Charles John Elikwu

Enterobacter spp. are an important cause of healthcare-associated bloodstream infections that are uncommonly reported in Africa. This study utilized whole-genome sequencing to characterize Enterobacter spp. from hospitals in Nigeria’s antimicrobial resistance surveillance system. Bloodstream Enterobacter spp. isolates from six sentinel tertiary-care hospitals recovered between 2014 and 2020 were re-identified and antimicrobial susceptibility-tested using VITEK 2 system. Illumina technology provided whole-genome sequences for genome nomenclature, antimicrobial resistance gene prediction, SNP phylogeny and multi-locus sequence typing via publicly available bioinformatics pipelines. Initial biochemical delineation often misclassifies Enterobacter, necessitating whole-genome sequencing for accurate classification. Among 98 Enterobacter received, Enterobacter hormaechei subspecies xiangfangensis predominated (43), followed by other E. hormaechei subspecies (18) and Enterobacter spp. such as Enterobacter cloacae (26), Enterobacter roggenkampii (4), Enterobacter bugandensis (3), Enterobacter kobei (2), Enterobacter asburiae (1) and Enterobacter cancerogenus (1). Resistance to extended-spectrum cephalosporins, aminoglycosides, phenicols, macrolides and carbapenems in E. hormaechei was attributed to known resistance genes. E. hormaechei isolates belonged to clusters III, IV and VIII based on hsp60 typing and clades A, B, C and D according to Sutton and Co’s nomenclature. This and other recent reports from Nigeria reveal the extensive diversity of E. hormaechei, as well as clusters representing potential outbreaks. E. hormaechei, often misidentified and rarely reported from Nigeria, is the most common Enterobacter spp. isolated from blood culture in this study. Uncovering underappreciated species as important bloodstream pathogens and retrospective detection of likely outbreaks emphasize the value of genomic surveillance in resource-limited settings.

Enterobacter spp. are an important cause of healthcare-associated bloodstream infections uncommonly reported in Africa. This study used whole genome sequencing (WGS) to characterise Enterobacter spp. from hospitals in Nigeria’s antimicrobial resistance (AMR) surveillance system. Blood-culture isolates of Enterobacter from six such tertiary-care hospitals recovered between 2014 and 2020 were re-identified and antimicrobial susceptibility-tested using VITEK2. Illumina technology provided whole genome sequences for genome nomenclature, antimicrobial resistance gene prediction, Single Nucleotide Polymorphism (SNP) phylogeny, and multi-locus sequence typing via publicly available bioinformatics pipelines. Initial biochemical delineation often misclassified Enterobacter , necessitating whole-genome sequencing for accurate classification. Among 98 Enterobacter received, Enterobacter hormaechei subspecies xiangfangensis predominated (43), followed by other E. hormachei subspecies (18), E. cloacae (26), E. roggenkampii (4), E. bugandensis (3), E. kobei (2), E. asburiae (1) and E. cancerogenous (1). Cephalosporins, aminoglycoside, chloramphenicol, macrolide, and carbapenem resistance in E. hormaechei was attributed to known resistance genes. They belonged to clusters III, IV, and VIII based on hsp60 typing and clades A, B, C, and D according to Sutton and Co’s nomenclature. These isolates and other Enterobacter species recently reported from Nigeria reveal extensive E. hormaechei diversity, as well as clusters representing potential outbreaks . Enterobacter hormaechei , often misidentified and rarely reported from Nigeria, is this study’s most common blood culture isolated Enterobacter spp. Uncovering underappreciated species as important bloodstream pathogens and retrospective detection of likely outbreaks emphasise the value of genomic surveillance in resource-limited settings. DATA SUMMARY: All sequence reads were submitted to the European Nucleotide Archive (ENA) under the project ID PRJEB29739 ( https://www.ebi.ac.uk/ena/browser/view/PRJEB29739 ). Accessions can be found in Table S1. IMPACT STATEMENT: Accurate identification of Enterobacter is essential in healthcare settings as misidentification can lead to selecting antimicrobials to the genus is intrinsically resistant resistant before susceptibility testing results are available. Also, misidentification can compromise microbiology support for infection prevention and control. We show that E. hormaechei , which is never reported from clinical laboratories in Nigeria, is frequently misidentified using conventional methods like tube- or strip biochemical testing and VITEK systems. Whole genome sequence data demonstrates that E. hormaechei and E. cloacae are the most common Enterobacter isolated from bloodstream infections in Nigeria. Enhanced identification methods for surveillance play pivotal roles in improving patient care, optimising antibiotic stewardship, and combating the evolving challenges posed by this pathogen. Overall, this study reveals the effectiveness of WGS in correctly identifying this important pathogen.

