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Abstract Background The emergence and spread of β-lactamase-producing Klebsiella spp. has been associated with a substantial healthcare burden resulting in therapeutic failures. We sought to describe the proportion of phenotypic resistance to commonly used antibiotics, characterize β-lactamase genes among isolates with antimicrobial resistance (AMR), and assess the correlates of phenotypic AMR in Klebsiella spp. isolated from stool or rectal swab samples collected from children being discharged from hospital. Methods We conducted a cross-sectional study involving 245 children aged 1–59 months who were being discharged from hospitals in western Kenya between June 2016 and November 2019. Whole stool or rectal swab samples were collected and Klebsiella spp. isolated by standard microbiological culture. β-lactamase genes were detected by PCR whilst phenotypic antimicrobial susceptibility was determined using the disc diffusion technique following standard microbiology protocols. Descriptive analyses were used to characterize phenotypic AMR and carriage of β-lactamase-producing genes. The modified Poisson regression models were used to assess correlates of phenotypic beta-lactam resistance. Results The prevalence of β-lactamase carriage among Klebsiella spp. isolates at hospital discharge was 62.9% (154/245). Antibiotic use during hospitalization (adjusted prevalence ratio [aPR] = 4.51; 95%CI: 1.79–11.4, p

Introduction Children with moderate or severe wasting are at particularly high risk of recurrent or persistent diarrhoea, nutritional deterioration and death following a diarrhoeal episode. Lactoferrin and lysozyme are nutritional supplements that may reduce the risk of recurrent diarrhoeal episodes and accelerate nutritional recovery by treating or preventing underlying enteric infections and/or improving enteric function.Methods and analysis In this factorial, blinded, placebo-controlled randomised trial, we aim to determine the efficacy of lactoferrin and lysozyme supplementation in decreasing diarrhoea incidence and improving nutritional recovery in Kenyan children convalescing from comorbid diarrhoea and wasting. Six hundred children aged 6–24 months with mid-upper arm circumference

Summary: Background: Children in low and middle-income countries remain vulnerable following hospital-discharge. We estimated the incidence and correlates of hospital readmission among young children admitted to nine hospitals in sub-Saharan Africa and South Asia. Methods: This was a secondary analysis of the CHAIN Network prospective cohort enrolled between 20th November 2016 and 31st January 2019. Children aged 2–23 months were eligible for enrolment, if admitted for an acute illness to one of the study hospitals. Exclusions were requiring immediate resuscitation, inability to tolerate oral feeds in their normal state of health, had suspected terminal illness, suspected chromosomal abnormality, trauma, admission for surgery, or their parent/caregiver was unwilling to participate and attend follow-up visits. Data from children discharged alive from the index admission were analysed for hospital readmission within 180-days from discharge. We examined ratios of readmission to post-discharge mortality rates. Using models with death as the competing event, we evaluated demographic, nutritional, clinical, and socioeconomic associations with readmission. Findings: Of 2874 children (1239 (43%) girls, median (IQR) age 10.8 (6.8–15.6) months), 655 readmission episodes occurred among 506 (18%) children (198 (39%) girls): 391 (14%) with one, and 115 (4%) with multiple readmissions, with a rate of: 41.0 (95% CI 38.0–44.3) readmissions/1000 child-months. Median time to readmission was 42 (IQR 15–93) days. 460/655 (70%) and 195/655 (30%) readmissions occurred at index study hospital and non-study hospitals respectively. One-third (N = 213/655, 33%) of readmissions occurred within 30 days of index discharge. Sites with fewest readmissions had the highest post-discharge mortality. Most readmissions to study hospitals (371/450, 81%) were for the same illness as the index admission. Age, prior hospitalisation, chronic conditions, illness severity, and maternal mental health score, but not sex, nutritional status, or physical access to healthcare, were associated with readmission. Interpretation: Readmissions may be appropriate and necessary to reduce post-discharge mortality in high mortality settings. Social and financial support, training on recognition of serious illness for caregivers, and improving discharge procedures, continuity of care and facilitation of readmission need to be tested in intervention studies. We propose the ratio of readmission to post-discharge mortality rates as a marker of overall post-discharge access and care. Funding: The Bill & Melinda Gates Foundation (OPP1131320).

