Blood culture surveillance in a secondary care hospital in Benin: epidemiology of bloodstream infection pathogens and antimicrobial resistance

Abstract

Background: Although global surveillance of antimicrobial resistance (AMR) is considered key in the containment of AMR, data from low- and middle-income countries, especially from sub-Saharan Africa, are scarce. This study describes epidemiology of bloodstream infections and antimicrobial resistance rates in a secondary care hospital in Benin.

Methods: Blood cultures were sampled, according to predefined indications, in BacT/ALERT FA Plus and PF Plus (bioMérieux, Marcy-l'Etoile, France) blood culture bottles (BCB) in a district hospital (Boko hospital) and to a lesser extent in the University hospital of Parakou. These BCB were incubated for 7 days in a standard incubator and twice daily inspected for visual signs of growth. Isolates retrieved from the BCB were processed locally and later shipped to Belgium for reference identification [matrix-assisted laser desorption/ionization time-of-flight spectrometry (MALDI-TOF)] and antibiotic susceptibility testing (disk diffusion and E-tests).

Results: From October 2017 to February 2020, 3353 BCB were sampled, corresponding to 3140 blood cultures (212 cultures consisting of > 1 BCB) and 3082 suspected bloodstream infection (BSI) episodes. Most of these cultures (n = 2471; 78.7%) were sampled in children < 15 years of age. Pathogens were recovered from 383 (12.4%) cultures, corresponding to 381 confirmed BSI. 340 of these pathogens were available and confirmed by reference identification. The most common pathogens were Klebsiella pneumoniae (n = 53; 15.6%), Salmonella Typhi (n = 52; 15.3%) and Staphylococcus aureus (n = 46; 13.5%). AMR rates were high among Enterobacterales, with resistance to third-generation cephalosporins in 77.6% of K. pneumoniae isolates (n = 58), 12.8% of Escherichia coli isolates (n = 49) and 70.5% of Enterobacter cloacae isolates (n = 44). Carbapenemase production was detected in 2 Escherichia coli and 2 Enterobacter cloacae isolates, all of which were of the New Delhi metallo-beta lactamase type. Methicillin resistance was present in 22.4% of S. aureus isolates (n = 49).

Conclusion: Blood cultures were successfully implemented in a district hospital in Benin, especially among the pediatric patient population. Unexpectedly high rates of AMR among Gram-negative bacteria against commonly used antibiotics were found, demonstrating the clinical and scientific importance of clinical bacteriology laboratories at this level of care.

Keywords: Antimicrobial resistance; Bloodstream infections; Low- and middle-income countries; Sepsis; sub-Saharan Africa.

Fig. 1

Location of Benin within Western Africa and location of Boko within Benin. Boko is situated in the Borgou province, close to the second largest city of the country, Parakou. The capital city, Cotonou, is located at 400 km distance. (Map generated with “Maps” function in Excel, Microsoft. © GeoNames, Microsoft, Tom Tom, Wikipedia)

Fig. 2

Breakdown of blood culture data from Boko, Benin. BCB blood culture bottle; BSI bloodstream infection

Fig. 3

Detail of Fig. 2. Breakdown of blood culture data stratified by age of patient. BCB blood culture bottles; BSI bloodstream infection episode; NTS non-Typhi Salmonella. For more detail of children < 5 years of age, see Fig. 4

Fig. 4

Further detail of Fig. 3; breakdown of data for children < 5 years age, stratified by age (≤ 28 days of > 28 days of age). BCB blood culture bottles; BSI bloodstream infection episode; NTS non-Typhi Salmonella