Pseudomonas aeruginosa will aid surveillance and diagnostic initiatives and can be crucial in early and appropriate antibiotic therapy. We conducted a systematic review examining risk factors of acquisition of resistant P. aeruginosa among hospitalized patients.Identifying risk factors predicting acquisition of resistant P. aeruginosa, among hospitalized patients. Random effects model meta-analysis was conducted when at least three or more studies were sufficiently similar.MEDLINE®, EMBASE®, and Cochrane Central were searched between 2000 and 2016 for studies examining independent risk factors associated with acquisition of resistant P. aeruginosa and 26 publications (29 studies) examined resistant P. aeruginosa. The acquisition of MDR P. aeruginosa, as compared with non-MDR P. aeruginosa, was significantly associated with intensive care unit (ICU) admission (3 studies: summary adjusted odds ratio [OR] 2.2) or use of quinolones (4 studies: summary adjusted OR 3.59). Acquisition of MDR or XDR compared with susceptible P. aeruginosa was significantly associated with prior hospital stay (4 studies: summary adjusted OR 1.90), use of quinolones (3 studies: summary adjusted OR 4.34), or use of carbapenems (3 studies: summary adjusted OR 13.68). The acquisition of MDR P. aeruginosa compared with non-P. aeruginosa was significantly associated with prior use of cephalosporins (3 studies: summary adjusted OR 3.96), quinolones (4 studies: summary adjusted OR 2.96), carbapenems (6 studies: summary adjusted OR 2.61), and prior hospital stay (4 studies: summary adjusted OR 1.74). The acquisition of carbapenem-resistant P. aeruginosa compared with susceptible P. aeruginosa, was statistically significantly associated with prior use of piperacillin-tazobactam (3 studies: summary adjusted OR 2.64), vancomycin (3 studies: summary adjusted OR 1.76), and carbapenems (7 studies: summary adjusted OR 4.36).Of the 54 eligible articles, 28 publications (31studies) examined multi-drug resistant (MDR) or extensively drug resistant (XDR) P. aeruginosa. These findings provide guidance in identifying patients that may be at an elevated risk for a resistant infection and emphasize the importance of antimicrobial stewardship and infection control in hospitals.Prior use of antibiotics and prior hospital or ICU stay was the most significant risk factors for acquisition of resistant The online version of this article (10.1186/s13756-018-0370-9) contains supplementary material, which is available to authorized users. Pseudomonas aeruginosais is one of the most common gram-negative bacteria causing nosocomial and healthcare-associated infections (HAIs) in hospitalized patients [P. aeruginosa as a critical priority pathogen that desperately requires new treatment options [P. aeruginosa in HAIs and among hospitalized patients is a major public health problem [P. aeruginosa infections in the hospital setting are associated with poor outcomes including increased resource utilization and costs, morbidity, and mortality [There is an alarming increase in antibiotic-resistant Gram-negative infections –3. Amongpatients . The Wor options . Increas problem . MDR P. ortality .P. aeruginosa account for 13–19% of HAIs each year in the US. The increasing level of resistance in MDR P. aeruginosa is often attributed to patient-to-patient transmission of resistant strains as well as newly acquired resistance owing to previous antibiotic exposure. As per standardized international terminology, MDR is defined as non-susceptibility to at least one agent in three or more antimicrobial categories and XDR is defined as non-susceptibility to at least one agent in all but two or fewer antimicrobial categories  [P. aeruginosa when selecting treatment is warranted to ensure timely and appropriate initial therapy. Lack of effective antibacterial therapies against P. aeruginosa infections severely limit effective therapeutic options and consequently, lead to inappropriate initial therapy that adversely impacts health outcomes [P. aeruginosa, which can be a detrimental delay for these patients.MDR egories) . In seveP. aeruginosa in nosocomial infections and HAIs. Identifying risk factors predicting acquisition of MDR P. aeruginosa or identifying subgroups of patients who are at an increased risk for acquisition of MDR P. aeruginosa in the hospital setting will assist in providing timely and appropriate treatment. While a recent review examined the risk factors independently associated with extensively drug-resistant (XDR) P. aeruginosa, there has not been a comprehensive analysis of contemporary literature reporting all levels of resistance (MDR or XDR or resistant) of P. aeruginosa infections [P. aeruginosa from various sites among inpatients, hospitalized in any of the following setting including wards, intensive care units, and other types of inpatient settings.There are considerable gaps and inconsistencies in knowledge regarding risk factors associated with the occurrence of MDR fections . This syP. aeruginosa), mode of infection , and risk factor assessment . Additionally, search terms for Gram-negative infections, beta-lactamases, and metallo-beta-lactamases attributed to carbapenem resistance were included to increase the yield of studies with resistant (single drug class) P. aeruginosa. These three databases were searched because they index most of the published citations. To supplement this search, we reviewed reference lists of eligible studies using an iterative process to maximize inclusion of relevant data. We did not perform grey literature searches or systematically search for unpublished data. We reviewed abstracts from conference proceedings if they were indexed in the three aforementioned databases.We performed a systematic search in the MEDLINE, Cochrane Library, and EMBASE databases for citations indexed from January 01, 2000 through December 31, 2016. The initial search strategy  or resistant to any one class of drug. Non- P. aeruginosa was also defined by the individual studies and varied in definition to include pathogens other than P. aeruginosa.Our primary objective was to examine studies evaluating risk factors associated with acquisition of MDR or XDR, or resistant P. aeruginosa were included. Risk factors were categorized into patient characteristics, hospital characteristics, and treatment characteristics.Studies evaluating patients hospitalized in a ward, intensive or critical care unit, or any other inpatient healthcare setting (including chronic care facilities), were eligible for inclusion. Studies examining patients with either hospital-acquired or community-acquired were included, provided that they were evaluated in a hospital /inpatient setting. Risk factors that predict acquisition of MDR or XDR, or resistant P. aeruginosa versus resistant P. aeruginosa (to any one class of antibiotic); MDR or XDR P. aeruginosa versus susceptible P. aeruginosa; MDR or XDR P. aeruginosa versus control (any other Gram-negative pathogen or any infection with unspecified pathogen); resistant P. aeruginosa versus susceptible P. aeruginosa. The outcome of interest was microbiologically confirmed acquisition of MDR or XDR, or resistant P. aeruginosa. For studies that reported both the outcome of acquisition of MDR or XDR P. aeruginosa and single-drug resistant P. aeruginosa, we included the study only once (for the outcome of acquisition of MDR or XDR P. aeruginosa) in the analysis. We accepted all study designs except non-comparative studies, case reports, and case series. Studies that reported multivariable results adjusting for any potential confounders were eligible. No minimum study duration or follow-up time was required for inclusion.The exposure and comparators of interest included: MDR or XDR P. aeruginosa resistant due to metallo-beta-lactamases. Studies published in languages other than English were excluded.We excluded studies of mixed infections that had more than 20% Gram-positive infections (to ensure most (80%) of the evaluated infections in eligible studies were Gram-negative infections) and studies solely examining All citations identified by literature searches were independently screened by two researchers. Upon the start of citation screening, we implemented a training session where all researchers screened the same articles and conflicts were discussed. We iteratively continued training until we reached consensus regarding the nuances of the eligibility criteria for screening. During double-screening, we resolved conflicts through group discussions.We assessed the methodological quality of each study based on predefined criteria using the Agency for Healthcare Research and Quality (AHRQ) and the New-Castle Ottawa risk of bias tool, which probes risk of selection, performance, detection, attrition, reporting, and other potential biases. Each study was extracted by one experienced methodologist . The extraction was reviewed and confirmed by at least one other methodologist. Any disagreements were resolved by discussion amongst the study team. Data were extracted into customized Microsoft Excel™ forms. We tested the data extraction forms on several studies and revised as necessary before full data extraction. Extracted data included variables addressing population characteristics, including severity of illness, description of exposure and comparator groups, sites of infection, outcome definitions, enrolled and analyzed sample sizes, study design features, and multivariate results. Any missing or unavailable data were deemed as not reported information. We performed random effects model meta-analyses of eligible studies if at least three or more studies were sufficiently similar in population, exposure, and outcomes . If apprp < 0.10) and quantified the extent of heterogeneity with the I2 statistic. It is common practice to interpret I2 > 50% as representing substantial inconsistency or significant statistical heterogeneity [All analyses were performed in Stata version 14  with the metan, metareg, and metabias functions. We tested between study heterogeneity with the Q statistic  that examined risk factors for acquisition of MDR or XDR P. aeruginosa [Of the 28 articles  reported data on MDR studies uisition , 37, 39,ruginosa –34, 38, ruginosa , 36. Theruginosa , 27, 28.ruginosa .P. aeruginosa or both types of resistance and the remaining were control patients. The descriptions of study control groups varied across studies: susceptible P. aeruginosa (5 studies [P. aeruginosa (without MDR phenotype) (14 studies [P. aeruginosa (without XDR phenotype) (2 studies [P. aeruginosa (any pathogen other than P. aeruginosa)  studies , 39); no studies , 33); no studies , 26, 30) studies , 37). No studies , 19. TheP. aeruginosa (without MDR phenotype); susceptible P. aeruginosa; and any controls (non P. aeruginosa or undescribed controls). In analyses of risk for acquisition of MDR P. aeruginosa, 21 articles in 23 studies [P. aeruginosa acquisition and two included both MDR P. aeruginosa and XDR P. aeruginosa (MDR P. aeruginosa acquisition being the most commonly reported) [For meta-analysis, we categorized studies based on three control groups: non-MDR  studies , 37, 39)eported) .P. aeruginosa in meta-analysis are described in the following results sections. Additional risk factors that had a statistically significant association with acquisition of MDR P. aeruginosa but were not eligible for meta-analysis are listed in Additional file The risk factors statistically significantly associated with acquisition of MDR P. aeruginosa as a comparator reported risk factors associated with acquisition of MDR P. aeruginosa [P. aeruginosa. Two other predictors, surgery and prior use of carbapenems, were not associated with an increased risk of acquisition  were not associated with a risk of acquisition of MDR P. aeruginosa in meta-analysis , urinary catheter (2 studies). The following factors were not associated with an increased risk of XDR P. aeruginosa: ceftazidime use, days of ciprofloxacin use, number of different antibiotics used during time at risk (i.e. time between admission and isolation of bacteria in index cases).Six studies reported risk factors for acquisition of XDR controls –34, 38.  