MLST is considered the gold standard to determine the structure of S. suis populations. This powerful method uses genetic variation that accumulates very slowly in housekeeping genes to investigate the genetic diversity of S. suis and its use has allowed global and long-term epidemiology. King et al. established the MLST scheme for S. suis in 2002, using seven different house-keeping genes (cpn60, dpr, recA, aroA, thrA, gki, and mutS) ^[18][26]. Since its establishment, this MLST scheme has been adopted by multiple laboratories throughout the world and used to determine the STs of S. suis strains isolated from pig and human cases of infection [1].

Thus far (28 November 2019), a total of 1245 STs have been recorded in the S. suis MLST database (https://pubmlst.org/ssuis/). This method has revealed the presence of many clonal complexes (CCs) within the S. suis population in the database. Among the different CCs identified, the most important causes of infections in human and pig have been CC1, CC16, CC20, CC25, CC28, CC94, CC104, CC233/379, and CC221/234 (Figure 1) ^{[1][4][17][19]}[1,4,17,33]. Different CCs were found to be distributed in different regions of the world [1]. CC1 was found mostly in Europe, Asia (Cambodia, China, Korea, Japan, Thailand, and Vietnam), Australia, and South America (Argentina), while CC20 (ST20) was described as being important in the Netherlands ^{[1][19][20][21][22][23]}[1,33,34,35,36,37]. Furthermore, ST7 (CC1), responsible for the 1998 and 2005 epidemics, was mostly present in China [1] and CC16 and CC94 were predominant in Europe, although human cases were reported in Thailand ^[17][19][17,33]. CC25 or CC28 were reported in North America and were also recovered in Thailand, Korea, Japan, and Australia ^{[1][4][19][20][21][22][23]}[1,4,33,34,35,36,37]. Finally, CC104 (ST101, ST104, ST391-ST393, ST512-ST514), and CC233/379 (ST233 and ST379) were endemic to Thailand ^[1][19][1,33]. In North America, the structure of S. suis strains is more complicated and pathotypes are different from Europe and Asia ^[24][38]. Serotypes 1, 1/2, 2, 7, 14, and 23 as well as ST1, ST13, ST28, ST94, ST108, ST961, and ST977 have recently been described as pathogenic strains in the USA ^[24][38].

An alternative MLST approach using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MS-MLST) has been reported to be more rapid in providing typing results than dideoxy sequencing ^[22][36]. While both MS-MLST and conventional MLST had 100% concordance in their classification of sequence types (STs), in addition to faster time-to-results, MS-MLST had lower labor requirements and per-isolate costs. MS-MLST analysis was easier to instrument when large numbers of isolates were involved ^[22][36]. However, MS-MLST requires a high initial investment in the MALDI-TOF MS equipment and software. Therefore, this approach may not be readily available to most laboratories, particularly those in developing countries.

Although informative, MLST is a high-cost and time-consuming method that is not ideal for screening large numbers of isolates. MLST is also unavailable in many laboratories in developing countries. Therefore, polymerase chain reaction (PCR)-based approaches ^{[24][25][26][27][28]}[38,39,40,41,42] to identify the most important S. suis CCs (PCR-CC) were developed allowing for the rapid screening of a large number of isolates at a relatively modest cost (summarized in Table 2).