Prevalence of anaerobic bacteria in surgical site infections in Lagos University Teaching Hospital.

Background: Surgical site infection (SSI) is the second most common cause of nosocomial infection, after urinary tract infection. Sequelae of SSI include increased healthcare costs and worse patient outcomes. There is a paucity of research studies on the impact of anaerobic organisms on SSIs in Nigeria. The aim of this study was to determine the role of anaerobic bacteria in SSI encountered at the Lagos University Teaching Hospital (LUTH). Materials and Methods: A total of 438 patients were consecutively recruited into this study from general surgery, obstetrics and gynaecology and paediatric units of the LUTH from 1 July through 31 December 2019. Two surgical wound specimens were collected from all patients with suspected SSIs. One was for anaerobic culture using Brucella blood agar incubated in an anaerobic jar that secured anaerobiosis using the anaerobic gas pack. The other swab was used for aerobic culture on blood agar incubated on air at 37oC. Identifications and antibiotic sensitivity testing were performed according to standard laboratory procedures. Result: The overall incidence of SSI in the study was 12.3%. The incidence of anaerobic SSI was 1.1%. The distribution of anaerobic infections by medical specialty unit was as follows; general surgery (1.6%), obstetrics and gynaecology (0.8%) and paediatrics (0.9%). Bacteroides species was the only anaerobic isolate. The risk factors associated with the development of SSI by multiple logistic regression analysis were duration of surgery greater than 2 h (OR 1.418; 95% CI 1.834-9.286; P = 0.001) and NNIS risk index 2 and 3 - (OR 2.165; 95% CI 2.366-32.086; P = 0.001). Conclusions: The prevalence of anaerobic SSI was 1.1%. Duration of surgery greater than 2 h and NNIS risk index 2 and 3 were independent predictors of SSI.

High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020.

Acinetobacter baumannii causes difficult-to-treat infections mostly among immunocompromised patients. Clinically relevant A. baumannii lineages and their carbapenem resistance mechanisms are sparsely described in Nigeria. This study aimed to characterize the diversity and genetic mechanisms of carbapenem resistance among A. baumannii strains isolated from hospitals in southwestern Nigeria. We sequenced the genomes of all A. baumannii isolates submitted to Nigeria's antimicrobial resistance surveillance reference laboratory between 2016 and 2020 on an Illumina platform and performed in silico genomic characterization. Selected strains were sequenced using the Oxford Nanopore technology to characterize the genetic context of carbapenem resistance genes. The 86 A. baumannii isolates were phylogenetically diverse and belonged to 35 distinct Oxford sequence types (oxfSTs), 16 of which were novel, and 28 Institut Pasteur STs (pasSTs). 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. The majority (n = 54) of the isolates were carbapenem resistant, particularly the IC7 (pasST25; 100%) and IC9 (pasST85; >91.7%) strains. blaOXA-23 (34.9%) and blaNDM-1 (27.9%) were the most common carbapenem resistance genes detected. All blaOXA-23 genes were carried on Tn2006 or Tn2006-like transposons. Our findings suggest that a 10-kb Tn125 composite transposon is the primary means of blaNDM-1 dissemination. Our findings highlight an increase in blaNDM-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 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. Our study characterized 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.

Antimicrobial use among paediatric inpatients in a Nigerian tertiary hospital: A three-year point prevalence survey.

Aim: Antimicrobials are among the most widely prescribed therapeutic agents among paediatric population. Irrational use of these agents increases the risk of antimicrobial resistance. We described the prevalence and pattern of antimicrobial use among paediatric inpatients from 2017 to 2019. Subject and Method: The study was a repeated point prevalence survey over a 3-year period using the global point prevalence standardized tools among all paediatric inpatients. The prevalence of antimicrobial use, the prescription indicators and patterns of antimicrobial use were estimated. Result: Among 191 paediatric inpatients assessed, the 3-year period prevalence antimicrobial use was 85.9% (164/191) with prevalence of 80.6% in 2017, 94.6% in 2018, and 83.6% in 2019. Antimicrobial agents used ranged from one agent (20.1%) to five different agents (5.5%). Parenteral route (66.6%) was the preferred route of administration. The reason for the use of antimicrobial agents (92.6%) and the stop/review date (99.5%) were mostly well documented. Only 4.5% of the antimicrobial use were targeted. There were no antimicrobial guidelines or policy guiding the use of antimicrobial agents, except the national guideline on the treatment of malaria and tuberculosis. Ceftriaxone, a third generation cephalosporin was the most commonly used agent across the period under review. Community-acquired infection was the commonest indication for antimicrobial use. Conclusion: Our findings of high antimicrobial prevalence has raised the attention for the need to develop hospital-based antimicrobial guideline and antimicrobial stewardship program to protect the vulnerable children, their contacts and the environment from the impact of antimicrobial resistance.

Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria.

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.

A mini- national surveillance study of resistance profiles of Staphylococcus Aureus isolated from clinical specimens across hospitals in Nigeria.

BACKGROUND: Infections with Staphylococcus aureus cause significant morbidity and mortality worldwide. Resistant strains of S. aureus to commonly used antibiotics are being increasingly encountered in clinical practice, necessitating the need to determine the resistance pattern in Nigeria. METHODS: Antibiotic susceptibility testing was performed on 360 S. aureus isolates from clinical specimen from seven hospitals across the six geo-political regions of Nigeria using Kirby Bauer disc diffusion technique, and E-test for vancomycin. Cefoxitin 30 µg disc was used to determine methicillin resistance, and D-test for inducible clindamycin resistance. RESULTS: Methicillin-resistant S. aureus was confirmed in 176 (48.9%) of the isolates, 346 (96%) for penicillin G and 311 (86.4%) for trimethoprim. 175 (99.4%) of the 176 resistant to methicillin were susceptible to vancomycin. Linezolid, tigecycline, chloramphenicol and clindamycin had susceptibilities of 341 (94.7%), 332 (92.2%), 298 (82.8%) and 290 (80.6%) respectively. Inducible clindamycin resistance was elucidated in 25 (29.1%) of the 86 isolates. Generally, MRSA isolates were more resistant than methicillin-sensitive S. aureus (MSSA) to all antibiotics tested. CONCLUSION: Staphylococcus aureus rates of resistance are high and call for urgent action such as antibiotic stewardship programmes and periodic surveillance to enhance clinical outcomes. While targeted therapy is preferred, options for empiric treatment include chloramphenicol, clindamycin, linezolid or vancomycin.

Bacterial Vaginosis and Pregnancy Outcome in Lagos, Nigeria.

Background. Bacterial vaginosis (BV) is a complex clinical syndrome characterized by alterations in the normal vaginal flora and a malodorous discharge when symptomatic. In pregnancy, BV has been associated with adverse outcomes such as miscarriage, premature rupture of membranes, preterm birth, and low birth weight. This study was conducted to determine the prevalence and associations of BV and pregnancy outcomes among pregnant women in Lagos University Teaching Hospital (LUTH). Methods. We conducted a prospective observational study with high vaginal swabs obtained from consecutive newly registered antenatal women between 14 and 36 weeks gestation. The women were monitored until delivery, and their pregnancy outcome and demographic data were obtained using an interviewer-administered questionnaire. Results. Bacterial vaginosis was diagnosed by Nugent score in 64 of 246 women, giving a prevalence rate of 26%. Bacterial vaginosis was significantly associated with preterm delivery (risk ratio [RR], 2.68; 95% confidence interval [CI], 1.44-4.98), low birth weight (RR, 3.20; 95% CI, 1.29-7.94), and premature rupture of membranes (RR, 6.75; 95% CI, 3.11-14.67). The association between BV and miscarriage (<28 weeks gestation) and neonatal admission for various morbidities was not statistically significant. Conclusions. The prevalence rate of BV among pregnant women in LUTH is high and is significantly associated with adverse pregnancy outcome. Routine screening and treatment of women preconceptually may enable interventions to prevent these adverse outcomes.

Feasibility and cost analysis of programmatic implementation of Microscopic-Observation Drug Susceptibility (MODS) assay in Nigeria.

Objectives: Detection of Multi-drug resistant tuberculosis in Nigeria still remains a challenge. We evaluated the feasibility of programmatic implementation of the Microscopic-Observation Drug Susceptibility (MODS) assay, a rapid culture and drug susceptibility testing technique for drug susceptibility testing in a low resource setting. Method: In a novel laboratory setting in Nigeria, we obtained data from the market on the cost of materials necessary for MODS assay. Three routinely collected sputum specimens from 160 tuberculosis suspects were evaluated by smear microscopy while only the early morning specimen was used for MODS culture. Results: MODS assay detected M. tuberculosis in 97.7% (42/43) of smear positive and 6.0% (7/117) of smear negative TB suspects. There was a statistically significant advantage of a single MODS culture over 3 smear microscopies (P=0.019). The modal time from culture of specimen to detection of M. tuberculosis and availability of drug susceptibility result for MODS was 7days with a mean of 8.4 days (Range= 5-13 days). Culture and susceptibility result was available in 18.4% (9/49) of patients within 5days of culture. Turnaround time for smear microscopy in the centers was 3 days. Cost of processing one specimen by MODS assay in the study was USD2.65. Multi-Drug resistant tuberculosis (MDR-TB) was detected in 4.1% (2/49) while Isoniazid mono-resistance was detected in 2.0% (1/49) of the culture positive cases. All the drug resistant isolates were from re-treatment cases with a statistically significant association (P=0.005). Conclusion: The MODS technique is simple, and its implementation in this novel setting was feasible. MODS can be scaled up to meet the demand for MDR-TB confirmation in XpertMTB/Rif deployed sites in Nigeria.