Summary: Background: Growth faltering is well-recognized during acute childhood illness and growth acceleration during convalescence, with or without nutritional therapy, may occur. However, there are limited recent data on growth after hospitalization in low- and middle-income countries. Methods: We evaluated growth following hospitalization among children aged 2–23 months in sub-Saharan Africa and South Asia. Between November 2016 and January 2019, children were recruited at hospital admission and classified as: not-wasted (NW), moderately-wasted (MW), severely-wasted (SW), or having nutritional oedema (NO). We describe earlier (discharge to 45-days) and later (45- to 180-days) changes in length-for-age [LAZ], weight-for-age [WAZ], mid-upper arm circumference [MUACZ], weight-for-length [WLZ] z-scores, and clinical, nutritional, and socioeconomic correlates. Findings: We included 2472 children who survived to 180-days post-discharge: NW, 960 (39%); MW, 572 (23%); SW, 682 (28%); and NO, 258 (10%). During 180-days, LAZ decreased in NW (−0.27 [−0.36, −0.19]) and MW (−0.23 [−0.34, −0.11]). However, all groups increased WAZ (NW, 0.21 [95% CI: 0.11, 0.32]; MW, 0.57 [0.44, 0.71]; SW, 1.0 [0.88, 1.1] and NO, 1.3 [1.1, 1.5]) with greatest gains in the first 45-days. Of children underweight (

Objectives This study evaluated the prevalence and correlates of guideline non-adherence for common childhood illnesses in low-resource settings.Design and setting We used secondary cross-sectional data from eight healthcare facilities in six Asian and African countries.Participants A total of 2796 children aged 2–23 months hospitalised between November 2016 and January 2019 with pneumonia, diarrhoea or severe malnutrition (SM) and without HIV infection were included in this study.Primary outcome measures We identified children treated with full, partial or non-adherent initial inpatient care according to site-specific standard-of-care guidelines for pneumonia, diarrhoea and SM within the first 24 hours of admission. Correlates of guideline non-adherence were identified using generalised estimating equations.Results Fully adherent care was delivered to 32% of children admitted with diarrhoea, 34% of children with pneumonia and 28% of children with SM when a strict definition of adherence was applied. Non-adherence to recommendations was most common for oxygen and antibiotics for pneumonia; fluid, zinc and antibiotics for diarrhoea; and vitamin A and zinc for SM. Non-adherence varied by site. Pneumonia guideline non-adherence was more likely among patients with severe disease (OR 1.82; 95% CI 1.38, 2.34) compared with non-severe disease. Diarrhoea guideline non-adherence was more likely among lower asset quintile groups (OR 1.16; 95% CI 1.01, 1.35), older children (OR 1.10; 95% CI 1.06, 1.13) and children presenting with wasting (OR 6.44; 95% CI 4.33, 9.57) compared with those with higher assets, younger age and not wasted.Conclusions Non-adherence to paediatric guidelines was common and associated with older age, disease severity, and comorbidities, and lower household economic status. These findings highlight opportunities to improve guidelines by adding clarity to specific recommendations.

Abstract Background The increasing spread of fluoroquinolone resistant enteric bacteria is a global public health concern. Children recently discharged from the hospital are at high risk of carriage of antimicrobial resistance (AMR) due to frequent exposure to antimicrobials during inpatient stays. This study aimed to determine the prevalence, correlates of ciprofloxacin (CIP) non-susceptibility, and distribution of plasmid-mediated quinolone resistance (PMQR) genes in Escherichia coli (E. coli) and Klebsiella spp isolated from children under five years being discharged from two Kenyan Hospitals. Methods E. coli and Klebsiella spp were isolated from fecal samples from children discharged from hospital and subjected to antimicrobial susceptibility testing (AST) by disc diffusion and E-test. CIP non-susceptible isolates were screened for seven PMQR genes using multiplex polymerase chain reaction (PCR). Poisson regression was used to determine the association between the carriage of CIP non-susceptible isolates and patient characteristics. Results Of the 280 CIP non-susceptible isolates: 188 E. coli and 92 Klebsiella spp isolates identified among 266 discharged children, 195 (68%) were CIP-non-susceptible with minimum inhibitory concentrations (MICs) of ≥ 1 µg/mL. Among these 195 isolates, 130 (67%) had high-level CIP MIC = ≥ 32 µg/mL). Over 80% of the isolates had at least one PMQR gene identified: aac(6’)lb-cr (60%), qnrB (24%), oqxAB (22%), qnrS (16%), and qepA (6%), however, qnrA was not identified in any isolates tested. Co-carriage of qnrB with acc(6’)-lb-cr was the most predominant accounting for 20% of all the isolates. Ceftriaxone use during hospital admission and the presence of extended spectrum beta-lactamase (ESBL) production were significantly associated with the carriage of CIP non-susceptible E. coli and Klebsiella spp. Conclusion CIP non-susceptibility is common among E. coli and Klebsiella spp isolated from hospital discharged children in Kenya. Carriage and co-carriage of PMQR, including the newly identified qepA gene, were frequently observed. These findings suggest that children leaving the hospital may serve as an important reservoir for transmission of resistant E. coli and Klebsiella spp to the community. Enhanced surveillance for AMR determinants is critical to inform interventions to control antimicrobial-resistant bacteria.

