Taxonomy of the Family Enterobacteriaceae

The Changing Face of the Family Enterobacteriaceae (Order: "Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes

The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.

Evaluation of the Complex Nomenclature of the Clinically and Veterinary Significant Pathogen Salmonella

Salmonella encompasses a vast and highly related population of clinically and veterinary significant pathogens. The genus is responsible for an array of diseases such as typhoid fever and salmonellosis (a variety of illnesses including gastroenteritis), which cause public health issues globally. Even with the global recognition of Salmonella as a significant human and veterinary pathogen, the highly complex and evolving nomenclature system of Salmonella is problematic for clinicians, veterinarians, and microbiologists to comprehend. The present paper offers a review of the ever developing nomenclature for this bacterial species.

'Nissabacter archeti' gen. nov., sp. nov., a new member of Enterobacteriaceae family, isolated from human sample at Archet 2 Hospital, Nice, France

We propose the main characteristics of a new bacterium species named Nissabacter archeti strain 2134 (CSURP3445 = LT631518), isolated from pustule scalp of a 29-year-old man at hospital Archet 2, Nice, south of France.

Evolution of Salmonella nomenclature: a critical note

Salmonellae are widely distributed but nomenclaturally controversial pathogens of both humans and animals. Despite elaborate studies, much still remain to be discovered about these organisms. Although Salmonella nomenclature has proved to be rather complex, in 2005, Salmonella enterica finally gained official approval as the type species of the genus Salmonella. In addition, one other species has been approved and recognised in the genus Salmonella, namely, Salmonella bongori. New serovars (serotypes) are continually being discovered each year and reported in the journal Research in Microbiology. Salmonella serovars and their antigenic formulae are listed in the White-Kauffmann-Le Minor scheme and updated by the World Health Organization's Collaborating Centre for Reference and Research on Salmonella at the Pasteur Institute, Paris, France.

The genus Hafnia: from soup to nuts

The genus Hafnia, a member of the family Enterobacteriaceae, consists of gram-negative bacteria that are occasionally implicated in both intestinal and extraintestinal infections in humans. Despite the fact that the genus currently contains only a single species (H. alvei), more extensive phylogenetic depth (two or more species) is apparent based upon DNA relatedness and 16S rRNA gene sequencing studies. Hafnia causes a variety of systemic infections, including septicemia and pneumonia; however, its role as a gastrointestinal pathogen is controversial. Many of the data supporting a role for hafniae as enteric pathogens were incorrectly attributed to this genus rather than to the actual pathogen, Escherichia albertii. There are numerous gaps in our understanding of this genus, including ecologic habitats and population genetics, disease-producing role in animals, phenetic and genetic methods useful in distinguishing genomospecies within the H. alvei complex, and bona fide pathogenicity factors.

Re-speciation of the original reference strains of serovars in the Citrobacter freundii (Bethesda-Ballerup group) antigenic scheme of West and edwards

The antigenic scheme for the Bethesda-Ballerup group of bacteria established by West and Edwards in 1954 has continued to be applied as a serotyping scheme for Citrobacter freundii. In 1993, however, the classification of the Citrobacter was drastically revised and the species C. freundii redefined by Brenner et al. Accordingly, to judge the propriety to continuously use a single antigenic scheme for the C. freundii complex, the 90 reference strains listed in the antigenic scheme for C. freundii by West and Edwards were characterized phenotypically and specified based on the revised classification. Of these 90 strains, two strains of Hafnia alvei and one of Escherichia coli were found. Among the remaining 87 reference strains, Citrobacter youngae was the predominant species (40 strains), followed by Citrobacter braakii (25 strains), Citrobacter werkmanii (13 strains), and the unnamed Citrobacter genospecies 10 of Brenner et al (six strains). Citrobacter freundii, as redefined, accounted for only three strains and ranked behind the other four species. No overlapping with most of the 42 O-groups and 82 H-antigens was recognized between species with few exceptions. O-groups 1-9 inclusive, which were estimated to represent more than 90% of the former C.freundii strains, occurred in strains of C. youngae and C. braakii; and all nine strains of O-group 29, formerly known as the Ballerup group, were identified as C. braakii. These findings suggest that further study of the serotyping system is needed for all H2S-producing Citrobacter species.

Deoxyribonucleic acid restriction and modification systems in Salmonella: chromosomally located systems of different serotypes

With the use of four different phages, Salmonella strains representing 85 different serotypes were examined to determine their restriction-modification phenotype. They fell into one of three groups on this basis: group 1, those which lacked the common LT system; group 2, those in which only the LT system could be recognized; and group 3. those which possessed the LT system and at least one other system shown with some serotypes to be closely linked to serB. The specificity of the serB-linked restriction-modification system was unique for each serotype, but different strains of the same serotype expressed the same specificity. Two of the systems were shown to behave in genetic crosses as functional alleles of the S. typhimurium SB system. It is possible that these serB-linked restriction-modification systems constitute a large multiallelic series of genes extending throughout the Salmonella genus and Escherichia coli. We suggest that the division of the Salmonella into the three restriction-modification groups may be significant in defining a "biological grouping" of the different serotypes within the genus which may ultimately be useful in describing the Salmonella species. From the genetic relatedness between the genes of some of the Salmonella restriction-modification systems with those of the E. coli systems, we deduce that the restriction endonuclases produced by the Salmonella serB-linked systems are of type 1. Determination of the nucleotide sequences of the recognition sites of the restriction endonucleases of selected Salmonella systems should further our understanding of specificity with these enzymes.

