In Lao PDR, the epidemiology of varicella infection is uncertain, since it is not a notifiable disease and VZV outbreaks are rarely reported as fever/rash (F/R) diseases.N = 3139) and investigated VZV and 6 other viruses in patients during F/R outbreaks and in an ad hoc sentinel site in the context of the national reporting system .We estimated the seroprevalence of VZV (IgG ELISA) in different age cohorts  also occurred in this age group mostly during the first year of primary school . During a dengue outbreak, 6% had varicella. At our F/R sentinel site, 14% of children with viral etiology were laboratory diagnosed as varicella and among others, a sizeable number of measles (N = 12) and rubella cases (N = 25) was detected compared to those reported for the whole country (N = 56 and 45), highlighting nationwide a large challenge of underreporting or misdiagnosis of these notifiable diseases because of lack of diagnostic laboratory capacity.At least 80% of the sampled population had evidence of VZV infection before the age of 15. The largest increase in seroprevalence occurred between the age groups 1 to 5 and 6 to 7 year-oldsWe recommend strengthening the clinical and laboratory diagnosis of VZV, measles and rubella, the surveillance and reporting of notifiable F/R diseases by retraining of healthcare workers and by setting up sentinel sites and enhancing laboratory capacity.The online version of this article (10.1186/s12879-019-3990-7) contains supplementary material, which is available to authorized users. Fever and rash (F/R) are common presentations of viral or bacterial infections in children. Viral infections associated with F/R syndromes include measles, rubella, dengue, chikungunya, parvovirus B19, human herpesvirus 6 (HHV6) and 7 (HHV7), Epstein Barr virus, cytomegalovirus, varicella zoster virus (VZV) and others [Although typically a mild disease, primary VZV infection may occasionally also be fatal, especially in neonates, the elderly and immunocompromised individuals . InfectiPrimary VZV infections usually occur during early childhood at least in temperate climates. Some studies suggest that in tropical countries exposure and seroconversion occur less frequently and later in adolescence, leaving a significant proportion of adults, including pregnant women and even elderly susceptible to primary infection –8.Vaccination can significantly reduce varicella-associated disease burden and hospitalization , 10. VZVLao PDR is a land-locked country in Southeast Asia with high humidity and high ambient temperatures. No VZV seroprevalence data exist from the general Lao population and the epidemiology of varicella infection is uncertain, since it is not a notifiable disease. Moreover, VZV outbreaks are rarely reported as F/R disease . Here, wAll protocols were approved by the Lao National Ethics Committee for Health Research (NECHR). Written informed consent was obtained from adult participants and the parents or legal guardians of children and infants. Additional file The National Centre for Laboratory and Epidemiology (NCLE) was notified of a suspected measles outbreak in a remote region of Pakseng district, Luang Prabang Province in January 2015. The investigation team included provincial health staff, epidemiologists and laboratory scientists from NCLE, WHO, and Institut Pasteur du Laos (IPL). Clinical diagnosis was performed by the local physicians and 29 blood samples were collected from children and 2 from adults who had rash within the previous 28 days. Measles and rubella IgM testing was performed by NCLE as described previously . Samplesn = 207; mean age 9.4 ± 0.7 months) were recruited when coming for routine measles vaccination to a central hospital in Vientiane and to Luang Prabang provincial hospital in 2011 and 2012 (NECHR ref. 001/2012). Pre-school children  were randomly selected from 26 villages in Kuan and Xamtai districts in Houaphan province in 2013 as described elsewhere [n = 1731; mean age 13.1 ± 3.7 years) were recruited in four different provinces  during a measles and rubella (M/R) supplementary immunisation activity in 2011/2012 (NECHR ref. 001/2012). Pregnant women  were recruited from antenatal clinics in Vientiane and Luang Prabang in 2012 (NECHR ref. 001/2012). IgG antibodies were detected using anti-varicella IgG ELISA kits according to manufacturer’s instructions .Samples from 3139 participants aged 9 months to 46 years, living in different Lao Provinces, were collected between 2011 and 2015. Infants . F/R multiplex kits (Fast Track Diagnostics) were used to detect parvovirus B19 and HHV6 and 7 DNA in serum, and measles and enterovirus RNA in throat swabs. Because HHV6 and HHV7 detection in throat swabs is likely to be due to chronic infection and detection in blood is more indicative of acute infection , 16, we In participants who were IgM borderline or positive, rubella RNA and VZV DNA were detected from throat swabs and oral fluid, respectively, using published primers , 17. SeqBetween March 2012 and September 2013, 108 plasma samples were collected in Vientiane Capital from dengue suspected cases. All these adults and children presented with F/R disease as part of the Lao National dengue surveillance network had no laboratory evidence for an active dengue virus infection. These dengue negative samples were tested for IgM antibodies against measles, rubella, VZV and parvovirus B19 by ELISA (Euroimmun).p values less than 0.05 were considered significant.Statistics were analysed using SPSS package v.21. Chi-squared, independent student t-tests and linear regression were used as appropriate. A total of 35 sera were collected during a F/R outbreak in Houitone village, Pakseng district, clinically suspected to be measles, were negative for both measles and rubella IgM but 30/34  of them were varicella IgM positive. The median age of cases was 6 years ) with 50% females. Clinical signs and epidemiology were compatible with varicella diagnosis . Three o2 = 0.94, p = 0.017). The largest increase in seroprevalence was between the 1 to 5 age bracket (9.3%) and the 6 to 7 year olds  including 36.9% from urban areas  and 63.1% from semi-urban areas . Overall, 55.6% had IgG antibodies against VZV. The seroprevalence increased with age in both urban and semi-urban areas from 2.4% in infants to 91.5% in women of child bearing age and was significantly correlated with age  occurred in children between 0 and 5 years of age. 28.6% (146/511) of participants had confirmed viral etiology (Table Adenovirus IgM was the most commonly detected (7.8%), with 17 (43.6%) co-infections or with persisting IgM from a past infection.VZV IgM was detected in 20 subjects, two thirds of which were below the age of 5 Table . MeaslesA total of 108 cases with F/R, that were suspected to have dengue, but were not confirmed, were included in this part of the study. The median age of the participants was 20 years with a range of 0 to 60 years. In this cohort IgM antibodies were detected against parvovirus B19 , measles , rubella  and VZV . Most IgM positive cases  were above the age of 10 years.Our age-stratified seroprevalence findings show that more than 80% of the sample population above the age of 15 had previous varicella infection. In our setting about half of the population seroconverted during the first 2 years of primary school. This is corroborated by the median age of 6 years of the patients in the outbreak in Northern Lao PDR. 90% of the VZV cases in the F/R patients at the Children’s Hospital in Vientiane occurred also before the age of 11. At least 90% of the adult population in this study had been infected. Similarly, an anti-VZV antibody seroprevalence of 95% was recently been reported from a cohort of more than 1100 healthcare workers from three different Lao provinces . With anThe outbreak in Houitane Village, Pakseng District was caused by clade 2 varicella zoster viruses, which were also detected throughout the year 2015, 500 km further south in Vientiane Capital together with at least one other clade (i.e. clade 5). Both clade 2 and clade 5 viruses were also reported from other Asian countries (reviewed in ).Our findings also have some important implications for F/R including M/R surveillance. F/R disease (but not explicitly varicella) is one of 17 diseases reportable to the Lao Early Warning and Response Network (EWARN) surveillance system including the Indicator Based Surveillance (IBS) and Event Based Surveillance (EBS). In general, health facilities do not have the capacity to perform laboratory diagnosis on-site. Therefore, specimens of all suspected F/R cases are supposed to be sent to the National Measles reference laboratory at NCLE for diagnostic confirmation by ELISA and PCR. Testing for other F/R causing pathogens remains challenging in the country.Nevertheless, few F/R outbreaks are ever notified and brought to the attention of the public health authorities, despite the high incidence of varicella observed in our study, suggesting that disease surveillance and EWARN reporting need to be strengthened.The outbreak in Northern Lao PDR was initially reported as F/R disease and clinically misdiagnosed as measles, before being confirmed as a varicella outbreak. In the Children’s Hospital, the primary paediatric hospital in the country, about 14% (20/146) of the children with a viral etiology of F/R disease were varicella patients. Also in suspected but unconfirmed dengue cases, 6% were varicella IgM-positive. Thus, overlapping symptoms and a dearth of clinical experience tend to blur the clinical differential diagnosis of varicella and other F/R diseases including M/R in the Lao setting.In 2015 during the 12 months of our surveillance in the Children’s Hospital in Vientiane, we detected about 500 F/R cases including 12 measles and 25 rubella cases. These are sizeable numbers compared to the 56 measles and 45 rubella cases and the 579 F/R cases reported the same year for the whole country. Also, 3 measles and 22 rubella cases were “hidden” in a cohort of patients (March 2012–September 2013) with F/R suspected to be dengue, compared to 103 and 161 notifications for measles and rubella, in 2012–2013. All of this is evidence of insufficient control of measles (and rubella) despite regular and comprehensive supplementary immunization campaigns at least for measles in addition to the routine outreach vaccinations recommended at 9–24 months of age. It is also an indication of severe underreporting of M/R cases  and a weakness of the F/R surveillance and reporting system.Among children with F/R about 8% were positive for adenovirus IgM. As adenoviral infections are often subclinical, many of these may not have been the primary reason for seeking medical care  but rathIn conclusion, we find that varicella has its highest incidence in school children and nearly the whole adult study population has evidence of previous infection. Nevertheless, because of competing programmes, vaccination against varicella may not be indicated for Lao PDR. Our study also warrants several recommendations. (i) Despite considerable efforts of the country to invigorate routine outreach vaccination with large supplementary immunization campaigns, our sentinel surveillance detected a sizeable number of M/R cases that would otherwise have gone unnoticed. Therefore, there is an urgent need to improve M/R surveillance and reporting. (ii) While case based surveillance must continue, even a few sentinel sites could help to monitor surveillance sensitivity to support regional elimination targets. (iii) Including varicella in the list of notifiable diseases may improve F/R and M/R reporting. (iv) Healthcare workers should be retrained in the clinical diagnosis and reporting of F/R diseases in order to increase the sensitivity and specificity of the Lao reporting system and (v) Resources should be made available to ensure that F/R diseases are systematically laboratory investigated at least for M/R and for VZV if clinical diagnosis is unclear.Additional file 1:Figure S1. Over-view of cohorts and methodology used. Flow-chart detailing the methodology of the 4 cohorts used in this study. (PPTX 41 kb)