Summary: Background: Effective methods of preventing and identifying childhood wasting are required to achieve global child health goals. Family mid-upper arm circumference (MUAC) programs train caregivers to screen their child for wasting with MUAC tapes. We assessed the effectiveness of a two-way short message service (SMS) platform (referred to as the Maternally Administered Malnutrition Monitoring System [MAMMS]) in western Kenya. Methods: In this individual-level randomised controlled trial in two rural countries in western Kenya, children (aged 5–12 months) were randomly allocated (1:1) to receive either standard care (SOC) or MAMMS. Randomisation method was permuted-block randomisation with a block size of 10. Eligible participants were children attending maternal child health clinics in the two counties whom had a MUAC between 12.5 and 14.0 cm. The MAMMS group received two MUAC tapes and weekly SMS reminders to screen their child's MUAC. The SOC group received routine community health volunteer services and additional quarterly visits from the study team. The primary analysis used a cox proportional hazards model to compare SOC and MAMMS time-to-diagnosis of wasting (MUAC

Abstract Interventions to reduce childhood stunting burden require clinical trials with a primary outcome of linear growth. When growth is measured longitudinally, there are several options for including baseline measurements in the analysis. This study compares the performance of several methods. Randomized controlled trials evaluating a hypothetical intervention to improve length‐for‐age z‐score (LAZ) from birth through 24 months of age were simulated. The intervention effect was evaluated using linear regression and five methods for handling baseline measurements: comparing final measurements only (FINAL), comparing final measurement adjusted for baseline (ADJUST), comparing the change in the measurement over time (DELTA), adjusting for baseline when comparing the changes over time (DELTA+ADJUST) and adjusting for baseline in two‐step residuals approach (RESIDUALS). We calculated bias, precision and power of each method for scenarios with and without a baseline imbalance in LAZ. Using a 0.15 effect size at 18 months, FINAL and DELTA required 1200 and 1500 enroled participants, respectively, to reach 80% power, whereas ADJUST, DELTA+ADJUST and RESIDUALS only required 900 participants. The adjusted models also produced unbiased estimates when there was a baseline imbalance, whereas the FINAL and DELTA methods produced biased estimates, as large as 0.07 lower and higher, respectively, than the true effect. Adjusted methods required smaller sample size and produced more precise results than both DELTA and FINAL methods in all test scenarios. If randomization fails, and there is an imbalance in LAZ at baseline, DELTA and FINAL methods can produce biased estimates, but adjusted models remain unbiased. These results warn against using the FINAL or DELTA methods.

Summary: We aimed to establish if enteric permeability was associated with similar biological processes in children recovering from hospitalization and relatively healthy children in the community. Extreme gradient boosted models predicting the lactulose-rhamnose ratio (LRR), a biomarker of enteric permeability, using 7,500 plasma proteins and 34 fecal biomarkers of enteric infection among 89 hospitalized and 60 community children aged 2–23 months were built. The R2 values were calculated in test sets. The models performed better among community children (R2: 0.27 [min-max: 0.19, 0.53]) than hospitalized children (R2: 0.07 [min-max: 0.03, 0.11]). In the community, LRR was associated with biomarkers of humoral antimicrobial and cellular lipopolysaccharide responses and inversely associated with anti-inflammatory and innate immunological responses. Among hospitalized children, the selected biomarkers had few shared functions. This suggests enteric permeability among community children was associated with a host response to pathogens, but this association was not observed among hospitalized children.

Summary: Background: A better understanding of which children are likely to die during acute illness will help clinicians and policy makers target resources at the most vulnerable children. We used machine learning to characterise mortality in the 30-days following admission and the 180-days after discharge from nine hospitals in low and middle-income countries (LMIC). Methods: A cohort of 3101 children aged 2–24 months were recruited at admission to hospital for any acute illness in Bangladesh (Dhaka and Matlab Hospitals), Pakistan (Civil Hospital Karachi), Kenya (Kilifi, Mbagathi, and Migori Hospitals), Uganda (Mulago Hospital), Malawi (Queen Elizabeth Central Hospital), and Burkina Faso (Banfora Hospital) from November 2016 to January 2019. To record mortality, children were observed during their hospitalisation and for 180 days post-discharge. Extreme gradient boosted models of death within 30 days of admission and mortality in the 180 days following discharge were built. Clusters of mortality sharing similar characteristics were identified from the models using Shapley additive values with spectral clustering. Findings: Anthropometric and laboratory parameters were the most influential predictors of both 30-day and post-discharge mortality. No WHO/IMCI syndromes were among the 25 most influential mortality predictors of mortality. For 30-day mortality, two lower-risk clusters (N = 1915, 61%) included children with higher-than-average anthropometry (1% died, 95% CI: 0–2), and children without signs of severe illness (3% died, 95% CI: 2–4%). The two highest risk 30-day mortality clusters (N = 118, 4%) were characterised by high urea and creatinine (70% died, 95% CI: 62–82%); and nutritional oedema with low platelets and reduced consciousness (97% died, 95% CI: 92–100%). For post-discharge mortality risk, two low-risk clusters (N = 1753, 61%) were defined by higher-than-average anthropometry (0% died, 95% CI: 0–1%), and gastroenteritis with lower-than-average anthropometry and without major laboratory abnormalities (0% died, 95% CI: 0–1%). Two highest risk post-discharge clusters (N = 267, 9%) included children leaving against medical advice (30% died, 95% CI: 25–37%), and severely-low anthropometry with signs of illness at discharge (46% died, 95% CI: 34–62%). Interpretation: WHO clinical syndromes are not sufficient at predicting risk. Integrating basic laboratory features such as urea, creatinine, red blood cell, lymphocyte and platelet counts into guidelines may strengthen efforts to identify high-risk children during paediatric hospitalisations. Funding: Bill & Melinda Gates Foundation OPP1131320.

