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.

BACKGROUND:Typhoid Fever remains a major cause of morbidity and mortality in low-income settings. The Severe Typhoid in Africa programme was designed to address regional gaps in typhoid burden data and identify populations eligible for interventions using novel typhoid conjugate vaccines. METHODS:A hybrid design, hospital-based prospective surveillance with population-based health-care utilisation surveys, was implemented in six countries in sub-Saharan Africa. Patients presenting with fever (≥37·5°C axillary or ≥38·0°C tympanic) or reporting fever for three consecutive days within the previous 7 days were invited to participate. Typhoid fever was ascertained by culture of blood collected upon enrolment. Disease incidence at the population level was estimated using a Bayesian mixture model. FINDINGS:27 866 (33·8%) of 82 491 participants who met inclusion criteria were recruited. Blood cultures were performed for 27 544 (98·8%) of enrolled participants. Clinically significant organisms were detected in 2136 (7·7%) of these cultures, and 346 (16·2%) Salmonella enterica serovar Typhi were isolated. The overall adjusted incidence per 100 000 person-years of observation was highest in Kavuaya and Nkandu 1, Democratic Republic of the Congo (315, 95% credible interval 254-390). Overall, 46 (16·4%) of 280 tested isolates showed ciprofloxacin non-susceptibility. INTERPRETATION:High disease incidence (ie, >100 per 100 000 person-years of observation) recorded in four countries, the prevalence of typhoid hospitalisations and complicated disease, and the threat of resistant typhoid strains strengthen the need for rapid dispatch and implementation of effective typhoid conjugate vaccines along with measures designed to improve clean water, sanitation, and hygiene practices. FUNDING:The Bill & Melinda Gates Foundation.

Salmonella enterica serovar Typhi is endemic in Nigeria where S. Gallinarum is rarely reported. Probable S. Gallinarum was blood-cultured from three Ibadan patients within 10-days leading to suspicion of an outbreak. All three isolates were re-identified using VITEK-2, whole genome sequenced on Illumina and Oxford Nanopore platforms and confirmed as S. Typhi genotype 3.1.1. Two isolates from the same household had no single nucleotide polymorphisms, suggesting a point-source, but the third was an independent infection event. The isolates formed small colonies, were negative for motility by hanging drop method, and in Sulphide-Indole-Motility medium at 24h, but positive after 48h incubation. Hybrid genome assemblies revealed chromosomal fragment arrangements with imbalances on either side of ori and ter, which has been shown to slow S. Typhi growth. Suspected S. Gallinarum isolates in typhoid endemic areas should be evaluated biochemically and for motility after extended incubation, and verified by serological or molecular methods. ### Competing Interest Statement The authors have declared no competing interest.

ABSTRACTSalmonella enterica serovar Typhi is endemic in Nigeria whereS. Gallinarum is rarely reported. ProbableS. Gallinarum was blood-cultured from three Ibadan patients within 10-days leading to suspicion of an outbreak. All three isolates were re-identified using VITEK-2, whole genome sequenced on Illumina and Oxford Nanopore platforms and confirmed asS. Typhi genotype 3.1.1. Two isolates from the same household had no single nucleotide polymorphisms, suggesting a point-source, but the third was an independent infection event. The isolates formed small colonies, were negative for motility by hanging drop method, and in Sulphide-Indole-Motility medium at 24h, but positive after 48h incubation. Hybrid genome assemblies revealed chromosomal fragment arrangements with imbalances on either side oforiandter, which has been shown to slowS. Typhi growth. SuspectedS. Gallinarum isolates in typhoid endemic areas should be evaluated biochemically and for motility after extended incubation, and verified by serological or molecular methods.Main contributions of the researchThis study demonstrates that slow-growingSalmonellaTyphi can be mis-identified asS. Gallinarum in resource-limited endemic countries.Extended motility testing and confirmatory testing can avoid S. Gallinarum miss-calls.The genetic basis for slow-growth may be chromosomal rearrangements at rrn operons, which are known to occur in S.Typhi