The odds ratio of MDROs, defined as specific pathogens  resistant to three or more antibiotic classes, were calculated using a multivariable logistic regression model across eGFR strata. Of 94,445 total microbial culture records, 7,288 first positive cultures matched to infection diagnosis were selected. Among them, 5,028 (68.9%) were potential MDROs. The odds of infections by MDROs was 19% and 41% higher in those with eGFR between 30–59 ml/min/1.73 m2 : 1.19, 95% CI:1.02–1.38, P = 0.022) and eGFR < 30 ml/min/1.73 m2 , respectively. Patients with impaired renal function have a higher risk of infections by MDROs. Kidney dysfunction at admission may be an indicator for need of closer attention to microbial culture results requiring subsequent change of antibiotics.Antibiotic resistance is a major global health threat. High prevalences of colonization and infection with multi-drug resistance organisms (MDROs) have been reported in patients undergoing dialysis. It is unknown if this finding extends to patients with mild and moderate/severe kidney disease. An observational study included all adult incident patients hospitalized with a discharge diagnosis of infection in four hospitals from Guangzhou, China. Inclusion criteria: Serum creatinine measurement at admission together with microbial culture confirmed infections. Exclusion criterion: Undergoing renal replacement therapy. Four categories of Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) estimated glomerular filtration rate (eGFR) were compared: eGFR ≥ 105, 60–104 (reference), 30–59, and <30 ml/min/1.73 m As recently stated by the United Nations (UN) and World Health Organization (WHO), ABR has escalated into a global crisis that must be prioritized3.Antibiotic resistance (ABR) is a major growing global threat because even common infections and minor injuries may becoming life threatening due to the increasing incidence of infections caused by multi-drug resistant organisms (MDROs)5. Patients with CKD are not only the victims of infection, but plausibly also a reservoir of antibiotic-resistant pathogens. An increased risk of infection has been reported in individuals with CKD, especially in those undergoing dialysis6. Higher rates of infection in patients with CKD result in more frequent use of antibiotics7 and more frequent hospitalization9, thereby increasing their exposure to microbes, including MDROs10.Chronic kidney disease (CKD) as well is a global health problem, affecting 10–15% of the population worldwidevancomycin-resistant enterococci (VRE), or methicillin-resistant Staphylococcus aureus (MRSA), have been reported in patients undergoing dialysis14. However, it is currently unknown if non-dialysis CKD patients are at higher risk of infections caused by MDROs. Studying these infections is relevant given the potential nephrotoxicity of second and third line antibiotics15. What is worse, these patients can potentially transmit MDROs to patients in other sections of the healthcare facilities.High prevalences of colonization by, and infection due to MDROs, such as 4, pre-admission baseline kidney function, such as estimated glomerular filtration rate (eGFR), is not always available when patients are admitted to hospital. In clinical practice, eGFR at the time of admission represents an important indicator of kidney function that may help to inform clinical decision making, even though reduced eGFR at admission may represent acute and/or chronic kidney dysfunction.Since the recognition of CKD remains lowThe aim of this study was to explore the association between kidney function at admission and the risk of infections by MDROs in patients hospitalized with infections. Secondly, we tried to identify specific microbial patterns of infection among them. The existence of such patterns would help to inform public planning strategies to cope with antibiotic resistance.Staphylococcus aureus, Enterococcus spp., Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter spp. accounted for 68.9%  of the first positive cultures. Among them, 51.0%  were MDROs . After excluding those without positive microbial results or infection diagnoses that were not matched to a culture confirmed sample, a total of 7,228 incident hospitalized patients with the first positive microbial culture results were included. Of these, 509 patients had eGFR available at a prior outpatient visit 1–12 months before hospitalization. Those samples with positivity for 2). The most common comorbidities were cerebrovascular disease (35.0%), diabetes mellitus (30.3%), chronic obstructive pulmonary disease (18.6%), and cancer (17.9%). Undefined infection-related hospitalizations (IRHs) were the most common IRHs (64.0%), followed by community-acquired (26.0%) and healthcare-associated IRHs (10.0%). The prevalence of comorbidities was higher in lower eGFR categories , 58.6% were females and the mean age was 70 years. The majority  had normal or near-normal kidney function . When categorized according to specific sample source, the same pattern remained only in the sputum (P < 0.01). There were no significant differences observed for culture positive rates in midstream urine (P = 0.6), venous blood (P = 0.7) or other specimen types (P = 0.7)  across decreasing eGFR strata, while the proportion of G+ increased (from 14% to 18%). Among the G+ bacteria noted, Staphylococcus aureus (SA) was the most common among patients with eGFR ≥ 30 ml/min/1.73 m2, and Enterococcus spp. the most common one among patients with eGFR < 30 ml/min/1.73 m2. Among the G− bacteria, Escherichia coli (E.coli) was the most common of all, followed by Klebsiella : 1.19, 95% CI:1.02–1.38, P = 0.022) and eGFR < 30 ml/min/1.73 m2 , respectively.The results of multivariable logistic regression models showed increased odds of MDROs across lower eGFR strata. Compared to eGFR 60–104 ml/min/1.73 mIn subgroup analysis, the trends persisted across sex, age strata, single pneumonia, single urinary tract infections, sepsis, community-acquired infection, health-care associated infection and in patients with or without diabetes, although they did not reach statistical significance Fig. .Figure 3In those with eGFR values determined 1–12 months prior to hospitalization, a sensitivity analysis demonstrated consistently higher risk of MDROs in those with lower eGFR categories, although the results were not statistically significant in this relatively small group . The finding in the current study of such an association is of potential clinical relevance. The main clinical application of this study lies in the need to consider the presence of renal dysfunction at admission as a signal to pay closer attention to the microbial culture results, given that identified pathogens may be potentially resistant to first-line initial antibiotics. Therefore, a subsequent modification of the initial antimicrobial therapy is needed if resistance to the current therapy exists. Our study also identifies patients with impaired renal function as a high-risk group for MDROs infections in need of close monitoring.14. To our knowledge, there are no data to suggest whether or not the association may extend to milder levels of reduced renal function not requiring dialysis. Shorr et al. documented that long-term hemodialysis was an independent risk factor associated with infection due to antibiotic resistant bacteria16. An analysis from the CDC Active Bacterial Core surveillance (ABCs) system showed that the incidence of invasive MRSA infection in dialysis patients was 23.3 cases per 1000 persons, a rate that was 100 times greater than that in the general population14. Similar statistics have been reported from the United Kingdom (UK), where 4.2% of all episodes of MRSA bacteremia occurred among dialysis patients17. Our findings showed that higher odds of infection caused by MDROs were observed as the eGFR declined below 60 ml/min/1.73 m2, and were even higher in the group eGFR < 30 ml/min/1.73 m2 compared to the group with eGFR between 60–104 ml/min/1.73 m2.Previous studies have mainly focused on the higher risk of infection caused by MDROs, such as MRSA and VRE, in patients undergoing hemodialysis 1. Patients with reduced eGFR have a higher risk of antimicrobial exposure due to their susceptibility to infections20, either prescribed by physicians or self-prescribed. Infection susceptibility due to immune dysfunction has also been proposed in patients with impaired renal function, including increased production of reactive oxygen species (ROS), accumulation of toxic products, and functional abnormalities of monocytes, T lymphocytes and natural killer cells22. Furthermore, patients with more severely reduced renal function generally have more frequent contact with healthcare personnel and environments , as well as other patients, due to comorbidities and complications6. This increases their potential exposure to MDROs. The high proportion of MDROs in our study is comparable to that of other studies in China 24. China is one of the leading antibiotic prescribing countries in the world and is facing the problem of misuse and overuse of antibiotics27. This might be the reason for the higher proportion of MDROs in the microbial results in our study than those in other western countries. The Chinese central government has started to address this problem with a more stringent antimicrobial stewardship policies since 2012, including restriction of antibiotic prescription to doctors, prevention of self-prescription, development of audit and inspection systems, and investigation and reassignment of responsibility to hospital management staff who violate rational use policies. These initiatives may take some time to mitigate the increased susceptibility of patients with reduced eGFR due to MDRO infection28. For physicians in clinical practice, close attention to eGFR at admission should inform clinical decision-making regarding rational prescription of initial and subsequent antibiotics in order to control the antibiotic resistance problem.Many factors might contribute to the higher odds of MDRO infections in patients with reduced renal function. Frequent exposure to antibiotics is the main driver of ABR31. There was no significant difference in culture positive rates among patients with different eGFR categories in our sample  To define renal function, we used a single measurement of eGFR at admission, which may have resulted in misclassification of true eGFR as patients’ renal function may not have been in steady state at the time. Thus, it was not possible to determine with certainty whether patients with low eGFR values at hospital admission had acute kidney injury, chronic kidney disease