Risk Factors for Community-Acquired Urinary Tract Infections Caused by ESBL-Producing Enterobacteriaceae –A Case–Control Study in a Low Prevalence Country

Community-acquired urinary tract infection (CA-UTI) is the most common infection caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, but the clinical epidemiology of these infections in low prevalence countries is largely unknown. A population based case-control study was conducted to assess risk factors for CA-UTI caused by ESBL-producing E. coli or K. pneumoniae. The study was carried out in a source population in Eastern Norway, a country with a low prevalence of infections caused by ESBL-producing Enterobacteriaceae. The study population comprised 100 cases and 190 controls with CA-UTI caused by ESBL-producing and non-ESBL-producing E. coli or K. pneumoniae, respectively. The following independent risk factors of ESBL-positive UTIs were identified: Travel to Asia, The Middle East or Africa either during the past six weeks (Odds ratio (OR) = 21; 95% confidence interval (CI): 4.5–97) or during the past 6 weeks to 24 months (OR = 2.3; 95% CI: 1.1–4.4), recent use of fluoroquinolones (OR = 16; 95% CI: 3.2–80) and β-lactams (except mecillinam) (OR = 5.0; 95% CI: 2.1–12), diabetes mellitus (OR = 3.2; 95% CI: 1.0–11) and recreational freshwater swimming the past year (OR = 2.1; 95% CI: 1.0–4.0). Factors associated with decreased risk were increasing number of fish meals per week (OR = 0.68 per fish meal; 95% CI: 0.51–0.90) and age (OR = 0.89 per 5 year increase; 95% CI: 0.82–0.97). In conclusion, we have identified risk factors that elucidate mechanisms and routes for dissemination of ESBL-producing Enterobacteriaceae in a low prevalence country, which can be used to guide appropriate treatment of CA-UTI and targeted infection control measures.     

Antimicrobial resistance including Extended Spectrum Beta Lactamases (ESBL) among E. coli isolated from kenyan children at hospital discharge

BackgroundChildren who have been discharged from hospital in sub-Saharan Africa remain at substantial risk of mortality in the post-discharge period. Antimicrobial resistance (AMR) may be an important factor. We sought to determine the prevalence and risk factors associated with AMR in commensal Escherichia coli (E. coli) from Kenyan children at the time of discharge.Methodology/Principle findingsFecal samples were collected from 406 children aged 1–59 months in western Kenya at the time of discharge from hospital and cultured for E. coli. Susceptibility to ampicillin, ceftriaxone, cefotaxime, ceftazidime, cefoxitin, imipenem, ciprofloxacin, gentamicin, combined amoxicillin/clavulanic acid, trimethoprim-sulfamethoxazole, azithromycin, and chloramphenicol was determined by disc diffusion according to guidelines from the Clinical and Laboratory Standards Institute (CLSI). Poisson regression was used to determine associations between participant characteristics and the presence of extended-spectrum beta-lactamases (ESBL) producing E. coli. Non-susceptibility to ampicillin (95%), gentamicin (44%), ceftriaxone (46%), and the presence of ESBL (44%) was high. Receipt of antibiotics during the hospitalization was associated with the presence of ESBL (aPR = 2.23; 95% CI: 1.29–3.83) as was being hospitalized within the prior year (aPR = 1.32 [1.07–1.69]). Open defecation (aPR = 2.02; 95% CI: 1.39–2.94), having a toilet shared with other households (aPR = 1.49; 95% CI: 1.17–1.89), and being female (aPR = 1.42; 95% CI: 1.15–1.76) were associated with carriage of ESBL E. coliConclusions/SignificanceAMR is common among isolates of E. coli from children at hospital discharge in Kenya, including nearly half having detectable ESBL.     

Determinants of Antimicrobial Resistance in Escherichia coli Strains Isolated from Faeces and Urine of Women with Recurrent Urinary Tract Infections

