Escherichia Coli: What Is and Which Are?

Overcoming Microbial Inhibition of S. Sonnei Through the Exploitation of Genomically Predicted Antibiotic Resistance Profiles for the Development of Food Enrichment Media

Linking outbreaks of Shigella spp. to specific foods is challenging due to poor selectivity of current enrichment media. We have previously shown that enrichment media, tailored to the genomically-predicted antimicrobial resistance (AMR) of Shiga toxigenic E. coli strains, enhances their isolation from foods. This study investigates the application of this approach for Shigella isolation. The AMR gene profiles of 21,908 published S. sonnei genomes indicated a high prevalence of genes conferring resistance to streptomycin (aadA, aph(3″)-Ib, aph(6)-Id, 92.8%), sulfonamides (sul1, sul2, 74.8%), and/or trimethoprim (dfrA, 96.2%). Genomic analysis and antibiotic susceptibility testing conducted with a panel of 17 outbreak-associated S. sonnei strains confirmed the correlation of AMR gene detection with resistance phenotypes. Supplementation of Shigella Broth (SB) with up to 400 µg/mL of trimethoprim or sulfadiazine did not suppress the growth of sensitive strains, whereas 100 µg/mL of streptomycin increased the selectivity of this broth. All three antibiotics increased the selectivity of modified Tryptone Soya Broth (mTSB). Based on these results, supplemented media formulations were developed and assessed by measuring the relative growth of S. sonnei in cultures coinoculated with a strain of bacteriocin-producing E. coli that is inhibitory to Shigella growth. S. sonnei was not recovered from cocultures grown in SB or mTSB without antibiotics. In contrast, media supplemented with streptomycin at 50 and 100 µg/mL, trimethoprim at 25 and 50 µg/mL, and sulfadiazine at 100 µg/mL increased the relative proportion of S. sonnei in postenrichment cultures. The enhanced recovery of resistant S. sonnei strains achieved in this study indicates that, in cases where genomic data are available for clinical S. sonnei isolates, customization of selective enrichment media based on AMR gene detection could be a valuable tool for supporting the investigation of foodborne shigellosis outbreaks.

Tracing the Evolutionary Pathways of Serogroup O78 Avian Pathogenic Escherichia coli

Avian pathogenic E. coli (APEC) causes severe economic losses in the poultry industry, and O78 serogroup APEC strains are prevalent in chickens. In this study, we aimed to understand the evolutionary pathways and relationships between O78 APEC and other E. coli strains. To trace these evolutionary pathways, we classified 3101 E. coli strains into 306 subgenotypes according to the numbers and types of single nucleotide polymorphisms (RST0 to RST63-1) relative to the consensus sequence (RST0) of the RNA polymerase beta subunit gene and performed network analysis. The E. coli strains showed four apparently different evolutionary pathways (I-1, I-2, I-3, and II). The thirty-two Korean O78 APEC strains tested in this study were classified into RST4-4 (45.2%), RST3-1 (32.3%), RST21-1 (12.9%), RST4-5 (3.2%), RST5-1 (3.2%), and RST12-6 (3.2%), and all RSTs except RST21-1 (I-2) may have evolved through the same evolutionary pathway (I-1). A comparative genomic study revealed the highest relatedness between O78 strains of the same RST in terms of genome sequence coverage/identity and the spacer sequences of CRISPRs. The early-appearing RST3-1 and RST4-4 prevalence among O78 APEC strains may reflect the early settlement of O78 E. coli in chickens, after which these bacteria accumulated virulence and antibiotic resistance genes to become APEC strains. The zoonotic risk of the conventional O78 APEC strains is low at present, but the appearance of genetically distinct and multiple virulence gene-bearing RST21-1 O78 APEC strains may alert us to a need to evaluate their virulence in chickens as well as their zoonotic risk.