or a combination of the two. A sensitivity analysis examining the relationship between eGFR values determined 1–12 months prior to hospitalization and MDROs demonstrated consistent findings to those of the main analysis, although the results were not statistically significant, possibly due to the more limited sample size. (2) We only focused on the first positive culture as the outcome, which was influenced by culture positive rate, previous hospitalization, antibiotic use before admission or admission from a nursing homeOur study suggests that patients with CKD at admission have a higher likelihood of having MDRO infections. This information may increase the awareness among physicians about the prognostic value of creatinine tests at admission, and aid in the choice of initial antibiotics.This was an observational study using electronic health records.32. GDHCM serves as one of the main referral centers for the area, with over 5 million outpatient visits and 70,000 inpatients per year. The four hospitals share the same electronic medical record database (EMRD), developed by International Business Machines Corporation (IBM), and which includes both inpatient and outpatient medical records.We used electronic healthcare data from four hospitals belonging to a healthcare conglomerate, Guangdong Provincial Hospital of Chinese Medicine (GDHCM), China. GDHCM is located in Guangzhou city with a population of 13,080,500 residents as of 2015International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM), between August 2012 and December 2015 (see Supplementary Table 33), had a positive microbial culture result in which the type of sample matched the type of infection, and had at least one serum creatinine (sCr) measurement available at admission. Patients receiving renal replacement therapy  were excluded. For patients with multiple hospital admissions, only the first admission record was used. The reasons why discharge diagnosis was used to confirm a hospitalization with infection included (1) need to capture all infections, including community acquired infection and health-care associated infection; (2) evidence was not always present to establish an infection diagnosis at admission. In the case of multiple infection diagnoses during the same hospitalization, only one infection-related diagnosis was used and only if the type of first positive culture aligned with the discharge diagnosis (Supplementary Table Patients were eligible for inclusion in the study if they were adults ≥18 years), were hospitalized with at least one discharge diagnosis of infection according to the 8 years, The protocol was reviewed and approved by the Ethical Committee of Guangdong Provincial Hospital of Chinese Medicine, China (B2016-194-01). Due to the retrospective nature of the study, informed consent was waived. All patient data were anonymized and de-identified prior to analysis.34. Patients were divided into four categories of eGFR: eGFR ≥ 105, 60–104, 30–59, and <30 ml/min/1.73 m2, with eGFR of 60–104 ml/min/1.73 m2 serving as the reference group because this range showed the lowest risk of infection in a previous study and higher eGFR, for example eGFR ≥ 105 ml/min/1.73 m2 might indicate malnutrition, which would be predisposed to high risk of infection9.Estimated glomerular filtration rate (eGFR) was estimated from serum creatinine (sCr) concentration at admission , using the CKD Epidemiology Collaboration (CKD-EPI) formula35. Microbiological tests based on Gram staining, microscopic observation of bacterial morphotypes, characteristics in culture medium and various specific biochemical reactions were applied to identify bacteria according to Clinical and Laboratory Standards Institute (CLSI) procedures36. Antibiotic susceptibility testing was also performed according to CLSI procedures, and micro-organisms were tested using a susceptibility panel35. The antibiotics panel used for susceptibility testing was applied according to CLSI guidelines and local prescription pattern. Minimum inhibitory concentrations (MICs) were determined by susceptibility analysis system . The antibiotic susceptibility was interpreted using the CLSI MIC breakpoints at the time the test was conducted35. The standard and quality of the laboratory in GDHCM is certified by the International Organization for Standardization, ISO 15189.Sampling and culture were performed according to standard proceduresStaphylococcus aureus, Enterococcus spp., Enterobacteriaceae , Pseudomonas aeruginosa and Acinetobacter spp., and acquired non-susceptibility to at least one agent in three or more antibiotic classes, defined by European Centre for Disease Prevention and Control (ECDC) and the Centers for Disease Control and Prevention (CDC)37. The first positive culture was used to avoid the influence of the initial antimicrobial therapy on culture result and different culture results during the same hospitalization.MDROs were limited to a first culture positive pathogen of 38, comorbid conditions were ascertained from the discharge diagnosis, including myocardial infarction, congestive heart failure, peripheral vascular disease, cerebrovascular disease, dementia, chronic pulmonary disease, rheumatologic disease, peptic ulcer disease, mild liver disease, diabetes without chronic complication, diabetes with chronic complication, hemiplegia or paraplegia, any malignancy, moderate or severe liver disease, metastatic solid tumor and AIDS/HIV. According to the GDHCM policy, discharge diagnosis was forced to include all the comorbid conditions from patients’ medical histories. Numbers of cultures, types of specimens and types of infection-related hospitalizations (IRHs) were extracted from the EMRD.Patient age and sex were extracted from the medical records. According to the classification of Charlson comorbidities index using an established ICD-10 algorithmIRHs were sub-classified as health care-associated IRH (HAIRHs), community-acquired IRH (CAIRHs), and undefined IRH (UIRHs). HAIRHs were defined as the onset of infection after 48 hours following admission and confirmed by health care-associated infection report in the database which was audited by infection control healthcare professionals in GDHCM. CAIRHs were defined as those with infection diagnosis at admission. UIRHs were those that did not fulfill any of the criteria above.Numerical variables were summarized using mean ± standard deviation, or median and interquartile range, as appropriate, while categorical variables were summarized using proportions. Differences in baseline characteristics and the proportion of MDROs in the first culture result between groups of patients within the 4 different eGFR categories were compared using ANOVA, Mann-Whitney U test, chi-square test, Fisher´s exact test, or Wilcoxon rank-sum test, as appropriate. All the data extracted from EMRD in our study were complete, with no missing data and loss to follow-up.2 at outpatient visit 1–12 months preceding hospitalization and eGFR < 60 ml/min/1.73 m2 at admission. Reduced renal function at admission with pre-existing reduced renal function was defined as eGFR < 60 ml/min/1.73 m2 both at preceding outpatient visits and at admission. We also performed a sensitivity analysis to estimate the relative risk of MDROs in the first culture result across different eGFR strata using log binomial model. All statistical analyses were performed using STATA version 14.2 .Multivariable logistic regression was used to calculate the adjusted odds ratio (AOR) of MDROs in the first culture result among different categories of eGFR. Covariates included age group , sex, and Charlson comorbidity index . A P-value < 0.05 was considered significant. Additionally, we repeated the main analysis in subgroups: different sex, age groups, diabetes groups, cause-specific infection-related outcomes including blood stream infections or sepsis, pneumonia and urinary tract infections and types of hospitalization. In light of the fact that reduced eGFR values at admission may have represented pre-existing renal impairment, we performed a sensitivity analysis in those with and without pre-existing reduced renal function. Reduced renal function at admission without pre-existing renal impairment was defined as eGFR 60–104 ml/min/1.73 mSupplementary materials


The benefit of palliative chemotherapy (PC) in patients with advanced solid tumors and poor performance status (ECOG-PS) has not been prospectively validated, which makes treatment decision challenging. We aimed to evaluate the overall survival, factors associated with early mortality, and adoption of additional procedures in hospitalized patients with advanced cancer and poor ECOG-PS treated with PC.We analyzed a retrospective cohort of patients with advanced cancer treated with PC during hospitalization at an academic cancer center in Brazil from 2014 to 2016. Eligibility criteria included: ECOG-PS 3–4 and start of first-line PC; or ECOG-PS ≥ 2 and start of second or subsequent lines. Primary endpoint was 30-day survival from start of PC. Kaplan-Meier method was used for survival estimates and Cox regression for factors associated with 30-day mortality.P = 0.016), hypercalcemia , and elevated bilirubin  were significantly associated with 30-day mortality.Two hundred twenty-eight patients were eligible. 21.9, 66.7 and 11.4% of patients had ECOG-PS 2, 3 and 4, respectively. 49.6% had gastrointestinal tumors. Median follow-up was 49 days (range 1–507). 98.2% of patients had died, 32% during the index hospitalization. The 30-day and 60-day survival rates were 55.7 and 38.5%, respectively. 30% of patients were admitted to the intensive care unit. In a multivariable analysis, ECOG-PS 3/4 (HR 2.01; Patients with advanced cancer and poor ECOG-PS had short survival after treatment with inpatient PC. Inpatient PC was associated with aggressive end-of-life care. Prognostic markers such as ECOG-PS, hypercalcemia and elevated bilirubin can contribute to the decision-making process for these patients. Palliative chemotherapy (PC) is a non-curative treatment given to cancer patients diagnosed with unresectable or metastatic disease to improve patients’ symptomatic control and/or quality of life, or to prolong survival , 2. HoweDue to the lack of robust predictive biomarkers of benefit from conventional cytotoxic chemotherapy, general prognostic markers such as performance status and patient comorbidities are usually used to select patients that are eligible for this type of therapy . One of The American Cancer Society of Clinical Oncology (ASCO) previously published recommendations against the use of cancer-directed therapy for patients with solid tumors and poor ECOG-PS  . AdditioOn the other hand, a previous retrospective analysis of 240 consecutive patients conducted in our institution showed that 48.6% of patients with metastatic colorectal cancer with an ECOG-PS 3–4 achieved some clinical benefit in terms of symptom improvement, experienced a low rate of serious adverse events (21.7%) and overall survival was longer compared to patients treated with best supportive care (BSC)  [Another retrospective analysis of 199 patients with advanced cancer who started PC while hospitalized , showed a hospital discharge rate of 77% and 72% of patients were able to receive subsequent cycles of chemotherapy [Therefore, a better understanding of the consequences of the use of PC in those