Dehydration is a major cause of death among children with wasting and diarrhea. We reviewed the evidence for the identification and management of dehydration among these children. Two systematic reviews were conducted to assess 1) the diagnostic performance of clinical signs or algorithms intended to measure dehydration, and 2) the efficacy and safety of low-osmolarity ORS versus ReSoMal on mortality, treatment failure, time to full rehydration, and electrolyte disturbances (management review). We searched PubMed/Medline, Embase, and Global Index Medicus for studies enrolling children 0-60 months old with wasting and diarrhea. The diagnostic review included four studies. Two studies found the Integrated Management of Childhood Illness (IMCI) and the Dehydration: Assessing Kids Accurately (DHAKA) algorithms had similar diagnostic performance, but both algorithms had high false positive rates for moderate (41% and 35%, respectively) and severe (76% and 82%, respectively) dehydration. One further IMCI algorithm study found a 23% false positive rate for moderate dehydration. The management review included six trials. One trial directly compared low osmolarity ORS to ReSoMal and found no difference in treatment failure rates, although ReSoMal had a shorter duration of treatment (16.1 vs. 19.6 hours, p = 0.036) and a higher incidence of hyponatremia. Both fluids failed to correct a substantial number of hypokalemia cases across studies. In conclusion, the IMCI dehydration assessment has comparable performance to other algorithms among wasted children. Low osmolarity ORS may be an alternative to ReSoMal for children with severe wasting, but might require additional potassium to combat hypokalemia.

The epidemiology of pediatric COVID-19 in sub-Saharan Africa and the role of fecal-oral transmission in SARS-CoV-2 are poorly understood. Among children and adolescents in Kenya, we identify correlates of COVID-19 infection, document the clinical outcomes of infection, and evaluate the prevalence and viability of SARS-CoV-2 in stool. We recruited a prospective cohort of hospitalized children aged two months to 15 years in western Kenya between March 1 and June 30 2021. Children with SARS-CoV-2 were followed monthly for 180-days after hospital discharge. Bivariable logistic regression analysis was used to identify the clinical and sociodemographics correlates of SARS-CoV-2 infection. We also calculated the prevalence of SARS-CoV-2 detection in stool of confirmed cases. Of 355 systematically tested children, 55 (15.5%) were positive and were included in the cohort. The commonest clinical features among COVID-19 cases were fever (42/55, 76%), cough (19/55, 35%), nausea and vomiting (19/55, 35%), and lethargy (19/55, 35%). There were no statistically significant difference in baseline sociodemographic and clinical characteristics between SARS-CoV-2 positive and negative participants. Among positive participants, 8/55 (14.5%, 95%CI: 5.3%-23.9%) died; seven during the inpatient period. Forty-nine children with COVID-19 had stool samples or rectal swabs available at baseline, 9 (17%) had PCR-positive stool or rectal swabs, but none had SARS-CoV-2 detected by culture. Syndromic identification of COVID-19 is particularly challenging among children as the presenting symptoms and signs mirror other common pediatric diseases. Mortality among children hospitalized with COVID-19 was high in this cohort but was comparable to mortality seen with other common illnesses in this setting. Among this small set of children with COVID-19 we detected SARS-CoV-2 DNA, but were not able to culture viable SARs-CoV-2 virus, in stool. This suggests that fecal transmission may not be a substantial risk in children recently diagnosed and hospitalized with COVID-19 infection.