Background Acinetobacter baumannii cause difficult-to-treat infections mostly among immunocompromised patients. Clinically relevant A. baumannii lineages and their carbapenem resistance mechanisms are sparsely described in Nigeria.Objective This study aimed to characterise the diversity and genetic mechanisms of carbapenem resistance among A. baumannii strains isolated from hospitals in southwestern Nigeria.Methods We sequenced the genomes of all A. baumannii isolates submitted to Nigeria’s antimicrobial resistance surveillance reference laboratory between 2016 – 2020 on an Illumina platform and performed in silico genomic characterisation. Selected strains were sequenced using the Oxford Nanopore technology to characterise the genetic context of carbapenem resistance genes.Results The 86 A. baumannii isolates were phylogenetically diverse and belonged to 35 distinct sequence types (STs), 16 of which were novel. Thirty-eight (44.2%) isolates belonged to none of the known international clones (ICs). Over 50% of the isolates were phenotypically resistant to 10 of 12 tested antimicrobials. Majority (n=54) of the isolates were carbapenem-resistant, particularly the IC7 (100%) and IC9 (>91.7%) strains. bla OXA-23 (34.9%) and bla NDM-1 (27.9%) were the most common carbapenem resistance genes detected. All bla OXA-23 genes were carried on Tn 2006 or Tn 2006 -like transposons. Our findings suggest that the mobilisation of a 10kb Tn 125 composite transposon is the primary means of bla NDM-1 dissemination.Conclusion Our findings highlight an increase in bla NDM-1 prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverse A. baumannii lineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings.Importance Acinetobacter baumannii are increasingly clinically relevant due to their propensity to harbour genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Our study characterised the diversity and antimicrobial resistance profiles of clinical A. baumannii in southwestern Nigeria using whole-genome sequencing. We also identified the key genetic elements facilitating the dissemination of carbapenem resistance genes within this species. This study provides key insights into the clinical burden and population dynamics of A. baumannii in hospitals in Nigeria and highlights the importance of routine whole-genome sequencing-based surveillance of this and other previously understudied pathogens in Nigeria and other similar settings.

Acinetobacter baumannii bacteria are increasingly clinically relevant due to their propensity to harbor genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing.

AbstractBackgroundAcinetobacter baumanniicause difficult-to-treat infections mostly among immunocompromised patients. Clinically relevantA. baumanniilineages and their carbapenem resistance mechanisms are sparsely described in Nigeria.ObjectiveThis study aimed to characterise the diversity and genetic mechanisms of carbapenem resistance amongA. baumanniistrains isolated from hospitals in southwestern Nigeria.MethodsWe sequenced the genomes of allA. baumanniiisolates submitted to Nigeria’s antimicrobial resistance surveillance reference laboratory between 2016 – 2020 on an Illumina platform and performedin silicogenomic characterisation. Selected strains were sequenced using the Oxford Nanopore technology to characterise the genetic context of carbapenem resistance genes.ResultsThe 86A. baumanniiisolates were phylogenetically diverse and belonged to 35 distinct sequence types (STs), 16 of which were novel. Thirty-eight (44.2%) isolates belonged to none of the known international clones (ICs). Over 50% of the isolates were phenotypically resistant to 10 of 12 tested antimicrobials. Majority (n=54) of the isolates were carbapenem-resistant, particularly the IC7 (100%) and IC9 (>91.7%) strains.blaOXA-23(34.9%) andblaNDM-1(27.9%) were the most common carbapenem resistance genes detected. AllblaOXA-23genes were carried on Tn2006or Tn2006-like transposons. Our findings suggest that the mobilisation of a 10kb Tn125composite transposon is the primary means ofblaNDM-1dissemination.ConclusionOur findings highlight an increase inblaNDM-1prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverseA. baumanniilineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings.ImportanceAcinetobacter baumannii are increasingly clinically relevant due to their propensity to harbour genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Our study characterised the diversity and antimicrobial resistance profiles of clinical A. baumannii in southwestern Nigeria using whole-genome sequencing. We also identified the key genetic elements facilitating the dissemination of carbapenem resistance genes within this species. This study provides key insights into the clinical burden and population dynamics of A. baumannii in hospitals in Nigeria and highlights the importance of routine whole-genome sequencing-based surveillance of this and other previously understudied pathogens in Nigeria and other similar settings.