For women with recurrent urinary tract infections (rUTI), the contribution of antibiotic use versus patient-related factors in determining the presence of antimicrobial resistance in faecal and urinary Escherichia coli, obtained from the same patient population, has not been assessed yet. Within the context of the ‘Non-antibiotic prophylaxis for recurrent urinary tract infections’ (NAPRUTI) study, the present study assessed determinants of antimicrobial resistance in E. coli isolated from urinary and faecal samples of women with rUTIs collected at baseline. Potential determinants of resistance were retrieved from self-administered questionnaires. From 434 asymptomatic women, 433 urinary and 424 faecal samples were obtained. E. coli was isolated from 146 (34%) urinary samples and from 336 (79%) faecal samples, and subsequently tested for antimicrobial susceptibility. Multivariable analysis showed trimethoprim/sulfamethoxazole (SXT) use three months prior to inclusion to be associated with urine E. coli resistance to amoxicillin (OR 3.6, 95% confidence interval: 1.3–9.9), amoxicillin-clavulanic acid (OR 4.4, 1.5–13.3), trimethoprim (OR 3.9, 1.4–10.5) and SXT (OR 3.2, 1.2–8.5), and with faecal E. coli resistance to trimethoprim (OR 2.0, 1.0–3.7). The number of UTIs in the preceding year was correlated with urine E. coli resistance to amoxicillin-clavulanic acid (OR 1.11, 1.01–1.22), trimethoprim (OR 1.13, 1.03–1.23) and SXT (OR 1.10, 1.01–1.19). Age was predictive for faecal E. coli resistance to amoxicillin (OR 1.02, 1.00–1.03), norfloxacin and ciprofloxacin (both OR 1.03, 1.01–1.06). In conclusion, in women with rUTI different determinants were found for urinary and faecal E. coli resistance. Previous antibiotic use and UTI history were associated with urine E. coli resistance and age was a predictor of faecal E. coli resistance. These associations could best be explained by cumulative antibiotic use.     

Epidemiology of Antimicrobial Resistance in Escherichia coli Isolates from Raccoons (Procyon lotor) and the Environment on Swine Farms and Conservation Areas in Southern Ontario

Antimicrobial resistance is a global threat to livestock, human and environmental health. Although resistant bacteria have been detected in wildlife, their role in the epidemiology of antimicrobial resistance is not clear. Our objective was to investigate demographic, temporal and climatic factors associated with carriage of antimicrobial resistant Escherichia coli in raccoons and the environment. We collected samples from raccoon paws and feces and from soil, manure pit and dumpsters on five swine farms and five conservation areas in Ontario, Canada once every five weeks from May to November, 2011–2013 and tested them for E. coli and susceptibility to 15 antimicrobials. Of samples testing positive for E. coli, resistance to ≥ 1 antimicrobials was detected in 7.4% (77/1044; 95% CI, 5.9–9.1) of raccoon fecal samples, 6.3% (23/365; 95% CI, 4.0–9.3) of paw samples, 9.6% (121/1260; 8.0–11.4) of soil samples, 57.4% (31/54; 95% CI, 43.2–70.8) of manure pit samples, and 13.8% (4/29; 95% CI, 3.9–31.7) of dumpster samples. Using univariable logistic regression, there was no significant difference in the occurrence of resistant E. coli in raccoon feces on conservation areas versus farms; however, E. coli isolates resistant to ≥ 1 antimicrobials were significantly less likely to be detected from raccoon paw samples on swine farms than conservation areas and significantly more likely to be detected in soil samples from swine farms than conservation areas. Resistant phenotypes and genotypes that were absent from the swine farm environment were detected in raccoons from conservation areas, suggesting that conservation areas and swine farms may have different exposures to resistant bacteria. However, the similar resistance patterns and genes in E. coli from raccoon fecal and environmental samples from the same location types suggest that resistant bacteria may be exchanged between raccoons and their environment.     

Taking care of a diarrhea epidemic in an urban hospital in Bangladesh: Appraisal of putative causes,presentation, management,and deaths averted