Abstract Objective The purpose of this study was to assess the distribution of HIV-program staff and the extent to which their availability influences HIV programmatic and patient outcomes. Methods The study was a facility level cross-sectional survey. Data from October 2018 to September 2019 were abstracted from HIV program reports conducted in 18 districts of Côte d’Ivoire. The distribution of staff in clinical, laboratory, pharmacy, management, lay, and support cadres were described across high and low antiretroviral therapy (ART) volume facilities. Non-parametric regression was used to estimate the effects of cadre categories on the number of new HIV cases identified, the number of cases initiated on ART, and the proportion of patients achieving viral load suppression. Results Data from 49,871 patients treated at 216 health facilities were included. Low ART volume facilities had a median of 8.1 staff-per-100 ART patients, significantly higher than the 4.4 staff-per-100 ART patients at high-ART volume facilities. One additional laboratory staff member was associated with 4.30 (IQR: 2.00–7.48, p

Human subjects research protections have historically focused on mitigating risk of harm and promoting benefits for research participants. In many low-resource settings (LRS), complex and often severe challenges in daily living, poverty, geopolitical uprisings, sociopolitical, economic, and climate crises increase the burdens of even minimal risk research. While there has been important work to explore the scope of ethical responsibilities of researchers and research teams to respond to these wider challenges and hidden burdens in global health research, less attention has been given to the ethical dilemmas and risk experienced by frontline researcher staff as they perform research-related activities in LRS. Risks such as job insecurity, moral distress, infection, or physical harm can be exacerbated during public health crises, as recently highlighted by the COVID-19 pandemic. We highlight the layers of risk research staff face in LRS and present a conceptual model to characterize drivers of this risk, with particular attention to public health crises. A framework by which funders, institutions, principal investigators, and/or research team leaders can systematically consider these additional layers of risk to researchers and frontline staff is an important and needed addition to routine research proposals and protocol review.

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

We present a computationally efficient galaxy archetype-based redshift estimation and spectral classification method for the Dark Energy Survey Instrument (DESI) survey. The DESI survey currently relies on a redshift fitter and spectral classifier using a linear combination of principal component analysis-derived templates, which is very efficient in processing large volumes of DESI spectra within a short time frame. However, this method occasionally yields unphysical model fits for galaxies and fails to adequately absorb calibration errors that may still be occasionally visible in the reduced spectra. Our proposed approach improves upon this existing method by refitting the spectra with carefully generated physical galaxy archetypes combined with additional terms designed to absorb data reduction defects and provide more physical models to the DESI spectra. We test our method on an extensive data set derived from the survey validation (SV) and Year 1 (Y1) data of DESI. Our findings indicate that the new method delivers marginally better redshift success for SV tiles while reducing catastrophic redshift failure by 10%-30%. At the same time, results from millions of targets from the main survey show that our model has relatively higher redshift success and purity rates (0.5%-0.8% higher) for galaxy targets while having similar success for QSOs. These improvements also demonstrate that the main DESI redshift pipeline is generally robust. Additionally, it reduces the false-positive redshift estimation by 5%−40% for sky fibers. We also discuss the generic nature of our method and how it can be extended to other large spectroscopic surveys, along with possible future improvements.

We measure the clustering of Lyman Alpha Emitting galaxies (LAEs) selected from the One-hundred-square-degree DECam Imaging in Narrowbands (ODIN) survey, with spectroscopic follow-up from Dark Energy Spectroscopic Instrument (DESI). We use DESI spectroscopy to optimize our selection and to constrain the interloper fraction and redshift distribution of our narrow-band selected sources. We select samples of 4000 LAEs at z = 2.45 and 3.1 in 9 sq.deg. centered on the COSMOS field with median Lyα fluxes of ≈ 10-16 erg s-1 cm-2. Covariances and cosmological inferences are obtained from a series of mock catalogs built upon high-resolution N-body simulations that match the footprint, number density, redshift distribution and observed clustering of the sample. We find that both samples have a correlation length of r 0 = 3.0 ± 0.2 h-1 Mpc. Within our fiducial cosmology these correspond to 3D number densities of ≈ 10-3 h3 Mpc-3 and, from our mock catalogs, biases of 1.7 and 2.0 at z = 2.45 and 3.1, respectively. We discuss the implications of these measurements for the use of LAEs as large-scale structure tracers for high-redshift cosmology.

Broad absorption line (BAL) quasars are characterized by gas clouds that absorb flux at the wavelength of common quasar spectral features, although blueshifted by velocities that can exceed 0.1c. BAL features are interesting as signatures of significant feedback, yet they can also compromise cosmological studies with quasars by distorting the shape of the most prominent quasar emission lines, impacting redshift accuracy and measurements of the matter density distribution traced by the Lyman α forest. We present a catalogue of BAL quasars discovered in the Dark Energy Spectroscopic Instrument (DESI) survey Early Data Release, which were observed as part of DESI Survey Validation, as well as the first two months of the main survey. We describe our method to automatically identify BAL quasars in DESI data, the quantities we measure for each BAL, and investigate the completeness and purity of this method with mock DESI observations. We mask the wavelengths of the BAL features and re-evaluate each BAL quasar redshift, finding new redshifts which are 243 km s−1 smaller on average for the BAL quasar sample. These new, more accurate redshifts are important to obtain the best measurements of quasar clustering, especially at small scales. Finally, we present some spectra of rarer classes of BALs that illustrate the potential of DESI data to identify such populations for further study.

