Temporal trends of skin and soft tissue infections caused by methicillin-resistant Staphylococcus aureus in Gabon.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is one of the leading causes of mortality due to bacterial antimicrobial resistance. While S. aureus is common in skin and soft tissue infections (SSTI) in Africa, data on MRSA rates are scarce and reports vary widely across the continent (5%-80%). In this study, we describe the proportion of MRSA causing SSTI in Lambaréné, Gabon, over an 11-year period. METHODS: We retrospectively analyzed data from 953 bacterial specimens collected from inpatients and outpatients with SSTI at the Albert Schweitzer Hospital, Lambaréné, Gabon, between 2009 and 2019. We determined temporal changes in the prevalence of MRSA and identified risk factors for SSTI with MRSA. RESULTS: 68% of all specimens with bacterial growth yielded S. aureus (n = 499/731), of which 7% (36/497) with antimicrobial susceptibility testing were identified as MRSA. Age above 18 years, admission to the surgical ward, and deep-seated infections were significantly associated with MRSA as the causative agent. After an initial decline from 7% in 2009, there was a marked increase in the proportion of MRSA among all S. aureus from SSTI from 3 to 20% between 2012 and 2019. The resistance rate to erythromycin was significantly higher in MRSA than in methicillin-susceptible S. aureus (73% vs. 10%), and clindamycin resistance was detected exclusively in MRSA isolates (8%). CONCLUSION: The increasing proportion of MRSA causing SSTI over the 11-year period contrasts with many European countries where MRSA is on decline. Continuous surveillance of MRSA lineages in the hospital and community along with antibiotic stewardship programs could address the increasing trend of MRSA.

Genomic epidemiology of Streptococcus pyogenes from pharyngeal and skin swabs in Gabon.

The disease burden of Streptococcus pyogenes is particularly high in low- and middle-income countries. However, data on the molecular epidemiology of S. pyogenes in such regions, especially sub-Saharan Africa, are scarce. To address this, whole-genome sequencing (WGS) of S. pyogenes from Gabon was performed to identify transmission clusters and provide valuable genomic data for public repositories. A total of 76 S. pyogenes isolates from 73 patients, collected between September 2012 and January 2013, were characterized by short-read whole-genome sequencing. The predominant emm types were emm58.0, emm81.2 and emm223.0 with 9.2% (7 of 76), 7.9% (6 of 76), and 6.6% (5 of 76), respectively. Single-nucleotide polymorphism analysis revealed 16 putative transmission clusters. Four of these were household transmissions. Four antimicrobial genes (lmrP, tetM, tetL, and thfT) were found in the S. pyogenes isolates from this study. All strains carried lmrP. Of the 76 isolates, 64 (84.2%) carried at least one tetracycline resistance gene (tetM or tetL). Comparisons with other publicly available African genomic data revealed a significant correlation between geographical location and genetic diversity of S. pyogenes, with Gabonese strains showing similarities to those from Kenya and certain Oceanian regions. Our study showed that transmission of S. pyogenes can occur at the community/household level and that high-resolution molecular typing is needed to monitor changes in circulating clones and to detect community outbreaks. Advocacy for the adoption of WGS for comprehensive molecular characterization of S. pyogenes and data sharing through public repositories should be encouraged to understand the molecular epidemiology and evolutionary trajectory of S. pyogenes in sub-Saharan Africa. IMPORTANCE: The study conducted in Gabon underscores the critical importance of addressing the limited knowledge of the molecular epidemiology of Streptococcus pyogenes in low- and middle-income countries, particularly sub-Saharan Africa. Our molecular analysis identified predominant emm types and unveiled 16 putative transmission clusters, four involving household transmissions. Furthermore, the study revealed a correlation between geographical location and genetic diversity, emphasizing the necessity for a comprehensive understanding of the molecular epidemiology and evolutionary trajectory of S. pyogenes in various regions. The call for advocacy in adopting whole-genome sequencing for molecular characterization and data sharing through public repositories is crucial for advancing our knowledge and implementing effective strategies to combat the spread of S. pyogenes in sub-Saharan Africa.

Species identification and drug susceptibility testing of non-tuberculous mycobacteria by Line Probe Assay in Lambaréné, Gabon-a cross-sectional study.

