Infections caused by multi-drug resistant Enterobacterales (MDR-E) are difficult to treat and cause significant mortality, especially in developing countries. This study characterized the phenotypic and genotypic profiles of 49 randomly selected beta-lactam resistant MDR-E previously isolated from patients being managed in hospitals in Nigeria using whole genome sequencing. The study isolates exhibited 85.5% resistance to 3rd generation cephalosporins and 65.3% resistance to carbapenems. The blaTEM-1B (29, 59.2%), blaCTX-M-15 (38, 77.6%), and blaNDM-1 (17, 51.5%) were the most common penicillinase, ESBL, and carbapenem resistant genes across isolates, respectively. Seventeen (45%) of blaCTX-M-15 was carried on the insertion sequence ISEc9 while blaNDM-1 (11, 64.7%) were associated with ISEc33. None of the 21 plasmids detected were associated with β-lactamase genes. Higher resistance rates were found in E. coli ST-88 (n = 2) and the high-risk ST-692 (n = 2). For Klebsiella species, the high-risk clones ST-476 (n = 8) and ST-147 (n = 3) predominated and had higher phenotypic resistance rates and higher number of AMR genes. The mechanisms and pattern of antibiotic resistance differ from patterns previously described with isolates harbouring a wide range of AMRGs. The detection of several chromosomally mediated carbapenemases in our study also represents a significant finding that warrants further investigation to better understand its' implications for clinical practice and public health. The selected MDR-Es were found to be pan-susceptible to tigecycline and had very low resistance to fosfomycin, suggesting a potential for these as empiric treatments. A surveillance approach incorporating both conventional laboratory techniques and modern molecular techniques is essential for the comprehensive characterization of the emergence and dissemination of antimicrobial resistance in Enterobacterales infections within Nigeria.

Objectives: Bacteremia due to invasive Salmonella enterica has been reported earlier in children in Nigeria. This study aimed to detect the virulence and antibiotic resistance genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria. Method: From June 2015 to June 2018, 4163 blood cultures yielded 83 Salmonella isolates. This is a secondary cross-sectional analysis of the Salmonella isolates. The Salmonella enterica were isolated and identified using standard bacteriology protocol. Biochemical identifications of the Salmonella enterica were made by Phoenix MD 50 identification system. Further identification and confirmation were done with polyvalent antisera O and invA gene. Antimicrobial susceptibility testing was done following clinical and laboratory standard institute guidelines. Resistant genes and virulence genes were determined using a real-time polymerase chain reaction. Result: Salmonella typhi 51 (61.4%) was the most prevalent serovar, followed by Salmonella species 13 (15.7%), choleraesuis 8 (9.6%), enteritidis 6 (7.2%), and typhimurium 5 (6.1%). Fifty-one (61.4%) of 83 Salmonella enterica were typhoidal, while 32 (38.6%) were not. Sixty-five (78.3%) of the 83 Salmonella enterica isolates were resistant to ampicillin and trimethoprim-sulfamethoxazole, followed by chloramphenicol 39 (46.7%), tetracycline 41 (41.4%), piperacillin 33 (33.9%), amoxicillin-clavulanate, and streptomycin 21 (25.3%), while cephalothin was 19 (22.9%). Thirty-nine (46.9%) of the 83 Salmonella enterica isolates were multi-drug resistant, and none were extensive drug resistant or pan-drug resistant. A blaTEM 42 (50.6%), floR 32 (38.6%), qnrA 24 (28.9%), tetB 20 (20.1%), tetA 10 (10.0%), and tetG 5 (6.0%) were the antibiotic resistance genes detected. There were perfect agreement between phenotypic and genotypic detection of antimicrobial resistance in tetracycline, ciprofloxacin, and chloramphenicol, while beta-lactam showed κ = 0.60 agreement. All of the Salmonella enterica isolates had the virulence genes invA, sopB, mgtC, and sip4D, while 33 (39.8%), 45 (51.8%), and 2 (2.4%) had ssaQ, spvC, and ljsGI-1, respectively. Conclusion: Our findings showed multi-drug resistant Salmonella enterica in children with bacteremia in northern Nigeria. In addition, significant virulence and antimicrobial resistance genes were found in invasive Salmonella enterica in northern Nigeria. Thus, our study emphasizes the need to monitor antimicrobial resistance in Salmonella enterica from invasive sources in Nigeria and supports antibiotic prudence.

Journal Article Corrected proof Unraveling Neonatal Sepsis: Sharper Tools Needed for Unexpected Organisms Get access Ian C Michelow, Ian C Michelow Pediatrics and Infectious Diseases, Connecticut Children's Medical Center, University of Connecticut School of Medicine, Connecticut, CT, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Stephen K Obaro Stephen K Obaro Pediatrics and Infectious Diseases, University of Nebraska Medical Center, Omaha, NE, USA Correspondence: S. K. Obaro, MD, PhD, Professor of Pediatrics and Infectious Diseases. (stephen.obaro@unmc.edu). https://orcid.org/0000-0002-7526-1075 Search for other works by this author on: Oxford Academic PubMed Google Scholar Clinical Infectious Diseases, ciad338, https://doi.org/10.1093/cid/ciad338 Published: 05 June 2023 Article history Received: 22 April 2023 Editorial decision: 25 May 2023 Accepted: 01 June 2023 Published: 05 June 2023 Corrected and typeset: 18 July 2023