Comparison of media for isolation of salmonellae and shigellae from fecal specimens

Five transport media, eight plating media, and three enrichment broth media for the isolation of salmonellae and shigellae were evaluated. Eight laboratories in widely separated regions of the United States participated in this evaluation by submitting 490 fecal specimens in the transport media provided. The results suggest that the newer transport media may not offer any advantage over the use of buffered glycerol-saline in the isolation of these enteric pathogens. Shigellae were best isolated by direct inoculation, whereas salmonellae were isolated in greater numbers after tetrathionate (without Brilliant Green) enrichment with subsequent culturing on the plating medium. The use of a variety of plating media is recommended for the recovery of a larger number of these enteric pathogens.

Salmonella enteritidis serotype 50-1,2,3: Z4, Z24:-

Characteristics of a new Salmonella serotype, subgenus IV, are reported. Culture 5534-68 was recovered from the intestinal tract of Anolis biporcatus, an arboreal lizard found in deep forest tracts in Panama Province, Republic of Panama. The antigenic composition of this new serotype was found to be 50(1, 2, 3):z(4), z(24):-.

Undescribed serotype of Salmonella: Salmonella enteritidis ser. Lovelace

A new serotype of Salmonella is described. Culture 1505-68, serotype 13,22,36:l, v:1,5, was recovered from the stool of a female patient and designated Salmonella enteritidis ser. Lovelace.

New Salmonella serotype: Salmonella enteritidis ser. Ordonez

The antigenic formula of a new serotype, Salmonella enteritidis serotype Ordonez, was characterized as (1),13,23,37:y:l,w.

Two additional Salmonella serotypes. Salmonella enteritidis ser 58:a:- and Salmonella enteritidis ser 44:z36, z38:-

The antigenic compositions of two additional Salmonella serotypes isolated from the feces of man were determined to be 58:a:- and 44:Z(36), Z(38)-.

COLIFORM BACTERIA IN SEA WATER AND SHELLFISH: I. LACTOSE FERMENTATION AT 35.5° AND 44 °C

Of 6452 coliform strains isolated from sea water and shellfish specimens by membrane filtration (MF) and Violet Red Bile (VRB) agar techniques, 4728 (73.3 per cent) fermented lactose with the production of acid and gas within 48 hours at 35.5 °C; these cultures were incubated in Eijkman medium, in a water-bath at 44 °C, for 48 hours. Gas-positive tests were recorded for 94.6 per cent of Escherichia coli type I strains and 37.7 per cent of E. coli type II strains; 6.7 per cent of the "non-faecal" strains (represented by 10 coliform biotypes) were also gas-positive at 44 °C. The capacity of selected strains to ferment lactose at higher temperatures (44.5° to 46.0 °C) was also studied.A total of 1724 (26.7 per cent) of the cultures produced completely typical coliform colonies on MF membranes or VRB agar plates but were incapable of rapid lactose fermentation at 35.5 °C on subsequent isolation. Aerobacter biotypes were predominant (77 per cent), and 47.4 per cent of the cultures liquefied gelatin. The probable effect of lactose-degraded coliform bacteria on coliform density estimates made by the MF technique is discussed.

The serological classification of Bacteriaceae

1. Four different Bacteriaceae possessing the same Vi antigen showed, after exposure to heat, striking differences in the physico-chemical behaviour of the Vi antigen. The most noticeable differences observed were those in the changes in Vi-agglutinability and O-inagglutinability of the bacteria; lesser differences were noted in the agglutinogenic activity of the Vi antigen, and none in its agglutinin-binding capacity.

2. Treatment with alcohol altered the TVi antigen of one of the species (Bact. coli5396/38) in a way different from that seen in the other three species.

3. On the other hand, dilute acid or alkali produced the same chemical changes in the TVi antigen of all four Bacteriaceae.

4. The TVi antigen present in the four Bacteriaceae appears to be one and the same substance; it cannot be differentiated by the customary serological methods. Its different physico-chemical state after exposure to heat or alcohol is, therefore, conditioned by other constituents of the bacterial cell, which may, or may not, be antigenic.

5. The simultaneous O- and Vi-inagglutinability resulting from heating at 75° C. is particularly impressive since it does not appear to be specially related to any one of the known antigenic components.

6. These findings invalidate the basis on which the L, A and B antigens ofBact. colihave been differentiated.

7. There is also no valid reason for designating the labile somatic antigens ofSalmonellaand other Bacteriaceae as K antigens. These antigens have the general characters of the Vi antigen ofSalm. typhi, are demonstrated by methods developed in the study of the typhoid Vi antigen, and are not associated with typical capsules.

8. The M (mucoid) antigens ofSalmonellaand ofBact. coliare in many respects different from the Vi antigens and should be classified separately.

I gratefully acknowledge the valuable technical assistance received from Mr F. J. Flynn throughout the work reported in this and the preceding papers of this series.