BackgroundIn April 2018, a diarrhea epidemic broke out in Dhaka city and adjoining areas, which continued through May. The Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), a dedicated diarrheal disease hospital, had a large upsurge in patient visits during the epidemic. An enhanced understanding of the epidemiology of this epidemic may help health-related professionals better prepare for such events in the future. This study examined the microbial etiology and non-pathogen factors associated with diarrhea during the epidemic. The study also evaluated the patients’ presentation and clinical course and estimated the potential mortality averted by treating patients during the epidemic.Methodology/Principal findingsData from the patients who were treated at Dhaka Hospital during the diarrhea epidemic between April 2 and May 12, 2018 and were enrolled into the Diarrheal Disease Surveillance System (DDSS) at icddr,b were compared with the DDSS-enrolled patients treated during the seasonally-matched periods in the flanking years using logistic regression. icddr,b Dhaka Hospital treated 29,212 diarrheal patients during the 2018 epidemic period (and 25,950 patients per comparison period on average). Vibrio cholerae was the most common pathogen isolated (7,946 patients; 27%) and associated with diarrhea during the epidemic (adjusted odds ratio [AOR] 1.5, 95% CI: 1.1–2.0). The interaction of Vibrio cholerae with ETEC (AOR 2.7, 95% CI: 1.3–5.9) or Campylobacter (AOR 2.4, 95% CI: 1.1–5.1) was associated with further increased odds of diarrhea during the epidemic. In children under five years old, rotavirus was the most common pathogen (2,029 patients; 26%). Those who were adolescents (AOR 2.0, 95% CI: 1.3–3.1) and young adults (AOR 1.9, 95% CI: 1.4–2.5) compared to children younger than five years, resided within a 10 km radius of Dhaka Hospital (AOR 1.6, 95% CI: 1.1–2.2) compared to those living outside 20 km, borrowed money or relied on aid to pay for the transport to the hospital (AOR 1.6, 95% CI: 1.2–2.0), used tap water (AOR 1.8, 95% CI: 1.4–2.4) for drinking compared to tubewell water, and disposed of the solid waste directly outside the house (AOR 4.0, 95% CI: 2.7–5.9) were more likely to present with diarrhea during the epidemic. During the epidemic, patients were more likely to present with severe dehydration (odds ratio [OR] 1.6, 95% CI: 1.3–2.0) and require inpatient admission (OR 2.5, 95% CI: 1.9–3.3), intravenous rehydration (OR 1.7, 95% CI: 1.4–2.1), and antibiotics (OR 2.2, 95% CI: 1.8–2.7). The in-hospital case fatality rate was low (13 patients; 0.04%), and the hospital averted between 12,523 and 17,265 deaths during the epidemic.Conclusions/SignificanceVibrio cholerae played the primary role in the 2018 diarrhea epidemic in Dhaka. Campylobacter, enterotoxigenic Escherichia coli, and rotavirus had a secondary role. Adolescents and adults, residents of the metropolitan area, and those who were relatively poor and lacked safe water, sanitation, and hygiene (WASH) practices comprised the most vulnerable groups. Despite the increased disease severity during the epidemic, the case fatality rate was less than 0.1%. icddr,b Dhaka Hospital saved as many as 17,265 lives during the epidemic.     

A Decline in HIV and Syphilis Epidemics in Chinese Female Sex Workers (2000–2011): A Systematic Review and Meta-Analysis

Background

Female sex workers (FSWs) play an important role in transmitting HIV and syphilis from high-risk groups to the general population. However, the trends in HIV and syphilis epidemics in Chinese FSWs in the period after 2000 are unclear to date.

Methods

The Preferred Reporting Items for Systematic Reviews and Meta-Analyses Statement was followed. Seven databases were searched for published peer-reviewed articles. The incidence of HIV and syphilis in FSWs in different time periods, provinces and workplaces in China were separately pooled by meta-analysis. Correlation analysis was conducted between HIV and syphilis incidence and study time, respectively.

Results

After 1,662 articles were screened, 190 published papers were included in the final analysis. Estimated HIV prevalence was 0.284% (95% CI: 0.080–0.488%) in the period 2000–2002, 0.211% (95% CI: 0.149–0.273%) in 2003–2005, 0.242% (95% CI: 0.190–0.294%) in 2006–2008 and 0.041% (95% CI: 0.024–0.058%) in 2009–2011. The corresponding syphilis prevalence was 9.669% (95% CI: 7.810–11.529%), 4.970% (95% CI: 4.384–5.556%), 4.404% (95% CI: 4.032–4.775%) and 3.169% (95% CI: 2.738–3.600%), respectively. Spearman rank correlation coefficients were −0.165 (p = 0.002) between HIV prevalence and study time, and −0.209 (p = 0.000) between syphilis prevalence and study time. The combined HIV prevalence was 0.318% (95% CI: 0.156–0.479%) in medium and high-tier workplaces and 0.393% (95% CI: 0.176–0.610%) in low-tier workplaces. The corresponding syphilis prevalence was 3.216% (95% CI: 2.192–4.240%) and 13.817% (95% CI: 10.589–17.044%), respectively.

Conclusions

Our data suggested a decline in HIV and syphilis epidemics in FSWs in China on a national level during the study period (2000–2011). FSWs in low-tier workplaces should be given more attention in the future to ensure they are included in prevention programs for HIV and sexually transmitted diseases.     

The Efficacy and Safety of Linezolid and Glycopeptides in the Treatment of Staphylococcus aureus Infections