IntroductionDiarrhoea can be debilitating in young children. Few aetiological investigations in Africans living with human immunodeficiency virus (HIV) have been performed since antiretrovirals became widely available.MethodsStool specimens from children with diarrhoea living with HIV, and HIV-uninfected controls, recruited at two hospitals in Ibadan, Nigeria, were screened for parasites and occult blood, and cultured for bacteria. Following biochemical identification of at least five colonies per specimen, diarrhoeagenic Escherichia coli and Salmonella were confirmed by PCR. Data were line-listed and comparisons were made using Fisher’s Exact test.ResultsOnly 10 children living with HIV could be enrolled during the 25-month study period and 55 HIV-uninfected children with diarrhoea were included for comparison. The most common pathogens overall were enteroaggregative E. coli (18/65, 27.7%), enteroinvasive E. coli (10/65, 15.4%), Cryptosporidium parvum (8/65, 12.3%) and Cyclospora cayetanensis (7/65, 10.8%). At least one pathogen was detected from seven of ten children living with HIV and 27 (49.1%) HIV-uninfected children. Parasite detection was associated with HIV positive status (p=0.03) with C. parvum specifically recovered more commonly from children living with HIV (p=0.01). Bacterial-parasite pathogen combinations were detected in specimens from four of ten children living with HIV but only 3(5.5%) HIV-uninfected children (p=0.009). Stools from five of ten children living with HIV and 7(12.7%) HIV-negative children (p = 0.014) contained occult blood.DiscussionEven though children living with HIV present infrequently to Ibadan health facilities with diarrhoea, their greater propensity for mixed and potentially invasive infections justifies prioritizing laboratory diagnosis of their stools.

Background:Many sub-Saharan African patients receive clinical care from extramurally-supported research and surveillance. Dur- ing the COVID-19 pandemic, pausing these activities reduces pa- tient care, surveillance, and research staff employment, increasing pandemic losses. In Oyo State, Nigeria, we paused a multi-country invasive salmonellosis surveillance initiative and a rural clinical bac- teriology project. Objective:Working with research partners raises health facility con- cerns about SARS-CoV-2 transmission risks and incurs infection pre- vention costs, so we developed and implemented re-opening plans to protect staff and patients and help health facilities deliver care. Methods:Our reopening plan included appointing safety and per- sonal protective equipment (PPE) managers from existing project staff cadres, writing new standard operating procedures, implement- ing extensive assessed training, COVID-19 testing for staff, procuring and managing PPE, and providing secondary bacteraemia blood culture support for COVID-19 patients in State isolation facilities. Results:Surveillance data showed that the pandemic reduced care access and negatively affected patient unsupervised antibacterial use. The re-opening plan repurposed human and material resources from national and international extramurally-supported programs to mitigate these effects on public health. Conclusions:A structured reopening plan restarted care, surveil- lance, and infection prevention and control.

Whole- genome sequencing (WGS) is finding important applications in the surveillance of antimicrobial resistance (AMR), providing the most granular data and broadening the scope of niches and locations that can be surveilled. A common but often overlooked application of WGS is to replace or augment reference laboratory services for AMR surveillance. WGS has supplanted traditional strain subtyping in many comprehensive reference laboratories and is now the gold standard for rapidly ruling isolates into or out of suspected outbreak clusters. These and other properties give WGS the potential to serve in AMR reference functioning where a reference laboratory did not hitherto exist. In this perspective, we describe how we have employed a WGS approach, and an academic-public health system collaboration, to provide AMR reference laboratory services in Nigeria, as a model for leapfrogging to national AMR surveillance.

Background:Acinetobacter baumannii are of major human health importance because they cause life-threatening nosocomial infections and often are highly resistant to antimicrobials. Specific multidrug-resistant A. baumannii lineages are implicated in hospital outbreaks globally. We retrospectively investigated a suspected outbreak of carbapenem-resistant A. baumannii (CRAB) colonizing patients in an intensive care unit (ICU) of a tertiary hospital in Southwest Nigeria where genomic surveillance of Acinetobacter has hitherto not been conducted.Methods:A prospective observational study was conducted among all patients admitted to the ICU between August 2017 and June 2018. Acinetobacter species were isolated from rectal swabs and verified phenotypically with the Biomerieux Vitek 2 system. Whole genome sequencing (WGS) was performed on the Illumina platform to characterize isolates from a suspected outbreak during the study period. Phylogenetic analysis, multilocus sequence typing, and antimicrobial resistance gene prediction were carried out in silico.Results:Acinetobacter isolates belonging to the A. baumannii complex were recovered from 20 (18.5%) ICU patients. Single nucleotide polymorphism (SNP) analysis and epidemiological information revealed a putative outbreak clone comprising seven CRAB strains belonging to the globally disseminated international clone (IC) 2. These isolates had ≤2 SNP differences, identical antimicrobial resistance and virulence genes, and were all ST1114/1841.Conclusion:We report a carbapenem-resistant IC2 A. baumannii clone causing an outbreak in an ICU in Nigeria. The study findings underscore the need to strengthen the capacity to detect A. baumannii in human clinical samples in Nigeria and assess which interventions can effectively mitigate CRAB transmission in Nigerian hospital settings.