Antimicrobial resistance (AMR) is a global security threat that accounts for about 700 000 deaths annually. Studies have shown that antimicrobial resistance could result in a 2% to 3.5% reduction in global Gross Domestic Product by 2050 and a loss of between 60 and 100 trillion US dollars, worth of economic output resulting in significant and widespread human suffering. Low- and middle-income countries (LMICs) will be worse hit by an unchecked rise of AMR. For example, it is predicted that AMR could kill about 4.1 million people in Africa by 2050 if it is not curbed. Similarly rising rates of AMR will lead to increased treatment costs and an inability to attain universal health coverage, in LMICs with fragile health systems. Sadly, AMR is driven by the inappropriate use of antimicrobials, especially antibiotics. Inappropriate antibiotic use is a pertinent problem in LMICs where regulatory frame works are weak. Inappropriate antibiotic use in LMICs is a multifaceted problem that cuts across clinical and veterinary medicine and agriculture. Therefore, efforts geared at curbing inappropriate antibiotic use in LMICs must identify the factors that drive this problem (i.e. inappropriate antibiotic use) in these countries. A clear knowledge of these factors will guide effective policy and decision making to curb inappropriate antibiotic use and ultimately AMR. The focus of this review is to discuss the factors that drive inappropriate antibiotic use in LMICs.

Background: Infection with cytomegalo virus is usually asymptomatic however in pregnant women the risk of congenital infection and foetal abnormalities makes antenatal screening for CMV infection necessary. The aim of this study was to determine the sero-prevalence and risk factors for CMV infection among pregnant women in Babcock University Teaching Hospital (BUTH), Ilishan Remo, Ogun State, Nigeria. Methods: The study was a cross-sectional descriptive study conducted between January and May, 2017 on patients attending the antenatal clinic of Babcock University Teaching Hospital. Enzyme Linked Immunosorbent Assay (ELISA) Kits were used to determine IgM and IgG anti CMV antibody titresin venous blood samples obtained from study participants. Results: A total of 80 patients were recruited into the study. The mean age was 30 years.All (100%) respondents were sero-positive for anti CMV IgG antibodies while 28.75% of respondents were seropositive for anti CMV IgM antibodies. Conclusion: There was a highsero-prevalence rate of CMV infection in the study. Screening of pregnant women for CMV infection is necessary due to the risk of congenital infection and fetal defects.

Coronavirus infection became a global pandemic in March 2020. The number of hospitalized cases in Nigeria and Ogun State has been on a steady increase with a concomitant rise in Mortality. This necessitates a coordinated and a more systemic approach in the management of this deadly disease. As a result of the potential effects of the disease on the socio-economic development of Ogun State, the state government granted Babcock University Teaching Hospital, Ilishan-Remo the permission to diagnose, admit and manage cases in line with Nigeria Centre for Disease Control (NCDC)/World Health Organization (WHO) guidelines. This led to the establishment of a molecular laboratory and a COVID-19 task force to oversee the treatment of confirmed cases of COVID-19 disease. This protocol is developed to serve as a template for the diagnosis, admission, treatment of cases of COVID-19 diseases presenting for care in the hospital and to prevent the spread of the disease among healthcare workers within the hospital environment.