BACKGROUND: Non-tuberculous mycobacteria (NTM) are a group of bacteria that cause rare lung infections and are increasingly recognized as causative agents of opportunistic and device-associated infections in humans. In Gabon, there is a lack of data on NTM species identification and drug susceptibility. The aim of this study was to identify the frequency of NTM species and their genotypic susceptibility pattern to commonly used antibiotics for NTM infections in Gabon. METHODS: A cross-sectional study was conducted at the CERMEL TB laboratory from January 2020 to December 2022, NTM subspecies identification and drug susceptibility testing to macrolides and aminoglycosides were performed using the genotype NTM-DR kit. RESULTS: The study found that out of 524 culture-positive specimens, 146 (28%) were NTM, with the predominant group being Mycobacterium avium complex (MAC) and Mycobacterium abscessus complex (MABC). All MAC isolates were fully susceptible to macrolides and aminoglycosides, while five MABC isolates carried mutations indicative of reduced susceptibility to macrolide and aminoglycoside drugs. CONCLUSIONS: These findings suggest that clinicians may use macrolides and aminoglycosides to manage NTM infections caused by MAC, but further investigation is required to determine MABC drug susceptibility.

Resistance patterns among drug-resistant tuberculosis patients and trends-over-time analysis of national surveillance data in Gabon, Central Africa.

OBJECTIVE: Routinely generated surveillance data are important for monitoring the effectiveness of MDR-TB control strategies. Incidence of rifampicin-resistant tuberculosis (RR-TB) is a key indicator for monitoring MDR-TB. METHODS: In a longitudinal nationwide retrospective study, 8 years (2014-2021) of sputum samples from presumptively drug-resistant tuberculosis patients from all regions of Gabon were referred to the national tuberculosis reference laboratory. Samples were analysed using GeneXpert MTB/RIF and Genotype MTBDRsl version 2/Line Probe Assay. RESULTS: Of 3057 sputum samples from presumptive tuberculosis patients, both from local hospital and from referral patients, 334 were RR-TB. The median patient age was 33 years (interquartile range 26-43); one third was newly diagnosed drug-resistant tuberculosis patients; one-third was HIV-positive. The proportion of men with RR-TB was significantly higher than that of women (55% vs 45%; p < 0.0001). Patients aged 25-35 years were most affected (32%; 108/334). The cumulative incidence of RR-TB was 17 (95% CI 15-19)/100,000 population over 8 years. The highest incidences were observed in 2020 and 2021. A total of 281 samples were analysed for second-line drug resistance. The proportions of study participants with MDR-TB, pre-XDR-TB and XDR-TB were 90.7% (255/281), 9% (25/281) and 0.3% (1/281), respectively. The most-common mutations in fluoroquinolones resistance isolates was gyrA double mutation gyrA MUT3B and MUT3C (23%; 4/17). Most (64%; 6/8) second-line injectable drugs resistance isolates were characterised by missing both rrs WT2 and MUT2 banding. CONCLUSION: The increasing incidence of MDR-TB infection in Gabon is alarming. It is highest in the 25-35 years age category. The incidence of MDR-TB infection in treatment-naïve patients calls for case finding and contact tracing strategy improvement.

Building sustainable clinical trial sites in Sub-Saharan Africa through networking, infrastructure improvement, training and conducting clinical studies: The PanACEA approach.

INTRODUCTION: The Pan-African Consortium for the Evaluation of Anti-Tuberculosis Antibiotics (PanACEA) was designed to build tuberculosis (TB) trial capacity whilst conducting clinical trials on novel and existing agents to shorten and simplify TB treatment. PanACEA has now established a dynamic network of 11 sub-Saharan clinical trial sites and four European research institutions. OBJECTIVES: In 2011, a capacity development program, funded by the European & Developing Countries Clinical Trials Partnership (EDCTP), was launched with four objectives, aiming at strengthening collaborating TB research sites to reach the ultimate goal of becoming self-sustainable institutions: networking; training; conducting clinical trials; and infrastructure scaling-up of sites. METHODS: Assessment in six sub-Saharan TB-endemic countries (Gabon, Kenya, South Africa, Tanzania, Uganda and Zambia) were performed through a structured questionnaire, site visits, discussion with the PanACEA consortium, setting of milestones and identification of priorities and followed-up with evaluations of each site. The results of this needs-based assessment was then translated into capacity development measures. RESULTS: In the initial phase, over a four-year period (March 2011 - June 2014), the programme scaled-up six sites; conducted a monitoring training program for 11 participants; funded five MSc and four PhD students, fostering gender balance; conducted four epidemiological studies; supported sites to conduct five Phase II studies and formed a sustainable platform for TB research (panacea-tb.net). CONCLUSION: Our experience of conducting TB clinical trials within the PanACEA programme environment of mentoring, networking and training has provided a sound platform for establishing future sustainable research centres. Our goal of facilitating emergent clinical TB trial sites to better initiate and lead research activities has been mostly successful.

