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MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa).

Lo CI, Fall B, Sambe-Ba B, Diawara S, Gueye MW, Mediannikov O, Sokhna C, Faye N, Diemé Y, Wade B, Raoult D, Fenollar F - PLoS ONE (2015)

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal.

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.

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Sixteen clinical isolates not identified in Dakar (Senegal).
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pone.0145889.g001: Sixteen clinical isolates not identified in Dakar (Senegal).

Mentions: One isolate was accurately identified as Escherichia hermannii in Dakar but not in Marseille; PCR and sequencing of the rpoB sequence confirmed the identification of Escherichia hermannii. Sixteen out of 191 (8.4%) isolates were not identified by MALDI-TOF MS in Dakar (Fig 1). Among these 16 isolates, 6 were correctly identified at the species level in Marseille (2 isolates of Exiguobacterium aurantiacum, 1 isolate of A. baumannii, 1 of Kytococcus schroeteri, 1 of Bacillus flexus, and 1 of C. albicans). Four isolates were only identified at the genus level in Marseille, and molecular biology with sequencing was necessary to allow their identification (1 isolate of Corynebacterium aurimucosum, 1 of S. haemolyticus, 1 of Paenibacillus amylolyticus, and 1 of B. cereus). Finally, 6 (3%) isolates were not identified with either MALDI-TOF MS. PCR followed by sequencing allowed the identification of 1 isolate of Rothia mucilaginosa, 1 of Staphylococcus arlettae, 1 of Bacillus amyloliquefaciens, 1 of Bacillus nealsonii, and 1 of Exiguobacterium profundum. In addition, the last isolate exhibited 95% 16S rRNA nucleotide sequence identity with Necropsobacter rosorum (NR_114550.1), the phylogenetically closest validated species (Fig 1), suggesting that this isolate corresponded to a new bacterial species, which we named “Necropsobacter massiliensis”. The Genbank accession number for the 16S rRNA sequence of “Necropsobacter massiliensis” is HG428679. The full genome sequencing and the characterization of “Necropsobacter massiliensis” have been performed [25].


MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa).

Lo CI, Fall B, Sambe-Ba B, Diawara S, Gueye MW, Mediannikov O, Sokhna C, Faye N, Diemé Y, Wade B, Raoult D, Fenollar F - PLoS ONE (2015)

Sixteen clinical isolates not identified in Dakar (Senegal).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4696746&req=5

pone.0145889.g001: Sixteen clinical isolates not identified in Dakar (Senegal).
Mentions: One isolate was accurately identified as Escherichia hermannii in Dakar but not in Marseille; PCR and sequencing of the rpoB sequence confirmed the identification of Escherichia hermannii. Sixteen out of 191 (8.4%) isolates were not identified by MALDI-TOF MS in Dakar (Fig 1). Among these 16 isolates, 6 were correctly identified at the species level in Marseille (2 isolates of Exiguobacterium aurantiacum, 1 isolate of A. baumannii, 1 of Kytococcus schroeteri, 1 of Bacillus flexus, and 1 of C. albicans). Four isolates were only identified at the genus level in Marseille, and molecular biology with sequencing was necessary to allow their identification (1 isolate of Corynebacterium aurimucosum, 1 of S. haemolyticus, 1 of Paenibacillus amylolyticus, and 1 of B. cereus). Finally, 6 (3%) isolates were not identified with either MALDI-TOF MS. PCR followed by sequencing allowed the identification of 1 isolate of Rothia mucilaginosa, 1 of Staphylococcus arlettae, 1 of Bacillus amyloliquefaciens, 1 of Bacillus nealsonii, and 1 of Exiguobacterium profundum. In addition, the last isolate exhibited 95% 16S rRNA nucleotide sequence identity with Necropsobacter rosorum (NR_114550.1), the phylogenetically closest validated species (Fig 1), suggesting that this isolate corresponded to a new bacterial species, which we named “Necropsobacter massiliensis”. The Genbank accession number for the 16S rRNA sequence of “Necropsobacter massiliensis” is HG428679. The full genome sequencing and the characterization of “Necropsobacter massiliensis” have been performed [25].

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal.

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.

Show MeSH
Related in: MedlinePlus