Commercial Aspergillus IgG antibody assays have become pivotal in the current diagnosis of chronic pulmonary aspergillosis (CPA). However, diagnostic cutoffs have been found to vary from manufactures’ recommendations in different settings. This study aimed to establish the Aspergillus IgG reference range among Nigerians and determine a diagnostic cutoff for CPA. Sera from 519 prospectively recruited healthy blood donors and 39 previously confirmed cases of CPA were analysed for Aspergillus IgG levels using the Bordier test kit (Bordier Affinity Products SA, Crissier, Switzerland). Accuracy versus cutoff profile and receiver operating characteristics (ROC) curve were analysed for both CPA cases and controls using the R-Studio (2020), (Window desktop, version 4.0.2 software with R packages “nnet” and “ROCR”). Among healthy blood donors, 141 (27.2%) were aged 16–25 years with median (interquartile range, IQR) of 22 (20–24) years; 304 (58.6%) were aged 26–40 years with median (IQR) of 32 (29–36) years; while 74 (14.2%) were aged 41–60 years with median (IQR) of 46 (44–49.75). Median IgG level in respective age groups were 0.069 (0.009–0.181), 0.044 (0.014–0.202) and 0.056 (0.01–0.265) with no significant difference found in the three age categories (p = 0.69). The overall diagnostic cutoff for the diagnosis of CPA was 0.821 with an accuracy of 97.1% and area under the curve (AUC) = 0.986. The optimal diagnostic cutoff for diagnosing CPA in Nigerians using the Bordier kit was 0.821 which is lower than the manufacturer’s recommended cutoff of 1.0. The determination of this cutoff among Nigerians will significantly enhance accurate identification of CPA and assessment of its true burden in Nigeria.

Introduction: Diarrhoea, in general, is well investigated but the epidemiology of Functional Diarrhoea (FDr) as a disease entity has not been adequately evaluated globally, and more especially, in the sub-Saharan African population. Aim: To determine the prevalence and risk factors of FDr, and the associated quality of life in a Nigerian community. Materials and Methods: The study was a community-based cross-sectional survey involving 515 consenting adults aged 18-70 years. Data collection was done from February to March 2019. Ten participants were excluded because of inappropriately filled questionnaires, thus leaving a total of 505 subjects. The research instrument contained sociodemographic information, the Rome IV Functional Bowel Disorder questionnaire, the Short Form 12, version 2 Health Survey (SF-12v2) questionnaire, the Beck Depression and Anxiety Inventories, the Pittsburgh Sleep Quality Index (PSQI), and the Early Trauma Inventory-Self Report. Respondents who were positive for FDr were the cases while those who had no FDr were the controls in the data analysis. Independent Student t-test was used to compare means. The odds ratios of prospective risk factors of FDr were calculated with logistic regression. Odds Ratios (OR) >1 and p-value ≤0.05 were considered significant. Results: The mean age of the participants was 32.7±12.9 years. Six participants {1.2% (95% CI, 0.4%-2.4%)} had FDr with a 1:2 Male/Female ratio. Functional diarrhoea had a statistically significant association with depression (18.0±12.8 vs 8.2±9.5, p-value=0.021) only among the possible risk factors considered. The mean SF-12v2 scale scores, except Vitality, were lower in subjects with FDr than the controls, though only Social Functioning was statistically significant (p-value=0.003). Conclusion: The prevalence of FDr is low in the present study population. The disease is associated with depression and it impacts the Health-Related Quality of Life (HRQoL) negatively.