BACKGROUND:Salmonellosis causes significant morbidity and mortality in Africa. Information on lineages of invasive Salmonella circulating in Nigeria is sparse. METHODS:Salmonella enterica isolated from blood (n = 60) and cerebrospinal fluid (CSF, n = 3) between 2016 and 2020 from five tertiary hospitals in southwest Nigeria were antimicrobial susceptibility-tested and Illumina-sequenced. Genomes were analysed using publicly-available bioinformatic tools. RESULTS:Isolates and sequence types (STs) from blood were S. Typhi [ST1, n = 1 and ST2, n = 43] and invasive non-typhoidal Salmonella (iNTS) (S. Enteritidis [ST11, n = 7], S. Durham [ST10, n = 2], S. Rissen [ST8756, n = 2], S. Chester [ST2063, n = 1], S. Dublin [ST10, n = 1], S. Infantis [ST603, n = 1], S. Telelkebir [ST8757, n = 1] and S. Typhimurium [ST313, n = 1]). S. Typhi ST2 (n = 2) and S. Adabraka ST8757 (n = 1) were recovered from CSF. Most S. Typhi belonged to genotype 3.1.1 (n = 44), carried an IncY plasmid, had several antibiotic resistance genes (ARGs) including blaTEM-1 (n = 38), aph(6)-Id (n = 32), tet(A) (n = 33), sul2 (n = 32), dfrA14 (n = 30) as well as quinolone resistance-conferring gyrA_S83Y single-nucleotide polymorphisms (n = 37). All S. Enteritidis harboured aph(3")-Ib, blaTEM-1, catA1, dfrA7, sul1, sul2, tet(B) genes, and a single ARG, qnrB19, was detected in S. Telelkebir. Typhoidal toxins cdtB, pltA and pltB were detected in S. Typhi, Rissen, Chester, and Telelkebir. CONCLUSION:Most invasive salmonelloses in southwest Nigeria are vaccine-preventable infections due to multidrug-resistant, West African dominant S. Typhi lineage 3.1.1. Invasive NTS serovars, including some harbouring typhoidal toxin or resistance genes, represented a third of the isolates emphasizing the need for better diagnosis and surveillance.

Escherichia coli bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasiveness. In Nigeria, the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified and whole-genome sequenced 68 2016–2018 bloodstream E. coli isolates from three sentinel sites in South-Western Nigeria and susceptibility tested 67 of them. Resistance to antimicrobials commonly used in Nigeria was high, with 67 (100 %), 62 (92.5 %), 53 (79.1 %) and 37 (55.2 %) showing resistance to trimethoprim, ampicillin, ciprofloxacin and aminoglycosides, respectively. Thirty-five (51 %) isolates carried extended-spectrum β-lactamase genes and 32 (91 %) of these were multidrug resistant. All the isolates were susceptible to carbapenems and colistin. The strain set included globally disseminated high-risk clones from sequence type (ST)12 (2), ST131 (12) and ST648 (4). Twenty-three (33.8 %) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprising O16:H5 and O25:H4 sub-lineages. The second was an ST10–ST167 complex clade comprising strains carrying O-antigen and capsular genes of likely Klebsiella origin, identical to those of avian pathogenic E. coli Sanji, and serotyped in silico as O89, O101 or ONovel32, depending on the tool used. Four temporally associated ST90 strains from one sentinel were closely related enough to suggest that at least some of them represented a retrospectively detected outbreak cluster. Our data implicate a broad repertoire of E. coli isolates associated with bloodstream infections in South-West Nigeria. Continued genomic surveillance is valuable for tracking clones of importance and for outbreak identification.

