Defining pathogenic bacterial species in the genomic era

Abstract

Actual definitions of bacterial species are limited due to the current criteria of definition and the use of restrictive genetic tools. The 16S ribosomal RNA sequence, for example, has been widely used as a marker for phylogenetic analyses; however, its use often leads to misleading species definitions. According to the first genetic studies, removing a certain number of genes from pathogenic bacteria removes their capacity to infect hosts. However, more recent studies have demonstrated that the specialization of bacteria in eukaryotic cells is associated with massive gene loss, especially for allopatric endosymbionts that have been isolated for a long time in an intracellular niche. Indeed, sympatric free-living bacteria often have bigger genomes and exhibit greater resistance and plasticity and constitute species complexes rather than true species. Specialists, such as pathogenic bacteria, escape these bacterial complexes and colonize a niche, thereby gaining a species name. Their specialization allows them to become allopatric, and their gene losses eventually favor reductive genome evolution. A pathogenic species is characterized by a gene repertoire that is defined not only by genes that are present but also by those that are lacking. It is likely that current bacterial pathogens will disappear soon and be replaced by new ones that will emerge from bacterial complexes that are already in contact with humans.

Keywords: allopatry; evolution; gene loss; pathogens; speciation; sympatry.

Figure 1

Our definition of bacterial species.

Figure 2

Pleomorphism of microbes. (A.1) Cocci, (A.2) diplococci, (A.3–5) streptococci, (A.6) staphylococci, (B.1) bacilli, (B.2) diplobacilli, (B.3) streptobacilli, and (B.4) coccobacilli.

Figure 3

Time-scale comparison between animal and bacterial species.

Figure 4

Vaccine principle established by Pasteur. P. multocida virulence is attenuated by multiple culture passages under the same laboratory conditions. The attenuation coincides with genomic loss. Injection of the attenuated strain protected chickens from future P. multocida infection.

Figure 5

Shigella dysenteriae and Escherichia coli strains. (A) The metabolic capacity of S. dysenteriae (ii) is limited compared to E. coli (i). (B) Sequence deletions in non-pathogenic E. coli strains (K-12; O6-H1; ED1a, and HS, IAI1), pathogenic E. coli strains (O103:H2, O157:H7, UT189, 536, O7:K1, O-127:H6, and O1:139:H28), and S. dysenteriae. Pathogenic strains of E. coli are divided into four groups: enterohemorrhagic (EHEC), uropathogenic (UPEC), enteropathogenic (EPEC), and enterotoxigenic (ETEC). Examples of three different genomic regions around melA (green rectangle), cadA (red circle), and yjcV (blue rectangle) genes are shown. Deletions occurred around these genes in most pathogenic strains, but they remain in non-pathogenic strains. Most pathogenic strains have plasmids, represented by empty circles. Genome size is reported in base pairs. The pink triangle represents Shiga toxin, which is found in S. dysenteriae, E. coli O103:H2, and E. coli O157:H7 (cadA: gene coding for lysine decarboxylase; melA: gene coding for melA protein, alpha-galactosidase activity; and yjcV: gene coding for d-allose transport system permease protein).

Figure 6

Genetic events leading to speciation of pathogenic bacteria. Polymerase errors can introduce new genes and/or delete existing ones. Recombination events cause duplication, deletion, or fusion of genes and yield new gene architecture. Bacteria may gain genes through horizontal gene transfers, thereby gaining fitness and the ability to better adapt to new environments. Finally, gene loss resulting from deletion events and a significant restriction of the number of ribosomal operons occurs once bacteria become specialized in a host organism whose metabolic substrates can be used by bacteria. Gene gain is subsequently decreased.

Figure 7

The resistome. Sympatric species have a higher resistance capacity compared to allopatric species, which are more sensitive to the action of antibiotics. (A) Gut microbes unaffected by antibiotics possess resistance genes, probably acquired through HGT. (B) Specialized species are more sensitive and may not resist some antibiotics. Their resistome is limited because of their isolation and their inability to exchange genes. Blue arrows represent resistance genes.

Figure 8

Examples of sympatric and allopatric bacteria. (A) The gut microbiota comprise millions of bacterial species, such as Bacteroidetes, Firmicutes, Lactobacillus, and Escherichia, and fungi. Each of these sympatric species exchanges genes at an intermediate rate, placing them between free-living non-specialized bacteria and isolated obligate intracellular parasites. Therefore, their resistance to antibiotics is also intermediate compared to free-living and pathogenic bacteria whose sensitivity to antibiotics is increased. (B) R. prowazekii inhabits the endothelium in humans. R. prowazekii is an allopatric bacterium and is therefore a specialized isolated pathogen that suffers from ongoing genome reduction. In contrast, it no longer gains any genes through HGT.

Figure 9

Species complexes and the rise of specialists. Non-specialized bacteria form complexes and engage in high rates of gene exchange. Some specialists may emerge from a complex and progressively adapt a balance between gene gain and gene loss (favoring gene loss). The more specialized a species is, the more important genome reduction becomes. This limits its capacity to obtain new characteristics.

Figure 10

Phylogenomic tree of E. coli strains and S. dysenteriae based on their gene repertoires. Pathogenic and non-pathogenic species form two separate groups.