Background: An ongoing outbreak of pneumonia associated with a novel coronavirus was reported in Wuhan city, China. This new virus was named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the Coronavirus Study Group (CSG) of the International Committee on Taxonomy of Viruses. That disease, caused by the SARS-CoV-2, has been named coronavirus disease 2019 (COVID-19) by the WHO. The outbreak has since spread across the globe, including countries in Africa. Main body: The dominant mode of transmission is from the respiratory tract, via droplets or indirectly via fomites, and to a lesser extent via aerosols. The rapidity with which the infection spread throughout the world was unexpected. The disease has now affected 212 countries, areas, or territories, with more than 2.1 million total confirmed cases and over 144 thousand fatalities as at the time of writing. It, therefore, behooves countries of the world to take firm public health measures for the pandemic is to be contained. Conclusion: Nigeria, with a population of at least 170 million people, is of global interest because a rapid rise in the number of infected people will have serious implications not only for the country but for the whole African continent.%MCEPASTEBIN%

Genital Chlamydia trachomatis infection causes significant morbidity and mortality in women. A number of epidemiologic studies have suggested that Polymerase Chain Reaction (PCR) is more accurate as a diagnostic tool for Chlamydia trachomatis. However, the use of serological markers may be cost effective and practical in diagnosing and estimating the burden of the disease in resource limited countries.This study was aimed at determining the serological markers (IgG, IgM and IgA) of Chlamydia trachomatis, evaluate the association between Chlamydia trachomatis infection and the sociodemographic characteristics and clinical diagnosis of the participants. This was a cross sectional hospital-based study in which blood samples from 145 consenting participants were tested for IgG, IgM and IgA antibodies against Chlamydia trachomatis using enzyme linked immunosorbent assay and their clinical diagnosis, retrieved from their case notes. The cumulative prevalence of seropositivity for Chlamydia trachomatis (IgG, IgM, IgA) was 112 (77.2%) while 33 (22.8%) were seronegative. The overall predominant seromarker was IgG 91(62.8%) while IgM and IgA accounted for 85(58.6%) and 54(37.2%) respectively. A statistically significant association was found between Chlamydia trachomatis infection and PID (p value = 0.031), primary infertility (p value 0.011) and level of income (p value= (0,045).

Malaria is an endemic disease in Nigeria that is a major cause of morbidity and mortality in children, especially those under the age of five years old. The home management of malaria has been shown to reduce the rate of morbidity and mortality linked to malaria. The objectives of this study were therefore to determine the knowledge on cause, signs and symptoms of malaria, health seeking behaviour of respondents, preventive measures and Knowledge, Attitude and Practice (KAP) of home management of malaria among mothers in Babcock University for their children. This research was done between April and June, 2018 in Babcock University, Ilishan-Remo, Ogun State. A descriptive study with a cross sectional study design was used. The study population was 274 mothers. A structured questionnaire was used as the instrument for this study. This study revealed that 96.7% of the respondents knew about malaria as a disease. 72.6% of them attributed it to the vector, mosquito, while 4.7% attributed it to the malaria parasite, Plasmodium. The commonest recognisable clinical symptom of malaria was headache (75.5%) of the study population. None of the respondents took their children to the native doctor or to Church when symptoms of malaria arose. Rather, they took them to the hospital (80.3%) or to the Pharmacy (11.3%). Regarding preventive measures, 76.6% of them made use of insecticides, which was the commonest preventive measure. In the modality of treatment, it is shown in this study that 69.0% of the mothers knew about Artemisinin Combination Therapy (ACT), which is the recommended treatment drug for malaria treatment by the World Health Organization (WHO). It was also the commonest treatment modality used (68.6%). The commonest ACT combination used was Coartem (Artemether/Lumefantrine) with 59.5% of the respondents patronizing it. The study also showed that mothers in Babcock University are well aware of the dangers of poor compliance (86.5%) and thus ensure that their children completed the drug dose. The mothers in Babcock University have good knowledge, attitude and awareness of home management practices of malaria for their children. These practices are effective in reducing malaria incidence, owing to the fact that majority of them are well educated, as proven by statistical analysis.