patients is required to avoid unnecessary or potentially harmful therapies and misguided decisions in end-of-life care –13. IdenIn this study, we aimed to evaluate the outcomes of patients with advanced cancer and poor ECOG-PS treated with inpatient PC, including the overall survival, factors associated with early mortality, and the rate of invasive procedures performed. We hypothesized that inpatient PC in this scenario would be associated with short overall survival, indirectly compared with ECOG-PS 0 or 1 cancer patients, and aggressive medical care near the end of life.Instituto do Câncer do Estado de São Paulo - ICESP), between January 2014 and September 2016.This was a retrospective study of consecutive hospitalized patients with advanced and incurable solid tumors and poor ECOG-PS who were treated with PC during hospitalization at a large academic and public cancer center  and primary tumors of the central nervous system (CNS). Patients with primary CNS tumors were excluded because they frequently present poor ECOG-PS due to neurologic deficits even at disease diagnosis. To obtain our sample, we reviewed data from all consecutive patients that received chemotherapy during hospitalization according to the hospital records and included those that met eligibility criteria. The medical records were available at the cancer center (ICESP) database. Accessing the database required a permission, which was obtained with the Research Center of ICESP.Data was collected from the electronic medical records and included: age, gender, primary tumor site, clinical stage (based on imaging studies), number of metastatic sites, main symptom(s) at hospitalization, line of chemotherapy and regimen (single agent versus combination), Charlson Comorbidity Index score, and body mass index. Charlson Comorbidity Index is a scale used to predict mortality based on patient comorbidities . Main syLaboratory tests at admission were reviewed to determine the hemoglobin (Hb) levels, total leukocyte and lymphocyte count, creatinine (Cr), alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (Bb), and calcium levels. Data on additional procedures used during hospitalization and place of death were also collected. Additional procedures recorded were blood transfusions, palliative radiotherapy, surgical procedures and/or admission to the intensive care unit (ICU).The primary endpoint of the study was 30-day survival rate from the start of the first inpatient chemotherapy cycle. Secondary endpoints included median survival, 60-day survival rate from the start of the first inpatient chemotherapy cycle, prognostic factors associated with survival, rate of additional procedures performed, and hospital discharge rate after starting chemotherapy.The prognostic factors evaluated were sex, age, primary tumor site, number of sites of metastases , main symptom that led to hospitalization, ECOG-PS (3–4 vs 2), body mass index and Charlson index (≤ 6 vs > 6 points), and laboratory abnormalities. The cutoff value for the number of sites of metastases was chosen based on previous studies suggesting that the presence of more than 2 metastatic sites is associated with shorter overall survival , 16. As 3), lymphopenia (lymphocytes ≤1500 per mm3), hypercalcemia , elevated liver function tests (LFT) , renal impairment (defined by Cr ≥ 1.5 mg/dL), and elevated bilirubin . Both clinical and laboratory variables were categorized based on clinical relevance for interpretation of the results in the clinical setting. Information on the clinical variables was available for all patients since it is systematically registered in electronic records during hospitalization at ICESP. For the laboratory tests, the median value was used for missing value imputation. The rates of missing data for the laboratory variables ranged from 0 to 17%.The laboratory tests were categorized according to the presence or absence of the following laboratory abnormalities: anemia (defined by Hb < 10 g/dL), leukocytosis .Survival analysis was performed using the Kaplan-Meier method. Factors associated with 30-day mortality were evaluated with univariable and multivariable analysis by using Cox regression. Prognostic factors with A total of 979 patients with solid tumors received PC during hospitalization between 2014 and 2016. Of these, 228 consecutive patients fulfilled the eligibility criteria and were included in the analysis. The CONSORT diagram is presented in Fig. N = 223; 97.8%), and only 5 patients (2.2%) had a locally advanced disease not amenable for treatment with curative intent. Patients were predominantly treated with a combination chemotherapy regimen .Median age was 56 years (range 21–79). The majority of patients were female (58%) and chemotherapy-naïve (66%). The most common primary tumor sites were gastrointestinal (49.6%) and breast (18.4%). The proportions of ECOG-PS 2, 3 and 4 were 21.9, 66.7, and 11.4%, respectively. The majority of patients had metastatic disease at presentation . Other common causes of admission included dyspnea, pain, and sepsis.Seventy-one patients (31.1%) were hospitalized because of gastrointestinal symptoms, including 40 patients (17.5%) with malignant bowel obstruction (Patient characteristics are summarized in Table Median follow–up was 49 days (range 1–507 days). Two hundred and twenty-four patients had died (98.2%), and median overall survival was 38.5 days. 30-day and 60-day survival rates were 55.7 and 38.5%, respectively. Seventy-three patients (32%) died during the same admission in which PC was started. Thirty-one patients (13.8%) died in the intensive care unit (ICU), twenty-seven patients (12%) died in an inpatient hospice facility and two patients (0.8%) died at home.N = 155) were discharged from the hospital after receiving PC, and 100 patients (43.8%) received at least one more cycle of PC as an outpatient after the index hospitalization. Outcomes of interest are summarized in Table Median duration of index hospitalization was 16 days range 2–87 days). Eighty-six patients (37%) required invasive procedures during the index hospitalization, which included 68 patients (30%) that required intensive care unit admission and 37 (16%) that underwent surgical procedures. One hundred and three patients (45%) received blood transfusions, and 22 patients (9.6%) received palliative radiotherapy. Approximately 68% of patients (–87 days.P = 0.012), hypercalcemia , elevated LFTs  and elevated bilirubin .In univariable analysis, 30-day mortality was positively correlated with presence of gastrointestinal symptoms at admission , ECOG-PS (3–4 vs 2) . In the multivariable analysis, three prognostic factors were independently associated with 30-day mortality: ECOG-PS (3–4 vs 2) , hypercalcemia , and elevated bilirubin .Among these variables, only ECOG-PS, hypercalcemia, and elevated bilirubin met inclusion criteria for the multivariable model. Gastrointestinal symptoms and elevated LFTs were not included because they were positively correlated with elevated bilirubin  and poor performance status had a low survival rate after receiving PC. Median OS was 38.5 days, and 30- and 60-day survival rates were 55.7 and 38.5%, respectively, highlighting that these patients had very poor outcomes regardless if they had initiated active cancer treatment or, in some cases, had received invasive life support interventions .Previous phase II/III clinical trials and meta-analysis have shown that cytotoxic chemotherapy improved survival and quality of life compared to BSC alone across different primary solid tumors –19. HoweA Spanish single-center study with eligibility criteria similar to ours analyzed 92 patients and showed that mOS was 33 days from the last course of chemotherapy . A CanadP = 0.02) [Importantly, the use of chemotherapy near the end of life has been associated with more invasive procedures near death, including ICU admissions, delays in hospice referrals, and increased treatment costs –25. In aA combination of several factors has been described as a possible reason for why medical oncologists offer PC to poor performance status patients. These factors include: (i) physicians overestimate prognosis of metastatic cancer patients ; (ii) liOur findings suggest an over-prescription of PC in this population because almost half of the patients (44.3%) died within 30 days of starting treatment. As mentioned previously, ASCO’s recommendation supports that 20–50% 30-day mortality rate after starting chemotherapy is excessive and requires revision of patient selection criteria for this type of treatment , 30, 31.Valuable efforts have been made in an attempt to determine prognostic markers that can help identify the patients with very short life expectancy, and therefore, not likely to benefit from PC . In our Another retrospective study conducted at ICESP with predominantly outpatients reinforce that ECOG-PS 3–4 was a predictor of 90-mortality. In contrast to our results, Caires-Lima et al. cohort found that elevated creatinine was a statistically significant predictor factor of early mortality . ValidatOur study has inherent limitations due to its retrospective nature. Other potential limitations are: (i) the lack of a control group; (ii) there was no systematic report of treatment related toxicities precluding the data collection; (iii) we were not able to obtain information related to quality of life and radiologic response; (iv) our study included a large variety of cancer types, with heterogeneous prognoses and a high proportion of stomach and pancreatic/biliary tumors, which could be associated with poor prognosis and may have contributed to a worse outcome in the population; and (v) unmeasured confounding factors (e.g. disease burden and high volume of metastatic disease) are also a potential source of bias.On the other hand, the strengths of our cohort include: (i) its robust sample size, which, to the best of our knowledge, is the largest single-center cohort of patients with advanced cancer and poor performance status who started PC during hospitalization; (ii) our broad inclusion criteria allow a great representation of this population and a proper evaluation of risk factors associated with early mortality; (iii) we analyzed real-world data, which is potentially generalizable to other public academic institutions; (iv) the assistance for hospitalized patients with advanced malignancies may be influenced by local culture; and (v) we provide data on the oncologic care for this Latin America population, which is scarcely represented in previous studies.Based on our results, we suggest that physicians should be aware of the outcomes of inpatient PC in this scenario and the factors associated with early mortality to allow better decision-making. Importantly, this information should also be shared with patients and their families to allow more informed decisions.A multicenter and international exchange of experiences would be helpful in order to build a collaborative line of work , concentOur study showed that patients with advanced solid tumors and poor performance status treated with inpatient PC had a poor prognosis and short survival. PC in the inpatient setting is associated with aggressive end-of-life care, including ICU admission. Elevated bilirubin, hypercalcemia, and ECOG-PS 3–4 are associated with 30-day mortality and may be used to aid in treatment decisions for this patient population.