Car windshield fragments as cheap alternative glass beads for homogenization of Mycobacterium tuberculosis cultures in a resource-limited setting.

Tuberculosis is a global health problem which has been compounded by the emergence and rapid spread of drug resistant strains. Phenotypic drug susceptibility testing of Mycobacterium tuberculosis usually requires homogenization of cultures using 3-5mm glass beads. In resource limited settings, these important material may either not be readily available in the country as in our case requiring that one orders them from abroad or they may be too expensive. In both situations, this would impact on the usually lean budget. In our centre were we recently introduced tuberculosis culture and drug susceptibility testing using the Microscopic Observation Drug Susceptibility (MODS) technique, we successfully used glass fragments from a broken car windshield obtained from a mechanic workshop to homogenize solid cultures to prepare positive controls. All cultures homogenized with these local beads gave consistent MODS results. The challenge of the limited availability of resources for research in resource limited settings can be met by adapting available materials to achieve results.

Candidaemia in a tertiary hospital in Nigeria.

BACKGROUND: Candidaemia is a widely-studied and reviewed topic in the developed world; however, there is a dearth of information on nosocomial candidaemia in Nigeria, despite the increasing use of more invasive therapeutic modalities, immunosuppressive agents and increasing incidence of immunosuppression as a result of malignancies and HIV. OBJECTIVES: To determine the hospital-based frequency of candidaemia in a tertiary hospital in Ibadan, Nigeria. METHOD: This was a prospective descriptive study which included 230 immunosuppressed patients. All isolates were identified to the species level using both conventional and automated methods. Thereafter, all Candida species isolated were tested for antifungal susceptibility using the broth microdilution method. RESULTS: Candidaemia occurred in 12 (5.21%) of the 230 study patients, with C. tropicalis accounting for 50% of the infections. Four patients (33.3%) presented with C. parapsilosis, one (8.3%) with C. albicans and one (8.3%) with a mixed infection of C. albicans and C. tropicalis. All 12 isolates were sensitive to fluconazole (minimal inhibitory concentration < 8 mg/mL). Univariate analysis revealed that old age, multiple surgeries and long-term hospitalisation were significant contributing factors for the occurrence of candidaemia. Eleven (91.7%) of the 12 patients with candidaemia had Candida colonisation of other sterile sites including the bladder, peritoneum and trachea. Furthermore, bivariate analysis revealed that mucositis (p = 0.019) and diarrhoea (p = 0.017) were significantly associated with an increased risk of candidaemia. The crude mortality rate of candidaemia was 91.7%. CONCLUSION: This study highlights the significance of nosocomial candidaemia and the need for proactive laboratory investigation and clinical management of this life-threatening disease.

Fluconazole susceptibility and ERG11 gene expression in vaginal candida species isolated from Lagos Nigeria.

Fluconazole resistance is an important type of resistance in Candida because in most countries, fluconazole is the drug of choice for vulvovaginal candidiasis. Candida species resist fluconazole by various mechanisms but there is paucity of data on these in our environment. Such mechanisms include among others, over-expression of the ERG11 gene, which codes for synthesis of the target enzymes in the fungus. The aim of this study was to screen Candida spp. resistant to fluconazole for the expression of ERG11 gene. Fluconazole susceptibility test was performed on 28 clinical strains of Candida species previously obtained from students of a School of Nursing in Lagos, Nigeria. They were identified by API Candida, CHROMagar candida and germ tube test. Using 25 mcg discs, fluconazole susceptibility was determined by the disc diffusion method and results were interpreted in accordance with the Clinical Laboratory Standard Institute (CLSI) criteria; sensitive (S), resistant (R) and susceptible dose dependent (SDD). The R and SDD isolates were subsequently evaluated for the presence of ERG11 gene. Of the 28 clinical isolates, 14 were identified as C. albicans and six as C. tropicalis. The remaining isolates were identified as C. glabrata (2), C. famata (2) C. kefyr (2) one each of C. parapsilosis and C. guilliermondii respectively. In this study, 18 were susceptible (S) to fluconazole, eight were SDD and two were resistant to the antifungal agent. Out of the 14 C. albicans isolates, 12 were susceptible, one showed high level resistance and similar number showed susceptible dose dependence. ERG11 was detected in three susceptible dose dependent Candida species. This analysis demonstrates that susceptible dose dependence should not be overlooked as it may be associated with the presence of ERG11 gene and resistance to fluconazole. There is a need to consider routine antifungal susceptibility testing for Candida species causing vulvovaginitis.