To assess the effectiveness and safety of linezolid in comparison with glycopeptides (vancomycin and teicoplanin) for the treatment of Staphylococcus aureus infections, we conducted a meta-analysis of relevant randomized controlled trials. A thorough search of Pubmed and other databases was performed. Thirteen trials on 3863 clinically assessed patients were included. Linezolid was slightly more effective than glycopeptides in the intent-to-treat population (odds ratio [OR], 1.05; 95% confidence interval [CI], 1.01–1.10), was more effective in clinically assessed patients (OR 95% CI: 1.38, 1.17–1.64) and in all microbiologically assessed patients (OR 95% CI: 1.38, 1.15–1.65). Linezolid was associated with better treatment in skin and soft-tissue infections (SSTIs) patients (OR 95% CI: 1.61, 1.22–2.12), but not in bacteraemia (OR 95% CI: 1.24, 0.78–1.97) or pneumonia (OR 95% CI: 1.25, 0.97–1.60) patients. No difference of mortality between linezolid and glycopeptides was seen in the pooled trials (OR 95% CI: 0.98, 0.83–1.15). While linezolid was associated with more haematological (OR 95% CI: 2.23, 1.07–4.65) and gastrointestinal events (OR 95% CI: 2.34, 1.53–3.59), a significantly fewer events of skin adverse effects (OR 95% CI: 0.27, 0.16–0.46) and nephrotoxicity (OR 95% CI: 0.45, 0.28–0.72) were recorded in linezolid. Based on the analysis of the pooled data of randomized control trials, linezolid should be a better choice for treatment of patients with S. aureus infections, especially in SSTIs patients than glycopeptides. However, when physicians choose to use linezolid, risk of haematological and gastrointestinal events should be taken into account according to the characteristics of the specific patient populations.     

Gastrointestinal Infections and Diarrheal Disease in Ghanaian Infants and Children: An Outpatient Case-Control Study

IntroductionDiarrheal diseases are among the most frequent causes of morbidity and mortality in children worldwide, especially in resource-poor areas. This case-control study assessed the associations between gastrointestinal infections and diarrhea in children from rural Ghana.MethodsStool samples were collected from 548 children with diarrhea and from 686 without gastrointestinal symptoms visiting a hospital from 2007–2008. Samples were analyzed by microscopy and molecular methods.ResultsThe organisms most frequently detected in symptomatic cases were Giardia lamblia, Shigella spp./ enteroinvasive Escherichia coli (EIEC), and Campylobacter jejuni. Infections with rotavirus (adjusted odds ratio [aOR] = 8.4; 95% confidence interval [CI]: 4.3–16.6), C. parvum/hominis (aOR = 2.7; 95% CI: 1.4–5.2) and norovirus (aOR = 2.0; 95%CI: 1.3–3.0) showed the strongest association with diarrhea. The highest attributable fractions (AF) for diarrhea were estimated for rotavirus (AF = 14.3%; 95% CI: 10.9–17.5%), Shigella spp./EIEC (AF = 10.5%; 95% CI: 3.5–17.1%), and norovirus (AF = 8.2%; 95% CI 3.2–12.9%). Co-infections occurred frequently and most infections presented themselves independently of other infections. However, infections with E. dispar, C. jejuni, and norovirus were observed more often in the presence of G. lamblia.ConclusionsDiarrheal diseases in children from a rural area in sub-Saharan Africa are mainly due to infections with rotavirus, Shigella spp./EIEC, and norovirus. These associations are strongly age-dependent, which should be considered when diagnosing causes of diarrhea. The presented results are informative for both clinicians treating gastrointestinal infections as well as public health experts designing control programs against diarrheal diseases.     

Efficacy and Safety of Lenalidomide for Treatment of Low-/Intermediate-1-Risk Myelodysplastic Syndromes with or without 5q Deletion: A Systematic Review and Meta-Analysis

BackgroundLenalidomide could effectively induce red blood cell (RBC) transfusion independence (TI) in patients with lower-risk (Low/Intermediate-1) myelodysplastic syndrome (MDS) with or without 5q deletion. However whether lenalidomide ultimately improves the overall survival (OS) of lower-risk MDS patients and reduces the progression to AML remains controversial.MethodA meta-analysis was conducted to examine the efficacy and safety of lenalidomide in the treatment of lower-risk MDS. Efficacy was assessed according to erythroid hematologic response (HI-E), cytogenetic response (CyR), OS and AML progression. Safety was evaluated based on the occurrence rates of grades 3–4 adverse events (AEs).ResultsSeventeen studies were included consisting of a total of 2160 patients. The analysis indicated that the overall rate of HI-E was 58% with 95% confidence interval (CI) of 43–74%. The pooled estimates for the rates of CyR, complete CyR, and partial CyR were 44% (95% CI 19–68%), 21% (95% CI 13–30%) and 23% (95% CI 15–32%), respectively. The patients with 5q deletion had significantly higher rate of HI-E and CyR than those without 5q deletion (P = 0.002 and 0.001, respectively). The incidences of grades 3–4 neutropenia, thrombocytopenia, leukopenia, anemia, deep vein thrombosis, diarrhea, fatigue and rash were 51% (95% CI 30–73%), 31% (95% CI 20–42%), 9% (95% CI 5–13%), 7% (95% CI 2–12%), 3% (95% CI 2–5%), 3% (95% CI 1–5%), 2% (95% CI 1–4%) and 2% (95% CI 1–3%), respectively. Lenalidomide significantly improved OS (HR: 0.62, 95% CI 0.47–0.83, P = 0.001) and lowered the risk of AML progression in del(5q) patients (RR: 0.61, 95% CI 0.41–0.91, P = 0.014).ConclusionsIn spite of the AEs, lenalidomide could be effectively and safely used for the treatment of lower-risk MDS patients with or without 5q deletion.     