Abstract Background Environmental enteric dysfunction (EED) is an acquired enteropathy of the small intestine, characterized by enteric inflammation, villus blunting and decreased crypt-to-villus ratio. EED has been associated with poor outcomes, including chronic malnutrition (stunting), wasting and reduced vaccine efficacy among children living in low-resource settings. As a result, EED may be a valuable interventional target for programs aiming to reduce childhood morbidity in low and middle-income countries. Main text Several highly plausible mechanisms link the proposed pathophysiology underlying EED to adverse outcomes, but causal attribution of these pathways has proved challenging. We provide an overview of recent studies evaluating the causes and consequences of EED. These include studies of the role of subclinical enteric infection as a primary cause of EED, and efforts to understand how EED-associated systemic inflammation and malabsorption may result in long-term morbidity. Finally, we outline recently completed and upcoming clinical trials that test novel interventions to prevent or treat this highly prevalent condition. Conclusions Significant strides have been made in linking environmental exposure to enteric pathogens and toxins with EED, and in understanding the multifactorial mechanisms underlying this complex condition. Further insights may come from several ongoing and upcoming interventional studies trialing a variety of novel management strategies.

Summary: Background: Mass drug administration of azithromycin to children in sub-Saharan Africa has been shown to improve survival in high-mortality settings. The period after hospital discharge is a time of elevated risk unaddressed by current interventions and might provide an opportunity for targeting empirical azithromycin administration. We aimed to assess the efficacy of azithromycin administered at hospital discharge on risk of death and rehospitalisation in Kenyan children younger than 5 years. Methods: In this double-blind, placebo-controlled randomised trial, children were randomly assigned (1:1) to receive a 5-day course of azithromycin (oral suspension 10 mg/kg on day 1, followed by 5mg/kg per day on days 2–5) or identically appearing and tasting placebo at discharge from four hospitals in western Kenya. Children were eligible if they were aged 1–59 months at hospital discharge, weighed at least 2 kg, and had been admitted to hospital for any medical reason other than trauma, poisoning, or congenital anomaly. The primary outcome was death or rehospitalisation in the subsequent 6-month period in a modified intention-to-treat population, compared by randomisation group with Cox proportional hazards regression and Kaplan-Meier. Azithromycin resistance in Escherichia coli isolates from a random subset of children was compared by randomisation group with generalised estimating equations. This trial is registered with ClinicalTrials.gov, NCT02414399. Findings: Between June 28, 2016, and Nov 4, 2019, 1400 children were enrolled in the trial at discharge from hospital, with 703 (50·2%) randomly assigned to azithromycin and 697 (49·8%) to placebo. Among the 1398 children included in the modified intention-to-treat analysis (702 in the azithromycin group and 696 in the placebo group), the incidence of death or rehospitalisation was 20·4 per 100 child-years in the azithromycin group and 22·5 per 100 child-years in the placebo group (adjusted hazard ratio 0·91, 95·5% CI 0·64–1·29, p=0·58). Azithromycin resistance was common in commensal E coli isolates from enrolled children before randomisation (37·7% of 406 isolates) despite only 3·7% of children having received a macrolide antibiotic during the hospitalisation. Azithromycin resistance was slightly higher at 3 months after randomisation in the azithromycin group (26·9%) than in the placebo group (19·1%; adjusted prevalence ratio 1·41, 95% CI 0·95–2·09, p=0·088), with no difference observed at 6 months (1·17, 0·78–1·76, p=0·44). Interpretation: We did not observe a significant benefit of a 5-day course of azithromycin delivered to children younger than 5 years at hospital discharge despite the overall high risk of mortality and rehospitalisation. These findings highlight the need for more research into mechanisms and interventions for prevention of morbidity and mortality in the post-discharge period. Funding: Eunice Kennedy Shriver National Institute of Child Health & Human Development.

