Computational protocol: Staphylococcus aureus Complex in the Straw-Colored Fruit Bat (Eidolon helvum) in Nigeria

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Protocol publication

[…] All isolates were spa typed; multilocus sequence typing (MLST) was done exemplarily for one isolate of each spa type. Related MLST sequence types (ST) were grouped in clonal clusters (CC) if they shared at least six of the seven alleles of the MLST housekeeping genes as implemented in eBURST (http://eburst.mlst.net/).The concatenated sequences of the seven MLST genes were used to construct a Neighbor-Joining (NJ) tree as implemented in MEGA7 (www.megasoftware.net). The phylogenetic distance between groups was calculated using the Maximum Composite Likelihood method. Additional STs were included in the phylogenetic tree. They comprise major STs of S. aureus in Africa (ST15, ST121, ST152) (Schaumburg et al., ), an early branching S. aureus from the DR Congo (ST2353) (Schaumburg et al., ), S. aureus from Gabonese bats (ST2984, ST3259, ST3301, ST3302) (Held et al., ), S. argenteus (ST75, ST850, ST1304, ST1850, ST2198) (Ng et al., ; Schuster et al., ), and S. schweitzeri (e.g., ST1700, ST1822, ST2296, ST2465) (Schaumburg et al., , ).To analyze the position of the isolates in the overall S. aureus population, we screened the S. aureus MLST Database website (http://pubmlst.org/saureus/, sited at the University of Oxford) for the most closely related STs. These STs and others from our study were used to construct a minimum spanning tree (MST) as implemented in the SeqSphere+ software (version 2.4.0, Ridom GmbH, Münster, Germany). […]

Pipeline specifications

Software tools BURST, MEGA, SeqSphere+
Databases MLST.net PubMLST
Applications Phylogenetics, WGS analysis
Organisms Staphylococcus aureus, Homo sapiens, Chandipura virus, Pampus argenteus
Chemicals Penicillins, Tetracycline