Crassostrea gigas (C. gigas) in industry. But few work has been done to study the genetic architecture of nutritional traits of the oyster. In this study, we constructed a high-density genetic map of C. gigas to help assemble the genome sequence onto chromosomes, meanwhile explore the genetic basis for nutritional traits via quantitative trait loci (QTL) mapping.Both growth and nutritional traits are important economic traits of C. gigas were successfully anchored to 10 linkage groups (LGs) of the consensus map. Using this high-qualified genetic map, we then conducted QTL analysis for growth and nutritional traits, the latter of which includes glycogen, amino acid (AA), and fatty acid (FA). Overall, 41 QTLs were detected for 17 traits. In addition, six candidate genes identified in the QTL interval showed significant correlation with the traits on transcriptional levels. These genes include growth-related genes AMY and BMP1, AA metabolism related genes PLSCR and GR, and FA metabolism regulation genes DYRK and ADAMTS.The constructed genetic map contained 5024 evenly distributed markers, with an average marker interval of 0.68 cM, thus representing the densest genetic map produced for the oyster. According to the high collinearity between the consensus map and the oyster genome, 1574 scaffold (about 70%) of the genome sequence of C. gigas.Using the constructed high-qualified linkage map, this study not only assembled nearly 70% of the oyster genome sequence onto chromosomes, but also identified valuable markers and candidate genes for growth and nutritional traits, especially for AA and FA that undergone few studies before. These findings will facilitate genome assembly and molecular breeding of important economic traits in The online version of this article (10.1186/s12864-018-4996-z) contains supplementary material, which is available to authorized users. Crassostrea gigas (C. gigas) originated in Asia, and has become an important cultured mollusc in many countries as a result of its rapid growth rate and high yield [C. gigas was estimated to be 625,925 metric tons with a value of approximately 1.34 billion dollars . As an edible aquatic product, quality and flavour plays a key role in the commercial value of C. gigas. Growth and nutritional traits are not only associated with the oyster production but also important indicators of oyster quality. Oysters are rich in glycogen, essential amino acids (EAAs), unsaturated fatty acids (UFAs), and vitamins [C. gigas. Compared with the growth traits, which have got great attention in previous phenotype-dependent selective breeding programs [C. gigas, other than glycogen [The Pacific oyster, gh yield , 2. In 2vitamins , 8. The vitamins . Becauseprograms –14, few glycogen , have bes FAO, 20. As an eglycogen , the oysglycogen ), which C. gigas, but also conducted QTL mapping for many economic traits, including AAs and FAs that had never undergone QTL mapping or association analysis in this species. This work assists to assemble the genome sequence of C. gigas onto chromosomes, meanwhile help illuminate the genetic mechanism of important economic traits so as to promote MAS programs of C. gigas.Linkage analysis is an important tool for quantitative trait loci (QTL) mapping, marker-assisted selection (MAS) programs, and genome assembly. For the oyster, a total of 20 articles have reported studies concerning genetic map construction or QTL mapping –38. To dIn July 2013, the mapping family was constructed by mating one maternal oyster  with another paternal oyster . All oysters were pasted with different labels on the shell to distinguish from natural spat before culturing in the sea in September 2013. In January 2015, a total of 169 F1 offsprings were randomly selected from this family as the mapping population. Mantles of the oysters were stored at − 80 °C for DNA and RNA extraction and the other tissues were sampled and stored at − 20 °C for nutrients detection. DNA was extracted with a DNeasy® Blood & Tissue Kit  according to the user’s instructions. RNA was extracted using TRIzol reagent  according to manufacturer’s protocol. cDNA was reverse-transcribed from 1 μg of total RNA in a 20-ul reaction mixture using PrimeScript RT reagent kit with gDNA Eraser  following the manufacturer’s instructions. All experiments were conducted with approval from the Experimental Animal Ethics Committee, Institute of Oceanology, Chinese Academy of Sciences, China.Growth and nutritional traits were analysed for all 169 full-sib offsprings. Growth traits include shell height (SH), shell length (SL), shell width (SW), body weight (BW) and weight of soft tissue (STW), while nutritional traits include glycogen, 18 AAs, and 22 FAs. All nutritional traits were detected using the dry soft tissue that was dried with the freeze dryer . Glycogen content was detected using a liver/muscle glycogen assay kit  according to the instructions. AAs were detected using an automatic amino-acid analyser LC-3000  according to Chinese national standard GB/T 18246–2000. FAs were detected and analysed using a gas chromatograph  method  with sliAciI-BfaI restriction enzyme-cut combination was selected. After the DNA concentrations of 171 individuals (two parents and 169 full-sib progenies) were quantified to 20 ng/μL by Qubit 2.0 , the GBS library was constructed with slight modifications to the reported method [AciI and BfaI, respectively. The length of the barcode ranged from 4 to 13 bp. A total of 9 kinds of adapter 1 and 10 kinds of adapter 2, were used , and low-quality reads  were removed. After all reads were trimmed to 112 bp using a Perl script, Stacks software was used to distinguish and genotype the mapping population . First, P < 0.01 in Chi-square goodness-of-fit tests were excluded. Sex-specific and averaged linkage maps were constructed using JoinMap4.1 [Prior to map construction, a segregation distortion test was performed. There are four categories of markers according to the segregation patterns: lm x ll , nn x np , and ef x eg and ab x cd (markers from both parents with 1:1:1:1 segregation ratio in the family). Markers showing significant segregation distortion with inMap4.1 . MarkersinMap4.1 .C. gigas. We quantified the number of scaffold that contains at least two markers, and then analysed the distribution of the markers on the same scaffold.To evaluate the collinearity between the genetic map and genome assembly, the sequences of the markers, which were extracted from the tsv file produced by cstacks, were mapped onto the genome of P < 0.05 for each trait. Mapping step size was set to 0.1 cM, and only QTLs with a LOD score exceeding the threshold were regarded as significant. To further confirm the QTL mapping results, we conducted association analysis between traits and genotypes using Tassel 5.0 with the MLM (PCA + K) method [C. gigas.MapQTL6.0 software was employed to detect QTLs for all detected traits using interval mapping (IM) and restricted multiple QTL model (rMQM) . The LOD) method . Conside-△△CT method. Besides, elongation factor (EF) primers were used as the internal control primers [For each gene identified in the QTL, we firstly genotyped the full-family by the nearest marker of the gene. Then we compared the phenotypic values of the individuals that with different genotypes to ensure that the marker was indeed associated with the trait. Samples with the genotype that showed higher and lower phenotypic values were then named ‘high group’ and ‘low group’, respectively. Based on the genotyping results, we selected eight samples with the highest phenotypic values from ‘high group’ and eight samples with the lowest phenotypic values from ‘low group’, respectively. Further, we compared the gene mRNA expression levels between the two groups. The real-time reverse transcript polymerase chain reaction (qRT-PCR) experiment was performed using SYBR® Premix Ex Taq™ II (Tli RNaseH Plus)  on ABI 7500 Fast Real time Thermal Cycler  according to the instructions. The expression levels of the gene were calculated with the 2 primers , and a rAdditional file P < 0.01). In total, 5094 markers were retained for the genetic map construction.After reads were demultiplexed and cleaned using Perl scripts and process_radtags program, a total of 860.7 million (M) clean reads were generated. There were, on average, 7.54 and 4.3 M clean reads for parents and progeny, respectively, which corresponded to an actual sequencing depth of 27× on average. Using data from the parents, a catalogue of 296,187 markers was built. Based on this catalogue, 55,792 polymorphic markers with more than 5× sequencing depth were identified across all the samples. We calculated the missing rate for all the polymorphic markers, and found that most of the markers (59.63%) were missing in more than half of the population  . High consistency between sex-specific maps laid the basis for generating a high-qualified consensus map.Marker distribution pattern on each LG showed a similar slope among different LGs, which indicated similar recombination rates of different LGs and evenly spaced markers on the consensus map Fig. . Similaraps Fig. . The aveaps Fig. . RecombiC. gigas. Results showed that all 5024 markers were aligned to 1574 scaffold, covering 68.81% of the oyster genome. Overall, 3809 markers with a unique genome position and an alignment length of over 100 bp were used for further analysis. These 3809 markers were distributed on 1303 scaffold of the genome, and 761 of those scaffold had more than one marker. Overall, 86.47% of the scaffold with at least two markers (658 of 761) were located on the same LG of the consensus map  is a metalloproteinase that can regulate the formation of the extracellular matrix and dorsal-ventral patterning in early embryos [GIPR), which is responsible for insulin secretion, has been reported to be associated with obesity and weight gain [AMY) has been widely reported to affect growth, e.g. AMY inhibits the growth of Porphyromonas gingivalis [AMY was correlated with growth traits in Litopenaeus vannamei [FGFR), was found to be significantly correlated with four growth traits in common carp [We detected a total of 41 QTLs for 17 of the 46 traits Table . For gro embryos ; While gght gain –50. Two ngivalis , and polvannamei ; While fmon carp .Table 3QZFPs), such as ZFP729, ZFP668, and ZFP37  (Table SDH) can catalyse the oxidation of succinate to fumarate, with the reduction of ubiquinone to ubiquinol during the citric acid cycle [GP) catalyses the rate-limiting step in glycogenolysis in animals by releasing glucose-1-phosphate from the terminal alpha-1,4-glycosidic bond [rBAT) in qTau_4 with a PVE of 9% , glycine (Gly), Tau, histidine (His), proline (Pro), and valine  Table . The corS) Table . P5CS caS) Table . Succinaid cycle ; While gdic bond . Tau wasdic bond , 63, 64.DYRK), can prevent metabolic disorders like obesity by reducing fat mass [ADAMTS), was widely reported to be associated with adipogenesis, fat content, and obesity [GHSR). GHSR polymorphisms are associated with carcass traits in sheep, and individuals with a mutant ‘TC’ genotype exhibit greater levels of abdominal fat [PLSCR). PLSCR proteins are responsible for the translocation of phospholipids between the two monolayers of a membrane lipid bilayer, and are critical to the normal regulation of lipid metabolism [A total of eight QTLs were detected for six FAs . Eight QTLs detected for FAs were distributed on six LGs, which indicated that different genes