studies , 34); no(1 study ); suscep(1 study ); and su(1 study ).The mosn = 9877 subjects) that examined risk factors for acquisition of carbapenem-resistant P. aeruginosa [P. aeruginosa studies.Twenty-three studies in 21 articles . The mean age ranged from 44 years to 67 years (cases) and from 41 years to 66 years (controls). Most studies included a mix of patients with respiratory, wound, genitourinary, and bloodstream as the source of infection.The descriptions of control groups varied across studies. For the purpose of analysis, we categorized the controls into two categories: susceptible P. aeruginosa  , 45, 64.P. aeruginosa in Table P. aeruginosa [P. aeruginosa [P. aeruginosa resistant to the newer cephalosporins, namely, cefepime and ceftazidime [Of the seven studies that reported data on acquisition of other (non-carbapenem) resistant ruginosa , 63, thrruginosa , 52, 53,tazidime , 45.-resistant P. aeruginosa for the following factors: admissions in prior year, ICU stay, time at risk, transfer, severe morbidity or higher comorbid score, and prior use of antibiotics .No meta-analysis could be conducted as there were fewer than three studies for this comparison on any particular category of predictor , 63. TwoP. aeruginosa [P. aeruginosa  . Both length of hospital stay before culture and prior use of carbapenem were not associated with an increased risk for resistance to higher generation cephalosporins in one study [Two studies , 45 repone study .P. aeruginosa, XDR P. aeruginosa, and other resistant P. aeruginosa. Our meta-analysis identified that the risk factors for acquisition of MDR or XDR P. aeruginosa varied with regard to the type of control used for comparison. ICU stays (either as current or prior to current episode of infection) and use of quinolones was significantly associated with acquisition of MDR or XDR P. aeruginosa, compared with resistant or susceptible P. aeruginosa. Use of prior antibiotics including, cephalosporins, quinolones, or carbapenems, and prior hospital admissions predicted an increased risk of MDR or XDR P. aeruginosa versus non-P. aeruginosa.This systematic review of the literature summarizes risk factors that predict acquisition of MDR P. aeruginosa are a worldwide public health problem. Resistant strains of P. aeruginosa are associated with high mortality and increased resource utilization [P. aeruginosa may be associated with misuse or overuse of antimicrobials. Our meta-analysis found a consistent association between the use of quinolones and acquisition of MDR or XDR P. aeruginosa P. aeruginosa. However, association between carbapenem use and acquisition of MDR or XDR P. aeruginosa was not consistent across comparisons. While some primary studies did report a relationship between MDR or XDR P. aeruginosa and prior use of antibiotics [P. aeruginosa and the significance of their association can vary by the type of comparator examined. Nonetheless, our results confirm that prior use of specific antimicrobials is an important risk factor for acquisition of MDR or XDR P. aeruginosa. Antimicrobial resistance occurs over time, often mediated by gene mutations and misuse or overuse of antimicrobials may accelerate this process. Understanding the epidemiology of MDR or XDR P. aeruginosa will be necessary to overcome infections with these resistant pathogens.The increasing rates of MDR or XDR, or resistant lization . The emeibiotics , 30, ourP. aeruginosa, which examined multivariate risk factors reported in eight included articles [P. aeruginosa. Our review, in which a meta-analysis was performed, demonstrated that admission location, prior admission, or use of quinolones was significantly associated with acquisition of MDR or XDR P. aeruginosa. In addition to reviewing MDR or XDR P. aeruginosa, we reviewed single drug-resistant P. aeruginosa. In meta-analysis, prior use of piperacillin-tazobactam, vancomycin, or carbapenems were significantly associated with acquisition of carbapenem-resistant versus susceptible P. aeruginosa. In meta-analysis, prior fluoroquinolone use was a statistically significant predictor of subsequent quinolone-resistant versus susceptible P. aeruginosa.This review finding can be supported in the context of a recent review on MDR or XDR articles . The autP. aeruginosa, and risk factors included in the study. As a result, a combined meta-analysis may misrepresent the true picture. We mitigated these issues by using a random effects model in our analyses and by limiting analyses to similar comparators. However, in many instances there were risk factors that were statistically significant in two studies, but unfortunately a third study was not available to permit the exploration of this factor through meta-analysis. Additionally, our study results may not be generalizable to all regions as studies from certain regions  were overrepresented in our sample published literature.There are limitations associated with this systematic literature review. To begin with, the study inclusion criteria were limited to published studies indexed in English. Secondly, studies eligible for inclusion were heterogeneous with respect to the definition of exposure, site of infection with P. aeruginosa as controls. The description of these controls was unclear if the control group did or did not include MDR infection of a non-Pseudomonas bacteria. The results section describes variability across studies with regard to study characteristics, outcome assessment, and the relationship between risk factors and the outcome of acquisition of resistant P. aeruginosa. We could not conduct additional subgroup analyses by site of infection, or explain differences across studies using stratified analyses due to the small number of available studies for any particular comparison. An insufficient number of studies (< 10 studies) precluded evaluatingthe potential for publication bias with funnel plots and Egger’s tests for small study effects [Confounding in observational studies reporting unadjusted data is a well-known source of bias. To mitigate this bias, we included risk factors that were analyzed in multivariate analyses. The choice of the control group  may also have influenced the results. We attempted to address this issue using similar comparison groups in the meta-analyses. As with any evidence synthesis, the limitations of the data available in primary studies will transfer into limitations of the systematic review. For example, the control group was not well defined in studies, specifically in studies that reported non-  effects .P. aeruginosa infections. Depending on local epidemiology, this finding is useful in identifying patients at high risk for resistant P. aeruginosa that may benefit from alternate empiric treatment. Further, these findings emphasize the need for antimicrobial stewardship and infection control in hospitals and continued need for the development of new antimicrobial agents with activity against MDR P. aeruginosa [Consistently, across comparisons, prior use of antibiotics and prior ICU stay was a significant risk predictor for acquisition of MDR or XDR ruginosa . The impAdditional file 1:Table S1. Search Strategy. Table S2. Patient–related Multivariate Risk Factors of Acquistion of MDR P. aeruginosa. Table S3. Antibiotic Treatment–related Multivariate Risk Factors of Acquistion of MDR P. aeruginosa. Table S4. Other Treatment–related Multivariate Risk Factors of Acquistion of MDR and XDR P. aeruginosa. Table S5. Hospital–related Multivariate Risk Factors of Acquistion of MDR and XDR P. aeruginosa. Table S6. Patient–related Multivariate Risk Factors of Acquistion of Carbapenem-resistant P. aeruginosa. Table S7. Antibiotic Treatment–related Multivariate Risk Factors of Acquistion of Carbapenem-resistant P. aeruginosa. Table S8. Other Treatment–related Multivariate Risk Factors of Acquistion of Carbapenem-resistant P. aeruginosa. Table S9. Hospital–related Multivariate Risk Factors of Acquistion of Carbapenem-resistant P. aeruginosa. Table S10. Multivariate Risk Factors of Acquistion of Resistant P. aeruginosa. Figure S1. Meta-analysis of Risk Factors for Carbapenem versus Susceptible P. aeruginosa Acquisition. Figure S2. Meta-analysis of Prior Use of Carbapenem as a Risk Factor for Carbapenem versus Susceptible P. aeruginosa Acquisition. Figure S3. Meta-analysis of Prior Use of Fluoroquinolones as a Risk Factor for Quinolone-resistant versus Susceptible P. aeruginosa Acquisition. (DOCX 182 kb)


Bacteroides fragilis constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen. Antimicrobial resistance (AMR) and the prevalence of AMR genes are increasing, and prediction of antimicrobial susceptibility based on sequence information could support targeted antimicrobial therapy in a clinical setting. Complete identification of insertion sequence (IS) elements carrying promoter sequences upstream of resistance genes is necessary for prediction of AMR. However, de novo assemblies from short reads alone are often fractured due to repeat regions and the presence of multiple copies of identical IS elements. Identification of plasmids in clinical isolates can aid in the surveillance of the dissemination of AMR, and comprehensive sequence databases support microbiome and metagenomic studies. We tested several short-read, hybrid and long-lead assembly pipelines by assembling the type strain B. fragilis CCUG4856T (=ATCC25285=NCTC9343) with Illumina short reads and long reads generated by Oxford Nanopore Technologies (ONT) MinION sequencing. Hybrid assembly with Unicycler, using quality filtered Illumina reads and Filtlong filtered and Canu-corrected ONT reads, produced the assembly of highest quality. This approach was then applied to six clinical multidrug-resistant B. fragilis isolates and, with minimal manual finishing of chromosomal assemblies of three isolates, complete, circular assemblies of all isolates were produced. Eleven circular, putative plasmids were identified in the six assemblies, of which only three corresponded to a known cultured Bacteroides plasmid. Complete IS elements could be identified upstream of AMR genes; however, there was not complete correlation between the absence of IS elements and antimicrobial susceptibility. As our knowledge on factors that increase expression of resistance genes in the absence of IS elements is limited, further research is needed prior to implementing AMR prediction for B. fragilis from whole-genome sequencing. Genome assemblies from the assembly pipeline validation are available at https://doi.org/10.5281/zenodo.2648546. Genome assemblies corresponding to each stage of the process of the assembly are available at https://doi.org/10.5281/zenodo.2661704. Full commands and scripts used are available from GitHub (https://github.com/thsyd/bfassembly), as well as a static version (https://doi.org/10.5281/zenodo.2683511).Sequence read files  were generated for each isolate . After filtering, adapter removal and down sampling, a median of 449 022 741 bases  was available per isolate with 87–96 % Q30 bases corresponding to calculated read depths of 75–103 %. The mol% G+C content of the reads for each isolate  were very consistent and within the expected range for the genus ides 40– mol%  assembled from mobilome metagenomic sequencing of the uncultured caecum content from a rat trapped at Bispebjerg Hospital in Copenhagen, Denmark  (Table S3) . blastn B. fragilis isolates was observed using progressiveMauve (not shown) , as well as the final genome assemblies, have been deposited in NCBI/ENA/DDBJ under BioProject accession numbers PRJNA525024, PRJNA244942, PRJNA244943, PRJNA244944, PRJNA253771, PRJNA254401 and PRJNA254455 (2019).1. Sydenham TV et al., fastq format of demultiplexed ONT reads trimmed of adapters and barcode sequences, https://doi.org/10.5281/zenodo.2677927 (2019).2. Sydenham TV et al., Genome assemblies from the assembly pipeline validation, https://doi.org/10.5281/zenodo.2648546 (2019).3. Sydenam TV et al., Reference assembly of B. fragilis CCUG4856T, https://www.ncbi.nlm.nih.gov/assembly/GCF_000025985.1/ (2005).4.Cerdeño-Tárraga AM et al., Genome assemblies corresponding to each stage of the process of the assembly of the six MDR isolates, https://doi.org/10.5281/zenodo.2661704.5. Sydenham TV et al., Sequences of the plasmid replication domain families were downloaded from the Pfam database (https://pfam.xfam.org/). Specifically, the full-length sequences for all sequences in the full alignments were downloaded for: PF01051, PF01402, PF01446, PF01719, PF01815, PF02486, PF03090, PF03428, PF04796, PF05732, PF06504, PF06970, PF07042 and PF10134 (2019).6. El-Gebali S Click here for additional data file.Click here for additional data file.


