Abstract
Our team in Europe has developed the routine clinical laboratory identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). To evaluate the utility of MALDI-TOF MS in tropical Africa in collaboration with local teams, we installed an apparatus in the Hôpital Principal de Dakar (Senegal), performed routine identification of isolates, and confirmed or completed their identification in France. In the case of discordance or a lack of identification, molecular biology was performed. Overall, 153/191 (80.1%) and 174/191 (91.1%) isolates yielded an accurate and concordant identification for the species and genus, respectively, with the 2 different MALDI-TOF MSs in Dakar and Marseille. The 10 most common bacteria, representing 94.2% of all bacteria routinely identified in the laboratory in Dakar (Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus haemolyticus, Enterobacter cloacae, Enterococcus faecalis, and Staphylococcus epidermidis) were accurately identified with the MALDI-TOF MS in Dakar. The most frequent misidentification in Dakar was at the species level for Achromobacter xylosoxidans, which was inaccurately identified as Achromobacter denitrificans, and the bacteria absent from the database, such as Exiguobacterium aurientacum or Kytococcus schroeteri, could not be identified. A few difficulties were observed with MALDI-TOF MS for Bacillus sp. or oral streptococci. 16S rRNA sequencing identified a novel bacterium, “Necropsobacter massiliensis.” The robust identification of microorganisms by MALDI-TOF MS in Dakar and Marseille demonstrates that MALDI-TOF MS can be used as a first-line tool in clinical microbiology laboratories in tropical countries.
Highlights
The routine identification of bacteria and fungi by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a true revolution in clinical microbiology laboratories [1,2]
Two hundred clinical isolates obtained by conventional culture procedures in the clinical microbiology laboratory of the Hôpital Principal de Dakar (Senegal) and tested for identification using MALDI-TOF MS (VITEK1 MS-RUO) were sent to the clinical microbiology laboratory of the University Hospital in Marseille to confirm or complete the identification performed in Africa using another mass spectrometer (MicroFlex LT, Bruker Daltonik)
191 out of 202 clinical isolates from Senegal were included in the analyses; 11 isolates were excluded from the analysis due to either contamination or an inability to be cultured in France
Summary
The routine identification of bacteria and fungi by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a true revolution in clinical microbiology laboratories [1,2]. This technique is a powerful and robust tool for accurately identifying bacteria and fungi in less than 1 hour without a priori knowledge of the type of microorganisms; it is more cost-effective than current phenotypic testing methods, despite the initial cost of the instrument and the maintenance costs, and perhaps most importantly, it is easy to use [1,2]. We installed a MALDI-TOF MS platform in the Hôpital Principal de Dakar in Senegal [8]
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