might be associated with different kinds of FAs Table . Two genfat mass ; while a obesity –72. qC20inal fat . For C17tabolism –76.P < 0.05) between groups with different genotypes and phenotypic values , 5094 markers were used to construct the genetic map, of which, 5024 (98.62%) were successfully assigned to 10 LGs with the unique marker density of 0.68 cM . In thiC. gigas. Based on the high collinearity between the linkage map and the oyster genome, we successfully assembled nearly 70% of the oyster genome sequence onto chromosomes for the first time. Besides, we provided valuable markers and candidate genes for growth, and firstly for AA and FA traits of C. gigas by QTL mapping. Six genes that can influence the traits by transcriptional regulation may be causative genes for further studies concerning qualified traits improvement. In a whole, our findings will promote genetic dissection and molecular breeding of important economic traits in C. gigas.In this study, we used ddGBS method to generate a high-density genetic map with the most markers for Additional file 1:Adaptors and primers used in this study. (XLS 34 kb)Additional file 2:Histogram of growth and nutritional traits. Individual panels show (A) growth and glycogen, (B) amino acid, and (C) fatty acid. Full names for the abbreviation are as follows: shell height (SH), shell length (SL), shell width (SW), body weight (BW), weight of the soft tissue (STW), total amino acids (All_AA), glutamic acid (Glu), taurine (Tau), aspartic acid (Asp), lysine (Lys), alanine (Ala), leucine (Leu), glycine (Gly), proline (Pro), arginine (Arg), valine , serine (Ser), isoleucine (Ile), threonine (Thr), phenylalanine (Phe), tyrosine (Tyr), histidine (His), cysteine (Cys), methionine (Met), total fatty acids (All_FA), C20:5ω3 (EPA), and C22:6ω3 (DHA). (TIF 552 kb)Additional file 3:Phenotype values and variance. Full names for the abbreviation are shown in Additional file Additional file 4:Amino acid and fatty acid composition. (A) Amino acid composition, (B) Fatty acid composition. Full names for the abbreviation are shown in Additional file Additional file 5:P < 0.05) and (P < 0.01) was indicated by * and **, respectively. Full names for the abbreviation are shown in Additional file Correlation analysis of growth and nutritional traits. (A) Correlation analysis of (A) growth and glycogen, (B) amino acid, (C) fatty acid, and (D) representative traits. Digits above the diagonal show correlation coefficient, while patterns below the diagonal show scatter plots of correlation. Significance correlation Additional file 7:Detailed information of 5024 haplotype markers used for genetic map construction. (XLS 12914 kb)Additional file 8:Summary of the sex-specific maps. (XLS 35 kb)Additional file 9:QTL mapping for growth and nutritional traits. Full names for the abbreviation are shown in Additional file


Ricinus communis L.) is considered as a model system in seed biology studies because of its persistent endosperms throughout seed development.Little is known about the molecular basis of seed size formation in endospermic seed of dicotyledons. The seed of castor bean  and RNA-seq technologies, respectively. A total of 1416 protein species were identified, of which 173 were determined as differentially abundant protein species (DAPs). Additionally, there were 9545 differentially expressed genes (DEGs) between ZB306 and ZB107. Functional analyses revealed that these DAPs and DEGs were mainly involved in cell division and the metabolism of carbohydrates and proteins.These findings suggest that both cell number and storage-component accumulation are critical for the formation of seed size, providing new insight into the potential mechanisms behind seed size formation in endospermic seeds. Arabidopsis [Seeds are vitally important for the economic and nutritional value of most agricultural products. Consequently, improving the traits associated with seed phenotypes has increasingly received attention for its implications in modern agricultural research. Seed size is a major determinant of crop yield and is one of major traits concerned with the breeding of oil crops that is strongly selected for crop domestication . Seed sibidopsis , rice [4bidopsis , the rolbidopsis , but mucRicinus communis L., Euphorbiaceae, 2n = 20) is an desirable model system for studying seed biology because of the large and persistent endosperm. It is therefore ideal to study the mechanisms behind seed size formation, as the endosperm contains 60% fatty acids and 34% protein [The seed of castor bean , and 10,506 were unique after eliminating low-score spectra  between ZB107 and ZB306. Of these DAPs, 57 increased-abundance and 116 decreased-abundance protein species were detected in small-seed ZB306 compared to large-seed ZB107    Fig. . The sca04) Fig. , e.g., Sbidopsis . Thus, cTo confirm the reliability of comparative proteomic and transcriptomic analysis, expression patterns of the 15 candidate DAPs/DEGs were detected at different developmental stages in ZB107 and ZB306 based on qRT-PCR Fig. . For celArabidopsis [Citrus sinensis [In recent years, many proteomic studies have been conducted on the metabolic processes in castor bean seeds, e.g., we have learned more about the processes that manage carbon assimilation during the seed-filling phase of seed development, gained new insights into the biosynthesis of fatty acids, and discovered further mechanisms that are responsible for the biosynthesis of storage proteins during seed development and germination , 22, 31.bidopsis , Citrus sinensis , and ricsinensis . HoweverCastor bean typically has endospermic seeds, whose size is largely determined by the endosperm volume. In this study, we discovered that the endosperm size of castor bean was dependent on cell number rather than cell size, which was similar to the determination of grain size in rice and maize , 37. OurArabidopsis [Arabidopsis via influencing cell division and cell differentiation [Arabidopsis [Arabidopsis and Glycine max [It is known that primary metabolism mainly occurs during the early stage of seed development, and many protein species involved in carbohydrate and protein metabolism have been identified in this study. Central carbon metabolism (including glycolysis and TCA cycle) is a main physiological process during seed-filling . A totalbidopsis , 46, anontiation . The probidopsis . Moreovebidopsis , was inccine max . Taken tNicotiana tabacum [Brassica napus [Vicia faba, and overexpression of a potato SUS gene in maize seeds could increase the starch content [Arabidopsis seed [Arabidopsis [Comparative transcriptome analysis revealed that a total of 120 DEGs were involved in cell development, cell division, cell growth, and cell cycle control, suggesting that these genes might participate in controlling seed size through regulating cell division or cell cycle. In addition, a kinesin gene 29,171.t000006) involved in cell division was up-regulated in large-seed ZB107, which could potentially determine seed size by the regulation of cell number in  tabacum . Similarca napus , 53. In  content , 55. Fur content . Additio1.t000006sis seed . It is lsis seed . AHP4 , were always rich in protein species abundances and their transcript levels and protein species abundances were higher in large-seed ZB107 compared to small-seed ZB306 . These data could provide a crucial resource to further understand the molecular mechanisms governing seed size/weight in endospermic seeds of castor bean. We hope this research will help us to unravel the genetic foundation in the improvement of crop yields by increasing the seed size.Castor bean seeds are typically endospermic in dicotyledons because of their persistent endosperms in maturity. In this study, histological observation revealed that seed size was determined by cell number rather than cell size at the cellular level in the endosperm of castor bean. Combining with comparative transcriptomic and proteomic analyses of developing seeds from two inbred varieties of large-seed ZB107 and small-seed ZB306, we identified that most of DAPs/DEGs were functionally involved in cell division and storage reservoir accumulation, consistent with the formation of seed size in volume and weight. These identified DAPs/DEGs may play a critical role in governing the formation of seed size in castor bean. The correlative analysis between proteomic and transcriptomic data showed that many genes involved in cell division, carbohydrate metabolism, and protein metabolism were correlatively regulated at both transcript and protein levels, though the Pearson correlation coefficient was low (The seeds of castor bean elite inbred lines ZB107 (large-seed) and ZB306  were the primary materials in this study. ZB107 and ZB306 were both grown in the Xishuangbanna Tropical Botanical Garden of the Chinese Academy of Science . This region is characterized by an average temperature of 21 °C~ 22 °C. The seeds of ZB107 were collected 7, 21, 35, 49, and 63 DAF, corresponding to ZB306 at 7, 14, 28, 42, and 56 DAF. Each time, at least twenty seeds from five independent plants were used for experiments, and the same tests were performed across three biological replicates. Samples for iTRAQ and RNA-seq analyses were immediately frozen in liquid nitrogen and stored at − 80 °C, while the remaining samples were used for measuring fresh and dry weight.The individual seeds of all harvested materials were immediately weighed for average fresh weight using an analytical balance , while average dry weight of individual seeds was measured after drying samples at 65 °C for 48 h in an oven. Protein content was determined on the basis of dry mass using a Kjelmaster K-375 Automatic Steam Distillation System as previously described . Three sTo determine seed size, we photographed the projective area of mature dry seeds and endosperm. Ten seeds were freshly isolated from five independent plants of ZB107 at 63 DAF and ZB306 at 56 DAF. Seed coat and embryo were both dissected from seeds in order to measure the cell size of the endosperm. Endosperms were trimmed into appropriately sized samples, fixed in a formaldehyde-acetic acid solution for no less than 48 h at room temperature, dehydrated in a series of ethanol in ascending concentration, cleared in xylene, and embedded in paraffin as previously described by Nogueira et al.  with somWe used whole developing seeds of ZB107 at 21, 35, and 63 DAF as well as ZB306 at 14, 28, and 56 DAF for further proteomics analysis . The HPLC was performed at a flow rate of 1.0 mL/min with a 50 min HPLC gradient consisting of 100% buffer A for 5 min, 0~20% buffer B  for 15 min, 20%~ 40% buffer B for 10 min, 40%~ 100% buffer B for 10 min, and 100% buffer A for 10 min. The eluted peptides were collected and combined into twelve fractions. Each fraction was dried in a vacuum dryer and re-suspended in 0.1% formic acid (FA) for LC-MS/MS analysis.The iTRAQ-labeled peptides were fractionated using Agilent 1200 HPLC with strong cation exchange (SCX) chromatography. The dried iTRAQ-labeled peptides were diluted in buffer A  system (AB SCIEX). The peptide fractions were loaded onto a nanobored C18 column at a flow rate of 0.20 μL/min. An elution gradient of 5%~ 40% ACN (0.1% FA) within a 120 min gradient was used. The mass spectroscopy data were acquired using an ion spray voltage of 2.5 kV, curtain gas of 30 PSI, nebulizer gas of 5 PSI, and an interface heater temperature of 150 °C. We used an information-dependent