Infections caused by multi-drug resistant Escherichia coli cause significant morbidity and mortality especially in developing countries. In this study, we describe the molecular characteristics of E. coli isolated from clinical specimens and the patients' outcomes. Phenotypic methods were used in the identification and antimicrobial susceptibility testing of E. coli from clinical specimens from a tertiary hospital in Abuja, Nigeria. Whole genome sequencing was used to describe the antimicrobial resistance genes, serotypes, sequence types/clonal complexes, and mobile genetic elements. The mean age of the patients was 20.3 years with 70.1% females and majority of isolates 75% from urine, 21% from blood cultures, and 3% each from cerebrospinal fluid and endo-cervical swabs. Of the 107 non-duplicate E. coli isolates, 101 (94.3%) were resistant to ampicillin, 95 (88.8%) to trimethoprim/sulfamethoxazole, 86 (80.4%) to ceftriaxone, 60 (56.1%) to gentamicin, and eight (7.5%) to meropenem. There were 102 (95.3%) isolates that were multi-drug resistant (MDR). Expression of Extended Spectrum Beta Lactamase (ESBL) phenotype was detected in 54 (50%) and bla(CTX-M-15) genes detected in 75 (70.1%) isolates. The carbapenemase genes bla(NDM-1) and bla(NDM-5) were detected in six (5.6%), while the AmpC gene- bla(CMY-2), was detected in seven (6.5%) isolates. Two (1.9%) isolates simultaneously harboured the bla(OXA-1), bla(CMY-2), bla(CTX-M-15), and bla(NDM-5) genes. In total, 35 sequence types (STs) were found with the majority being ST131 (n = 23; 21.5%). The most common serotype was O25:H4 associated with all 23 strains of ST131, followed by O1:H6/ST648 (n = 6). The ST410, ST671, and ST101 strains displayed phenotypic resistance to wide array of antibiotic classes and harbored high numbers of antibiotic resistance genes via in-silico analysis. The ST410 strain in particular harbored a higher number of antibiotic resistance genes and was phenotypically resistant to a wider array of antibiotics. Four pairs of isolates were closely related with three isolates (ST131, ST38, ST652) having a pairwise SNP difference of zero. 71/72 75/76 52/14. The MDR E. coli lineages circulating in this setting pose a clinical and public health threat as they can hinder effective prevention and management of infections. The genetic diversity and MDR E. coli with the emergence of ST410 and ST101 clones is concerning because of the potential for rapid dissemination in hospitals and communities- further increasing the problems of antibiotic resistance. Continuous routine surveillance of E. coli infections for AMR in hospitals becomes imperative, aimed at development of effective antimicrobial stewardship programs, facilitating prudent use of antimicrobial agents, and limiting dissemination of resistant strains.

Pneumococcal serotype 35B is an important non- conjugate vaccine (non- PCV) serotype. Its continued emergence, post- PCV7 in the USA, was associated with expansion of a pre- existing 35B clone (clonal complex [CC] 558) along with post- PCV13 emergence of a non- 35B clone previously associated with PCV serotypes (CC156). This study describes lineages circulating among 35B isolates in South Africa before and after PCV introduction. We also compared 35B isolates belonging to a predominant 35B lineage in South Africa (GPSC5), with isolates belonging to the same lineage in other parts of the world. Serotype 35B isolates that caused invasive pneumococcal disease in South Africa in 2005-2014 were characterized by whole- genome sequencing (WGS). Multi- locus sequence types and global pneumococcal sequence clusters (GPSCs) were derived from WGS data of 63 35B isolates obtained in 2005-2014. A total of 262 isolates that belong to GPSC5 (115 isolates from South Africa and 147 from other countries) that were sequenced as part of the global pneumococcal sequencing (GPS) project were included for comparison. Serotype 35B isolates from South Africa were differentiated into seven GPSCs and GPSC5 was most common (49 %, 31/63). While 35B was the most common serotype among GPSC5/CC172 isolates in South Africa during the PCV13 period (66 %, 29/44), 23F was the most common serotype during both the pre- PCV (80 %, 37/46) and PCV7 period (32 %, 8/25). Serotype 35B represented 15 % (40/262) of GPSC5 isolates within the global GPS database and 75 % (31/40) were from South Africa. The predominance of the GPSC5 lineage within non- vaccine serotype 35B, is possibly unique to South Africa and warrants further molecular surveillance of pneumococci.

BACKGROUND:Children with acute febrile illness with no localizing signs often receive antibiotics empirically in most resource-poor settings. However, little is known about the burden of bacteremia in this category of patients, and an appraisal is thus warranted. This will guide clinical practice and promote rational antibiotics use.METHODS:We prospectively followed up 140 under-five children who presented with acute undifferentiated fever at the emergency/outpatient pediatric unit of a secondary healthcare facility. Baseline clinical and laboratory information was obtained and documented in a structured questionnaire. We compared baseline characteristics between participants with bacteremia and those without bacteremia. We further fitted a multivariable logistic regression model to identify factors predictive of bacteremia among the cohort.RESULT:The prevalence of bacteremia was 17.1%, and Salmonella Typhi was the most frequently (40.9%) isolated pathogen. The majority (78.6%) of the study participants were managed as outpatients. The participants who required admission were four times more likely to have bacteremia when compared to those managed as outpatients (AOR 4.08, 95% CI 1.19 to 14.00). There is a four times likelihood of bacteremia (AOR 4.75, 95% CI 1.48 to 15.29) with a fever duration of beyond 7 days. Similarly, participants who were admitted with lethargy were six times more likely to have bacteremia (AOR 6.20, 95% CI 1.15 to 33.44). Other significant predictors were tachypnea and lymphopenia.CONCLUSION:Among under-five children with acute undifferentiated fever, longer duration of fever, lethargy, inpatient care, tachypnea, and lymphopenia were the significant predictors of bacteremia.