Implementation of an antimicrobial stewardship programme in three regional hospitals in the south-east of Liberia: lessons learned.

Background: Antimicrobial stewardship (AMS) programmes can improve the use of antimicrobial agents. However, there is limited experience in the implementation of such programmes in low- and middle-income countries (LMICs). Objectives: To assess the effect of AMS measures in south-east Liberia on the quality of antimicrobial use in three regional hospitals. Methods: A bundle of three measures (local treatment guideline, training and regular AMS ward rounds) was implemented and quality indicators of antimicrobial use (i.e. correct compounds, dosage and duration) were assessed in a case series before and after AMS ward rounds. Primary endpoints were (i) adherence to the local treatment guideline; (ii) completeness of the microbiological diagnostics (according to the treatment guideline); and (iii) clinical outcome. The secondary endpoint was reduction in ceftriaxone use. Results: The majority of patients had skin and soft tissue infections (n = 108) followed by surgical site infections (n = 72), pneumonia (n = 64), urinary tract infection (n = 48) and meningitis (n = 18). After the AMS ward rounds, adherence to the local guideline improved for the selection of antimicrobial agents (from 34.5% to 61.0%, P < 0.0005), dosage (from 15.2% to 36.5%, P < 0.0005) and duration (from 13.2% to 31.0%, P < 0.0005). In total, 79.7% of patients (247/310) had samples sent for microbiological analysis. Overall, 92.3% of patients improved on Day 3 (286/310). The proportion of patients receiving ceftriaxone was significantly reduced after the AMS ward rounds from 51.3% to 14.2% (P < 0.0005). Conclusions: AMS measures can improve the quality of antimicrobial use in LMICs. However, long-term engagement is necessary to make AMS programmes in LMICs sustainable.

Knowledge and perception on antimicrobial resistance and antibiotics prescribing attitude among physicians and nurses in Lambaréné region, Gabon: a call for setting-up an antimicrobial stewardship program.

BACKGROUND: Africa is challenged by the emergence of antimicrobial resistance (AMR). In order to improve patient management and to optimise approaches to curb the spread of antimicrobial resistance, we examined knowledge and perceptions of AMR and antibiotics prescription practices of HCW (healthcare workers) in Lambaréné, Gabon. METHODS: We conducted a self-administered, questionnaire-based survey in HCW at the regional referral hospital, a medical research centre, and peripheral health care facilities. The proportions of correct responses to questions were determined and compared between physicians and nurses using Fisher's Exact test. RESULTS: A total of 47 HCW took part in the survey. Of those, 64% (30/47) recognised antibiotic resistance as a major public health issue in Gabon, but only 14/47 (30%) recognised it as a problem in their health facility. Of note, 37/47 (79%) recognised excessive use of antibiotics without microbiological confirmation in case of infection, and buying antibiotics without a prescription, as possible cause of antimicrobial resistance. Some HCW (28%; 13/47) reported having prescribed antibiotics because the patients asked for them; and a total of 15/47 (32%) responded that antibiotics could help patients recover faster when added to malaria treatment. Compared to nurses, most of the physicians recognised that excessive use of antibiotics without microbiological confirmation of infection could contribute to AMR spread (18/19 (95%) vs 19/28 (68%); p = 0.028). CONCLUSION: Most HCW recognised AMR as public health issue. However, a quarter of the participants did not know about the causes fostering the emergence of antimicrobial resistance. There is a need to perform regular HCW training in antimicrobial prescription, and to set up an antimicrobial stewardship program.

Creatine kinase-(MB) and hepcidin as candidate biomarkers for early diagnosis of pulmonary tuberculosis: a proof-of-concept study in Lambaréné, Gabon.

