THE GENUS SHIGELLA: (Dysentery Bacilli and Allied Species)

Impact of insertion sequences on convergent evolution of Shigella species

Shigella species are specialised lineages of Escherichia coli that have converged to become human-adapted and cause dysentery by invading human gut epithelial cells. Most studies of Shigella evolution have been restricted to comparisons of single representatives of each species; and population genomic studies of individual Shigella species have focused on genomic variation caused by single nucleotide variants and ignored the contribution of insertion sequences (IS) which are highly prevalent in Shigella genomes. Here, we investigate the distribution and evolutionary dynamics of IS within populations of Shigella dysenteriae Sd1, Shigella sonnei and Shigella flexneri. We find that five IS (IS1, IS2, IS4, IS600 and IS911) have undergone expansion in all Shigella species, creating substantial strain-to-strain variation within each population and contributing to convergent patterns of functional gene loss within and between species. We find that IS expansion and genome degradation are most advanced in S. dysenteriae and least advanced in S. sonnei; and using genome-scale models of metabolism we show that Shigella species display convergent loss of core E. coli metabolic capabilities, with S. sonnei and S. flexneri following a similar trajectory of metabolic streamlining to that of S. dysenteriae. This study highlights the importance of IS to the evolution of Shigella and provides a framework for the investigation of IS dynamics and metabolic reduction in other bacterial species.

Classification, identification, and clinical significance of Proteus, Providencia, and Morganella

This review presents the current taxonomy of the genera Proteus, Providencia, and Morganella, along with the current methods for the identification of each species within the three genera, incorporating both conventional biochemical and commercial methods. While all of these organisms are ubiquitous in the environment, individual case reports and nosocomial outbreak reports that demonstrate their ability to cause major infectious disease problems are presented. Lastly, anticipated antimicrobial susceptibility patterns are reviewed. Many of these organisms are easily controlled, but the advent of newer and more powerful antimicrobial agents has led to some problems of which laboratorians need to be aware.

Classification, identification, and clinical significance of Proteus, Providencia, and Morganella

This review presents the current taxonomy of the genera Proteus, Providencia, and Morganella, along with the current methods for the identification of each species within the three genera, incorporating both conventional biochemical and commercial methods. While all of these organisms are ubiquitous in the environment, individual case reports and nosocomial outbreak reports that demonstrate their ability to cause major infectious disease problems are presented. Lastly, anticipated antimicrobial susceptibility patterns are reviewed. Many of these organisms are easily controlled, but the advent of newer and more powerful antimicrobial agents has led to some problems of which laboratorians need to be aware.

Typing methods for Proteus rettgeri: comparison of biotype, antibiograms, serotype, and bacteriocin production

Two hunderd five strains of Proteus rettgeri from epidemic and nonepidemic sources were differentiated by a new biotyping scheme, agglutination in O antisera, antimicrobial resistance patterns, and a new scheme based on bacteriocin production. The P. rettgeri were divided into 10 groups by their fermentation of lactose, sucrose, D-mannitol, and salicin. These groups were then subdivided into 19 biotypes by other biochemical reactions. Bacteriocin production was tested by the cross-streak method. Thirty-four bacteriocin-sensitive indicator strains were evaluated, and 16 were selected for the final scheme and used to type the 205 P. rettgeri, which were divided into 15 bacteriocin types. Serologically, 43% of the P. rettgeri were O42, 13% were untypable, 4% were O15, and 3% each were O33, O64, and O84 in addition to 31 remaining serotypes. Strains of P. rettgeri from known outbreaks contained fewer biotypes, O groups, and bacteriocin types and were more resistant to antimicrobial agents than endemic strains. Strains with common patterns with all four marker systems were frequently associated with outbreaks. A strong correlation between multiple antibiotic resistance and bacteriocin production was shown.

Biotypes of Proteus rettgeri

Examination of 729 isolates of Proteus rettgeri showed that 674 reacted positively in tests for phenylalanine deamination, indole production, growth on citrate, and acid production from meso-inositol, and negatively for L-ornithine decarboxylation and acid production from lactose, maltose, D-xylose, and L-arabinose. Only 51 isolates differed in one, and four differed in two of these ten reactions, which were taken as the core characteristics of the species. On the basis of additional tests (acid production from salicin, L-rhamnose, D-mannitol, adonitol, and D-arabitol), the 729 isolates could be separated into five groups. Goups 1, 2, 3, and 4 could be further separated on the basis of the reaction with meso-erythritol, and group 5 could be subdivided on the basis of reaction with D-mannitol. Two metabolically distinct kinds of P. rettgeri were recognized. Isolates of the first kind (groups 1, 2, 3, and 4) each utilized both adonitol and D-arabitol and most utilized meso-erythritol. Isolates of the other kind (group 5) were negative with the three polyhydric alcohols but resembled, in their reactions, some strains of Providencia stuartii. These may be intermediates between P. rettgeri that catabolize these substrates and the Providencia.