Background: Current guidelines for the management of childhood wasting primarily focus on the provision of therapeutic foods and the treatment of medical complications. However, many children with wasting live in food-secure households, and multiple studies have demonstrated that the etiology of wasting is complex, including social, nutritional, and biological causes. We evaluated the contribution of household food insecurity, dietary diversity, and the consumption of specific food groups to the time to recovery from wasting after hospital discharge. Methods: We conducted a secondary analysis of the Childhood Acute Illness Network (CHAIN) cohort, a multicenter prospective study conducted in six low- or lower-middle-income countries. We included children aged 6–23 months with wasting (mid-upper arm circumference [MUAC] ≤ 12.5 cm) or kwashiorkor (bipedal edema) at the time of hospital discharge. The primary outcome was time to nutritional recovery, defined as a MUAC > 12.5 cm without edema. Using Cox proportional hazards models adjusted for age, sex, study site, HIV status, duration of hospitalization, enrollment MUAC, referral to a nutritional program, caregiver education, caregiver depression, the season of enrollment, residence, and household wealth status, we evaluated the role of reported food insecurity, dietary diversity, and specific food groups prior to hospitalization on time to recovery from wasting during the 6 months of posthospital discharge. Findings: Of 1286 included children, most participants (806, 63%) came from food-insecure households, including 170 (13%) with severe food insecurity, and 664 (52%) participants had insufficient dietary diversity. The median time to recovery was 96 days (18/100 child-months (95% CI: 17.0, 19.0)). Moderate (aHR 1.17 [0.96, 1.43]) and severe food insecurity (aHR 1.14 [0.88, 1.48]), and insufficient dietary diversity (aHR 1.07 [0.91, 1.25]) were not significantly associated with time to recovery. Children who had consumed legumes and nuts prior to diagnosis had a quicker recovery than those who did not (adjusted hazard ratio (aHR): 1.21 [1.01,1.44]). Consumption of dairy products (aHR 1.13 [0.96, 1.34], p = 0.14) and meat (aHR 1.11 [0.93, 1.33]), p = 0.23) were not statistically significantly associated with time to recovery. Consumption of fruits and vegetables (aHR 0.78 [0.65,0.94]) and breastfeeding (aHR 0.84 [0.71, 0.99]) before diagnosis were associated with longer time to recovery. Conclusion: Among wasted children discharged from hospital and managed in compliance with wasting guidelines, food insecurity and dietary diversity were not major determinants of recovery.

ObjectiveTo assess attitudes, perceptions, and practices of healthcare workers regarding hospital discharge and follow-up care for children under age five in Migori and Homa Bay, Kenya.MethodsThis mixed-methods study included surveys and semi-structured telephone interviews with healthcare workers delivering inpatient pediatric care at eight hospitals between November 2017 and December 2018.ResultsThe survey was completed by 111 (85%) eligible HCWs. Ninety-seven of the surveyed HCWs were invited for interviews and 39 (40%) participated. Discharge tasks were reported to be "very important" to patient outcomes by over 80% of respondents, but only 37 (33%) perceived their hospital to deliver this care "very well" and 23 (21%) believed their facility provides sufficient resources for its provision. The vast majority (97%) of participants underestimated the risk of pediatric post-discharge mortality. Inadequate training, understaffing, stock-outs of take-home therapeutics, and user fees were commonly reported health systems barriers to adequate discharge care while poverty was seen as limiting caregiver adherence to discharge and follow-up care. Respondents endorsed the importance of follow-up care, but reported supportive mechanisms to be lacking. They requested enhanced guidelines on discharge and follow-up care.ConclusionKenyan healthcare workers substantially underestimated the risk of pediatric post-discharge mortality. Pre- and in-service training should incorporate instruction on discharge and follow-up care. Improved post-discharge deaths tracking-e.g., through vital registry systems, child mortality surveillance studies, and community health worker feedback loops-is needed, alongside dissemination which could leverage platforms such as routine hospital-based mortality reports. Finally, further interventional trials are needed to assess the efficacy and cost-effectiveness of novel packages to improve discharge and follow-up care.

Introduction Over 52 million children under 5 years of age become wasted each year, but only 17% of these children receive treatment. Novel methods to identify and deliver treatment to malnourished children are necessary to achieve the sustainable development goals target for child health. Mobile health (mHealth) programmes may provide an opportunity to rapidly identify malnourished children in the community and link them to care.Methods and analysis This randomised controlled trial will recruit 1200 children aged 6–12 months at routine vaccine appointments in Migori and Homa Bay Counties, Kenya. Caregiver–infant dyads will be randomised to either a maternally administered malnutrition monitoring system (MAMMS) or standard of care (SOC). Study staff will train all caregivers to measure their child’s mid-upper arm circumference (MUAC). Caregivers in the MAMMS arm will be given two colour coded and graduated insertion MUAC tapes and be enrolled in a mHealth system that sends weekly short message service (SMS) messages prompting caregivers to measure and report their child’s MUAC by SMS. Caregivers in the SOC arm will receive routine monitoring by community health volunteers coupled with a quarterly visit from study staff to ensure adequate screening coverage. The primary outcome is identification of childhood malnutrition, defined as MUAC

Summary: Background: Host vulnerabilities associated with acute malnutrition could facilitate the ability of specific enteric pathogens to cause diarrhoea and associated mortality. Using data from the Global Enteric Multicenter Study, we assessed whether acute malnutrition modifies the association between common enteric pathogens and moderate-to-severe diarrhoea, and whether associations between enteric pathogens and death were modified by acute malnutrition. Methods: Children with moderate-to-severe diarrhoea and age-matched and community-matched controls were included in this post-hoc analysis if their mid-upper arm circumference had been measured and if they were older than 6 months of age. Acute malnutrition was defined as mid-upper arm circumference below 12·5 cm, capturing both severe acute malnutrition (