The control of sulphate activation in bacteria

1. ATP–sulphate adenylyltransferase (EC 2.7.7.4) and ATP–adenylyl sulphate 3′-phosphotransferase (EC 2.7.1.25) of Escherichia coli 9723, E. coli K₁₂ and Bacillus subtilis 1379 are each repressed by growth in the presence of cystine. Repression of the two enzymes in E. coli 9723 may be co-ordinate. 2. ATP–sulphate adenylyltransferase of Desulphovibrio desulphuricans, in which sulphate reduction is linked to the energy supply of the organism, is not repressed by growth in the presence of inorganic sulphite or cysteine. 3. Leuconostoc mesenteroides lacks all the enzymes between sulphate and cysteine whether grown on cysteine or glutathione.     

Prognostic Significance of KIT Mutations in Core-Binding Factor Acute Myeloid Leukemia: A Systematic Review and Meta-Analysis

The prognostic significance of KIT mutations in core-binding factor acute myeloid leukemia (CBF-AML), including inv(16) and t(8;21) AML, is uncertain. We performed a systematic review and meta-analysis of the effect of KIT mutations on the complete remission (CR) and relapse rates and overall survival (OS) of CBF-AML. PubMed, Embase, Web of Science, and the Cochrane Library were searched and relevant studies were included. Negative effect was indicated on relapse risk of CBF-AML (RR [relative risk], 1.43; 95%CI [confidence interval], 1.20–1.70) and t(8;21) AML (RR, 1.70; 95% CI, 1.31–2.21), not on OS of CBF-AML (RR, 1.09; 95% CI, 0.97–1.23), CR (OR [odds ratio], 0.95; 95% CI, 0.52–1.74), relapse risk (RR, 1.12; 95% CI, 0.90–1.41) or OS (RR, 1.03; 95% CI, 0.90–1.18) of inv(16) AML. Subgroup analysis of t(8,21) AML showed negative effect of KIT mutations on CR (OR, 2.03; 95%CI: 1.02–4.05), relapse risk (RR, 1.89; 95%CI: 1.51–2.37) and OS (RR, 2.26; 95%CI: 1.35–3,78) of non-Caucasians, not on CR (OR, 0.61; 95%CI: 0.19–1.95) or OS (RR, 1.12; 95%CI: 0.90–1.40) of Caucasians. This study indicates KIT mutations in CBF-AML to be included in the initial routine diagnostic workup and stratification system of t(8,21) AML. Prospective large-scale clinical trials are warranted to evaluate these findings.     

Estimates of Electronic Medical Records in U.S. Emergency Departments

Background

Policymakers advocate universal electronic medical records (EMRs) and propose incentives for “meaningful use” of EMRs. Though emergency departments (EDs) are particularly sensitive to the benefits and unintended consequences of EMR adoption, surveillance has been limited. We analyze data from a nationally representative sample of US EDs to ascertain the adoption of various EMR functionalities.

Methodology/Principal Findings

We analyzed data from the National Hospital Ambulatory Medical Care Survey, after pooling data from 2005 and 2006, reporting proportions with 95% confidence intervals (95% CI). In addition to reporting adoption of various EMR functionalities, we used logistic regression to ascertain patient and hospital characteristics predicting “meaningful use,” defined as a “basic” system (managing demographic information, computerized provider order entry, and lab and imaging results). We found that 46% (95% CI 39–53%) of US EDs reported having adopted EMRs. Computerized provider order entry was present in 21% (95% CI 16–27%), and only 15% (95% CI 10–20%) had warnings for drug interactions or contraindications. The “basic” definition of “meaningful use” was met by 17% (95% CI 13–21%) of EDs. Rural EDs were substantially less likely to have a “basic” EMR system than urban EDs (odds ratio 0.19, 95% CI 0.06–0.57, p = 0.003), and Midwestern (odds ratio 0.37, 95% CI 0.16–0.84, p = 0.018) and Southern (odds ratio 0.47, 95% CI 0.26–0.84, p = 0.011) EDs were substantially less likely than Northeastern EDs to have a “basic” system.

