bluuebunny/crossref_metadata_2025_split huggingface dataset:
Source attribution of salmonellosis by time and geography in New South Wales, Australia
Authors: McLure Angus , Shadbolt Craig , Desmarchelier Patricia M. , Kirk Martyn D. , Glass Kathryn 
Published: January 2022

Abstract
Background
Salmonella is a major cause of zoonotic illness around the world, arising from direct or indirect contact with a range of animal reservoirs. In the Australian state of New South Wales (NSW), salmonellosis is believed to be primarily foodborne, but the relative contribution of animal reservoirs is unknown.

Methods
The analysis included 4543 serotyped isolates from animal reservoirs and 30,073 serotyped isolates from domestically acquired human cases in NSW between January 2008 and August 2019. We used a Bayesian source attribution methodology to estimate the proportion of foodborne Salmonella infections attributable to broiler chickens, layer chickens, ruminants, pigs, and an unknown or unsampled source. Additional analyses included covariates for four time periods and five levels of rurality.

Results
A single serotype, S. Typhimurium, accounted for 65–75% of included cases during 2008–2014 but < 50% during 2017–2019. Attribution to layer chickens was highest during 2008–2010 (48.7%, 95% CrI 24.2–70.3%) but halved by 2017–2019 (23.1%, 95% CrI 5.7–38.9%) and was lower in the rural and remote populations than in the majority urban population. The proportion of cases attributed to the unsampled source was 11.3% (95% CrI 1.2%–22.1%) overall, but higher in rural and remote populations. The proportion of cases attributed to pork increased from approximately 20% in 2009–2016 to approximately 40% in 2017–2019, coinciding with a rise in cases due to Salmonella ser. 4,5,12:i:-.

Conclusion
Layer chickens were likely the primary reservoir of domestically acquired Salmonella infections in NSW circa 2010, but attribution to the source declined contemporaneously with increased vaccination of layer flocks and tighter food safety regulations for the handling of eggs.
Sero-molecular survey on Toxoplasma gondii infection among drug addicted and non-addicted individuals: a case–control study
Authors: Sharifzadeh Majid , Rezanezhad Hassan , Solhjoo Kavous , Kargar Jahromi Zahra , Shadmand Enayatollah , Shahabi Saeed , Taghipour Ali 
Published: January 2022

Abstract
Background
Up to now, epidemiological studies on the prevalence of Toxoplasma gondii infection among drug addicted individuals have been rarely performed. By designing an age and sex matched case–control study, we sought to determine the prevalence and associated factors with T. gondii infection in these population using serological and molecular techniques.

Methods
One hundred and thirty-seven drug addicted individuals and 141 healthy subjects were enrolled in this study. Informed consent as well as a standard questionnaire were obtained from all subjects participating. Blood samples were collected from each participant and the serum was screened for anti-Toxoplasma antibodies (IgG and IgM). PCR assay was performed using the primer pair targeting the RE and GRA6 genes of T. gondii. Then, PCR products were sequenced to determine genotype.

Results
The seroprevalence of T. gondii infection based on IgG titer was 34.3% in case and 9.9% in the control groups, revealing a statistically significant difference (OR = 4.37; 95% CI = 2.46–9.12; P = 0.001). After analyzing the variables studied through the questionnaire, age was the only significantly factor associated with the anti-T. gondii IgG antibody in case group. Considering PCR assays with RE genomic target, the prevalence of T. gondii infection was 5.1% in the case and 3.5% in control groups which the difference was no statistically significant (OR = 1.46; 95% CI = 0.45–4.73; P = 0.521). Subsequently, all sequenced samples were genotype #1 using the GRA6 genomic target.

Conclusions
T. gondii exposure is relatively high among drug addicted individuals in Iran, and there is a need for health policymakers and researchers to establish enlightenment and prevention programs for these population at risk of infection.
Nasopharyngeal colonisation dynamics of bacterial pathogens in patients with fever in rural Burkina Faso: an observational study
Authors: Martens Liesbeth , Kaboré Bérenger , Post Annelies , van der Gaast-de Jongh Christa E. , Langereis Jeroen D. , Tinto Halidou , Jacobs Jan , van der Ven André J. , de Mast Quirijn , de Jonge Marien I. 
Published: January 2022

Abstract
Background
Nasopharyngeal colonisation with clinically relevant bacterial pathogens is a risk factor for severe infections, such as pneumonia and bacteraemia. In this study, we investigated the determinants of nasopharyngeal carriage in febrile patients in rural Burkina Faso.