Background Population-level health and mortality data are crucial for evidence-informed policy but scarce in Nigeria. To fill this gap, we undertook a comprehensive assessment of the burden of disease in Nigeria and compared outcomes to other west African countries. Methods In this systematic analysis, using data and results of the Global Burden of Diseases, Injuries, and Risk Factors Study 2019, we analysed patterns of mortality, years of life lost (YLLs), years lived with disability (YLDs), life expectancy, healthy life expectancy (HALE), and health system coverage for Nigeria and 15 other west African countries by gender in 1998 and 2019. Estimates of all-age and age-standardised disability-adjusted life-years for 369 diseases and injuries and 87 risk factors are presented for Nigeria. Health expenditure per person and gross domestic product were extracted from the World Bank repository. Findings Between 1998 and 2019, life expectancy and HALE increased in Nigeria by 18% to 64.3 years (95% uncertainty interval [UI] 62.2-66.6), mortality reduced for all age groups for both male and female individuals, and health expenditure per person increased from the 11th to third highest in west Africa by 2018 (US$18.6 in 2001 to $83.75 in 2018). Nonetheless, relative outcomes remained poor; Nigeria ranked sixth in west Africa for age-standardised mortality, seventh for HALE, tenth for YLLs, 12th for health system coverage, and 14th for YLDs in 2019. Malaria (5176.3 YLLs per 100 000 people, 95% UI 2464.0-9591.1) and neonatal disorders (4818.8 YLLs per 100 000, 3865.9-6064.2) were the leading causes of YLLs in Nigeria in 2019. Nigeria had the fourth-highest under-five mortality rate for male individuals (2491.8 deaths per 100 000, 95% UI 1986.1-3140.1) and female individuals (2117.7 deaths per 100 000, 1756.7-2569.1), but among the lowest mortality for men older than 55 years. There was evidence of a growing non-communicable disease burden facing older Nigerians. Interpretation Health outcomes remain poor in Nigeria despite higher expenditure since 2001. Better outcomes in countries with equivalent or lower health expenditure suggest health system strengthening and targeted intervention to address unsafe water sources, poor sanitation, malnutrition, and exposure to air pollution could substantially improve population health. Copyright (C) 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.