Chlamydia and Vaginitis in Sexually Active Females: Classical Identification Methods for Effective Control

Laboratory diagnosis of Chlamydia and vaginitis in sexually active females has been limited by unavailability of a sequential method/rapid technique for simple diagnosis. Six hundred (600) adult females from hotel/brothel; Sexually Transmitted Infections (STIs) Clinic; Obstetrics/Gynaecology Clinic; Family Planning Clinic and Healthy controls were investigated for Chlamydia; Candida; trichomoniasis and bacterial vaginosis (BV). This was done using microscopy: wet mount; stained vaginal secretion and stained smear after culture. Results showed that there were 72infections in the female groups. The brothel and STI group had infection in the range (70-86). Chlamydial infection was highest in the STI group while Candida infection was highest in the healthy (control) females. Bacterial vaginosis was distributed in all groups. As p-value increased; f-value increased indicating constant co-infection of Candida and BV in Chlamydia positive females. Microscopy by direct detection from sample and stained smear after culture were in the range: 56-86. Direct microscopy for BV was 78.5and stained smear after culture; 57.1. Sensitivity and specificity of the techniques showed that detection of Chlamydia was less sensitive by direct microscopy of sample but sensitivity and specificity of stained smear after culture were high. Immunoassay (32.2) was also less sensitive. Sensitivity and specificity of wet mount microscopy for Candida; Trichomoniasis and BV were in the range 62.5 - 80and 62.5-97.8respectively. Wet mount has high sensitivity and specificity for detecting agents of vaginitis and may be useful for routine use and for diagnosis where disease is absent; thus; making identification more cost effective

The effects of antimicrobial therapy on bacterial vaginosis in non-pregnant women.

BACKGROUND: Bacterial vaginosis (BV) is a very common cause of vaginitis that has been associated with a high incidence of obstetric and gynaecologic complications and increased risk of HIV-1 transmission. This has led to renewed research interest in its treatment. OBJECTIVES: To assess the effects of antimicrobial agents on BV in non-pregnant women. SEARCH STRATEGY: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library), MEDLINE, EMBASE, LILACS, and African Healthline (December 2007); and proceedings of relevant international conferences (from 1981 to date). SELECTION CRITERIA: Randomised controlled trials comparing any two or more antimicrobial agents, or antimicrobial agents with placebo or no treatment, in women with clinical or Gram-stain criteria of BV. DATA COLLECTION AND ANALYSIS: Two authors independently assessed trial quality and extracted data from the original publications while the third author cross checked the data. MAIN RESULTS: Twenty-four trials involving 4422 participants were reviewed. Most examined symptomatic women only. Only seven trials analysed results by intention to treat; we re-analysed the remainder.Compared with placebo, clindamycin showed a lower rate of treatment failure (relative risk (RR) 0.25, 95% confidence interval (CI) 0.16 to 0.37). Clindamycin and metronidazole showed identical rates of treatment failure, irrespective of regimen type, at two and four-week follow up (RR 1.01, 95% CI 0.69 to 1.46; RR 0.91, 95% CI 0.70 to 1.18, respectively). Clindamycin tended to cause a lower rate of adverse events (RR 0.75, 95% CI 0.56 to 1.02); metallic taste, and nausea and vomiting were more common in the metronidazole group (RR 0.08, 95% CI 0.1 to 0.59; RR 0.23, 95% CI 0.10 to 0.51, respectively). Given intravaginally as gelatin tablets, lactobacillus was more effective than oral metronidazole (RR 0.20, 95% CI 0.05 to 0.08). Similarly, oral lactobacillus combined with metronidazole was more effective than metronidazole alone (RR 0.33, 95% CI 0.14 to 0.77). Clindamycin showed a lower rate of clinical failure than triple sulfonamide cream (RR 0.46, 95% CI 0.29 to 0.72). Hydrogen peroxide douche showed a higher rate of clinical failure (RR 1.75, 95% CI 1.02 to 3.00) and adverse events (RR 2.33, 95% CI 1.21 to 4.52) than a single 2 g dose of metronidazole. AUTHORS' CONCLUSIONS: Clindamycin preparations, oral metronidazole, and oral and intravaginal tablets of lactobacillus were effective for bacterial vaginosis. Hydrogen peroxide douche and triple sulphonamide cream were ineffective. Metronidazole caused metallic taste, nausea and vomiting. We need better-designed trials with larger sample sizes to test the effectiveness of promising drugs.