H. pylori infection in patients with ITP improved thrombocytopenia in about half of the cases. However, most included studies were observational case series. We performed the first meta-analysis of randomized trials to gain a better insight into the effect of H. pylori eradication in ITP patients.  Several recent reviews of published studies have shown that the eradication of  A systematic computerized search of the electronic databases including PubMed, EMBASE, Google Scholar, and Cochrane Library (up to December 2017) was conducted. P = 0.05). In the subgroup analysis, however, children in the eradication group failed to show statistically better response rate than those in the noneradication group .  From six studies, a total of 241 patients (125 in eradication group and 116 in control group) were included in the meta-analysis. Patients in the eradication group showed significantly higher overall platelet response rate than those in the control group (odds ratio = 1.93, 95% confidence interval: 1.01–3.71, H. pylori eradication has a significant therapeutic effect in patients with ITP. Considering the intrinsic limits in the design and sample size of the included studies, however, large randomized controlled trials are warranted to validate the therapeutic impact of H. pylori eradication in adults as well as children with ITP. This meta-analysis indicates that  Idiopathic or immune thrombocytopenic purpura (ITP) is an autoimmune-mediated acquired bleeding disorder of children as well as adults. It is characterized by the destruction of host platelet caused by anti-platelet antibodies . HoweverHelicobacter pylori (H. pylori) is the most common microbial pathogen that colonizes in the mucosal layer of the stomach. It is causally associated with a variety of gastrointestinal disorders including chronic gastritis, gastric mucosal atrophy, peptic ulcer, gastric mucosa-associated lymphoid tissue lymphoma, and gastric adenocarcinoma [H. pylori infection was initially proposed in 1998 by Gasbarrini et al. who reported a significant increase of platelet count after bacterial eradication in 8 of 11 ITP patients infected with H. pylori [H. pylori-associated ITP is still uncertain, several studies have suggested that H. pylori virulence factor, cytotoxin-associated gene A (CagA), stimulates the development of anti-CagA antibodies (Abs) that cross-react with platelet surface antigens (Ags), resulting in thrombocytopenia [H. pylori eradication led to an increase of platelet counts and even a regression of ITP [H. pylori in chronic ITP is effective in increasing platelet counts or not.arcinoma , 5. A pa. pylori . Althougytopenia –9. Many n of ITP –18. As on of ITP , howeverH. pylori infection in patients with chronic ITP improved thrombocytopenia in about half of the cases [H. pylori [H. pylori eradication in ITP patients.Several recent reviews of previously published studies have shown that the eradication of he cases –24. The he cases . Howeverhe cases –24, whic. pylori –21. TherHelicobacter pylori,” “H. pylori,” “thrombocytopenia,” “idiopathic thrombocytopenic purpura,” “immune thrombocytopenic purpura,” and “ITP.” The related article function in PubMed was used to identify all relevant articles. In addition, the bibliographic references of all retrieved studies and reviews were evaluated for additional eligible articles.The current study was conducted according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines , 26. A sH. pylori infection documented by reliable tests such as 13C-urea breath test (UBT), serologic test for antibody to H. pylori, stool antigen test, or histology of gastric mucosal biopsies; (iii) randomization of ITP patients infected with H. pylori to either bacterial eradication or noneradication; (iv) providing treatment outcomes (platelet counts or response rate) of these two groups. Reports published only in abstract form were not considered eligible.We only included randomized controlled trials in this meta-analysis. Retrospective or observational case control studies were excluded. Eligible studies should meet the following inclusion criteria: (i) patients with a diagnosis of chronic ITP according to the American Society of Hematology (ASH) guidelines ; (ii) H.Two reviewers (BJK and HJJ) independently screened relevant studies and extracted the data from each eligible study. If these two authors did not agree, the other investigator (JHK) was consulted to resolve the disagreement through discussion.H. pylori infection, duration of ITP, treatment, platelet counts (before and after treatment) or treatment outcomes, and relapse rate.The following data were extracted from the included studies: the first author, year of publication, country, number of patients, demographics , detecting methods for The methodological quality of the randomized trials was scored using the Jadad five-item scale, taking into account randomization, double-blinding process, and withdrawals . The finQ statistics and I2 inconsistency test. The fixed-effect model (Mantel–Haenszel method) was used for pooling homogeneous outcomes (P ≥ 0.1 and I2 ≤ 50%), and the random-effect model (DerSimonian–Laird method) was selected if significant heterogeneity was observed (P < 0.1 and I2 > 50%).We chose to record the overall response rate (ORR) as primary assessment criteria. The odds ratios (ORs) and 95% confidence intervals (CIs) for ORR were calculated indirectly from original articles. The effect size of ORR was pooled through OR and its 95% CI. The heterogeneity across studies was estimated by the H. pylori infection.The RevMan version 5.3 was used to combine the data. The plots show a summary estimate of the results from all the studies combined. The size of the squares represents the estimate from each study, reflecting the statistical “weight” of the study. Outcomes are provided as forest plots with diamonds representing the estimate of the pooled effect and the width of diamond implying its precision. The line of no effect is number one for binary outcomes, which depicts statistical significance if not crossed by the diamond . The OR P value of less than 0.05 for the summary estimate of OR and publication biases.The possibility of publication bias was assessed with a visual inspection of the graphical funnel plot . The staA total of 157 potentially relevant articles were initially found, but 111 of them were excluded after careful screening of the titles and abstracts. We retrieved 46 articles for full-text evaluation and further excluded 40 by the inclusion criteria. Finally, 6 studies were included in the meta-analysis –21.  FigH. pylori infection was UBT [H. pylori infection ranged from 25.9% [ was UBT , 18–21. om 25.9% . Bacteriom 25.9% , patient9/L [9/L was most commonly adopted [In most studies, complete response (CR) was defined as the achievement of a platelet count more than 150 × 109/L , 18–21.  adopted , 21 . Patients in the eradication group showed significantly higher ORR than those in the control group   were included in the meta-analysis of ORs for ORR. The fixed-effect model was selected because there was no significant heterogeneity among studies ( = 0.05) .P = 0.11) , and the fixed-effect model was used for pooling the data.In the subgroup analysis, children in the eradication group failed to show statistically higher ORR than those in the noneradication group  . There wP = 0.452, Egger's P = 0.465)  .H. pylori infection plays an etiological role in ITP, several randomized trials to date have shown the inconsistent results in the effect of bacterium eradication. In this meta-analysis of 6 randomized trials, we evaluated the therapeutic effect of H. pylori eradication in patients with ITP. Our results indicate that bacterium eradication has a significant impact on platelet recovery in ITP.Despite the findings indicating that ITP is considered an organ-specific autoimmune disease. It is mediated by anti-platelet Abs that bind to host platelets and megakaryocytes, accelerating platelet destruction by the reticuloendothelial system . The autH. pylori may contribute to the pathogenesis of chronic ITP [H. pylori eradication resulted in an increase of platelet counts in ITP [H. pylori in chronic ITP: the production of Ag-specific Abs that are cross-reactive with platelet surface glycoproteins (GP IIb/IIIa or GP Ib) due to molecular mimicry increased plasmacytoid dendritic cell numbers and variable host immune response to virulence factors such as vacuolating-associated cytotoxin gene A (VacA) and CagA [γRIIB expression on circulating monocytes is downregulated in H. pylori-infected ITP patients [H. pylori infection may play an important role in the development of ITP by activating the Fcγ receptor of monocytes/macrophages through downregulation of the inhibitory receptor FcγRIIB. Despite mounting evidence of the association of H. pylori and ITP, published studies are inconclusive due to the scarcity of controlled clinical trials to date and some reports presenting conflicting results [H. pylori in children with ITP remains controversial [H. pylori eradication has a critical impact on clinical diagnosis and treatment of ITP.Since the first report in 1998 , the acconic ITP –34. In as in ITP –18. Variand CagA , 34. A rpatients . Therefo results –21. Moreoversial , 37. TheH. pylori infection in ITP ranged from 58% [H. pylori [H. pylori eradication was successful, compared with untreated patients (weighted mean difference (WMD) of 40.77 × 109/L, 95% CI: 20.92–60.63) and those who failed eradication . Another systemic review with a meta-analysis of 1555 patients with ITP from 25 studies reported the weighted mean CR (platelet count more than 100 × 109/L) of 42.7% and ORR  of 50.3% after successful eradication of H. pylori [H. pylori-positive adult ITP patients resulted in about a 50% CR rate [H. pylori. Except for one [H. pylori eradication in the other studies [In the previous systemic reviews, the pooled prevalence of from 58%  to 65% [from 58% . The fir. pylori . There w. pylori . In addi CR rate . These f for one –24. Ther for one –21. Whil studies –19.H. pylori infection ranged from 30% [P = 0.05). This result suggests that H. pylori eradication in patients with ITP is effective in increasing platelet count. The recent ASH guidelines have recommended the examination and treatment of H. pylori infection in adult patients with ITP [H. pylori in children is not recommended. The prevalence of H. pylori infection