The scourge of COVID-19 has been global, but the most affected subgroups in the population have largely been older people and individuals with comorbid conditions that predispose them to increasingly severe disease and poor outcomes. Overall, the disease burden in children has been reasonably mild, even in those with comorbidities, such as oncological conditions. Protection from severe disease in children might be related to a lower expression of host factors required for viral replication, and to differences in the magnitude and timing of innate or adaptive immune responses. Data for recorded COVID-19 cases show that only 7% of children younger than 18 years with severe disease required intensive care, whereas 53% of adults who had severe disease required intensive care.1Castagnoli R Votto M Licari A et al.severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review.JAMA Pediatr. 2020; 174: 882-889Crossref PubMed Scopus (799) Google Scholar, 2Hoang A Chorath K Moreira A et al.COVID-19 in 7780 pediatric patients: a systematic review.EClinicalMedicine. 2020; 24100433Summary Full Text Full Text PDF Scopus (400) Google Scholar, 3US Centers for Disease Control and PreventionSevere outcomes among patients with coronavirus disease 2019 (COVID-19) — United States, February 12–March 16, 2020.Morb Mortal Wkly Rep. 2020; 69: 343-346Crossref PubMed Scopus (1557) Google Scholar Multisystem inflammatory syndrome in children, arguably the most dreaded presentation, typically presents between 3 and 6 weeks after SARS-CoV-2 exposure.4Ahmed M Advani S Moreira A et al.Multisystem inflammatory syndrome in children: a systematic review.EClinicalMedicine. 2020; 26100527Summary Full Text Full Text PDF PubMed Scopus (369) Google Scholar Most patients at presentation have a negative nasopharyngeal RT-PCR but are positive for serology. This temporal association and low PCR positivity rate suggest a postinfectious mechanism rather than acute viral infection. Children of African or Hispanic race or ethnicity are more frequently affected, whereas children of Asian or White race or ethnicity appear to be less often affected,5Dufort EM Koumans EH Chow EJ et al.Multisystem inflammatory syndrome in children in New York State.N Engl J Med. 2020; 383: 347-358Crossref PubMed Scopus (972) Google Scholar, 6Godfred-Cato S Bryant B Leung J et al.COVID-19-associated multisystem inflammatory syndrome in children—United States, March–July 2020.MMWR Morb Mortal Wkly Rep. 2020; 69: 1074-1080Crossref PubMed Scopus (0) Google Scholar and genetic susceptibility might account for this over-representation. The reasonably low incidence of COVID-19 in the general population of children, the unusual manifestation with multisystem inflammatory syndrome in older children and adolescents, and the absence of epidemiological data that incriminates children in the transmission of SARS-CoV-2, pose important immunological, ethical, and economic conundrums that require careful examination before the deployment of any COVID-19 vaccine in children. The following clinical observations are relevant for formulating COVID-19 vaccines for deployment in children. First, from an immunological perspective, the milder spectrum of disease in children might correlate with SARS-CoV-2 antigen processing and immunopathogenesis in children. Few immunological studies in children with multisystem inflammatory syndrome report abnormal immunophenotypes of plasmablasts,7Mathew D Giles JR Baxter AE et al.Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications.Science. 2020; 369eabc8511Crossref PubMed Google Scholar, 8Carter MJ Fish M Jennings A et al.Peripheral immunophenotypes in children with multisystem inflammatory syndrome associated with SARS-CoV-2 infection.Nat Med. 2020; 26: 1701-1707Crossref PubMed Scopus (274) Google Scholar elevated SARS-CoV-2 IgG, and proinflammatory cytokines.8Carter MJ Fish M Jennings A et al.Peripheral immunophenotypes in children with multisystem inflammatory syndrome associated with SARS-CoV-2 infection.Nat Med. 2020; 26: 1701-1707Crossref PubMed Scopus (274) Google Scholar Current vaccines that are authorised for emergency use, approved or in development, do not have a safety or immunogenicity profile in children. In the absence of a better understanding of the pathogenesis of this condition, using the same approach for delivering vaccines as in adults could exacerbate the incidence of this hyperinflammatory condition. Second, from a public health perspective, it will be necessary to immunise children if they are a major source of SARS-CoV-2 transmission and if the candidate vaccines block transmission. However, epidemiological reports up to now suggest that young children have a high likelihood of developing COVID-19 via household transmission, once a family member tests positive for COVID-19.1Castagnoli R Votto M Licari A et al.severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review.JAMA Pediatr. 2020; 174: 882-889Crossref PubMed Scopus (799) Google Scholar There is little evidence of secondary infection from children to others in the transmission pathways of COVID-19. Although emerging data suggest that some candidate vaccines can block transmission, vaccinating children cannot be justified if it is to give direct protection despite minimal burden of disease or to help to block transmission if children do not constitute a substantial reservoir for transmission. For other infections that can be prevented by vaccine, such as invasive pneumococcal disease, immunisation of children not only prevented infections in children, but also conferred indirect benefit by decreasing disease in older people, because of its effect on carriage reduction and blockage of transmission.9Tsaban G Ben-Shimol S Indirect (herd) protection, following pneumococcal conjugated vaccines introduction: a systematic review of the literature.Vaccine. 2017; 35: 2882-2891Crossref PubMed Scopus (86) Google Scholar For COVID-19, the reverse might be the case, with adults having to be vaccinated to confer protection on young children. Third, from an ethical perspective, there is a balance between risk and benefit in offering a COVID-19 vaccine to children that will offer minimal or no direct benefit to the recipient, no benefit to the public, and as yet, unknown medium-term and long-term risks to the recipient. Other important considerations include the economic and practical considerations in deploying a new vaccine into the routine childhood immunisation programmes. Without additional data and public enlightenment on the benefits of immunising young children, this deployment could further threaten childhood immunisation coverage that is already precariously low in several settings. Finally, because individuals are not equally susceptible and contagious, our current target to vaccinate 65–70% of the population to archive herd immunity might be an overestimate.10Fontanet A Cauchemez S COVID-19 herd immunity: where are we?.Nat Rev Immunol. 2020; 9: 1-2Google Scholar If young children are excluded, there will be more vaccines available for the more epidemiologically susceptible subgroups. Initiating efficacy trials in youths aged 12–18 years is a welcome development, but a new strategy might ultimately be required for immunising younger children, should this become necessary. I declare no competing interests.

Perennial outbreaks of meningococcal disease in the meningitis belt of Africa have been the norm for several decades. These outbreaks are largely unpredictable in size, location, and causative strain, but are caused predominantly by serogroup A. 1 Greenwood B Manson lecture. Meningococcal meningitis in Africa. Trans R Soc Trop Med Hyg. 1999; 93: 341-353 Summary Full Text PDF PubMed Scopus (279) Google Scholar In 2010, a serogroup A meningococcal conjugate vaccine (MenAfriVac) was deployed across the region in a mass vaccination campaign with a plan for phased introduction of MenAfriVac into national routine immunisation programmes across the region. 2 Djingarey MH Barry R Bonkoungou M et al. Introduction and rollout of a new group A meningococcal conjugate vaccine (PsA-TT) in African meningitis belt countries, 2010–2014. Clin Infect Dis. 2015; 61: S434-S441 Crossref PubMed Scopus (40) Google Scholar Meningococcal carriage 7 years after introduction of a serogroup A meningococcal conjugate vaccine in Burkina Faso: results from four cross-sectional carriage surveysOur results show the continued effect of MenAfriVac on serogroup A meningococcal carriage, for at least 7 years, among vaccinated and unvaccinated cohorts. Carriage prevalence of epidemic-prone serogroup C CC10217 and serogroup W CC11 was low. Continued monitoring of N meningitidis carriage will be crucial to further assess the effect of MenAfriVac and inform the vaccination strategy for future multivalent meningococcal vaccines. Full-Text PDF Open Access