BACKGROUND: The present study aimed to evaluate the diagnostic utility of creatine kinase-MB (CK-MB), hepcidin (HEPC), phospholipase A2 group IIA (PLa2G2A), and myosin-binding protein C (MYBPC1) for tuberculosis (TB). These four biomarkers are differentially regulated between quiescent Mycobacterium tuberculosis (Mtb) infected individuals (non-progressors to TB disease) and Mtb-infected TB disease progressors 6 months before the onset of symptoms. METHODS: We enrolled samples from patients experiencing moderate-to-severe pulmonary infections diseases including 23 TB cases confirmed by smear microscopy and culture, and 34 TB-negative cases. For each participant, the serum levels of the four biomarkers were measured using ELISA. RESULTS: The levels of CK-MB and HEPC were significantly reduced in patients with active TB disease. CK-MB median level was 2045 pg/ml (1455-4000 pg/ml) in active TB cases and 3245 pg/ml (1645-4000 pg/ml) in non-TB pulmonary diseases. Using the receiver operating characteristic curve (ROC) analysis, HEPC and CK-MB had the Area Under the Curve (AUC) of 79% (95% CI 67-91%) and 81% (95% CI 69-93%), respectively. Both markers correlated with TB diagnosis as a single marker. PLa2G2A and MYBPC1 with AUCs of 48% (95% CI 36-65%) and 62% (95% CI 48-76%) did not performed well as single biomarkers. The three markers'model (CK-MB-HEPC-PLa2G2A) had the highest diagnostic accuracy at 82% (95% CI 56-82%) after cross-validation. CONCLUSION: CK-MB and HEPC levels were statistically different between confirmed TB cases and non-TB cases. This study yields promising results for the rapid diagnosis of TB disease using a single marker or three biomarkers model.

High Diversity of emm Types and Marked Tetracycline Resistance of Group A Streptococci and Other ß-Hemolytic Streptococci in Gabon, Central Africa.

BACKGROUND: Group A ß-hemolytic streptococcus (GABHS) is a leading pathogen worldwide and post-streptococcal sequelae is a major cause of morbidity and mortality in resource-limited countries. The M protein (coded by the emm gene) is a key virulence factor and a component of GABHS vaccine candidates. As data on BHS in Central Africa are scarce, antibiotic resistance, emm diversity and potential vaccine coverage were investigated. METHODS: In a prospective cross-sectional study, 1014 Gabonese were screened for streptococcal throat carriage, tonsillopharyngitis and pyoderma by throat and skin smear tests. All BHS were isolated, species were identified and analysis of antibiotic resistance, emm types and emm clusters was performed. RESULTS: One hundred sixty-five BHS were detected, comprising 76 GABHS, 36 group C ß-hemolytic streptococcus (GCBHS) and 53 group G ß-hemolytic streptococcus (GGBHS) in 140 carrier, 9 tonsillopharyngitis and 16 pyoderma isolates. Eighty percentage of GABHS, 78% of GCBHS and 79% of GGBHS were tetracycline resistant. Forty-six emm types were identified. GABHS emm58, emm65 and emm81 were most prevalent (26%). Emm diversity of GABHS was the highest, GCBHS and GGBHS were less divers. Every second GABHS, every third GCBHS and every tenth GGBHS carrier was colonized with emm types detected in tonsillopharyngitis or pyoderma isolates. CONCLUSIONS: Tetracycline resistance and emm type diversity was high among BHS carriers in Gabon with a potential coverage of 58% by the 30-valent GABHS vaccine. A relevant overlap of carrier emm types with emm types found in tonsillopharyngitis and pyoderma characterizes a shared pool of circulating BHS strains.

Non-tuberculous mycobacteria isolation from presumptive tuberculosis patients in Lambaréné, Gabon.

OBJECTIVE: The prevalence of clinical cases of pulmonary non-tuberculous mycobacteria (NTM) is increasing worldwide. The aim of this study was to determine the proportion and the NTM species isolated from presumptive tuberculosis patients in Lambaréné, Gabon. METHOD: From January 2018 to December 2020, sputum samples from presumptive TB patients were analysed at the tuberculosis reference laboratory of the Centre de Recherches Médicales de Lambaréné. Two sputum samples were collected per patient, and culture was performed using Bactec MGIT 960. The GenoType Mycobacterium CM/AS was used for NTM isolates confirmation and species differentiation. RESULTS: Among 1363 sputum samples analysed, 285 (20.9%) were Auramin acid fast bacilli (AFB) smear-positive. NTM were isolated in 137/1363 (10%) of the samples. The most prevalent NTM species was Mycobacterium intracellulare (n = 74; 54%). CONCLUSION: These results show the presence of NTM among presumptive TB patients in Gabon, which could potentially complicate TB diagnosis. This presents a new public health challenge, and emphasises the need to consider NTM in planning the prevention and management of tuberculosis control.