is much lower in children than in adults with chronic ITP, suggesting that H. pylori play only a minor role in the development of childhood ITP [H. pylori eradication in children were highly variable and inconsistent among studies [P = 0.11). However, the subgroup analysis included only 4 studies with a small number of patients. Therefore, this finding seems not sufficient to determine the therapeutic efficacy of H. pylori eradication in childhood ITP. Larger randomized trials are necessary to confirm the beneficial role of H. pylori eradication in childhood ITP.In this meta-analysis of 6 randomized trials –21, the from 30% . Patienthood ITP . Platele studies –41. In tH. pylori infection in ITP still remain to be resolved, including the difference of efficacy among countries, factors predicting the platelet response, and mechanisms responsible for therapeutic effect associated with H. pylori eradication [H. pylori eradication between Western and Eastern series [H. pylori strains may, at least in part, account for the difference in the platelet responses. The frequency of CagA-positive strains varies among geographic locations. Eastern Asian H. pylori strains have been found as more pathogenic, correlating with an increased development of gastric adenocarcinoma in H. pylori-positive patients in East Asia [H. pylori strains detected in East Asia express CagA, whereas the proportion of CagA-positive H. pylori strains in Western countries was much lower [H. pylori eradication in patients with ITP [A number of questions regarding the eradication of dication . There wn series . Studiesast Asia , 43. Thech lower . Immune with ITP –9. Takahwith ITP . Kodama H. pylori infection. Especially one study [Our study has several inherent limitations that need to be discussed. First, this meta-analysis included a limited number of studies with a small sample size. Moreover, there were only two trials conducted in adults with ITP. Second, five studies were carried out in Asia and the remaining trial in South Africa. So the results might not be transferred to Caucasian populations. Third, the studies showed heterogeneity in the detection methods of ne study  adopted ne study . Fourth,H. pylori eradication has a significant therapeutic effect in patients with ITP. This result suggests that the detection and eradication of H. pylori infection need to be considered in patients with chronic ITP. Taking into account the intrinsic limits in the design and sample size of the included studies, however, large randomized controlled trials are warranted to validate the therapeutic impact of H. pylori eradication in adults as well as children with chronic ITP.In conclusion, our meta-analysis indicates that


Enterococcus durans KLDS6.0930 has previously been shown to have probiotic potential. However, being a potential clinical pathogen, it becomes necessary to evaluate its safety status for novel potential probiotic use. The purpose of this study is to systematically evaluate the safety of E. durans KLDS6.0930 based on its genomics, phenotypic characteristics and oral toxicity. The complete genome of E. durans KLDS6.0930 was sequenced and analyzed for safety-related genes. Antibiotic susceptibility and the production of harmful metabolites were tested. A 28-day repeated oral dose toxicity test was implemented in rats. In vitro, E. durans KLDS6.0930 was resistant to five antibiotics, with intrinsic resistances to four antibiotics and no identified genes for the last. E. durans KLDS6.0930 was not hemolytic and virulence factors were non-functional in its genome. E. durans KLDS6.0930 produced a small amount of tyramine and phenethylamine; genes encoding tyramine decarboxylase were identified. In addition, genotype and phenotype analyses showed that the strain did not have the ability to generate D-lactic acid, indole, or nitroreductase. In vivo, E. durans KLDS6.0930 did not induce adverse effects on the organs, hematological and serum biochemical parameters, or cecal bacterial populations in the oral toxicity test. These results indicate that E. durans KLDS6.0930 can be safely used as a potential probiotic for human consumption and animal feed. Enterococcus, a large genus of lactic acid bacteria (LAB), includes 54 species characterized as gram-positive, facultative anaerobic, and non-spore forming , bacteraemia (the third most commonly isolated agent), surgical site infections, bloodstream infections, endocarditis and diarrhea , Northeast Agricultural University (NEAU), Harbin, China. E. durans KLDS6.0930 was maintained in M17 broth  with 10% glycerol and stored at −20°C. Before use, E. durans KLDS6.0930 was activated through three propagation steps in M17 broth at 37°C for 24 h. Bacteria were harvested by centrifugation at 5,000 g for 10 min. Cell pellets were then washed twice with sterile normal saline and resuspended at the desired concentration in sterile normal saline. Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 25923 were incubated in Luria-Bertani (LB) broth and Tryptic Soy Broth (TSB) under aerobic conditions at 37°C, respectively.E. durans KLDS6.0930 genomic DNA was extracted using the DNeasy Tissue kit  following the manufacturer's instruction. Detailed information on the genome sequencing study can be found in our previous report  scheme, which was based on 49 genes encoding the bacterial ribosome protein subunits (rps genes), as performed in rMLST database website (http://pubmlst.org/rmlst/). The ribosomal protein sequences retrieved from the genomes were aligned with CLUSTALW software, while neighbor-joining method was used to infer the phylogenetic tree.E. durans KLDS6.0930 were compared with the comprehensive antibiotic resistance database         for antibiotics  against E. durans KLDS6.0930 was tested by incubating bacteria on blood agar (7% v/v sheep blood) for 48 h at 37°C  crystal violet for 15 min. The wells were then rinsed again with sterile saline and filled with 200 μL of acetone and ethanol solution . Absorbance at 595 nm was measured by using a microplate reader . The cut-off OD (ODc) was defined as three standard deviations above the mean OD of the negative control. The ability to form biofilm was classified according to Stepanovic et al. . Pretreatment and dansyl chloride derivatization of samples were performed as previously reported . A red ring was regarded as positive. E. coli ATCC25922 was used as a positive control. The activity of nitroreductase was determined using the assay kit according to the manufacturer's instructions . E. coli ATCC25922 was used as a positive control.The optical purity of the resulting lactic acid was estimated using an L/D-lactic acid enzymatic test kit following the manufacturer's instructions . The ability of Specific Pathogen Free (SPF) Sprague-Dawley (SD) rats aged 6–7 weeks were supplied by Vital River Laboratory Animal Technology Co., Ltd. . All rats were randomly put into plastic cages in an animal chamber under controlled environmental conditions with a 12-h light/dark cycle at a temperature of 23 ± 2°C and a relative humidity of 50 ± 20%. The rats were acclimatized to the laboratory conditions for 1 week before the start of the experiment and permitted with free access to drinking water and standard diet. The experimental protocol was approved by the guidelines of Animal Care and Use Committee of Northeast Agricultural University (SRM-06).E. durans KLDS6.0930 at 1 × 109 CFU/kg body weight (BW) once daily for 28 days. The control group was administered with 1 mL sterile normal saline. During the treatment period, all rats were observed daily for clinical signs of morbidity and mortality. BW and feed intake were monitored weekly. At the end of the dosing period, all rats were deprived of food and water for 16 h before humane sacrifice under diethyl ether anesthesia.This study was performed according to Organization for Economic Co-operation and Development (OECD) test guidelines OECD, . Male anHematological variables were analyzed in all rats at the end of the treatment period. Blood samples were collected in heparinized tubes to assess red blood cell count (RBC), white blood cell count (WBC), hemoglobin (HGB), platelet count (PLT), mean corpuscular volume (MCV), mean corpuscular hemoglobin concentration (MCHC), neutrophils, monocytes, lymphocytes, and eosinophils using an automatic hematological analyzer .Whole blood was centrifuged to obtain serum for analysis on an automatic biochemistry analyzer  for the following parameters: aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), total bilirubin (TBIL), total protein (TP), albumin (ALB), glucose (GLU), triglycerides (TG), total cholesterol (TC), high density lipoprotein cholesterol (HDL), low density lipoprotein cholesterol (LDL), urea (UREA), creatinine (CRE), sodium (Na), chloride (Cl), calcium (Ca), and inorganic phosphorus (P).Organs including heart, spleen, liver, kidney, lung, brain, adrenal thymus, epididymides , testes , ovaries , and uterus  were collected for gross necropsy and weighed. The organ index was calculated as a percentage of organ weight to terminal BW. Selected organs  were excised and fixed in 10% neutral buffered formalin for histopathology. The samples were then embedded in paraffin, cut into 5 μm thickness slices, and stained with hematoxylin-eosin for microscopic examination.In silico analysis of sequenced data was performed using quantitative insights into microbial ecology (QIIME) . Isolated DNA was examined by agarose gel electrophoresis and quantified using an ND-2000C spectrophotometer . Modified fusion primers 515F (5′-GTGCCAGCMGCCGCGGTAA-3′) and 806R (5′-GGACTACHVGGGTWTCTAAT-3′), containing a 6-bp error-correcting barcode were used to amplify the V4 hypervariable region of the bacterial 16S rRNA gene. The PCR products were quantified using an Agilent DNA 1000 Kit on an Agilent 2100 Bioanalyser , pooled together and sequenced using the Illumina Miseq . E. durans KLDS6.0930 at 2 × 108 CFU/mL was fluorescently labeled with carboxyfluorescein diacetate succinimidyl ester (cFDA-SE)  according to the manufacturer's instructions. Male rats were randomly divided in two groups of six rats each. The control group received 1 mL normal saline. The experimental group was treated with 2 × 108 CFU E. durans KLDS6.0930 labeled with cFDA-SE at by gavage in 1 mL of sterile normal saline. After administration for 1 day, test rats were anesthetized with diethyl ether and sacrificed for