Fast genome-based delimitation of Enterobacterales species

Average Nucleotide Identity (ANI) is becoming a standard measure for bacterial species delimitation. However, its calculation can take orders of magnitude longer than similarity estimates based on sampling of short nucleotides, compiled into so-called sketches. These estimates are widely used. However, their variable correlation with ANI has suggested that they might not be as accurate. For a where-the-rubber-meets-the-road assessment, we compared two sketching programs, mash and dashing, against ANI, in delimiting species among Esterobacterales genomes. Receiver Operating Characteristic (ROC) analysis found Area Under the Curve (AUC) values of 0.99, almost perfect species discrimination for all three measures. Subsampling to avoid over-represented species reduced these AUC values to 0.92, still highly accurate. Focused tests with ten genera, each represented by more than three species, also showed almost identical results for all methods. Shigella showed the lowest AUC values (0.68), followed by Citrobacter (0.80). All other genera, Dickeya, Enterobacter, Escherichia, Klebsiella, Pectobacterium, Proteus, Providencia and Yersinia, produced AUC values above 0.90. The species delimitation thresholds varied, with species distance ranges in a few genera overlapping the genus ranges of other genera. Mash was able to separate the E. coli + Shigella complex into 25 apparent phylogroups, four of them corresponding, roughly, to the four Shigella species represented in the data. Our results suggest that fast estimates of genome similarity are as good as ANI for species delimitation. Therefore, these estimates might suffice for covering the role of genomic similarity in bacterial taxonomy, and should increase confidence in their use for efficient bacterial identification and clustering, from epidemiological to genome-based detection of potential contaminants in farming and industry settings.

Gene flow and species boundaries of the genus Salmonella

The genus Salmonella comprises two species, Salmonella bongori and Salmonella enterica, which are infectious to a wide variety of animal hosts. The diversity within S. enterica has been further partitioned into 6-10 subspecies based on such features as host range, geography, and most recently, genetic relatedness and phylogenetic affiliation. Although Salmonella pathogenicity is attributable to large numbers of acquired virulence factors, the extent of homologous exchange in the species at large is apparently constrained such that the species and subspecies form distinct clusters of strains. To explore the extent of gene flow within and among subspecies, and to ultimately define true biological species, we evaluated patterns of recombination in over 1,000 genomes currently assigned to the genus. Those Salmonella subspecies containing sufficient numbers of sequenced genomes to allow meaningful analysis-i.e., subsp. enterica and diarizonae-were found to be reproductively isolated from one another and from all other subspecies. Based on the configuration of genomic sequence divergence among subspecies, it is expected that each of the other Salmonella subspecies will also represent a biological species. Our findings argue against the application of prescribed nucleotide-identity thresholds to delineate bacterial species and contend that the Biological Species Concept should not be disregarded for bacteria, even those, like Salmonella, that demonstrate complex patterns of species and subspecies divergence. IMPORTANCE The Biological Species Concept (BSC), which defines species boundaries based on the capacity for gene exchange, is widely used to classify sexually reproducing eukaryotes but is generally thought to be inapplicable to bacteria due to their completely asexual mode of reproduction. We show that the genus Salmonella, whose thousands of described serovars were formerly considered to be strictly clonal, undergoes sufficient levels of homologous recombination to be assigned to species according to the BSC. Aside from the two recognized species, Salmonella enterica and Salmonella bongori, several (and likely all) of the subspecies within S. enterica are reproductively isolated from one another and should each be considered a separate biological species. These findings demonstrate that species barriers in bacteria can form despite high levels of nucleotide identity and that commonly applied thresholds of genomic sequence identity are not reliable indicators of bacterial species status.

Investigating the Relationship between CRISPR-Cas Content and Growth Rate in Bacteria

CRISPR-Cas systems provide adaptive immunity for prokaryotic cells by recognizing and eliminating the recurrent genetic invaders whose sequences had been captured in a prior infection and stored in the CRISPR arrays as spacers. However, the biological/environmental factors determining the efficiency of this immune system have yet to be fully characterized. Recent studies in cultured bacteria showed that slowing the growth rate of bacterial cells could promote their acquisition of novel spacers. This study examined the relationship between the CRISPR-Cas content and the minimal doubling time across the bacteria and the archaea domains. Every completely sequenced genome could be used to predict a minimal doubling time. With a large data set of 4,142 bacterial samples, we found that the predicted minimal doubling times are positively correlated with spacer number and other parameters of the CRISPR-Cas systems, like array number, Cas gene cluster number, and Cas gene number. Different data sets gave different results. Weak results were obtained in analyzing bacterial empirical minimal doubling times and the archaea domain. Still, the conclusion of more spacers in slowly grown prokaryotes was supported. In addition, we found that the minimal doubling times are negatively correlated with the occurrence of prophages, and the spacer numbers per array are negatively associated with the number of prophages. These observations support the existence of an evolutionary trade-off between bacterial growth and adaptive defense against virulent phages. IMPORTANCE Accumulating evidence indicates that slowing the growth of cultured bacteria could stimulate their CRISPR spacer acquisition. We observed a positive correlation between CRISPR-Cas content and cell cycle duration across the bacteria domain. This observation extends the physiological conclusion to an evolutionary one. In addition, the correlation provides evidence supporting the existence of a trade-off between bacterial growth/reproduction and antiviral resistance.