Conclusions/Significance

EMRs are becoming more prevalent in US EDs, though only a minority use EMRs in a “meaningful” way, no matter how “meaningful” is defined. Rural EDs are less likely to have an EMR than metropolitan EDs, and Midwestern and Southern EDs are less likely to have an EMR than Northeastern EDs. We discuss the nuances of how to define “meaningful use,” and the importance of considering not only adoption, but also full implementation and consequences.     

Bacteriology and Changes in Antibiotic Susceptibility in Adults with Community-Acquired Perforated Appendicitis

This study evaluated bacterial etiology and antibiotic susceptibility in patients diagnosed with community-acquired perforated appendicitis over a 12-year-period. We retrospectively reviewed records of adult patients diagnosed with perforated appendicitis at an 800-bed teaching hospital between January 2000 and December 2011. In total, 415 culture-positive perforated appendicitis cases were analyzed. Escherichia coli was the most common pathogen (277/415, 66.7%), followed by Streptococcus species (61/415, 14.7%). The susceptibility of E. coli to ampicillin, piperacillin/tazobactam, ceftriaxone, cefepime, amikacin, gentamicin, and imipenem was 35.1%, 97.1%, 97.0%, 98.2%, 98.9%, 81.8%, and 100%, respectively. The overall susceptibility of E. coli to quinolones (ciprofloxacin or levofloxacin) was 78.7%. During the study period, univariate logistic regression analysis showed a significant decrease in E. coli susceptibility to quinolones (OR = 0.91, 95% CI 0.84–0.99, P = 0.040). We therefore do not recommend quinolones as empirical therapy for community-acquired perforated appendicitis.     

A meta-analysis reveals the effectiveness of probiotics and prebiotics against respiratory viral infection

Experimental experience suggests that microbial agents including probiotics and prebiotics (representative microbial agents) play a critical role in defending against respiratory virus infection. We aim to systematically examine these agents’ effect on respiratory viral infection and encourage research into clinical applications. An electronic literature search was conducted from published data with a combination of a microbial agents search component containing synonyms for microbial agents-related terms and a customized search component for respiratory virus infection. Hazard ratio (HR), risk ratio (RR) and standard deviation (SD) were employed as effect estimates. In 45 preclinical studies, the mortality rates decreased in the respiratory viral infection models that included prebiotics or prebiotics as interventions (HR: 0.70; 95% confidence interval (CI): 0.56–0.87; P=0.002). There was a significant decrease in viral load due to improved gut microbiota (SD: −1.22; 95% CI: −1.50 to −0.94; P<0.001). Concentrations of interferon (IFN)-α (SD: 1.05; 95% CI: 0.33–1.77; P=0.004), IFN-γ (SD: 0.83; 95% CI: 0.01–1.65; P=0.05) and interleukin (IL)-12 (SD: 2.42; 95% CI: 0.32–4.52; P=0.02), IL-1β (SD: 0.01; 95% CI: −0.37 to 0.40; P=0.94) increased, whereas those of TNF-α (SD: −0.58; 95% CI: −1.59 to 0.43; P=0.26) and IL-6 (SD: −0.59; 95% CI: −1.24 to 0.07; P=0.08) decreased. Six clinical studies had lower symptom scores (SD: −0.09; 95% CI: −0.44 to 0.26; P=0.61) and less incidence of infection (RR: 0.80; 95% CI: 0.64–1.01; P=0.06). Our research indicates that probiotics and prebiotics pose a defensive possibility on respiratory viral infection and may encourage the clinical application.     

Influence of Deforestation,Logging, and Fire on Malaria in the Brazilian Amazon

Malaria is a significant public health threat in the Brazilian Amazon. Previous research has shown that deforestation creates breeding sites for the main malaria vector in Brazil, Anopheles darlingi, but the influence of selective logging, forest fires, and road construction on malaria risk has not been assessed. To understand these impacts, we constructed a negative binomial model of malaria counts at the municipality level controlling for human population and social and environmental risk factors. Both paved and unpaved roadways and fire zones in a municipality increased malaria risk. Within the timber production states where 90% of deforestation has occurred, compared with areas without selective logging, municipalities where 0–7% of the remaining forests were selectively logged had the highest malaria risk (1.72, 95% CI 1.18–2.51), and areas with higher rates of selective logging had the lowest risk (0.39, 95% CI 0.23–0.67). We show that roads, forest fires, and selective logging are previously unrecognized risk factors for malaria in the Brazilian Amazon and highlight the need for regulation and monitoring of sub-canopy forest disturbance.     

MLH1 Promoter Methylation Frequency in Colorectal Cancer Patients and Related Clinicopathological and Molecular Features

Purpose

To describe the frequency of MLH1 promoter methylation in colorectal cancer (CRC); to explore the associations between MLH1 promoter methylation and clinicopathological and molecular factors using a systematic review and meta-analysis.