BACKGROUND:Pulmonary hypertension (PH), a complication of sickle cell anaemia (SCA), results in considerable morbidity. This study aims to determine the prevalence and associations of echocardiography-suggested PH in children with SCA.METHODS:We performed a cross-sectional comparative study involving 100 systematically sampled SCA subjects 3-14 y of age in their steady state with matched haemoglobin AA phenotype controls. Clinical, laboratory and echocardiography data (including tricuspid regurgitation velocity [TRV], mean pulmonary arterial pressure [mPAP] and tricuspid annular plane systolic excursion [TAPSE]) were obtained from all patients. Statistical analyses were performed using SPSS version 22 (IBM, Armonk, NY, USA). A p-value <0.05 was considered statistically significant.RESULTS:Of the 100 SCA subjects studied, 22 (22%) had echocardiographic findings suggestive of PH compared with none in the controls. The median TAPSE was significantly lower in the PH group (2.55 cm [interquartile range {IQR} 2.2-2.8]) compared with the no PH group (2.77 cm [IQR 2.4-3.2]) (p=0.03). No significant correlation existed between mPAP and age, nor any laboratory parameters studied. The odds ratio (OR) suggested PH significantly increased with an increase in the frequency of hospitalizations for vaso-occlusive crises within a 12-month period (OR 15.15 [95% CI 1.57 to 146.35], p=0.02) and a lifetime history of blood transfusion (OR 5.44 [95% CI 1.09 to 27.24], p=0.04).CONCLUSIONS:Echocardiography-suggested PH is common in children with SCA and is associated with poorer right ventricular function, frequent vaso-occlusive crises and blood transfusions.

Urogenital schistosomiasis is a neglected tropical disease caused by the parasite Schistosoma haematobium, which resides in the vasculature surrounding the urogenital system. Previous work has suggested that helminthic infections can affect the intestinal microbiome, and we hypothesized that S. haematobium infection could result in an alteration of immune system-microbiota homeostasis and impact the composition of the gut microbiota. To address this question, we compared the fecal microbiomes of infected and uninfected schoolchildren from the Argungu Local Government Area of Kebbi State, Nigeria, detecting significant differences in community composition between the two groups. Most remarkably, we observed a decreased abundance of Firmicutes and increased abundance of Proteobacteria - a shift in community structure which has been previously associated with dysbiosis. More specifically, we detected a number of changes in lower taxa reminiscent of inflammation-associated dysbiosis, including decreases in Clostridiales and increases in Moraxellaceae, Veillonellaceae, Pasteurellaceae, and Desulfovibrionaceae. Functional potential analysis also revealed an enrichment in orthologs of urease, which has been linked to dysbiosis and inflammation. Overall, our analysis indicates that S. haematobium infection is associated with perturbations in the gut microbiota and may point to microbiome disruption as an additional consequence of schistosome infection.

Introduction: Nearly 24% of the world's population carry hemoglobin (Hb) gene variants, with the large majority of affected births occurring in low-income countries. The most prevalent structural Hb variants are the recessive β-globin gene mutations, βS or S, βC or C, and βE or E1. Hb S mutation is prevalent in sub-Saharan Africa and in Central India. Hb C is common in West Africa, and Hb E is common in Southeast Asia and in India. Homozygotes or compound heterozygotes with βS (e.g., Hb SS or SC) have sickle cell disease (SCD), a chronic sickling disorder associated with pain, chronic multi-organ damage, and high mortality. While Hb EE causes only a mild microcytic anemia, Hb E in combination with β-thalassemia can lead to transfusion dependent thalassemia. Though carriers are typically asymptomatic, they may pass the mutations to their offspring. Screening is needed so that these disorders can be diagnosed early and managed in a timely manner2. For example, in low-income countries, due to lack of nationwide screening and comprehensive care programs, up to 80% of babies born with SCD are undiagnosed and less than half of them survive beyond 5 years of age2. The unmet need for affordable, portable, accurate point-of-care tests to facilitate decentralized hemoglobin testing in resource-constrained countries is well-recognized 2,3. Here, we present international multi-site clinical validation results and high diagnostic accuracy of the 'HemeChip' (Fig. 1), an affordable, 10-minute point-of-care microchip electrophoresis test for identifying common Hb variants S, C, and E. Methods: Institutional Review Board approvals were obtained at each study site, and blood samples were collected as part of the standard clinical care. Tests were performed by local users, including healthcare workers and clinical laboratory personnel. 315 children (6 weeks to 5 years of age) were tested in Kano, Nigeria. Study participants were enrolled at three hospitals, Amino Kano Teaching Hospital, Murtala Mohammed Specialist Hospital, and Hasiya Bayero Pediatric Hospital. 124 subjects (7 weeks to 63 years old) were included in the study at Siriraj Thalassemia Center in Bangkok, Thailand. 298 subjects (8 months to 65 years old) were tested at a referral testing facility of ICMR-National Institute of Research in Tribal Health, located at Late Baliram Kashayap Memorial Medical College, Jagdalpur, Chhattisgarh, India. Blood samples were tested with both HemeChip and the standard reference methods, high performance liquid chromatography or cellulose acetate electrophoresis. Reference test results were not available to the HemeChip users. Similarly, HemeChip test results were not available to the users of the standard reference tests. Clinical validation studies presented here were performed with a fully functional, portable HemeChip prototype developed at Case Western Reserve University (Fig. 1A). A commercial product has been developed based on this technology by Hemex Health Inc. under the product name, GazelleTM(Fig. 1B). Results and Discussion: Among the total 768 tests performed with HemeChip in all test sites, 732 were valid tests, as defined by the Standards for Reporting Diagnostic Accuracy (STARD)4. HemeChip correctly identified all subjects with Hb SS, Hb SC, Hb AS, Hb AE, and Hb EE with 100% accuracy (Table 1). Nine subjects with normal Hb (Hb AA) were identified as HbSS in Nigeria. No subjects with disease were identified as normal or trait by HemeChip. Three subjects with compound heterozygous Hb Sβ-thalassemia (2 subjects with Hb Sβ+-thalassemia, 1 subject with Hb Sβ0-thalassemia) were identified as Hb SS. Sensitivity was 100% for all Hb types tested. Specificity was 98.7% for Hb SS versus other Hb types, and 100% for all other Hb types tested. HemeChip displayed an overall diagnostic accuracy of 98.4% in comparison to standard reference methods for the Hb variants tested in all clinical testing sites (Table 1). HemeChip is a versatile point-of-care system that enables affordable, accurate, decentralized hemoglobin testing in resource-limited settings. References: 1. Weatherall DJ, Clegg JB. Bull World Health Organ. 2001;79(8):704-712. 2. Mburu J, Odame I. International Journal of Laboratory Hematology. 2019;41(S1):82-88. 3. Alapan Y, Fraiwan A, Kucukal E, et al. Expert Review of Medical Devices. 2016;13(12):1073-1093. 4. Bossuyt PM, Reitsma JB, Bruns DE, et al. BMJ : British Medical Journal. 2015;351:h5527. Disclosures Fraiwan: Hemex Health, Inc.: Equity Ownership, Patents & Royalties. Hasan:Hemex Health, Inc.: Equity Ownership, Patents & Royalties. An:Hemex Health, Inc.: Patents & Royalties. Thota:Hemex Health, Inc.: Employment. Piccone:Hemex Health, Inc.: Patents & Royalties. Little:Hemex Health, Inc.: Patents & Royalties; GBT: Research Funding. Gurkan:Hemex Health, Inc.: Consultancy, Employment, Equity Ownership, Patents & Royalties, Research Funding.