Methods
From March 2016 to June 2017, we recruited 924 paediatric and adult patients presenting with fever, hypothermia or suspicion of severe infection to the Centre Medical avec Antenne Chirurgicale Saint Camille de Nanoro, Burkina Faso. We recorded a broad range of clinical data, collected nasopharyngeal swabs and tested them for the presence of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus and Klebsiella pneumoniae by quantitative polymerase chain reaction. Using logistic regression, we investigated the determinants of carriage and aimed to find correlations with clinical outcome.

Results
Nasopharyngeal colonisation with S. pneumoniae, H. influenzae and M. catarrhalis was highly prevalent and strongly dependent on age and season. Females were less likely to be colonised with S. pneumoniae (OR 0.71, p = 0.022, 95% CI 0.53–0.95) and M. catarrhalis (OR 0.73, p = 0.044, 95% CI 0.54–0.99) than males. Colonisation rates were highest in the age groups < 1 year and 1–2 years of age and declined with increasing age. Colonisation also declined towards the end of the rainy season and rose again during the beginning of the dry season. K. pneumoniae prevalence was low and not significantly correlated with age or season. For S. pneumoniae and H. influenzae, we found a positive association between nasopharyngeal carriage and clinical pneumonia [OR 1.75, p = 0.008, 95% CI 1.16–2.63 (S. pneumoniae) and OR 1.90, p = 0.004, 95% CI 1.23–2.92 (H. influenzae)]. S. aureus carriage was correlated with mortality (OR 4.01, p < 0.001, 95% CI 2.06–7.83), independent of bacteraemia caused by this bacterium.

Conclusions
Age, sex and season are important determinants of nasopharyngeal colonisation with S. pneumoniae, H. influenzae and M. catarrhalis in patients with fever in Burkina Faso. S. pneumoniae and H. influenzae carriage is associated with clinical pneumonia and S. aureus carriage is associated with mortality in patients with fever. These findings may help to understand the dynamics of colonisation and the associated transmission of these pathogens. Furthermore, understanding the determinants of nasopharyngeal colonisation and the association with disease could potentially improve the diagnosis of febrile patients.
SARS-CoV2 infection in symptomatic patients: interest of serological tests and predictors of mortality: experience of DR Congo
Authors: Makulo Jean-Robert , Mandina Madone Ndona , Mbala Placide Kingebeni , Wumba Roger Dimosi , Akilimali Pierre Zalagile , Nlandu Yannick Mayamba , Odio Jerome Ossam , Bepouka Ben Izizag , Longokolo Murielle Mashi , Mukenge Eric Kasongo , Kamwiziku Guyguy , Muamba Jonathan Mutombo , Longo Augustin Luzayadio , Lufu Crispin Muanza , Keke Hervé Letin , Mbula Marcel Mambimbi , Situakibanza Hippolyte Nanituma , Sumaili Ernest Kiswaya , Kayembe Jean-Marie Ntuma 
Published: January 2022

Abstract
Background
In symptomatic patients, the diagnostic approach of COVID-19 should be holistic. We aimed to evaluate the concordance between RT-PCR and serological tests (IgM/IgG), and identify the factors that best predict mortality (clinical stages or viral load).

Methods
The study included 242 patients referred to the University hospital of Kinshasa for suspected COVID-19, dyspnea or ARDS between June 1st, 2020 and August 02, 2020. Both antibody-SARS-CoV2 IgM/IgG and RT-PCR method were performed on the day of admission to hospital. The clinical stages were established according to the COVID-19 WHO classification. The viral load was expressed by the CtN2 (cycle threshold value of the nucleoproteins) and the CtE (envelope) genes of SARS- CoV-2 detected using GeneXpert. Kappa test and Cox regression were used as appropriate.

Results
The GeneXpert was positive in 74 patients (30.6%). Seventy two patients (29.8%) had positive IgM and 34 patients (14.0%) had positive IgG. The combination of RT-PCR and serological tests made it possible to treat 104 patients as having COVID-19, which represented an increase in cases of around 41% compared to the result based on GeneXpert alone. The comparison between the two tests has shown that 57 patients (23.5%) had discordant results. The Kappa coefficient was 0.451 (p < 0.001). We recorded 23 deaths (22.1%) among the COVID-19 patients vs 8 deaths (5.8%) among other patients. The severe-critical clinical stage increased the risk of mortality vs. mild-moderate stage (aHR: 26.8, p < 0.001). The values of CtE and CtN2 did not influence mortality significantly.