AbstractEscherichia coli bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasion and, in recent years, invasive E. coli are increasingly multiply antimicrobial resistant. In Nigeria, E. coli is a common cause of bloodstream infections but the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified and whole genome-sequenced 68 bloodstream E. coli isolates recovered between 2016 and 2018 at three sentinel sites in southwestern Nigeria and susceptibility tested 67 of them. Resistance to antimicrobials commonly used in Nigeria was high, with 67(100%), 62 (92.5%), 53 (79%) and 37(55%) showing resistance to trimethoprim, ampicillin, ciprofloxacin and aminoglycosides, respectively. All the isolates were susceptible to carbapenems and colistin. The strain set included isolates from globally disseminated high risk clones including those belonging to ST12 (n=2), ST131 (n=12) and ST648 (n = 4). Twenty-three (33.82%) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprised of O16:H5 and O25:H4 sub-lineages. The second was an ST10-ST167 complex clade comprised of strains carrying capsular genes that may have originated in Klebsiella. We additionally determined that four temporally-associated ST90 strains from one sentinel were closely related enough to suggest that at least some of them represented a retrospectively detected outbreak cluster. Our data demonstrate that a broad repertoire of invasive E. coli isolates cause bloodstream infections in southwest Nigeria. In addition to pandemic lineages, particularly ST131, these include a previously undescribed lineage carrying an O-antigen cluster previously only reported from Klebsiella. Genomic surveillance is valuable for tracking these and other clones and for outbreak identification.Data SummaryPhylogenetic tree, clinical data, and epidemiological data were visualized using Microreact (https://microreact.org/project/hmj3KwxS1dmmFPCKFx6qeA-invasive-escherichia-coli-sw-nigeria-2016-2018). All the sequence data have been deposited in the ENA under the project ID PRJEB29739 (https://www.ebi.ac.uk/ena/browser/view/PRJEB29739). Accessions can be found in Table S6.

BACKGROUND:Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria.METHODS:We performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria. We conducted in silico multilocus sequence typing; AMR gene, virulence gene, plasmid, and K and O loci profiling; as well as phylogenetic analyses, using publicly available tools and Nextflow pipelines.RESULTS:Phylogenetic analysis revealed that the majority of the 134 K. pneumoniae and 5 K. quasipneumoniae isolates from Nigeria characterized are closely related to globally disseminated multidrug-resistant clones. Of the 39 K. pneumoniae sequence types (STs) identified, the most common were ST307 (15%), ST5241 (12%), ST15 (~9%), and ST25 (~6%). ST5241, 1 of 10 novel STs detected, is a single locus variant of ST636 carrying dfrA14, tetD, qnrS, and oqxAB resistance genes. The extended-spectrum β-lactamase (ESBL) gene blaCTX_M-15 was seen in 72% of K. pneumoniae genomes, while 8% encoded a carbapenemase. No isolate carried a combination of carbapenemase-producing genes. Four likely outbreak clusters from 1 facility, within STs 17, 25, 307, and 5241, were ESBL but not carbapenemase-bearing clones.CONCLUSIONS:This study uncovered known and novel K. pneumoniae lineages circulating in 3 hospitals in Southwest Nigeria that include multidrug-resistant ESBL producers. Carbapenemase-producing isolates remain uncommon. WGS retrospectively identified outbreak clusters, pointing to the value of genomic approaches in AMR surveillance for improving infection prevention and control in Nigerian hospitals.

BACKGROUND:There is limited information on the best practices for monitoring multicountry epidemiological studies. Here, we describe the monitoring and evaluation procedures created for the multicountry Severe Typhoid Fever in Africa (SETA) study.METHODS:Elements from the US Food and Drug Administration (FDA) and European Centre for Disease Prevention and Control (ECDC) recommendations on monitoring clinical trials and data quality, respectively were applied in the development of the SETA monitoring plan. The SETA core activities as well as the key data and activities required for the delivery of SETA outcomes were identified. With this information, a list of key monitorable indicators was developed using on-site and centralized monitoring methods, and a dedicated monitoring team was formed. The core activities were monitored on-site in each country at least twice per year and the SETA databases were monitored centrally as a collaborative effort between the International Vaccine Institute and study sites. Monthly reports were generated for key indicators and used to guide risk-based monitoring specific for each country.RESULTS:Preliminary results show that monitoring activities have increased compliance with protocol and standard operating procedures. A reduction in blood culture contamination following monitoring field visits in two of the SETA countries are preliminary results of the impact of monitoring activities.CONCLUSIONS:Current monitoring recommendations applicable to clinical trials and routine surveillance systems can be adapted for monitoring epidemiological studies. Continued monitoring efforts ensure that the procedures are harmonized across sites. Flexibility, ongoing feedback, and team participation yield sustainable solutions.