Nigeria leads the world in the number of cases of sickle cell disease (SCD). An estimated 150,000 babies are born annually in Nigeria with SCD, a heredity disorder, and 70-90% die before age 5. Only a small portion of affected infants and children in sub Saharan Africa (SSA) reach adolescence. Over 650 children die per day in sub-Saharan Africa from SCD. These dismal statistics are in sharp contrast to outcomes in high-income countries (HICs) where more than 90% of SCD patients reach adulthood. The World Health Organization (WHO) estimates that 70% of deaths could be prevented with a low cost diagnostic and treatment plan. Meaningful preventive care and treatment cannot be implemented without a structured plan for early diagnosis and patient tracking.Early diagnosis requires improved access to parents and guardians of children with SCD, and gaining this access remains a challenge in most of SSA. In 2015, Nigeria's Kano state government, with support from foreign partners, established a community-based program for newborn registration. This platform provides unique access to newborn babies in one of Nigeria's most populous cities, but still lacks a functioning patient testing, tracking, and monitoring system, which we plan to address in our ongoing study. This study will introduce mobile health in a low-income country with low literacy rate and hopefully accustom that segment of the population to more varied mobile health applications that will ultimately improve their health in the long run. Our current operational platform in Kano, Nigeria provides access to a large population with a high prevalence of SCD. We have previously completed pilot testing of 315 subjects for SCD using our microchip electrophoresis test. We are planning to test up to 4,500 additional subjects less than 5 years of age at Murtala Muhammed Specialist Hospital. The hospital staff includes 97 physicians and 415 nurses and outpatient clinics serve about 30,000 patients monthly. The maternity department has a 200-bed capacity and the antenatal clinic performs about 1,000 deliveries and serves an average of 3,000 mothers monthly. Enrollment is planned to start on September 15, 2019 and medical staff are currently being trained to run the tests. Our study is registered in the United States National Library of Medicine's ClinicalTrials.gov (Identifier: NCT03948516). Our technology is uniquely paired with an automatic reader and an Electronic Medical Record (EMR) and patient management solution to record POC test results, register new cases, and track patients for follow-up (Fig. 1). The reader enables automated interpretation of test results, local and remote test data storage, and includes geolocation (Global Positioning System) (Fig. 2). The system will generate reports for all cases of SCD, track hospital visits, appointments, lab tests, and will have mobile and dashboard applications for tracking patients and samples. The application will be installed on mobile devices provided to users. The proposed system will be compliant with the existing privacy standards to handle medical data (e.g., HIPAA in the US and GDPR in the EU). All communications between the parties will be secured via end-to-end encryption as a safeguard. We anticipate that our project will increase the rates of screening, diagnosis and timely treatment of SCD in Kano State of Nigeria. The project's broader impact will likely be the ability to track and monitor screening, disease detection, diagnosis and treatment, which can be scaled up to the whole nation of Nigeria, then to sub-Saharan Africa. The data obtained and analyzed will be the first of their kind and will be used to inform the design of programs to improve access to, and availability of, effective care for this underserved populations. The importance of increased access to diagnosis and treatment should not be underestimated - it is crucial for realizing effective management of people with SCD. The impact can be enhanced by complementing diagnosis and patient tracking with education for the families so they can provide or seek the necessary preventative treatment. Identification of the location of the patients in need would help identify the areas where family, parent, caregiver education should be provided. Disclosures Fraiwan: Hemex Health, Inc.: Equity Ownership, Patents & Royalties. Hasan:Hemex Health, Inc.: Equity Ownership, Patents & Royalties. An:Hemex Health, Inc.: Patents & Royalties. Thota:Hemex Health, Inc.: Employment. Gurkan:Hemex Health, Inc.: Consultancy, Employment, Equity Ownership, Patents & Royalties, Research Funding.