Conclusion
In symptomatic patients, serological tests are a support which makes it possible to refer patients to the dedicated COVID-19 units and treat a greater number of COVID-19 patients. WHO Clinical classification seems to predict mortality better than SARS-Cov2 viral load.
Intestinal microsporidiosis among HIV/AIDS patients receiving antiretroviral therapy in Sana’a city, Yemen: first report on prevalence and predictors
Authors: Al-Brhami Kwkab A. R. , Abdul‑Ghani Rashad , Al-Qobati Salah A. 
Published: January 2022

AbstractBackgroundIntestinal microsporidiosis is an opportunistic infection associated with persistent diarrhea among HIV/AIDS patients. In Yemen, however, its epidemiology is unknown. Therefore, this study determined its prevalence and predictors among HIV/AIDS patients receiving antiretroviral therapy (ART) in Sana’a city, the capital of Yemen.MethodsThis cross-sectional study included 402 patients receiving ART at Al-Jomhori Educational Hospital in Sana’a from November 2019 to December 2020. Data about demographics, clinical characteristics and risk factors were collected using a pre-designed questionnaire. Stool samples were collected and examined for microsporidian spores using the Gram-chromotrope Kinyoun staining. Blood samples were also collected and used for CD4 cell counting by flow cytometry. Univariate analysis was used to test the association of patients’ characteristics and risk factors with intestinal microsporidiosis. Multivariable logistic regression was then used to identify the independent predictors of infection. Statistical significance was considered atP-values < 0.05.ResultsIntestinal microsporidiosis was prevalent among 14.2% (57/402) of HIV/AIDS patients and was significantly associated with diarrhea (OR 3.4, 95% CI 1.7–6.6;P = 0.001). The significant independent predictors of infection were < 200 CD4 cells/µl (AOR 3.2, 95% CI 1.5–6.9;P = 0.003), not washing hands after contacting soil (AOR 2.5, 95% CI 1.1–5.4;P = 0.026) and before eating (AOR 3.1, 95% CI 1.5–6.4;P = 0.003), eating unwashed raw produce (AOR 2.5, 95% CI 1.2–5.3;P = 0.017) and absence of indoor latrines (AOR 6.2, 95% CI 1.5–25.9;P = 0.012).ConclusionsThe prevalence of intestinal microsporidiosis among HIV/AIDS patients in Sana'a is high and comparable to that reported from several other countries, being prevalent among approximately 14.0% of patients and significantly associated with diarrhea. It could be predicted among patients who have < 200 CD4 cells/µl, have poor hand hygiene after contacting soil and before eating, usually eat unwashed raw produce, or do not possess indoor latrines. Large-scale studies on its epidemiology and predictors among HIV/AIDS patients across the country are warranted.
Monocyte distribution width as a novel sepsis indicator in COVID-19 patients
Authors: Alsuwaidi Laila , Al Heialy Saba , Shaikh Nahid , Al Najjar Firas , Seliem Rania , Han Aaron , Hachim Mahmood 
Published: January 2022

Abstract
Background
The severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a highly transmittable virus which causes the novel coronavirus disease (COVID-19). Monocyte distribution width (MDW) is an in-vitro hematological parameter which describes the changes in monocyte size distribution and can indicate progression from localized infection to systemic infection. In this study we evaluated the correlation between the laboratory parameters and available clinical data in different quartiles of MDW to predict the progression and severity of COVID-19 infection.

Methods
A retrospective analysis of clinical data collected in the Emergency Department of Rashid Hospital Trauma Center-DHA from adult individuals tested for SARS-CoV-2 between January and June 2020. The patients (n = 2454) were assigned into quartiles based on their MDW value on admission. The four groups were analyzed to determine if MDW was an indicator to identify patients who are at increased risk for progression to sepsis.

Results
Our data showed a significant positive correlation between MDW and various laboratory parameters associated with SARS-CoV-2 infection. The study also revealed that MDW ≥ 24.685 has a strong correlation with poor prognosis of COVID-19.