acquisition (IDA) mode to acquire MS/MS data. Survey scans were acquired in 250 ms intervals, and as many as 35 product ion scans were collected with a 20 s exclusion window and a total cycle time of 2.5 s. A rolling collision energy setting was applied to all precursor ions for CID. The data acquisition rate was 4 s per spectrum.Ricinus communis database (ftp://ftp.tigr.org/pub/data/castorbean/release_0.1/). The following criteria were applied: iTRAQ 8-plex was chosen for quantification with unique peptides, peptide mass tolerance value was set at 20 ppm, and the tolerance of MS/MS was set at 0.6 Da. The quantitative protein species ratios were calculated and normalized by the median ratio of only unique peptides. For the quantification of protein species, a mass-to-charge ratio (m/z) of 117 was performed as the control sample in accordance with the peak area of m/z 121 reporter ions. A sequest score of HT > 0 for authentic proteins and ≥ 1 for unique peptides were used as the screening criteria. The miss values were maintained with the null values. Protein species with a fold change ≥1.5 or ≤ 0.67 and a p-value <0.05 in all three replicates were determined as differentially abundant protein species (DAPs).The raw data were converted into MGF files using Proteome Discoverer software . The identification of protein species was performed using the Mascot software (Matrix Science) against the The functions of all the protein species were annotated using the NCBI nr and SwissProt/Uniprot databases and further analyzed using the Cluster of Orthologous Groups of proteins (COG), Gene Ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. These identified DAPs were subjected to GO and KEGG enrichment analyses. Hierarchical clustering of protein species between the two samples was visualized using MeV 4.9.0 software.http://www.omicshare.com/tools/Home/Soft/getsoft). To identify the cis-elements in the promoter of genes involved in the hormone signal transduction pathways, 1500 bp upstream sequences of genes were extracted from reference genome and cis-elements were detected by querying the PlantCARE database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/).Total RNA was extracted from the same samples used for the proteomics analysis with the RNAprep Pure Plant Kit . RNA concentration and integrity were measured using the Agilent 2100 Bioanalyzer . Two RNA-seq libraries (ZB107 and ZB306) were constructed and sequenced on an Illumina HiSeq 2000 platform. After removing low-quality reads, the sequencing data were mapped to the castor bean reference genome using SOAP2 with default parameters . Reads pTo investigate the concordance between transcriptome and proteome during the seed development of ZB107 and ZB306, a correlation analysis was performed based on DAPs and their corresponding transcripts. The Pearson’s correlation coefficient was calculated for these data and scatter plots were created with the log2-transformed ratios of transcripts and corresponding protein species abundances.We selected fifteen genes to validate their expression patterns in the ZB306 and ZB107 seeds when at different developmental stages using qRT-PCR. Total RNAs were extracted independently from eight samples, including the seeds of ZB306 at 7, 14, 28, and 56 DAF along with the corresponding seeds of ZB107 at 7, 21, 35, and 63 DAF. At this stage, to facilitate the description of the seed development periods, we used the period of ZB306 to represent the corresponding developmental period of ZB107. The cDNA was synthesized with 1 μg total RNA using the TransScript All-in-One First-Strand cDNA Synthesis SuperMix for qPCR kit , and qRT-PCR was carried out according to our previous studies [t-test and one-way analysis of variance (ANOVA) followed by Tukey’s multiple comparison test (P < 0.05) was performed using SPSS18.0. The following asterisks indicate the results of significance testing: *p < 0.05 and ** p < 0.01. Different lowercase letters in the graphs indicate significant differences. Data represent mean values and error bars are SD.For all statistical significance analyses, at least three biological replicates were used for ZB107 and ZB306. Student’s Additional file 1: Table S1. Numbers of spectra, peptides, and protein species identified in the iTRAQ analysisAdditional file 2: Table S2. Peptide sequences of the identified protein species (XLS 904 kb)Additional file 3: Figure S1. The COG functional category analysis of all proteins.Additional file 4: Table S3. Eight protein species involved in cell cycle control, cell division, chromosome partitioningAdditional file 5: Figure S2. GO categories for all protein species identify in both ZB107 and ZB306.Additional file 6: Table S4. Total list of the differentially abundant protein species (XLS 128 kb)Additional file 7: Figure S3. Schematic representation of the DAPs and DEGs involved in carbohydrate metabolism of castor bean seed.Additional file 8: Table S5. Gene functional classes of protein species only detected in our comparative proteomicsAdditional file 9: Figure S4.Cis-element analysis of promoter sequences of genes in hormone signal transduction pathways.Additional file 10: Table S6. Correlation analysis of the DAPs and the corresponding genesAdditional file 11: Figure S5. The KEGG annotation of genes that were correlated between protein and transcript levels.Additional file 12: Figure S6. Workflow of identify DAPs/DEGs between large-seed ZB107 and small-seed ZB306.Additional file 13: Table S7. Summary of primers used in this study.


The Xpert® MTB/RIF assay  is a cartridge-based nucleic acid amplification assay for rapidly diagnosing tuberculosis and assessing antibiotic sensitivity. Although previous evidence supports the use of Xpert for diagnosing extrapulmonary tuberculosis (EPTB) in adults, information regarding the accuracy of Xpert for EPTB only in children is lacking. This meta-analysis was performed to assess the accuracy of Xpert for detecting EPTB in children.We searched the MEDLINE, EMBASE, and Cochrane Infectious Diseases Group Specialized Register from January 1, 2010 to July 16, 2019 for studies of the diagnostic performance wherein Xpert was analyzed against cultures or composite reference standards for < 18-year-old children with EPTB.In only pediatric studies, 8 studies including 652 samples were selected. The pooled sensitivity and specificity of Xpert for all samples were 71% (95% CI 0.63–0.79) and 97% (95% CI 0.95–0.99), respectively. The area under the summary receiver operating characteristic (sROC) curve was 0.89. For lymph node tissues or aspirates, the pooled sensitivity and specificity of Xpert were 80% (95% CI 0.70–0.88) and 94% (95% CI 0.89–0.97), respectively; for cerebrospinal fluid (CSF), these values were 42% (95% CI 0.22–0.63) and 99% (95% CI 0.95–1.00), respectively.Overall, Xpert displayed high specificity but modest sensitivity across various samples for diagnosing pediatric EPTB compared to the composite reference standard. Xpert sensitivity varied with the sampling site and was especially lower in CSF samples. Positive Xpert results may be considered to indicate a presumptive case of pediatric EPTB, whereas negative test results indicate that the possibility of pediatric EPTB should not be excluded. Tuberculosis (TB) is a serious threat to global public health and the leading cause of death from a single infectious disease worldwide, surpassing the rates of malaria and HIV/AIDS. Globally, there were an estimated 10.0 million incident cases of TB in 2018, with approximately 1 million (11%) among children < 15 years. However, the mortality rate was higher in children aged < 15 years, accounting for 14% of total deaths, which is greater than that in incident cases, suggesting poorer access to diagnosis and treatment [Extrapulmonary tuberculosis (EPTB) refers to TB occurring within a location in the body other than the lungs  . EPTB isTo diagnose EPTB, samples should be obtained from sites of suspected infection and cultured. The diagnosis of pediatric EPTB remains challenging because clinical specimens are potentially inaccessible for appropriate sampling and require invasive diagnostic procedures . FurtherThe Xpert® MTB/RIF assay  is a cartridge-based nucleic acid amplification assay for rapid TB diagnosis and rapid antibiotic sensitivity analysis. Currently, Xpert is used as a rapid assay for TB diagnosis as recommended by the World Health Organization (WHO) . Since 2We searched the MEDLINE, EMBASE, and Cochrane Infectious Diseases Group Specialized Register. Our last search was carried out on July 16, 2019. Furthermore, we manually reviewed the bibliographies of the included articles. The primary search terms were “Xpert,” “GeneXpert,” “Cepheid,” “MTB/RIF,” and “Tuberculosis.” The search methodology applied for each database is shown in Additional file The following inclusion criteria were used: (1) studies using Xpert as a diagnostic tool for detecting EPTB compared to a reference standard in each study, with all non-respiratory samples ; (2) studies evaluating the diagnostic performance of Xpert; and (3) studies providing pediatric (0–18 years) data. Studies were included regardless of HIV infection status.We excluded reviews, letters, editorials, expert opinions, animal experiments, and studies that only presented an abstract. Studies that did not include separate pediatric data were also excluded. We attempted to include all types of EPTB samples; however, studies reporting the use of gastric lavage samples were excluded because they were intended to diagnose pulmonary TB. Studies including samples from fewer than five patients and studies with no or insufficient data to construct a 2 × 2 contingency table to determine sensitivity and specificity were also excluded. If data were obtained in more than one article from the same author, the article with the most data was selected.Two review authors (YS Seo and JK Ahn) independently assessed the titles and abstracts in accordance with the inclusion and exclusion criteria, followed by a full-text review of the selected studies. Discrepancies regarding the inclusion of articles between the two authors were resolved by the third author (DS Kim).To compare the accuracy of Xpert, mycobacterial culturing or a CRS was used as a reference standard. The CRS was defined by the authors of each study. Because of the paucibacillary characteristics of extrapulmonary TB, the clinical diagnosis of TB was also included. The CRS included histopathological, smearing, and clinical response analysis to treatment with anti-TB therapy along with culturing.Qualitative assessment was performed using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool . All elip-value of < 0.10. In case of heterogeneity, different thresholds were considered to influence sensitivity and specificity. To assess the presence of a threshold effect, Spearman’s ρ correlation analysis was performed with ρ > 0.6 indicating a threshold effect. The sensitivities and specificities of Xpert in each study were determined and subjected to meta-analysis with a bivariate random-effects model. We plotted the summary receiver operating characteristic (sROC) curve with this model. R-package mada (version 3.5.1.) was used to generate forest plots and an ROC curve.We determined the sensitivity and specificity of Xpert with 95% confidence intervals compared to culturing or the CRS. To assess the heterogeneity among studies, the chi-square test was performed. Heterogeneity was