Methods

A literature search of the PubMed and Embase databases was conducted to identify relevant articles published up to September 7, 2012 that described the frequency of MLH1 promoter methylation or its associations with clinicopathological and molecular factors in CRC. The pooled frequency, odds ratio (OR) and 95% confidence intervals (95% CI) were calculated.

Results

The pooled frequency of MLH1 promoter methylation in unselected CRC was 20.3% (95% CI: 16.8–24.1%). They were 18.7% (95% CI: 14.7–23.6%) and 16.4% (95% CI: 11.9–22.0%) in sporadic and Lynch syndrome (LS) CRC, respectively. Significant associations were observed between MLH1 promoter methylation and gender (pooled OR = 1.641, 95% CI: 1.215–2.215; P = 0.001), tumor location (pooled OR = 3.804, 95% CI: 2.715–5.329; P<0.001), tumor differentiation (pooled OR = 2.131, 95% CI: 1.464–3.102; P<0.001), MSI (OR: 27.096, 95% CI: 13.717–53.526; P<0.001). Significant associations were also observed between MLH1 promoter methylation and MLH1 protein expression, BRAF mutation (OR = 14.919 (95% CI: 6.427–34.631; P<0.001) and 9.419 (95% CI: 2.613–33.953; P = 0.001), respectively).

Conclusion

The frequency of MLH1 promoter methylation in unselected CRC was 20.3%. They were 18.7% in sporadic CRC and 16.4% in LS CRC, respectively. MLH1 promoter methylation may be significantly associated with gender, tumor location, tumor differentiation, MSI, MLH1 protein expression, and BRAF mutation.     

Assessment of Risk Factors for Delayed Colonic Post-Polypectomy Hemorrhage: A Study of 15553 Polypectomies from 2005 to 2013

Background and Aim

Delayed colonic postpolypectomy bleeding is the commonest serious complication after polypectomy. This study aimed to utilize massive sampling data of polypectomy to analyze risk factors for delayed postpolypectomy bleeding.

Patients and Methods

The endoscopic data of 5600 patients with 15553 polyps removed (2005 to 2013) were analyzed retrospectively through univariate analysis and multiple logistic regression analysis to evaluate the risk factors for delayed bleeding.

Results

Delayed postpolypectomy bleeding occurred in 99 polyps (0.6%). The rates of bleeding for different polypectomy methods including hot biopsy forcep, biopsy forcep, Argon Plasma Coagulation (APC), Endoscopy piecemeal mucosal resection (EPMR), Endoscopic Mucosal Resection (EMR), and snare polypectomy were 0.1%, 0.0%, 0.0%, 6.9%, 0.9% and 1.0%, respectively. The risk factors for delayed bleeding were the size of polyps over 10 mm (odds ratio [OR] = 4.6, 95% CI, 2.9–7.2), pathology of colonic polyps (inflammatory/hyperplastic, OR = 1; adenomatous, OR = 1.4, 95% CI, 0.7–2.6; serrated, OR = 1.5, 95% CI, 0.2–11.9; juvenile, OR = 4.3, 95% CI, 1.8–11.0; Peutz-Jegher, OR = 3.3, 95% CI, 1.0–10.7), and immediate postpolypectomy bleeding (OR = 2.9, 95% CI, 1.4–5.9). In addition, although polypectomy method was not a risk factor, compared with hot biopsy forcep, snare polypectomy, EMR, and EPMR had increased risks of delayed bleeding, with ORs of 3.2 (0.4–23.3), 2.8 (0.4–21.7) and 5.1 (0.5–47.7), respectively.

Conclusion

Polyp size over 10 mm, pathology of colonic polyps (especially juvenile, Peutz-Jegher), and immediate postpolypectomy bleeding were significant risk factors for delayed postpolypectomy bleeding.     

Shiga Toxin-Producing Escherichia coli O157 Is More Likely to Lead to Hospitalization and Death than Non-O157 Serogroups – Except O104

