Retrospective analysis of antimicrobial resistance and bacterial spectrum of infection in Gabon, Central Africa

This retrospective analysis of antimicrobial resistance in Gabon, Central Africa consists of data from the microbiology laboratory of the Albert Schweitzer Hospital (HAS) in Lambaréné. All microbiological reports on bacterial pathogens between January 2009 and September 2012 were included. Ethical approval was not obtained as retrospective studies such as our study do not require ethical approval in Gabon. No inclusion or exclusion criteria were applied. The decision to take samples for microbiological culture and the selection of samples was made by the physicians. We used commercial blood culture bottles (BacT/ALERT, bioMérieux, Marcy l'Etoile, France) to assess bacteremia and sterile cotton (Transswab, MWE, Corsham, England) for superficial infections, urine samples were collected in sterile single-use pots for microbiological culture.

Standard culture based methods were used for species identification (API Test stripes, bioMérieux, France and BBL Enterotubes or BBL Oxi/Ferm Tube, BD, Germany). Antimicrobial susceptibility testing was performed using the disk-diffusion method and was reported according to Clinical Laboratory Standards Institute (CLSI) guidelines [7]. Inducible clindamycin resistance was not routinely tested in our laboratory and is therefore not reported. We report the non-susceptibility rates, which include both intermediate and resistant isolates. The production of extended-spectrum beta-lactamase was confirmed in all ceftriaxone resistant Enterobacteriaceae using the double-disks method according to the manufacturer’s instruction (Mast discs, Mast diagnostics, Bootle, UK). This test applies discs of three different beta-lactam antibiotics (ceftazidim 30 μg, cefotaxime 30 μg, cefpodoxime 10 μg) with and without clavulanic acid. Methicillin-resistance was confirmed for all cefoxitin-resistant Staphylococcus aureus using a PBP2a-agglutination test (PBP2’ Test Kit, Oxoid, Japan). As part of a clinical trial requirement, the microbiology laboratory at the HAS successfully participates in regular external quality assurance (EQA) programs addressing species identification and susceptibility testing. The EQA is part of the WHO/NICD Proficiency Testing Scheme, and is organized by the Contract Laboratory Services (CLS), Johannesburg, South Africa.

In our analysis, children (≤ 18 years old) and adults (> 18 year old) were assessed separately. Types of infection were categorized as "bloodstream infection" (sepsis, bacteremia), "ear, eye, nose, throat infection" (pharyngitis, upper-respiratory tract infection, conjunctivitis, otitis), "surgical site infection", "skin and soft tissue infection" (pyoderma, impetigo, pyomyositis, abscesses, ulcer), "urinary tract infection" and "wound infection" [8]. All data were entered in one excel spreadsheet and analyzed using 'R’, version 2.13.1 (http://​www.​cran.​r-project.​org) and the package "epicalc". Categorical variables were compared using Chi-square test. The odds ratio (OR) and the 95% confidence interval (95% CI) were calculated to assess the association. The significance level was p < 0.05.

The proportion of children was higher compared to adults (Table 1). Similarly, the isolates from different groups of infections were not equally distributed among children and adults (Table 2). In total, 34.1% (n = 434) of all cases received a pre-sampling antibiotic treatment. Of these, the majority received ampicillin/amoxicillin (37.6%, n = 163), cloxacillin (16.4%, n = 71), ceftriaxone (15.0%, n = 65), gentamicin (14.1%, n = 61), ciprofloxacin (11.8%, n = 51) or cotrimoxazole (3.0%, n = 13).

In total, 1271 isolates were included in this study comprising isolates from 2009 (n = 234), 2010 (n = 273), 2011 (n = 397) and 2012 (n = 367). Noteworthy, adults and children frequently share the three most common bacterial pathogens but the distribution of these pathogens was different in both groups. For instance, the most frequent isolate from blood cultures in children was Klebsiella pneumoniae (16.7%, n = 21) followed by S. aureus (11.9%, n = 15) and Salmonella enterica (11.1%, n = 14). Similarly, S. aureus was most frequently found in blood cultures from adults (18.5%, n = 15) followed by S. enterica (14.8%, n = 12) and Streptococcus pneumoniae (12.3%, n = 10, Table 3). The spectrum of bacterial pathogens was highly diverse for the majority of infections. For instance, the three most frequent species comprised only one half of all pathogens isolated from blood cultures, ear, eye, nose and throat infection (S. aureus, Pseudomonas aeruginosa, Proteus mirabilis) or surgical site infections (S. aureus, P. mirabilis, Escherichia coli and Enterococcus faecalis, respectively, Table 3). The bacterial spectrum was less diverse in skin and soft tissue infections as S. aureus dominated in children (74.8%, n = 116) and adults (75.7%, n = 28, Table 2). Urinary tract infections were dominated by E. coli, K. pneumoniae and P. mirabilis both in children and adults. Wound infections in children were frequently caused by S. aureus (46.1%, n = 35) and Streptococcus pyogenes (26.3%, n = 20, Table 2).

The overall proportion of methicillin resistant S. aureus (MRSA) was 5.8% (n = 19) and fluctuated during the studied period between 3.9% (n = 2, 2009), 10.9% (n = 7, 2010), 5.2% (n = 5, 2011) and 3.3% (n = 4, 2012). The non-susceptibility rates (methicillin, erythromycin and clindamycin) of S. aureus from bloodstream infection were lower than in non-invasive isolates (Tables 4 and 5). The non-susceptibility of streptococci against penicillin was 8.6% (non-invasive S. pyogenes), 6.7% (non-invasive S. pneumoniae, Table 5) and 25% (S. pneumoniae from bloodstream infection, Table 4). Noteworthy, the two major Gram-negative bacteria K. pneumoniae and E. coli were frequently non-susceptible to combinations of aminopenicillins with beta-lactamase inhibitors. The overall non-susceptibility against third generation cephalosporins in K. pneumoniae was 50.6% (n = 43), ESBL-production was confirmed in all but one cases (49.4%, n = 42). The proportion of ESBL-producers among all Enterobacteriaceae throughout the observation period was 15.0% (n = 15, 2009), 18.9% (n = 27, 2010), 13.5% (n = 20, 2011) and 13.2% (n = 15, 2012). Despite its wide use in the hospital and other health care facilities in the region, the non-susceptibility to ciprofloxacin was diverse and ranged from 0% (Salmonella enterica) to 97.1% (K. pneumoniae, Table 4). The non-susceptibility rates of P. aeruginosa were very low, non-susceptibility to ciprofloxacin was reported in only one isolate (2.6%, Table 3).