defined as a n = 844), EMBASE (n = 1180), and Cochrane (n = 201), 670 duplicates were excluded. After screening the titles, 1291 studies were excluded. After screening the abstracts, 162 studies were excluded for the following reasons: 139 studies did not fulfill the inclusion criteria and 23 studies were excluded because they were review studies, meta-analysis studies, or case reports. After reviewing the full-text of the remaining 102 studies, 94 studies were excluded for the following reasons: 14 studies included only abstracts, 6 studies did not contain EPTB samples, 11 studies had inadequate study protocols, and 63 studies did not separate pediatric data. Finally, we identified 8 studies that included 652 samples.Figure Table Quality assessment was performed using QUADAS-2, as summarized in Fig. The 8 studies were evaluated as described above Fig. . RegardlSix studies used Xpert to analyze lymph node samples obtained by fine-needle aspiration biopsy (FNAB) or lymph node biopsy rather than a CRS , 22–25. Five studies used Xpert to analyze CSF samples rather than a CRS –25. The Nine meta-analyses have been performed to assess the accuracy of Xpert for detecting EPTB Table  5, 9–16–169–16. The present study summarizes the overall performance of Xpert for diagnosing pediatric EPTB based on the currently available literature. Although previous systematic reviews analyzed data from both children and adult populations, no studies have reported distinct data for children , 9–16. TIn a recent meta-analysis reporting data primarily about adults, the pooled sensitivity varied among different types of specimens . However, the pooled specificity was relatively high between sample types  . These dSince 2013, the WHO has recommended Xpert rather than conventional tests for the diagnosis of TB meningitis and TB lymphadenitis in children. As per the 2013 WHO data, the pooled sensitivity and specificity of lymph node TB in children were 86% (95% CI 0.65–0.96) and 81% (95% CI 0.54––0.93), respectively. In the case of TB meningitis, the pooled specificity was 95% (95% CI 0.81–0.99) and sensitivity could not be determined because of insufficient data [Recently, the next-generation Xpert MTB/RIF assay, Xpert MTB/RIF Ultra assay (Cepheid) (ULTRA), was developed; its limit of detection was enhanced by ~ 8-fold compared to the previous Xpert MTB/RIF assay and it includes a larger chamber and additional molecular targets . In 2017EPTB is common in children but difficult to diagnose because the sampling methods are invasive. A point-of-care ultrasound (POCUS) protocol  is a noninvasive diagnostic tool developed to improve the diagnosis of EPTB in HIV-infected adults . AlthougThe present meta-analysis revealed high heterogeneity in patients with TB lymphadenitis and meningitis. Although the population was limited to those of the pediatric age and the samples were divided into subgroups, differences in the processing methods of samples and the small sample size may have resulted in high heterogeneity.In diagnosing pediatric EPTB, Xpert displayed high specificity regardless of the specimen type, but exhibited modest sensitivity, which varied among specimen types. Particularly, in CSF samples, Xpert displayed the lowest sensitivity compared to the CRS. Although positive Xpert results can be considered to indicate presumptive EPTB in children, EPTB cannot be ruled out based on negative test results. Future clinical trials are required to expand the evidence for using Xpert to diagnose pediatric EPTB with different forms of extrapulmonary specimens in various clinical settings.Additional file 1. Study search strategy


Surgical site infections (SSIs) were the most common healthcare-associated infection mainly in developing countries. Inappropriate use of surgical antibiotic prophylaxis, in terms of antibiotic choice, timing, and duration, can lead to the selection of resistant microorganisms and high costs. The aim of this study was to investigate the pattern of antibiotic use, incidence and predictors of SSIs at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia.From 131 patients, 55.7% were male study participants. Ninety (68.7%) patients received preoperative prophylaxis. Ceftriaxone was the most 76 (84.5%) prescribed agent for prophylaxis. Twenty-seven (20.6%) patients developed surgical site infection. Previous surgery AOR = 3.22 (95% CI [1.14–9.13]) and alcohol use AOR = 7.04  were independent predictors of SSIs in multivariate logistic regression analysis.The online version of this article (10.1186/s13104-018-3643-8) contains supplementary material, which is available to authorized users. Surgical site infection (SSI) is an infection that happens within 30 days of operation or after 1 year if the implant is placed at or near the surgical incision  and espeThe extent of microbial contamination at an incision site, host factors , the length of the preoperative hospital period, preoperative procedures and the duration and performance of the operation contribute to increased risks of SSIs . PatientSSIs can have a devastating impact on the patient’s course of treatment and is associated with increased treatment intensity, prolonged length of stay and higher costs . A studyAnother well-documented approach is to use pre and postoperative antimicrobial prophylaxis. From patients that received antimicrobial prophylaxis 30–90% are inappropriate; most antimicrobials are either given at the wrong time, wrong dosage and wrong strength which results in increased antibiotic usage, increased costs, prolonged hospitalization, super infection, antimicrobial resistance and reduction of surgical antimicrobial prophylaxis (SAP) used , 13.Although the high incidence of SSI is suspected in Ethiopia, the magnitude of the problem is not known in TASH. It becomes therefore essential to determine the pattern of antibiotic use in surgical wards and occurrence and predictors of SSIs.The study was conducted in Tikur Anbessa Specialized Hospital (TASH) Addis Ababa, Ethiopia. TASH is one of the largest tertiary level, referral and teaching hospitals in the country, affiliated to Addis Ababa University. TASH has approximately 570 beds and out of this, 150 are allocated to surgical patients.A prospective observational study was undertaken from April 1 to April 30, 2017. The source population was all inpatients admitted to the hospitals and undergone surgery, whereas the study population was all patients who had undergone operation and admitted to surgical ward during the study period.All surgical patients who had operated during the study period and hospitalized up to 30 days were considered as eligible for the study. However, patients from other wards of the hospital  and patients who died or left before third postoperative days and those not voluntary to participate were excluded from the study.Convenient sampling was used in as sampling technique in this study. Accordingly, all patients who had undergone surgical procedures are followed from admission until discharge, including any readmissions for infection. Accordingly, 131 patients were enrolled in our study.Socio-demographic characteristics of the patients, surgery-related information, antibiotic used  were collected using data abstraction tool from patient’s medical chart. The tool was developed from literatures and modified at it suits to study setting up and senior clinical pharmacist was consulted for its appropriateness. Patients were interviewed in case the information couldn’t be obtained from their chart to make the data complete. Antimicrobial use evaluation was done according to Center for Disease Prevention and Control (CDC) criteria for using antimicrobials in surgical site infection (SSI) prevention and treatment . In our Data was entered into and analyzed by SPSS version 20. Logistic regression analysis was used to identify predictors of SSI. In all cases, p-value less than 0.05 are taken as statistically significant. Variables which have a significant association at p-value < 0.25 in the bivariate logistic regression analysis were candidates for multivariate logistic regression analysis to identify predictors of SSIs.Ethical clearance was obtained from the ethics review committee of School of Pharmacy, College of Health Sciences, Addis Ababa University. Additionally written consent was taken from each participant before participating in the study.During the study period, a total of 158 patients underwent surgery in selected wards of the hospital. From the total, 27 patients were excluded by exclusion criteria (refused to provide consent or death or discharged too early after surgery) and finally, 131 patients were considered for analysis. The age of the patients ranged from 2 to 86 years with a mean of 41.15 ± 18.29 years. Twenty-two (16.8%) and 41 (31.3%) patients were smokers and alcohol drinkers respectively  stayed in hospital for more than 7 days before surgery was conducted. Fifty-seven (43.5%) of the study participants had various types of co-morbidities beside their surgery indications. Six (4.6%) of them had more than co-morbidities Table . About hAmong 131 patients, more than two-third of (68.7%) patients received preoperative antimicrobial prophylaxis. Out of the 43 and 64 patients who had a clean and clean contaminated wound, 15 (34.9%) and 58 (90.6%) patients received pre-operative antimicrobial prophylaxis respectively. From all patients that took preoperative antimicrobial prophylaxis eighty (88.9%) patients received antimicrobial prophylaxis for greater than 24 h after surgery. The majority of patients received ceftriaxone 76 (84.5%). The most commonly prescribed regimen among the combination regimens was ceftriaxone plus metronidazole 12 (13.3%)  patients before discharge. Among the detected SSIs, 23 (85.2%) and 4 (14.8%) were superficial and deep infections respectively.Bivariate logistic regression model showed seven variables were associated with the occurrence of SSIs at p < 0.25. Alcohol (p = 0.000), cigarette smoking (p = 0.05), preoperative blood transfusion (p = 0.05), contaminated p = 0.17) and clean wound (p = 0.12), previous surgery (p = 0.01), and duration of surgery (p = 0.20) were candidate variables for multivariate analysis. The remaining factors were not associated with SSIs in studied participants , . However, other socio-demographic and clinical characteristics were not independently predictors of SSIs , and another study reported similar association . Higher Some studies have examined the use of the ASA score as a predictor of SSI risk , 28. TheWe used smaller sample size and shorter study period which might have an impact on some of the results reported. Other factors have been known to influence the risk of SSIs, such as operation characteristics and nutritional status, antiseptic usage, and sterilization techniques and quality of operation theatre was not studied in this study.Additional file 1. Factors associated with SSIs occurrence among surgical patients in TASH (N = 131). It is additional material which describes bivariate logistic regression model showing seven variables were associated with the occurrence of SSIs at p < 0.25. Alcohol (p = 0.000), cigarette smoking (p = 0.05), preoperative blood transfusion (p = 0.05), contaminated (p = 0.17) and clean wound (p = 0.12), previous surgery (p = 0.01), and duration of surgery (p = 0.20) were candidate variables for multivariate analysis. The remaining factors were not associated with SSIs development in studied participants.