INTRODUCTION:Accelerating progress in reducing child deaths is needed in order to achieve the Sustainable Development Goal child mortality target. This will require a focus on vulnerable children-including young children, those who are undernourished or with acute illnesses requiring hospitalization. Improving adherence to inpatient guidelines may be an important strategy to reduce child mortality, including among the most vulnerable. The aim of our assessment of nine sub-Saharan African and South Asian hospitals was to determine adherence to pediatric inpatient care recommendations, in addition to capacity for and barriers to implementation of guideline-adherent care prior to commencing the Childhood Acute Illness and Nutrition (CHAIN) Cohort study. The CHAIN Cohort study aims to identify modifiable risk factors for poor inpatient and post discharge outcomes above and beyond implementation of guidelines. METHODS:Hospital infrastructure, staffing, durable equipment, and consumable supplies such as medicines and laboratory reagents, were evaluated through observation and key informant interviews. Inpatient medical records of 2-23 month old children were assessed for adherence to national and international guidelines. The records of children with severe acute malnutrition (SAM) were oversampled to reflect the CHAIN study population. Seven core adherence indicators were examined: oximetry and oxygen therapy, fluids, anemia diagnosis and transfusion, antibiotics, malaria testing and antimalarials, nutritional assessment and management, and HIV testing. RESULTS:All sites had facilities and equipment necessary to implement care consistent with World Health Organization and national guidelines. However, stockouts of essential medicines and laboratory reagents were reported to be common at some sites, even though they were mostly present during the assessment visits. Doctor and nurse to patient ratios varied widely. We reviewed the notes of 261 children with admission diagnoses of sepsis (17), malaria (47), pneumonia (70), diarrhea (106), and SAM (119); 115 had multiple diagnoses. Adherence to oxygen therapy, antimalarial, and malnutrition refeeding guidelines was >75%. Appropriate antimicrobials were prescribed for 75% of antibiotic-indicative conditions. However, 20/23 (87%) diarrhea and 20/27 (74%) malaria cases without a documented indication were prescribed antibiotics. Only 23/122 (19%) with hemoglobin levels meeting anemia criteria had recorded anemia diagnoses. HIV test results were infrequently documented even at hospitals with universal screening policies (66/173, 38%). Informants at all sites attributed inconsistent guideline implementation to inadequate staffing. CONCLUSION:Assessed hospitals had the infrastructure and equipment to implement guideline-consistent care. While fluids, appropriate antimalarials and antibiotics, and malnutrition refeeding adherence was comparable to published estimates from low- and high-resource settings, there were inconsistencies in implementation of some other recommendations. Stockouts of essential therapeutics and laboratory reagents were a noted barrier, but facility staff perceived inadequate human resources as the primary constraint to consistent guideline implementation.

Summary: Background: Shigella infections are a leading cause of diarrhoeal death among children in low-income and middle-income countries. WHO guidelines reserve antibiotics for treating children with dysentery. Reliance on dysentery for identification and management of Shigella infection might miss an opportunity to reduce Shigella-associated morbidity and mortality. We aimed to systematically review and evaluate Shigella-associated and dysentery-associated mortality, the diagnostic value of dysentery for the identification of Shigella infection, and the efficacy of antibiotics for children with Shigella or dysentery, or both. Methods: We did three systematic reviews (for mortality, diagnostic value, and antibiotic treatment of Shigella and dysentery), and meta-analyses where appropriate, of studies in resource-limited settings. We searched MEDLINE, Embase, and LILACS database for studies published before Jan 1, 2017, in English, French, and Spanish. We included studies of human beings with diarrhoea and accepted all study-specific definitions of dysentery. For the mortality and diagnostic value searches, we excluded studies that did not include an effect estimate or data necessary to calculate this estimate. The search for treatment included only randomised controlled trials that were done after Jan 1, 1980, and assessed antibiotics in children (aged

We describe the spectroscopic data processing pipeline of the Dark Energy Spectroscopic Instrument (DESI), which is conducting a redshift survey of about 40 million galaxies and quasars using a purpose-built instrument on the 4 m Mayall Telescope at Kitt Peak National Observatory. The main goal of DESI is to measure with unprecedented precision the expansion history of the universe with the baryon acoustic oscillation technique and the growth rate of structure with redshift space distortions. Ten spectrographs with three cameras each disperse the light from 5000 fibers onto 30 CCDs, covering the near-UV to near-infrared (3600-9800 Å) with a spectral resolution ranging from 2000 to 5000. The DESI data pipeline generates wavelength- and flux-calibrated spectra of all the targets, along with spectroscopic classifications and redshift measurements. Fully processed data from each night are typically available to the DESI collaboration the following morning. We give details about the pipeline's algorithms, and provide performance results on the stability of the optics, the quality of the sky background subtraction, and the precision and accuracy of the instrumental calibration. This pipeline has been used to process the DESI Survey Validation data set, and has exceeded the project's requirements for redshift performance, with high efficiency and a purity greater than 99% for all target classes.