Species identification by MALDI-TOF MS and gap PCR–RFLP of non-aureus Staphylococcus, Mammaliicoccus, and Streptococcus spp. associated with sheep and goat mastitis

Table 2 Detail of the 20 discordant species identification results between MALDI-TOF MS and gap PCR–RFLP integrated with gap gene sequencing

MALDI-TOF MS^a	Log score	ID by gap PCR-RFLP^b	ID by gap sequencing^c (% identity)^d
Staphylococci
Staphylococcus microti	1.99	–	Staphylococcus muscae (92.79%)
Staphylococcus microti	2.05	–	Staphylococcus muscae^e
Staphylococcus microti	2.06	–	Staphylococcus muscae^e
Staphylococcus microti	1.91	–	Staphylococcus muscae^e
Staphylococcus microti	1.76	–	Staphylococcus muscae^e
Staphylococcus microti	2.04	–	Staphylococcus simulans (99.89%)
Staphylococcus petrasii	2.1	Staphylococcus haemolyticus	–
Staphylococcus petrasii	2.03	Staphylococcus haemolyticus	–
Staphylococcus petrasii	2.24	–	Staphylococcus jettensis (99.29%)
Staphylococcus sciuri^f	2.23	–	Staphylococcus chromogenes (98.75%)
Staphylococcus sciuri^f	2.16	–	Staphylococcus hyicus (98.69%)
Staphylococcus xylosus	1.88	–	Staphylococcus devriesei^g
Staphylococcus xylosus	1.81^g	–	Staphylococcus pseudoxylosus (99.78%)
Staphylococcus cohnii	1.7^h	–	Staphylococcus haemolyticus (98.91%)
Staphylococcus lentus^f	1.8^h	–	Staphylococcus epidermidis (98.46%)
Staphylococcus succinus	1.93	Staphylococcus epidermidis	–
Unidentified	1.6	–	Staphylococcus haemolyticus (99.07%)
Unidentified	1.28	–	Staphylococcus haemolyticus (98.26%)
Unidentified	1.44	–	Staphylococcus devriesei (99.77%)
Streptococci
Streptococcus suis	1.78	–	Streptococcus ruminantium (98.15%)

^aBased on the Bruker MALDI Biotyper System Compass® Library Revision H (2021), covering 3893 species/entries.
^bSpecies identification was assigned by matching the enzyme digestion pattern of the gap gene amplicon with the reference strain.
^cAll amplicons producing an enzyme digestion pattern different than the reference strains were subjected to genomic sequencing for species identification.
^dPercent identity of the gap gene amplicon with sequences in the GenBank database using the Basic Local Alignment Search Tool (BLAST). Details are reported in Additional files 6 and 7.
^eBased on the restriction pattern of the Staphylococcus muscae isolate identified by gap sequencing.
^fThese species have been reclassified in the Mammaliicoccus genus [6].
^gBased on the restriction pattern of the Staphylococcus devriesei isolate identified by gap sequencing.
^hThe first round of MALDI-TOF MS identification was not successful and it was repeated.

ISSN: 1297-9716