Conclusions
Monitoring of monocytes provides a window into the systemic inflammation caused by infection and can aid in evaluating the progression and severity of COVID-19 infection.
Outcomes of surgical repair of Retinoschisis-associated retinal detachment compared to Rhegmatogenous retinal detachment
Authors: Garneau Jérôme , Hébert Mélanie , You Eunice , Lachance Alexandre , Bourgault Serge , Caissie Mathieu , Tourville Éric , Dirani Ali 
Published: January 2022

Abstract
Background
The aim of this study is to compare outcomes of primary retinal detachment (RD) repair in retinoschisis-associated RD (RSRD) and rhegmatogenous RD (RRD).

Methods
This is a retrospective observational cohort study. Charts of 2247 consecutive patients operated for RD repair at the Centre hospitalier universitaire de Québec – Université Laval between 2014 and 2018 were reviewed. Patients with RSRD and RRD were included to compare the visual and anatomical outcomes of both groups.

Results
There were 41 patients (1.8%) with RSRD and 1661 patients (74%) with RRD. RSRD patients had more primary repair failures (n = 9, 22%, vs. n = 166, 10%; p = 0.013). The primary anatomical success rates for pars plana vitrectomy with and without scleral buckle (PPV-SB vs. PPV) as primary repair method were similar in both RSRD patients (n = 11/14, 79% vs. n = 20/25, 80%; p = 0.92) and RRD patients (n = 751/827, 91% vs. n = 641/721, 89%; p = 0.21). At final follow-up, best corrected visual acuity (VA) in logarithm of the minimum angle of resolution (logMAR) was 0.30 [0.10, 0.88] and 0.18 [0.10, 0.40] (p = 0.03) in RSRD patients and RRD patients, respectively. Presence of retinoschisis was associated with worse final VA (β 0.082, p < 0.001). Other predictive variables included female sex, macula-off presentation, number of RD quadrants involved, longer symptoms duration, worse baseline VA, and primary repair failure. The greatest predictors were worse baseline VA, primary repair failure, and macula-off status at presentation. Presence of retinoschisis did not significantly increase risk of primary repair failure in multivariable analysis (OR 1.45, 95% CI: 0.50–4.17; p = 0.49). Symptoms duration was the greatest effect factor associated with for primary repair failure (OR 1.37, 95% CI: 1.12–1.69; p = 0.003).

Conclusions
RSRD is associated with more primary repair failure in univariate analysis, but not in multivariate analysis after adjusting for symptoms duration. It is however associated with worse final VA even after adjusting for primary repair failure. Both PPV and PPV-SB are valid repair methods for RSRD. However, RSRD remains a challenge to treat.
Suicidal ideation in patients with mental illness and concurrent substance use: analyses of national census data in Norway
Authors: Andersson Helle Wessel , Lilleeng Solfrid E. , Ruud Torleif , Ose Solveig Osborg 
Published: January 2022

Abstract
Background
Suicidal ideation may signal potential risk for future suicidal behaviors and death. We examined the prevalence of recent suicidal ideation in patients with mental illness and concurrent substance use and explored the clinical and sociodemographic factors associated with suicidal ideation in this patient subgroup, which represents a particular risk group for adverse psychiatric outcomes.

Methods
We used national cross-sectional census data in Norway collected from 25,525 patients in specialized mental health services. The analytic sample comprised 3,842 patients with concurrent substance use, defined as having a co-morbid substance use disorder or who reported recent regular alcohol use/occasional illicit drug use. Data included suicidal ideation measured in relation to the current treatment episode, sociodemographic characteristics and ICD-10 diagnoses. Bivariate and multivariate analyses were used to examine differential characteristics between patients with and without suicidal ideation.

Results
The prevalence of suicidal ideation was 25.8%. The suicidal ideation rates were particularly high for those with personality disorders, posttraumatic stress disorder, and depression, and for alcohol and sedatives compared with other substances. Patients with suicidal ideation were characterized by being younger, having single marital status, and having poorly perceived social relationships with family and friends.

Conclusion
Suicidal ideation in patients with mental illness and concurrent substance use was associated with a number of distinct characteristics. These results might help contribute to an increased focus on a subgroup of individuals at particular risk for suicidality and support suicide prevention efforts in specialized mental health services.
Association of serum creatinine levels and risk of type 2 diabetes mellitus in Korea: a case control study
Authors: Song Do Kyeong , Hong Young Sun , Sung Yeon-Ah , Lee Hyejin 
Published: January 2022

Abstract
Background
Reduced skeletal muscle has been suggested as a potential risk factor for type 2 diabetes mellitus (T2DM). Serum creatinine is the primary metabolite of creatine in skeletal muscle. Therefore, low serum creatinine levels may be associated with an increased risk of T2DM. We aimed to evaluate the association between serum creatinine levels and the risk of T2DM in Korea.