cecum tissue collection. Cecal contents were carefully removed, and the cecal wall was rinsed with 1 mL sterile normal saline. Samples were stored in the dark and subjected to flow cytometry (BD LSR Fortessa) using a 488 nm laser.SD). Statistical significance of data comparisons was calculated by an unpaired Student's t-test in the subacute toxicity assays. Values of P < 0.05 were considered to be statistically significant.All experiments were conducted at least in triplicate using independent assays. Values are expressed as means ± the standard deviation  in the E. durans KLDS6.0930 chromosome  was identified. This region contained 36 proteins including integrase, transposase, terminase, phage-like protein, tail protein, fiber protein, lysis protein, and hypothetical protein  encoding Type II-A CRISPR associated enzymes (Cas) was found in the genome of E. durans KLDS6.0930 , lincosamide (2), tetracycline (2), rifampin (1), aminocoumarin (1), trimethoprim (1), and peptide (1). Regarding the possibility of acquired resistance by horizontal gene transfer (HGT), the ResFinder software did not detect any acquired antibiotic resistance genes.Antibiotic resistance-related genes in ms Table . The genE. durans KLDS6.0930 to antibiotics was determined by measuring MICs, and the results were compared to the cut-off values for Enterococcus species as defined by EFSA  were aligned to VFDB using BLASTP. The results showed that E. durans KLDS6.0930 genome and plasmid 1 carry a total of 45 putative virulence factors , which contributes to adherence to extracellular matrix proteins and may cause endocarditis , encoding PilA-type pilus structures was present in plasmid 1 of E. durans KLDS6.0930. Non-health care-associated E. faecium strains have been reported to express PilA, PilE, and PilF as cell wall-anchored proteins without forming pilus structures  and an S-layer protein (LIU_RS11695), which may contribute to its adhesion. In addition, our previous study , serine protease (sprE), hyaluronidase (hyl), and cytolysin (cyl), which are commonly found in hospital-associated pathogenic strains of this species, were devoid of E. durans KLDS6.0930. In silico finding for cytolysin was confirmed by a phenotypic assay. After incubation on blood agar plates for 48 h, E. durans KLDS6.0930 did not exhibit any hemolytic effects  and a TDC gene cluster containing a TDC (LIU_RS00045), Na+/H+ antiporter (LIU_RS00035), tyrosine antiporter (LIU_RS00040), and tyrosine-tRNA ligase (LIU_RS00050).The biosynthetic pathway of different biogenic amines is shown in Figure E. durans KLDS6.0930. The second pathway is the conversion of arginine into citrulline and followed by catalysis to ornithine via arginine deiminase (ADI) and ornithine carbamoyl transferase (OCT). LIU_RS09825 and LIU_RS09820 encode these two enzymes, respectively, which indirectly catalyze the biosynthesis of ornithine accompanied by the generation of adenosine triphosphate (ATP)  encoding L-lactate dehydrogenase were identified in the genome of m Figure , which cGeneral behavior and physical activity of rats were not abnormal for both groups during the 28-days observation period. In terms of weight gain and daily food consumption, there was no statistically significant difference in both genders of the treatment group when compared to the control group Table .No gross pathological findings were observed in rats of both two groups. Statistical analysis showed that the relative organ weights included heart, liver, spleen, lung, kidney, brain, adrenal, thymus, testis, epididymis, uterus, and ovary were not significantly different between the treatment group and the control group in both sexes Table . FurtherE. durans KLDS6.0930 also did not result in any treatment-related effects on all rats of the treatment group compared with the control group. In summary, treatment with E. durans KLDS6.0930 did not cause any biological deviations outside of the normal ranges.Hematological and serum biochemistry parameters are reported in Tables E. durans KLDS6.0930 on cecal microbial diversity was determined by amplicon sequencing and analyzed by α-diversity and β-diversity. There were no significant differences in α-diversity, which include Simpson index, Shannon index, observed species and Chao1 index . Therefore, changes in cecal microbiota due to E. durans KLDS6.0930 treatment are not harmful.Additionally, the sample distance based on weighted UniFrac analysis is shown in Figure E. durans KLDS6.0930 administration specifically enriched the abundance of enterococci in treated rats, indirectly indicating E. durans KLDS6.0930 was present in the cecal content. Furthermore, we used cFDA-SE to trace E. durans KLDS6.0930 in the cecum . According to the present EFSA guidelines on the characterization of microbiological feed additives  . Interestingly, the MIC value of tetracycline for E. durans KLDS6.0930 was equal to the cut-off value for Enterococcus species. Based on EFSA guidelines  in foods (ten Brink et al., Biogenic amines have a strong impact on maintenance of normal physiological function of the human body. Nonetheless, they may be hazardous to human health if their levels in foods or beverages reach a critical threshold EFSA, . TherefoE. durans KLDS6.0930 also produced 10.48 ± 1.26 mg/L phenethylamine, under the threshold value of 30 mg/kg (ten Brink et al., E. durans KLDS6.0930 was not found to encode any of the genes related to phenethylamine. A previous study showed that a decarboxylase can decarboxylate different structural homologs (Benkerroum, Enterococcus can accept tyrosine and phenylalanine as substrates (Marcobal et al., Usually, phenylethylamine production is associated with tyramine production, as demonstrated for some Enterococci (Bover-Cid et al., in vivo studies can provide valuable information. The physiology of rats behaves similarly in some situations to that of humans, making rats a suitable model for toxicity studies. A 28-day repeated oral dose toxicity study was performed to assess the safety of E. durans KLDS6.0930 in a rat model. No significant strain-related toxigenic symptoms in the physical appearance of male or female rats were observed in any of the groups. Changes in food consumption, BW and organ weight are considered indicators of toxic effects of a test material. Hematological parameters are commonly used to detect inflammation and infections. Serum biochemical parameters are usually used to determine of organ-related problems. There were no significant differences in food consumption, BW, organ weight, serum biochemical parameters, or hematological parameters between the control and treatment groups, implying that E. durans KLDS6.0930 administration for 28 days did not cause any adverse effects. Histopathology showed that there were no anomalies or changes related to repeated oral application of E. durans KLDS6.0930 for 28 days. Notably, our results suggested that a daily dose of 1 × 109 CFU of E. durans KLDS6.0930 /kg BW daily intake was safe and did not give rise to any treatment-related toxicity effects.As a part of extensive safety assessments, Lactobacillus strains decreased pathogenic bacterial populations such as Salmonella and E. coli while increasing beneficial bacterial populations such as lactobacilli and bifidobacteria in the cecal contents of rats through the colony counting method (Parisa et al., L. plantarum counts in a dose-dependent manner by qPCR method. However, these methods focus on individual gut microbes and are not nearly as extensive and comprehensive enough when compared to next-generation sequencing. The effect of E. durans KLDS6.0930 on cecal microbiota diversity was evaluated by sequencing the 16S rRNA V4 region. No significant differences in α-diversity and β-diversity were detected between the control and treatment groups, indicating that E. durans KLDS6.0930 did not impact cecal microbiota diversity and abundance in healthy male and female rats. This result is consistent with our previous study (Li B. et al., E. durans KLDS6.0930 administration is safely modulates gut microbiota without causing detrimental effects on diversity.To support host health, cecal bacterial populations should be analyzed when evaluating the safety of probiotics. Parisa et al.  showed tE. durans KLDS6.0930 using multiple methods. The results in vitro demonstrated that E. durans KLDS6.0930 does not raise safety concerns regarding acquired antibiotic resistance genes, virulence factors, D-lactic acid, indole production, or nitroreductase activity, as supported by phenotypic and genomic data. The production levels of tyramine and phenethylamine were found to be well below established limits to cause harm to consumers. Furthermore, the in vivo studies showed that E. durans KLDS6.0930 is not toxic to male or female rats. These findings confirm that E. durans KLDS6.0930 is a non-pathogenic strain and can be used as a potential probiotic for human consumption and animal feed.In summary, we present a safety assessment of GH and BL designed the study. BL, MZ, DJ, SC, and SS performed experiments. BL, FL, MZ, LZ, and SE analyzed data. SE, BL, SC, and SS wrote manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


This article has been corrected: In the Materials and Methods section, regarding the Isolation of RNA, production of cRNA, array hybridization and scanning, the correct microarray GEO information is given below:Isolation of RNA, production of cRNA, array hybridization and scanninghttp://www.ncbi.nlm.nih.gov/geo).Total RNA was extracted using the Qiagen RNA isolation kit according to the manufacturer’s instructions  and copy RNA was prepared according to the Affymetrix Gene Chipâ Expression Analysis Technical Manual . Further details are given in our recent report [6]. The microarray study is MIAME compliant, and the raw data have been deposited in GEO database (GSE54829; 101808-101831. https://doi.org/10.18632/oncotarget.21981Original article: Oncotarget. 2017; 8:


Raoultella ornithinolytica P079F W, isolated from the feces of an infant residing in a neonatal intensive care unit during an ongoing study to characterize the neonate gut microbiota. P079F W will be used in studies investigating the role of the microbiome in neonatal infections.Here, we describe the draft genome sequence of  Raoultella ornithinolytica P079F W, isolated from the feces of an infant residing in a neonatal intensive care unit during an ongoing study to characterize the neonate gut microbiota. P079F W will be used in studies investigating the role of the microbiome in neonatal infections.Here, we describe the draft genome sequence of  Raoultella ornithinolytica is an inhabitant of aquatic environments, but it is recognized as an emerging and underreported cause of nosocomial infections  with informed and written consent obtained from the parents. The protocol for feces collection was laid out by the Norwich Research Park (NRP) Biorepository , was in accordance with the terms of the Human Tissue Act 2004, and was approved with license no. 11208 by the Human Tissue Authority. The infant had suspected sepsis against a background of prematurity , premature rupture of membranes, and respiratory distress. Chorioamnionitis and funisitis were confirmed on placental histology. Blood culture and lumbar puncture were unremarkable. The infant had a partial septic screen, and intravenous antibiotics (benzylpenicillin and gentamicin) were commenced during the first week of life. After 5 days of antibiotics, the infant showed no signs of infection.Here, we report the draft genome of an Klebsiella oxytoca [API20E code 524577(3/7)]. DNA was extracted from an overnight culture of P079F W using a phenol-chloroform method described fully by Kiu et al. (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/); no adapter trimming was required, and reads had an average Phred score of >25. MetaPhlAn2.6  being produced by BugBuilder v1.0.3b1 (default settings for Illumina assembly) , with a G+C content of 55.6% and 5,194 coding sequences (CDS) and 75 tRNAs (NCBI Prokaryotic Genome Annotation Pipeline [R. ornithinolytica NBRC 105727T (Assembly accession no. GCA_001598295), confirming its affiliation to this species (–https://bigsdb.pasteur.fr/klebsiella/) and encodes several virulence factors  according to a BLASTN search with the draft genome via VFanalyzer (Klebsiella data set) at http://www.mgc.ac.cn/cgi-bin/VFs/v5/main.cgi (marA (ARO:3000263), acrB (ARO:3000216), msbA (ARO:3003950), and PmrF   colonies. Strain P079F W was isolated along with strain P079F P  from theu et al.  and sequPipeline ) with th species –14. Genomain.cgi . The genistance) .QFTY00000000. Raw sequence reads have been deposited at DDBJ/EMBL/GenBank under accession no. SRR9048023. The version described in this paper is the first version, QFTY01000000.This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no.


As the central dogma of molecular biology, genetic information flows from DNA through transcription into RNA followed by translation of the message into protein by transfer RNAs (tRNAs). However, mRNA translation is not always perfect, and errors in the amino acid composition may occur. Mistranslation is generally well tolerated, but once it reaches superphysiological levels, it can give rise to a plethora of diseases. The key causes of mistranslation are errors in translational decoding of the codons in mRNA. Such errors mainly derive from tRNA misdecoding and misacylation, especially when certain codon-paired tRNA species are missing. Substantial progress has recently been made with respect to the mechanistic basis of erroneous mRNA decoding as well as the resulting consequences for physiology and pathology. Here, we aim to review this progress with emphasis on viral evolution and cancer development. Because of wobbling and superwobbling, it is possible to use 32 tRNA species for decoding all 64 possible codons , 22. In plastids , 25, 26.ANN, the NNU codons likely only pair with tRNAGNN, tRNAUNN, and tRNAINN as dictated by the revised wobble rules , as conversion of tRNAANN to tRNAINN is catalyzed by the tRNA-dependent adenosine deaminases 2 (ADAT2) [GNN, it will lead to a G•U wobble pair without concomitant amino acid misincorporation, as the same amino acid is coded by NNU and NNC (tRNAGNN) codons  code for different amino acids at the 2-fold degenerate codon box, resulting in leucine→phenylalanine, lysine→asparagine, glutamic acid→aspartic acid, glutamine→histidine, Stop→tyrosine, and selenocysteine→cysteine misdecoding ,,ANN, the (ADAT2) . Specifi) codons . If NNU decoding . Accordiectively –30. Misrectively . This tyectively , 22. Sucdecoding .GNN, the NNC codons are expected to pair with tRNAANN, tRNAUNN, and tRNAINN  code for different amino acids in twice-degenerated codons (U (tyrosine)-UAA (Stop) mismatch will truncate the elongation process of nascent peptide , and this predisposes organisms to a potential arginine→serine misincorporation  [CGU/CGC codons as cysteine UGU/UGC codons [GU codon misdecoded by tRNAAGG-Leu [Nonsense translation, so-called stop-codon readthrough, can result from aberrant decoding of stop codons by noncognate aminoacyl-tRNAs (examples are Gln[p codon) , 33. Thep codon) . PositioC codons , 36. By AGAG-Leu . Thus, sAGAG-Leu , 5 (Tabl−3 to 10−5) that strongly imply a universal role of this mismatch in translation errors [It has been reported that G•T mismatching occurs in both DNA and RNA duplex following tautomerization and ionization, and this plays important roles in replication and translation errors , 38. Then errors , 36. HenE. coli, four types of misacylated-tRNA—including Cys-tRNAPro, Ser-tRNAThr, Glu-tRNAGln, and Asp-tRNAAsn—do not evoke a correctional reaction [Faithful translation of the mRNA codons into protein is essential for cellular physiology. The fidelity of the translation machinery firstly depends on the specific coupling of amino acids to their cognate tRNA species, which is catalyzed by aminoacyl-tRNA synthetases (aaRSs) . aaRS isreaction . In bothreaction . In mycoreaction . Thus, breaction –45. AparHow could tRNA wobbling guarantee faithful decoding by the codon–anticodon duplex? During elongation, eEF-1A or EF-Tu delivers amino acid–coupled tRNA to the ribosome A site . SubsequE. coli does not compromise physiology of this organism and is even compatible with bacterial proliferation [The integrity of mRNA translation sustains essential cellular physiology in all domains of life. Low level of mistranslation, however, is well tolerated and even contributes to stress responses, as it creates a degree of diversity in the proteome  . Yeasts feration . aaRSs oferation . In mammferation .Ala mischarging with serine residues by an editing-defective AlaRS is associated with neurodegeneration [Rates of mistranslation vary dramatically between organisms and different environmental conditions . An overneration . In addineration . However−8 to 10−6 s/n/c for DNA viruses and from 10−6 to 10−4 s/n/c for RNA viruses [Viral genomes are dynamically mutated with frequent emergence of new quasispecies. The spectrum for the hypermutation of viral genomes, sometimes denominate as mutant clouds . Mutatio viruses . Apparen viruses . Within  viruses , 57. TheLittle is known of the consequences of an error-prone translation machinery on viral evolution. As discussed, erroneous protein synthesis is prone to occur especially when cells suffer cellular stresses like viral infection. In this situation, the viral RNA is possibly mistranslated during the inaccurate translation . SeveralAs for DNA viruses, the mechanisms driving viral mutation are more diverse and less well understood. Degradation of HIV-1 proviral DNA with G→A hypermutation has an important role in host responses to infection . This suGlu-UUC and tRNAArg-CCG in breast cancer [Malignant transformation is usually associated with accumulation of large numbers of DNA mutations. Once occurring in essential oncogenes and tumor suppressors, these are also intimately associated with cancer development and progression , 65. Thet cancer , 71. Mort cancer . For exat cancer . How thet cancer , 73–75. t cancer . The ribt cancer , 75. Thit cancer , 77. In t cancer . MoreoveIt is important to note that N→T missense mutations are widespread in cancer . This tyV600E melanoma cultures [Though mistranslation promotes carcinogenesis, it also offers possible targets for anticancer therapeutics. Targeting enzymes catalyzing U34 tRNA modification has been demonstrated the potential for treating melanoma . Depleticultures . Geneticcultures . Misincocultures , 84. Morcultures . These tcultures , 86.mRNA mistranslation universally occurs across all living organisms. It is generally well tolerated in physiology and even helps the organism adapt and withstand cell stresses. However, excessive mistranslation is pathogenic and implicated in many diseases. Mistranslation may also provide targets for drug and vaccine development, in particular against viral infection and cancer.Although mRNA mistranslation can be caused by a variety of mechanisms, tRNA misdecoding and tRNA misacylation are the key drivers. The former is largely attributed to the partially missing tRNAs and excessive wobbling decoding. Consequently, mRNA codons can be coupled to cognate or near-cognate tRNAs at position 3, leading to modulation of translation efficiency and misincorporation . By furtThe development of high-throughput sequencing and ribosome profiling technologies has greatly advanced our understanding of tRNA decoder . However