The clinical spectrum following infection with Shiga toxin-producing Escherichia coli (STEC) is wide ranging and includes hemorrhagic colitis and life-threatening hemolytic uremic syndrome (HUS). Severity of STEC illness depends on patients'' age and strongly on the infecting strains'' virulence. Serogroup O157 is often assumed to be more virulent than others. Age-adjusted population-based data supporting this view are lacking thus far.We conducted a large retrospective cohort study among patients of community-acquired gastroenteritis or HUS diagnosed with STEC infection, reported in Germany January 2004 through December 2011. Age-adjusted risks for reported hospitalization and death, as proxies for disease severity, were estimated for STEC serogroups separately, and compared with STEC O157 (reference group) using Poisson regression models with robust error estimation.A total of 8,400 case-patients were included in the analysis; for 2,454 (29%) and 30 (0.4%) hospitalization and death was reported, respectively. Highest risks for hospitalization, adjusted for age and region of residence, were estimated for STEC O104 (68%; risk ratio [RR], 1.33; 95% confidence interval [CI], 1.19–1.45), followed by STEC O157 (46%). Hospitalization risks for the most prevalent non-O157 serogroups (O26, O103, O91, O145, O128, O111) were consistently and markedly lower than for O157, with the highest RR for O145 (0.54; 95% CI, 0.41–0.70) and the lowest for O103 (0.27; 95% CI, 0.20–0.35). Mortality risk of O104 was similar to O157 (1.2% each), but the group of all other non-O157 STEC had only 1/10 the risk (RR, 0.09; 95% CI, 0.02–0.32) compared to O157.The study provides population-based and age-adjusted evidence for the exceptional high virulence of STEC O157 in relation to non-O157 STEC other than O104. Timely diagnosis and surveillance of STEC infections should prioritize HUS-associated E. coli, of which STEC O157 is the most important serogroup.     

STORMSeq: An Open-Source,User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5–10 hours to process a full exome sequence and $30 and 3–8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.     

Effect of Water,Sanitation, and Hygiene on the Prevention of Trachoma: A Systematic Review and Meta-Analysis

Background

Trachoma is the world''s leading cause of infectious blindness. The World Health Organization (WHO) has endorsed the SAFE strategy in order to eliminate blindness due to trachoma by 2020 through “surgery,” “antibiotics,” “facial cleanliness,” and “environmental improvement.” While the S and A components have been widely implemented, evidence and specific targets are lacking for the F and E components, of which water, sanitation, and hygiene (WASH) are critical elements. Data on the impact of WASH on trachoma are needed to support policy and program recommendations. Our objective was to systematically review the literature and conduct meta-analyses where possible to report the effects of WASH conditions on trachoma and identify research gaps.

Methods and Findings

We systematically searched PubMed, Embase, ISI Web of Knowledge, MedCarib, Lilacs, REPIDISCA, DESASTRES, and African Index Medicus databases through October 27, 2013 with no restrictions on language or year of publication. Studies were eligible for inclusion if they reported a measure of the effect of WASH on trachoma, either active disease indicated by observed signs of trachomatous inflammation or Chlamydia trachomatis infection diagnosed using PCR. We identified 86 studies that reported a measure of the effect of WASH on trachoma. To evaluate study quality, we developed a set of criteria derived from the GRADE methodology. Publication bias was assessed using funnel plots. If three or more studies reported measures of effect for a comparable WASH exposure and trachoma outcome, we conducted a random-effects meta-analysis. We conducted 15 meta-analyses for specific exposure-outcome pairs. Access to sanitation was associated with lower trachoma as measured by the presence of trachomatous inflammation-follicular or trachomatous inflammation-intense (TF/TI) (odds ratio [OR] 0.85, 95% CI 0.75–0.95) and C. trachomatis infection (OR 0.67, 95% CI 0.55–0.78). Having a clean face was significantly associated with reduced odds of TF/TI (OR 0.42, 95% CI 0.32–0.52), as were facial cleanliness indicators lack of ocular discharge (OR 0.42, 95% CI 0.23–0.61) and lack of nasal discharge (OR 0.62, 95% CI 0.52–0.72). Facial cleanliness indicators were also associated with reduced odds of C. trachomatis infection: lack of ocular discharge (OR 0.40, 95% CI 0.31–0.49) and lack of nasal discharge (OR 0.56, 95% CI 0.37–0.76). Other hygiene factors found to be significantly associated with reduced TF/TI included face washing at least once daily (OR 0.76, 95% CI 0.57–0.96), face washing at least twice daily (OR 0.85, 95% CI 0.80–0.90), soap use (OR 0.76, 95% CI 0.59–0.93), towel use (OR 0.65, 95% CI 0.53–0.78), and daily bathing practices (OR 0.76, 95% CI 0.53–0.99). Living within 1 km of a water source was not found to be significantly associated with TF/TI or C. trachomatis infection, and the use of sanitation facilities was not found to be significantly associated with TF/TI.

Conclusions

We found strong evidence to support F and E components of the SAFE strategy. Though limitations included moderate to high heterogenity, low study quality, and the lack of standard definitions, these findings support the importance of WASH in trachoma elimination strategies and the need for the development of standardized approaches to measuring WASH in trachoma control programs. Please see later in the article for the Editors'' Summary