Methods
We analyzed a total of 264,832 nondiabetic adults older than 40 years of age who had undergone a national health examination at least once from 2009 to 2015 in the Korean National Health Insurance Service Cohort. Hazard ratios for T2DM were calculated.

Results
In men, serum creatinine levels and the risk for T2DM showed an inverse J-shaped association. This association was confirmed after adjustment for age, body mass index (BMI), systolic blood pressure (SBP), diastolic blood pressure (DBP), and fasting plasma glucose. In women, there was a trend that serum creatinine levels were inversely associated with the risk of T2DM among those with serum creatinine below 1.1 mg/dl. However, serum creatinine levels were not significantly associated with the risk of T2DM after adjustment for age, BMI, SBP, DBP, and fasting plasma glucose.

Conclusions
Reduced levels of serum creatinine were significantly associated with an increased risk of T2DM in men with creatinine below 1.20 mg/dl. There was a trend that decreased levels of serum creatinine were associated with an increased risk of T2DM among women with serum creatinine below 1.1 mg/dl, although this result was not statistically significant.
Nursing students’ understanding of health literacy and health practices: a cross-sectional study at a university in Namibia
Authors: Munangatire Takaedza , Tomas Nestor , Mareka Violetha 
Published: January 2022

Abstract
Background
A poor understanding of health literacy and inadequate health practices among nurses can be detrimental to a population’s health. The starting point of solving this problem is through the provision of methodical health literacy and health practice education in the nursing curriculum. This study explored nursing students’ understanding of the concept of ‘health literacy’ and their health practices at a university in Namibia.

Methods
A descriptive cross-sectional study was carried out among 205 nursing students. A simple stratified sampling method was used and data were collected using a self-reporting Understanding of Health Literacy (UHL) questionnaire. Pearson correlation, independent t-test and One-way ANOVA were used to analyse the data.

Results
The overall mean Understanding of Health Literacy score was 13.04 ± 1.52. The majority (n = 157; 76.5%) of the students were found to have adequate health literacy scores, 21.5% had moderate health literacy scores, and only 2% had inadequate health literacy scores. The overall mean health practice score was 32.4 ± 5.50. Most (n = 106; 51.7%) of the students were found to have poor health practices, 44.4% had average health practices, and just 3.9% had good health practices. There was no significant relationship between the health literacy levels and health practices of the students (p = 0.63).

Conclusions
Nursing students have a good understanding of the concept of health literacy, but more effort can be made to translate this understanding into health literacy skills. There is a need to investigate the contributing factors to poor health practices, as well as develop strategies that can support good health practices among nursing students. These health literacy skills could then be transferred into the students' professional careers as nurses.
A peer learning intervention in workplace introduction - managers’ and new graduates’ perspectives
Authors: Pålsson Ylva , Engström Maria , Swenne Christine Leo , Mårtensson Gunilla 
Published: January 2022

Abstract
Background
Evaluation of a complex intervention are often described as being diminished by difficulties regarding acceptability, compliance, delivery of the intervention, recruitment and retention. Research of peer learning for nursing students have found several positive benefits while studies of peer learning for newly graduated nurses are lacking. This study aimed (1) to investigate the study process in terms of (a) first-line managers’ perspectives on the intervention study, the difficulties they face and how they handle these and (b) new graduates’ fidelity to the intervention and (2) to examine the effect of the peer learning intervention in workplace introduction for newly graduated nurses.

Methods
A mixed-methods approach using semi-structured interviews with eight managers, repeated checklist for fidelity and questionnaires conducted with 35 new graduates from June 2015 and January 2018, whereof 21 in the intervention group. The peer learning intervention’s central elements included pairs of new graduates starting their workplace introduction at the same time, working the same shift and sharing responsibility for a group of patients for 3 weeks. The intervention also included 3 months of regular peer reflection.

Results
Managers offered mostly positive descriptions of using peer learning during workplace introduction. The intervention fidelity was generally good. Because of recruitment problems and thereby small sample size, it was difficult to draw conclusions about peer learning effects and, thus, the study hypothesis could either be accepted or rejected. Thereby, the study should be regarded as a pilot.

Conclusions
The present study found positive experiences of, from managers, and fidelity to the peer learning intervention; regarding the experimental design, there were lessons learned.

Trial registration
Before starting data collection, a trial registration was registered at (Trial ID ISRCTN14737280).