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Aim: Staphylococcus epidermidis is a significant coagulase-negative staphylococci obtained from blood culture samples. However, there is limited information about phenol-soluble modulin (PSM), which is associated with virulence in S. epidermidis and its genetic relatedness in Nigeria. This study observed the presence of phenolsoluble modulin mec (psm-mec) gene and the multilocus sequence typing (MLST) of biofilm-positive Staphylococcus epidermidis (BPSE). Method: Twenty-two biofilm-positive S. epidermidis isolates obtained from paediatric blood culture at three hospitals in north-west and north-central Nigeria were evaluated for the molecular detection of the psm-mec gene using conventional polymerase chain reaction (PCR). The biofilm formation was previously assessed by molecular detection of the intercellular adhesion (icaA) gene and the methicillin resistance using cefoxitin disk agar diffusion. Internal fragments of the respective seven housekeeping genes was sequenced for 21 BPSE strains and matched with the central MLST database. Results: Out of 22 BPSE, only 4.5% had the psm-mec gene and it was methicillin resistant. About 91% methicillin resistance was observed among the psm-mec negative BPSE strains. Twenty-one BPSE strains were sequence type 1 (ST1) based on the MLST analysis of the seven housekeeping genes. Conclusion: Considering the very low presence of psm-mec gene, the BPSE may be carrying the ß-type PSMs related to biofilm formation and dissemination, and not the cytolytic a-type PSMs common in the aggressive form of S. epidermidis. Phenol-soluble modulin methicillin resistance island-encoded peptide toxin is involved in sepsis related methicillin-resistant S. epidermidis. The strains are genetically related to each other.

Objectives: The objective of this study was to assess the prevalence of maternal recto-vaginal extended-spectrum B-lactamase producing Enterobacteriacea (ESBL-E) colonization, identify risk factors for maternal and neonatal ESBL-E colonization, and subsequent impact on neonatal mortality. Methods: A prospective, cross-sectional study was conducted at the University of Abuja Teaching Hospital from April 2016 to May 2017. Maternal-neonatal pairs were screened for ESBL-E exposure at time of delivery. Neonatal mortality was assessed at 28 days. Results: A total of 1161 singleton deliveries were evaluated. In total, 9.7% (113/1161) of mothers and 4.3% (50/1161) of infants had ESBL-E-positive cultures at delivery. Maternal antibiotic exposure was associated with ESBL-E recto-vaginal colonization (18.6% (21/113) vs. 8.4% (88/1048), p < 0.001)). Maternal ESBL-E colonization (adjusted odds ratio (AOR) 14.85; 95% CI 7.83-28.15) and vaginal delivery (AOR 6.35; 95% CI 2.63-17.1) were identified as a risk factor for positive ESBL-E neonatal surface cultures. Neonatal positive ESBL-E surface cultures were a risk factor for neonatal mortality (stillbirths included, AOR 4.84; 95% CI 1.44-16.31). The finding that maternal ESBL-E recto-vaginal colonization appeared protective in regards to neonatal mortality (AOR 0.22; 95% CI .06-0.75) requires further evaluation. Conclusions: Maternal ESBL-E recto-vaginal colonization is an independent risk factor for neonatal ESBL-E colonization and neonates with positive ESBL-E surface cultures were identified as having increased risk of neonatal mortality. (C) 2019 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Carbapenem-resistant Klebsiella pneumoniae is of global health importance, yet there is a paucity of genome-based studies in Africa. Here we report fatal blood-borne NDM-5-producing K. quasipneumoniae subsp. similipneumoniae infections from Nigeria, Africa. New Delhi metallo-β-lactamase (NDM)-producing Klebsiella spp. are responsible for high mortality and morbidity, with the NDM-5 variant showing elevated carbapenem resistance. The prevalence of NDM-5 in Klebsiella has been limited primarily to K. pneumoniae , with only one isolate being collected from Africa. During an outbreak of sepsis in a teaching hospital in Nigeria, five NDM-5-producing K. quasipneumoniae subsp. similipneumoniae sequence type 476 isolates were identified. Given the increased resistance profile of these strains, this study highlights the emerging threat of bla NDM-5 dissemination in hospital environments. The observation of these NDM-5-producing isolates in Africa stresses the urgency to improve monitoring and clinical practices to reduce or prevent the further spread of resistance.

