsequent relapse.

Interferon regulatory factor 4 (IRF4) interacts with NFATc2 to modulate interleukin 4 gene expression.

Proteins of the nuclear factor of activated T cells (NFAT) family of transcription factors are critical for lymphocyte activation in the immune system. In particular, NFATs are important regulators of inducible IL-4 gene expression. Interferon regulatory factor 4 (IRF4) is an immune system-restricted interferon regulatory factor that is required for lymphocyte activation, but its molecular functions in the T lineage remain to be elucidated. We demonstrate that IRF4 potently synergizes with NFATc2 to specifically enhance NFATc2-driven transcriptional activation of the IL-4 promoter. This function is dependent on the physical interaction of IRF4 with NFATc2. IRF4 synergizes with NFATc2 and the IL-4-inducing transcription factor, c-maf, to augment IL-4 promoter activity as well as to elicit significant levels of endogenous IL-4 production. Furthermore, naïve T helper cells from mice lacking IRF4 are compromised severely for the production of IL-4 and other Th2 cytokines. The identification of IRF4 as a partner for NFATc2 in IL-4 gene regulation provides an important molecular function for IRF4 in T helper cell differentiation.