Corynebacterium urinapleomorphum nov. sp., Staphylococcus saprophyticus and Helicobacter pylori. The latter colonies were confirmed as H. pylori by immunohistochemistry and biochemical methods. H. pylori cultured from the gallbladder exhibited both the same DNA fingerprinting and Western cagA gene sequence with ABC-type EPIYA (Glu-Pro-Ile-Tyr-Ala) phosphorylation motifs as isolates recovered from the gastric mucus of the same patient, suggesting that gastric H. pylori can also colonize other organs in the human body. Taken together, here we report, for the first time, the identification and characterization of a community consisting of live S. saprophyticus; C. urinapleomorphum, and H. pylori in the gallbladder of a patient with acute cholecystitis. Their potential infection routes and roles in pathogenesis are discussed.Culture-independent studies have identified DNA of bacterial pathogens in the gallbladder under pathological conditions, yet reports on the isolation of corresponding live bacteria are rare. Thus, it is unclear which pathogens, or pathogen communities, can colonize the gallbladder and cause disease. Using light microscopy, scanning electron microscopy, culture techniques, phylogenetic analysis, urease assays and Western blotting, we investigated the presence of live bacterial communities in the gallbladder of a cholecystitis patient after cholecystectomy. 16S rRNA gene sequencing of isolated bacterial colonies revealed the presence of pathogens most closely resembling  Escherichia coli, Salmonella enteritidis, Acinetobacter baumannii, Citrobacter freundii, Enterobacter cloacae, and Klebsiella species. Within Gram-positives, Clostridium perfringens is most commonly observed. Additionally, in some Asian countries, the presence of Helicobacter pylori has been detected infrequently in the gallbladder by PCR [H. pylori infections could lead to gallbladder disease. In this report, an acute case of cholecystitis was presented to our hospital, and after surgical removal, the gallbladder was used for microbial analysis. Here, we present the results of studies using light microscopy, scanning electron microscopy, culture techniques, phylogenetic analysis, urease assays, and Western blotting to investigate the presence of live bacterial communities in the gallbladder of this patient.Acute cholecystitis is considered a serious, potentially life-threatening complication and is one of the most common surgically treated diseases. Bacterial infection is commonly reported in 50 to 90% of the cases ,2,3. Galr by PCR ,7,8. ThiH. pylori gastritis as determined by Warthin silver staining and culturing. After collecting a sample by endoscopy, a conventional triple antibiotics therapy for 7 days was prescribed to eradicate gastric H. pylori. As the nightly colics continued for the next three weeks, ultrasound diagnostics was performed revealing a thickened gallbladder wall and signs of inflammation, suspicious for cholecystitis. Two gallstones measuring up to 1.5 cm were detected before removal of the gallbladder by standard laparoscopic surgery. Histopathology suggested a microbial infection as the etiology for the observed pathological changes of the gallbladder.A 50-year-old male patient with a history of nightly lower abdominal pain for three months was transferred to the emergency room at Erlangen University Hospital. First routine examinations revealed that heart, spine, liver and kidney showed no pathological changes. The patient had no diarrhea, no fever and no apparent changes in blood values. Gastroscopy revealed a moderately chronic slightly active TM  [. PCR products with the expected sizes were produced from all colonies and were subsequently sequenced. Three different sequences corresponding to the three different colony morphologies were further analyzed by a BLAST  query to determine the identity of the isolated bacteria. Query and reference sequences were aligned using CLUSTAL in MEGA7  [Staphylococcus saprophyticus ATCC 15305  ,11. ThreGermany) ,13. PCR lysis 7)  and cluslysis 7) . Their elysis 7) . This anCC 15305 A. Isolat species B, but a n BM012B C. No othH. pylori were approximately 0.5–1 µm in diameter and varied in length from 2–3 µm. In addition, spherical round-shaped bacteria were observed, which could either represent Gram-positive species or coccoid forms of H. pylori (red arrows). These morphological results suggested the presence of live, spiral-shaped, and spherical bacteria in the gallbladder tissue, in agreement with the culture results and their above described identification. Notably, these bacteria were mostly detected focally and only in certain locations.To corroborate the above findings, the gallbladder tissue samples were subjected to microscopic investigation. First, the specimens were stained with hematoxylin–eosin and examined independently by two attending pathologists, who specialized in biliary diseases. Acute cholecystitis was diagnosed by the presence of predominantly mononuclear inflammatory infiltrates, fibrosis with thickening of the gallbladder wall, cholesteatosis, and metaplastic changes. Lymphoid aggregates were found in the wall of the gallbladder but not within the mucosa. Remarkably, the bacteria that were observed in the tissue were primarily bended, curved, and spiral-shaped bacteria that were in close association to the epithelial cells  expressed functional urease enzymes, with activity indistinguishable from that of the fully sequenced and stomach-derived H. pylori control strains 26695 and P12 [urease knockout mutant of the reference strain that was included as a negative control (S. saprophyticus and C. urinapleomorphum (our unpublished data). To further characterize these gallbladder H. pylori isolates, we performed protein profiling of total cell lysates using Coomassie staining. Bands migrating at positions typical of highly expressed proteins CagA, Urease A, and Urease B [Hp-1, Hp-2, and the two H. pylori control strains . The genetic profiles of these strains were analyzed using random amplified polymorphism DNA (RAPD) fingerprinting method as described in ref. [H. pylori typically display DNA sequence diversity between individuals, different isolates are easily distinguishable by RAPD, even with a single RAPD primer [cagA gene containing the EPIYA phosphorylation sequences and subjected the PCR products to sequencing. The results also showed identical cagA sequences for every strain and revealed a typical Western-type EPIYA-motif ABC arrangement (our unpublished data). Together, these data suggest that a single H. pylori strain of Western origin colonized both the stomach and the gallbladder.Lastly, we compared the croscopy  revealed gastric A and gal gastric B. These  in ref. ,26. BecaD primer . This anS. saprophyticus, C. urinapleomorphum, and H. pylori from the gallbladder of a patient with gallstones and symptoms of cholecystitis.Infections of the human gastrointestinal tract have been proposed to frequently propagate to the gallbladder ,28,29. RStaphylococcus saprophyticus, a Gram-positive, coagulase-negative Staphylococcus species, is a regular cause of community-acquired urinary tract infections [S. saprophyticus is commonly isolated from food such as meat, cheese, and vegetables, and often colonizes the human and animal gastrointestinal and genital tracts. S. saprophyticus causes about 10 to 20% of urinary tract infections, and patients commonly exhibit symptomatic cystitis. Similarly, Corynebacterium urinapleomorphum strain Marseille-P2799T (CSURP2799) has been isolated from a urine sample of a two-months-old child with gastroenteritis [H. pylori is commonly found in the human stomach and is responsible for diseases ranging from gastritis to severe malignancies [H. pylori is transmitted to the stomach have been widely unsuccessful [H. pylori in the gallbladder of cholecystitis patients [fections ,32. S. snteritis , while Hgnancies . Attemptccessful ,36. Somepatients ,6,7,8. HH. pylori in the gallbladder of a German patient. To our knowledge, this is the first report on the discovery of viable H. pylori from a gallbladder sample of a patient from the Western hemisphere, a phenomenon which deserves further investigation with large patient cohorts. Some of the bacteria were seen as intracellular, which is in agreement with earlier studies showing invasive H. pylori in gastric epithelial cells [cagA gene may represent a good marker as genome sequencing projects have never revealed two identical cagA genes from different strains. Here, we could demonstrate that the cagA gene sequences in the patient are identical from gallbladder and stomach, encoding a typical Western-type CagA with classical ABC composition in the EPIYA-motif phosphorylation sites, and not the ABD-type present in East Asian isolates [H. pylori, while the stomach was proven to harbor no H. pylori bacteria at all, for example, after eradication with antibiotics. In addition, it should be mentioned that H. pylori has never been found before together with live S. saprophyticus or C. urinapleomorphum at the same infection site. The regular habitat of these pathogens is the gastrointestinal or urogenital tract of humans, respectively. It can therefore be proposed that a gastrointestinal pathway, rather than transport through the bloodstream or other routes of infection, may be involved in the colonization of the gallbladder.Here, we unequivocally identified al cells . Using Risolates ,39. ExtrS. saprophyticus, C. urinapleomorphum, and H. pylori to gallbladder pathology is still unclear. Further studies are therefore necessary to investigate if this environment may represent a reservoir for survival and growth that could serve as a potential source for bacterial transmission. In this case, it is remarkable that the antibiotic therapy eradicated H. pylori from the stomach, but not from the gallbladder. The reason for this treatment failure is not clear and deserves further investigation.The possible contribution of H. pylori, a Warthin–Starry Silver stain was performed. In addition, α-H. pylori antibodies  were used to identify and localize H. pylori in the biopsy samples. Incubation for about 1 h at 4 °C was carried out for binding of the α-H. pylori primary antibody as described [ultra-view Universal Alkaline Phosphatase Red Detection Kit  according to the manufacturer’s protocol .All studies on human biopsy specimens were reviewed and approved through the FAU Ethics Bureau at Erlangen/Germany . The patient gave his informed consent for inclusion before he participated in the study. Routine biopsy specimens were fixed in 4% neutral buffered formalin and paraffinized in an increasing series of alcohol and xylene. The paraffin blocks were cut into 4-micron thick slices and stained with hematoxylin and eosin. For detection of escribed . Antibodg. The mixture was then centrifuged for 5 min at 500× g to remove larger particles and cell debris. Bacteria were then cultured in different amounts  on various culturing media including Mueller–Hinton agar plates, GC agar plates with 10% horse serum, H. pylori selective agar plates, and Columbia agar plates with 5% sheep blood. We used the gas generating systems Anaerogen and Campygen  for incubation of the agar plates in anaerobic jars or cultured the plates under aerobic conditions at 37 °C [Biopsy specimens were collected in sterile Falcon tubes, incubated with brain heart infusion (BHI) medium , and shaken at 37 °C for 15 min at 5000× at 37 °C ,42. ThesThe method was utilized in the initial phase of studies to examine the homogeneity, morphological features, and pureness of all grown bacteria. For this purpose, bacterial samples were analyzed by the conventional Gram-staining method using crystal violet, Gram’s iodine, acetone–ethanol (50:50 ratio), and 0.1% basic fuchsin solution as described .H. pylori strains were grown on GC agar plates under standard conditions as described above. To investigate for active urease enzyme activity, the bacteria were transferred to selective acidified GC agar plates complemented by the urease substrate urea and phenol red as a pH indicator according to a described protocol [All isolated protocol .