BACKGROUND:The relative contribution of bacterial infections to febrile disease is poorly understood in many African countries due to diagnostic limitations. This study screened pediatric and adult patients attending 4 healthcare facilities in Ibadan, Nigeria, for bacteremia and malaria parasitemia. METHODS:Febrile patients underwent clinical diagnosis, malaria parasite testing, and blood culture. Bacteria from positive blood cultures were isolated and speciated using biochemical and serological methods, and Salmonella subtyping was performed by polymerase chain reaction. Antimicrobial susceptibility was tested by disk diffusion. RESULTS:A total of 682 patients were recruited between 16 June and 16 October 2017; 467 (68.5%) were <18 years of age. Bacterial pathogens were cultured from the blood of 117 (17.2%) patients, with Staphylococcus aureus (69 [59.0%]) and Salmonella enterica (34 [29.1%]) being the most common species recovered. Twenty-seven (79.4%) of the Salmonella isolates were serovar Typhi and the other 7 belonged to nontyphoidal Salmonella serovarieties. Thirty-four individuals were found to be coinfected with Plasmodium falciparum and bacteria. Five (14.7%) of these coinfections were with Salmonella, all in children aged <5 years. Antimicrobial susceptibility testing revealed that most of the Salmonella and Staphylococcus isolates were multidrug resistant. CONCLUSIONS:The study demonstrates that bacteria were commonly recovered from febrile patients with or without malaria in this location. Focused and extended epidemiological studies are needed for the introduction of typhoid conjugate vaccines that have the potential to prevent a major cause of severe community-acquired febrile diseases in our locality.

This study, carried out in a rural community in Ogun state Nigeria, aims to determine the prevalence of soil-transmitted helminths, bacteria causing Chronic Suppurative Otitis Media (CSOM), and their coinfection among school-aged participants. Formol-ether sedimentation technique was used to check for helminth eggs in stool samples. Ear swabs collected were cultured on chocolate, blood and MacConkey agar plates. CD4+T lymphocyte count was derived using a flow cytometre. Study participants were between 5 and 19 years old. Three hundred participants were sampled, 108 (36%) were infected with helminth parasites: Ascaris lumbricoides (28.7%), hookworm (6.7%) and Strongyloides stercoralis (0.7%). The prevalence of helminth infection between the sexes was not statistically significant (χ2 = 0.497; P= 0.390), but statistically significant between the age groups (χ2 = 10.10; P=0.016). Mixed helminthic infections were found in only 3.3% of the study population. Seventeen participants (5.7%) were found to have CSOM. Bacteria isolated in the ear swabs were Pseudomonas aeruginosa, Staphylococcus aureus, Klebiella pneumoniae, Proteus mirabilis and Haemophilus influenzae. Only two percent (2%) of study population were co-infected with helminth and bacteria. Heavy intensity of helminths and heavy growth of bacteria was found in the coinfected when compared with single infected children. This study showed the presence of otitis media in the study area, and that helminthiasis might have an effect on its presentation. Efforts to control CSOM in the study site may need to consider the inclusion of mass deworming. Key words: Chronic suppurative otitis media (CSOM), helminth, bacteria, coinfection, Ogun State, Nigeria.

BACKGROUND:Patients admitted into the intensive care unit (ICU) usually have impaired immunity and are therefore at high risk of acquiring hospital associated infections. Infections caused by multidrug resistant organisms now constitute a major problem, limiting the choice of antimicrobial therapy.OBJECTIVES:This study was aimed at determining the antimicrobial resistance pattern of pathogens causing ICU infections in University College Hospital (UCH), Ibadan, Nigeria. The aetiological agents, prevalence and types ICU infections were also determined.METHODS:One year hospital associated infections surveillance was conducted in the ICU of UCH, Ibadan. Blood, urine, tracheal aspirate and wound biopsies specimens were collected under strict asepsis and sent to the Medical Microbiology laboratory of the same institution for immediate processing. All pathogens were isolated and identified by standard microbiological methods. Disk diffusion antibiotic susceptibility testing was performed and interpreted according to Clinical and Laboratory Standards Institute (CLSI) guidelines.RESULTS:The overall prevalence of ICU infections was 30.9% out of which 12.9% were bloodstream infections, 31.5% urinary tract infections, 38.9% pneumonia, and 16.7% skin and soft tissue infections. Klebsiella species andEscherichia coli were the predominant pathogens. Multidrug resistant organisms constituted 59.3% of the pathogens, MDR Klebsiella spp and MDR E. coli were 70.8% and 71.4% respectively. Resistance to Cefuroxime was the highest (92.9%) while Meropenem had the least resistance (21.4%).CONCLUSION:There is a high prevalence of multidrug resistant bacteria causing ICU infections. Application of more stringent infection control procedures and institution of functional antimicrobial stewardship are recommended to combat this problem.