OBJECTIVES:Acute febrile illness is a common cause of hospital admission, and its associated infectious causes, of which a key bacterial causative agent is Streptococcus pneumoniae, contribute to substantial morbidity and mortality. We sought to evaluate the utility of real-time (rt)-PCR on dried blood spots (DBS) for diagnosis of S. pneumoniae in acute febrile illness among children presenting to hospitals in Nigeria. We previously described preliminary results in a sample of 537 patients. Here we present data from a larger collection of 1038 patients.RESULTS:Using rt-PCR for Streptococcus pneumoniae on 1038 dried blood spots from children prospectively enrolled with acute febrile illness, including 79 healthy controls, we detected pneumococcal DNA in nine of 15 blood culture-positive specimens, one culture-negative specimen from a high-risk group, a culture-confirmed non-pneumococcal specimen and a healthy control. Six culture-positive isolates (40%) were negative. Sensitivity was 60%, specificity 99.7%, positive predictive value 75% and negative predictive value 99.4%. Rt-PCR of DBS has limited sensitivity in blood specimens from acute febrile illness in children.

Abstract BACKGROUND The severity of sickle cell anemia (SCA) has been associated with five specific haplotypes in the beta globin cluster, identifiable by distinct patterns of restriction fragment length polymorphism (RFLP). These RFLP-defined haplotypes, named according to the region where they were first discovered - Central Africa region (CAR), Benin, Senegal, Arabic-Indian, and Cameroon - suggested that the sickle cell mutation arose recently at least four independent times in Africa, each time on a different genetic background, and again in India - the Multi-centric Sickle Cell Model. The beta-globin locus, however, is prone to extensive structural rearrangements, and alongside observations of ancestral sequence haplotypes extending several hundreds of kilobases beyond the beta globin cluster, it has been suggested that there is more cis-variation in the beta-globin gene cluster than is evident from RFLP analyses, and current definitions of RFLP haplotypes may not accurately reflect the ancestral origin of the sickle mutation. This undescribed cis-variation is important to understanding inter-individual phenotype variation associated with the different haplotypes. To better define this variation, we have undertaken extended, long-range molecular haplotyping of the beta-globin cluster on differing RFLP haplotype backgrounds using real time single molecule sequencing (SMS). The SMS approach generates long, unbroken reads with uniform coverage, thereby allowing for detailed molecular phasing of RFLP haplotypes and identification of local structural variation that would otherwise be hidden within the complex repetitive elements of the beta-globin cluster. In so doing, we plan to evaluate the molecular evidence for a single origin for the sickle cell allele and identify potential cis-acting, disease-modifying, candidate variants within the beta globin cluster. METHODS DNA from 200 SCA patients from three countries in sub-Saharan Africa - Nigeria, Cameroon, and Kenya - were collected after informed consent. RFLP analysis revealed the majority of the patients to be homozygous for the Benin and CAR haplotypes, with a smaller sampling of Cameroon, Senegal, and Atypical haplotypes. From this group we selected 40 samples - representing the four main classical RFLP haplotypes in sub-Saharan Africa - were selected for SMS. PCR was used to tile barcoded amplicons across the cluster. SMS was performed on a Sequel machine (Pacific Biosciences). The resulting FASTQ sequences were de-multiplexed, read quality control filters were applied, and mapped to human reference genome Hg38, prior to annotation and calling of single nucleotide variants (SNV) and structural variants (SV). RESULTS Analyses have so far identified 227 insertions, 18 deletions, 7 duplications, 76 inversions and 13 translocations from long-read analyses of the initial 40 samples; the vast majority of these variants are not described in public variant databases. Atypical haplotypes demonstrated more translocation and duplication events than other haplotypes. Insertions ~48 kb upstream of the beta-globin locus control region and 1.3 kb upstream of gamma globin gene 2 (HBG2) were observed on 50% of Senegal and 45% of CAR haplotypes. Also, recurrent insertions ranging between 32bp and 1,184bp in length, 2.3 kb downstream of the beta globin gene (HBB), were seen on 50% of the Benin and 54% of the CAR haplotypes, but only once on Senegal haplotypes. CONCLUSIONS Our findings suggest there are more cis-SVs within the beta-globin gene cluster than previously described. Work to validate these SVs using orthogonal methods and complete similar analyses of SNVs is ongoing. Variation outside of the gene cluster will also be integrated with RFLP and within-cluster molecular haplotypes to investigate the ancestral origin of the mutation, and validated cis-acting variants will be used to identify markers associated with proxies of SCA disease modification. Disclosures No relevant conflicts of interest to declare.

Background: Susceptibility to invasive pneumococcal disease (IPD) is high in children with sickle cell disease (SCD). National guidelines in many countries recommend a combined schedule of 13-valent pneumococcal conjugate vaccine (PCV13) beginning after birth followed by the 23-valent polysaccharide vaccine (PPSV23) beginning at age 2 years. In Africa, where the burden of SCD is greatest, PPSV23 is generally unavailable and not routinely administered to children with SCD. To help inform optimal immunization regimens for children with SCD in West Africa, we sought to determine the prevalence and spatial distribution of IPD in the region. We focused specifically on the 24 combined pneumococcus strains covered by PCV13 (serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F) and PPSV23 (serotypes 1, 2, 3, 4, 5, 6B, 7F, 8, 9N, 9V, 10A, 11A, 12F, 14, 15B, 17F, 18C, 19A, 19F, 20, 22F, 23F, and 33F). This analysis also explored the epidemiology of IPD-associated serotypes after the introduction of routine PCV13 immunization in countries in West Africa.