® Genomic DNA Purification Kit  and subjected to PCR for the amplification of a ~1 kb segment of the 16S rRNA gene using universal primers 27F (5′-AGA GTT TGA TCM TGG CTC AG-3′) and 926R (5′-CCG TCA ATT CCT TTR AGT TT-3′), as well as 16S-FW (5′-GAA GAG TTT GAT CAT GGC TCA G-3′) and 16S-Rev (5′-ACG ACA GCC ATG CAG CAC CT-3′), respectively [https://blast.ncbi.nlm.nih.gov/Blast.cgi), and similar sequences were determined [http://www.megasoftware.net) [Bacterial DNA was isolated from all colonies using Wizardectively ,13. The termined . The resare.net) . Similarare.net) . The evoH. pylori strains 26695 and P12 were suspended in 1× SDS-PAGE buffer and boiled for 5 min [Total protein profiling of the bacteria was done using SDS polyacrylamide gel electrophoresis (SDS-PAGE) according to an adapted protocol . In brieor 5 min ,45. The H. pylori virulence proteins HtrA and GGT were raised against conserved peptide residues (HtrA amino acids 90–103: DKIKVTIPGSNKEY and GGT amino acids 175–188: RQAETLKEARERFL) derived from H. pylori strain 26695 [Bacterial samples were resolved in 6% and 8% SDS-PAGE gels, followed by Western blotting using the semidry blotting method. Mouse monoclonal anti-CagA antibodies were purchased from Austral-Biological . Polyclonal rabbit α-VacA antiserum was kindly provided by Prof. Timothy Cover . Additional polyclonal rabbit antisera against the in 26695 ,46. Thesin 26695 ,48.2, 10 μM CaCl2 at pH 6.9) containing 2% glutaraldehyde and 5% formaldehyde [2 . All samples were subsequently covered with 10 nm gold–palladium films using the sputter coating method . Specimen examination was performed by the Zeiss–Merlin field emission scanning electron microscope operating with Everhart–Thornley and in-lens SE-detectors in a 25:75 ratio at 5 kV acceleration voltage .Bacteria were fixed for 1 h on ice in cacodylate buffer , thirty cycles of , and a final incubation at 72 °C for 10 min.We applied the RAPD fingerprinting methodology to distinguish the identified isolates . The proisolates . PCR bufcagA gene subfragments from H. pylori strains were amplified by PCR using primers 48F (5′-AAA GGA TTG TCC CTA CAA GAA GC-3′) and 38R (5′-CTC GAG ATT TTT GGA AAC CAC CTT TTG-3′), followed by purification via NucleoSpin® Gel and PCR Clean-up columns . Sequences of cagA subfragments from the various strains were determined by GATC Biotech. The obtained sequences were analyzed by CLUSTAL Omega multiple sequence alignment analysis  and a BLASTX search to determine the EPIYA-motif patterns (available online: https://blast.ncbi.nlm.nih.gov/Blast.cgi).To analyze the origin of the strains, EPIYA-motifs in different CagA proteins,


Toxoplasma gondii infection in humans remain poorly known in Senegal. Although rodent surveys could help to assess the circulation of T. gondii, they have seldom been set up in sub-Saharan Africa. The aim of this study was to examine Toxoplasma seroprevalence in rodents from villages and towns across Senegal. Rodents were sampled in 40 localities using a standardised trapping protocol. Detection of T. gondii antibodies was performed on 1205 rodents, using a modified agglutination test (MAT) technique. Seroprevalence data were analysed depending on geography, the local rodent community, and individual characteristics of the rodent hosts. We found 44 seropositive rodents from four different species . Toxoplasma seroprevalence was low, averaging 4% in the localities. Higher Toxoplasma seroprevalence (up to 24%) was found in northern Senegal, a region known to be the heart of pastoral herding in the country.Risks related to  Toxoplasma gondii [T. gondii, all homoeothermic animals may act as intermediate hosts [T. gondii in commensal habitats [a gondii  is an ina gondii . In humate hosts . Rodentshabitats , 30.T. gondii infection in humans has been found to vary between 4% and 40% [Toxoplasma in animal populations has rarely been characterised in Senegal [In sub-Saharan Africa, human seroprevalence is highly variable, with reported values ranging from 4% to 83% . In Sene and 40% , 24. How Senegal .T. gondii obtained from 1205 rodents sampled in villages and towns in Senegal. Seroprevalence data were analysed regarding the geographical location of the sampling locality, its rodent community, and the individual characteristics of the rodent hosts.In this study, we provide serological data for Fieldwork was conducted in 40 localities in Senegal between 2011 and 2014 , Table 1Rodents were identified to the species level using morphologic tools . The rodT. gondii antibodies using a modified agglutination test (MAT) technique [T. gondii antibody-seronegative Swiss mice (not infected by T. gondii) and T. gondii antibody-seropositive Swiss mice   was spotted onto a 5 mm diameter circle on Whatman No. 3 paper and allowed to dry at RT for 24 h, before storage at RT in sealed bags. Antibody titres were determined by the last dilution where the agglutination pattern could be read in comparison with the negative and positive controls. Toxoplasma seroprevalence was finally calculated as the percentage of seropositive rodents in each sampling locality.Dried blood samples were used for the detection of echnique  adapted echnique . Two 5 mP values were obtained by stepwise model simplification using likelihood-ratio tests and were considered significant when p < 0.05. The final model was validated by the graphical checking of normality, independence and variance homogeneity of the residuals. All analyses were performed with R Software using the lme4 v1.1-8 [We carried out a generalised linear model (GLM) assuming a binomial distribution to test whether individual rodent seropositivity was related to geography , rodent community diversity (Simpson index) and relative abundance (estimated using trap success) at the locality of sampling, as well as rodent species, sex and body mass (this variable was centred-reduced to avoid the confounding effect of specific differences). The interactions between rodent species and geographical coordinates were also considered in the model. Using the Akaike information criterion with correction for samples of finite size (AICc), we carried out model selection from the full starting model. We then chose the most parsimonious model among those selected within two AIC units of the best model obtained. 4 v1.1-8  packagesMus musculus domesticus), 513 multimammate rats , 334 black rats (Rattus rattus), 39 Nile rats (Arvicanthis niloticus), 25 Dalton’s mice , three brown rats (Rattus norvegicus) and one fat mouse (Steatomys sp.) : 689 house mice (mys sp.) . Rodent mys sp.) .Mastomys spp., R. rattus, M. m. domesticus, A. niloticus and P. daltoni) were screened for Toxoplasma antibodies. Among them, we found 44 seropositive rodents  and M. natalensis , and the invasive M. m. domesticus , and R. rattus . No seropositive individuals were found among A. niloticus and P. daltoni, represented by very low sample sizes . Within localities, Toxoplasma seroprevalence (mean: 0.04 ± 0.06) ranged from zero  to 24% (code THC)  ; Table 1M. m. domesticus, R. rattus and Mastomys species). Rodent seropositivity was significantly related to latitude , with higher seroprevalence in northern localities , Simpson diversity , trap success , rodent species , sex  or body mass .Statistical analysis was restricted to data for the four species with sufficient sample sizes Mastomys ern part , 15, 18.Toxoplasma seroprevalence was relatively low (4%) in rodents from Senegal. This value closely matches that found in rodents elsewhere [T. gondii infection. The MAT technique is commonly used in diverse species of animals. It was shown to be a reliable indicator of infection in mice of several laboratory strains [Mus musculus offspring infected by vertical transmission from chronically infected dams, although the infection was confirmed by PCR [T. gondii strain has been observed in laboratory and wild mouse strains, indicating different innate immunological reactions linked to polymorphic variations in the IRG system [T. gondii infection among wild rodent species cannot be excluded. All these elements point out the benefit of combining different techniques of Toxoplasma detection in future studies, in order to evaluate their respective value for the screening of rodent communities in the wild.Mean lsewhere , 20, 22. strains , 26. Serd by PCR , 27. DivG system , 21. AlsToxoplasma seroprevalence is expected under Sahelian climatic conditions , which are poorly suitable for oocysts survival and sporulation [Toxoplasma seroprevalence in M. m. domesticus, R. rattus and M. natalensis) [Toxoplasma transmission but increases from south to north [Toxoplasma seroprevalence in rodents. For instance, the proximity of irrigated surfaces may play a role, as indicated by higher Toxoplasma seroprevalence found in rodents that were sampled within irrigated gardens in Niamey [Toxoplasma in Senegal [Toxoplasma seroprevalence found in rodents among the different localities [Low rulation  and may rulation . On the alensis) . Neverthto north  like then Niamey . Seropre Senegal , 12, 28. Senegal . Large pT. gondii infection were not related to variations in rodent communities among localities (R. rattus larger than M. m. domesticus), or in some individuals because of sex or body mass , or M. m. musculus and Mastomys species (that use crevices or cracks as burrows) are less at risk of being infected by T. gondii than fossorial mammals, because they are less in contact with potentially contaminated soil [Variations in calities . We wouls e.g., , 30). Ho. HoT. gos (e.g., , which rted soil .Toxoplasma seroprevalence in rodents at the scale of a Sahelian country. To obtain a clearer view of T. gondii epidemiology, similar studies in rural areas on other epidemiological agents such as cats, sheep and goats, are necessary. They will enable us to better understand the risk factors related to T. gondii in villages and towns of Senegal, which seem to be variable geographically.To our knowledge, this study is the first to focus on The authors declare that they have no conflict of interest.