Minimum Core Genome Sequence Typing of Bacterial Pathogens: a Unified Approach for Clinical and Public Health Microbiology

Abstract

Bacterial pathogens impose a heavy health burden worldwide. In the new era of high-throughput sequencing and online bioinformatics, real-time genome typing of infecting agents, and in particular those with potential severe clinical outcomes, holds promise for guiding clinical care to limit the detrimental effects of infections and to prevent potential local or global outbreaks. Here, we sequenced and compared 85 isolates of Streptococcus suis, a zoonotic human and swine pathogen, wherein we analyzed 32 recognized serotypes and 75 sequence types representing the diversity of the species and the human clinical isolates with high public health significance. We found that 1,077 of the 2,469 genes are shared by all isolates. Excluding 201 common but mobile genes, 876 genes were defined as the minimum core genome (MCG) of the species. Of 190,894 single-nucleotide polymorphisms (SNPs) identified, 58,501 were located in the MCG genes and were referred to as MCG SNPs. A population structure analysis of these MCG SNPs classified the 85 isolates into seven MCG groups, of which MCG group 1 includes all isolates from human infections and outbreaks. Our MCG typing system for S. suis provided a clear separation of groups containing human-associated isolates from those containing animal-associated isolates. It also separated the group containing outbreak isolates, including those causing life-threatening streptococcal toxic shock-like syndrome, from sporadic or less severe meningitis or bacteremia-only isolates. The typing system facilitates the application of genome data to the fields of clinical medicine and epidemiology and to the surveillance of S. suis. The MCG groups may also be used as the taxonomical units of S. suis to define bacterial subpopulations with the potential to cause severe clinical infections and large-scale outbreaks.

Population Analysis of Streptococcus suis Isolates from Slaughtered Swine by Use of Minimum Core Genome Sequence Typing

“…The full-length mrp gene was amplified and sequenced using a previously described method (18) or extracted from the draft sequence (GenBank accession numbers PRJNA171448 to PRJNA171478 and PRJNA171480 to PRJNA171483), as done in our previous study (8). Amplification of the sly and epf genes was performed using a previously described method (19,20).…”

“…Chromosomal DNA was prepared from all of the isolates as described previously (16). Thirty-five isolates were whole-genome sequenced by Solexa sequencing and were used in a previous study (8).…”

“…Based on the genome data of 85 isolates, we first identified the minimum number of SNPs needed to assign the 7 MCG groups. The SNPs chosen were based on the following criteria: (i) the target gene contained as many specific SNPs for different groups as possible and therefore required the fewest number of genes, (ii) the length of the amplified product was less than the reading length for the sequence reaction (900 bp), and (iii) the genes selected contained conserved regions without sequence variation among the 85 genome sequences available for S. suis (8) so that primers suitable for amplifying a diverse range of strains could be designed. MCG group 7 is defined by 3 subgroups, 7-1, 7-2, and 7-3, as there are no unique SNPs that define MCG group 7.…”

“…High genetic diversity within the species adds complexity to the understanding of the clonal relationships between strains, especially low-virulence strains (5)(6)(7). In a previous study, we developed a whole-genome sequencebased typing scheme to identify and classify S. suis populations as one of seven minimum core genome (MCG) groups (8). In that study, 13 epidemic strain-specific single nucleotide polymorphisms (SNPs), 553 group-specific SNPs, and 129 lineage-specific SNPs were found.…”

Le séquençage haut-débit

“…Ainsi, Loman et al [13] ont présenté une approche visant à identifier et caractériser par séquen-çage direct, à partir d'une matrice complexe (échantillons de fèces), les souches impliquées dans un épisode infectieux à Escherichia coli entérohémorragiques survenu en Allemagne en 2011. En premier lieu, cette approche a réussi à identifier/caractériser la souche principale [16]. Cette exploration peut être utilisée pour la prédiction et la prévention des maladies infectieuses (par exemple en adaptant une stratégie vaccinale).…”