Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase β-subunit

Abstract

The phylogeny of enterobacterial species commonly found in clinical samples was analysed by comparing partial sequences of their elongation factor Tu gene (tuf ) and of their F-ATPase b-subunit gene (atpD). An 884 bp fragment for tuf and an 884 or 871 bp fragment for atpD were sequenced for 96 strains representing 78 species from 31 enterobacterial genera. The atpD sequence analysis exhibited an indel specific to Pantoea and Tatumella species, showing, for the first time, a tight phylogenetic affiliation between these two genera. Comprehensive tuf and atpD phylogenetic trees were constructed and are in agreement with each other. Monophyletic genera are Cedecea, Edwardsiella, Proteus, Providencia, Salmonella, Serratia, Raoultella and Yersinia. Analogous trees based on 16S rRNA gene sequences available from databases were also reconstructed. The tuf and atpD phylogenies are in agreement with the 16S rRNA gene sequence analysis, and distance comparisons revealed that the tuf and atpD genes provide better discrimination for pairs of species belonging to the family Enterobacteriaceae. In conclusion, phylogeny based on tuf and atpD conserved genes allows discrimination between species of the Enterobacteriaceae. INTRODUCTIONMembers of the family Enterobacteriaceae are facultatively anaerobic, Gram-negative rods that are catalase-positive and oxidase-negative (Brenner, 1984). They are found in soil, water and plants, and also in animals ranging from insects to humans. Many enterobacteria are opportunistic pathogens. In fact, members of this family are responsible for about 50 % of nosocomial infections in the US (Brenner, 1984). Therefore, this family is of considerable clinical importance.The major classification studies on the family Enterobacteriaceae were based on phenotypic traits (Brenner et al., , 1999Dickey & Zumoff, 1988;Farmer et al., 1980Farmer et al., , 1985a such as biochemical reactions and physiological characteristics. However, phenotypically distinct strains may be closely related by genotypic criteria and may belong to the same genospecies (Bercovier et al., 1980;Hartl & Dykhuizen, 1984). Also, phenotypically close strains (biogroups) may belong to different genospecies, like Klebsiella pneumoniae and Enterobacter aerogenes (Brenner, 1984), for example. Consequently, identification and classification of certain species may be ambiguous with techniques based on phenotypic tests (Janda et al., 1999;Kitch et al., 1994;Sharma et al., 1990).More advances in the classification of members of the family Enterobacteriaceae have come from DNA-DNA hybridization studies (Brenner et al., , 1986(Brenner et al., , 1993Farmer et al., 1980Farmer et al., , 1985aIzard et al., 1981;Steigerwalt et al., 1976). The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, tuf and atpD gene sequences obtained in this study are listed in Furthermore, the phylogenetic significance of bacterial classification based on 16S rRNA gene sequences has been recognized by many workers Wayne et al., 1987). However, members of the family En...

Molecular detection of Escherichia coli in Wadi Hanifa, Saudi Arabia

“…The ISO 9308-1 was the technique of choice for us for the subsequent detection and enumeration of coliforms and E. coli in real samples of water, in the second part of the study. Our results are in accordance with those reported by Paradis et al [18] and Afnor [19] who reported that the membrane filtration technique is the method most widely used for the enumeration of coliforms in drinking water in Europe [20], have also demonstrated that PCR methods offer a higher level of specificity detection. Nevertheless, they have major limitations when applied to natural samples, including low amplification rates linked to the presence of inhibitor substances and the lack of information on the physiological activity of cells.…”

Molecular detection of Escherichia coli in Wadi Hanifa, Saudi Arabia

“…The ISO 9308-1 was the technique of choice for us for the subsequent detection and enumeration of coliforms and E. coli in real samples of water, in the second part of the study. Our results are in accordance with those reported by Paradis et al [18] and Afnor [19] who reported that the membrane filtration technique is the method most widely used for the enumeration of coliforms in drinking water in Europe [20], have also demonstrated that PCR methods offer a higher level of specificity detection. Nevertheless, they have major limitations when applied to natural samples, including low amplification rates linked to the presence of inhibitor substances and the lack of information on the physiological activity of cells.…”

Identification of Bacteria Associated with Post-Operative Wounds of Patients with the Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Approach

“…The listed species of bacteria belong to the large Enterobacteriaceae family, and the results from the phyloproteomic tree correlate with their genetic background. This is confirmed, among other things, by the studies by Paradis et al [ 44 ]. No close relationship was found for the bacteria of the genus Staphylococcus triggered on the MH medium as they were divided into three groups based on species ( S. haemolyticus , S. aureus , and S. epidermidis ).…”

Design and testing of a PCR assay to quantify coliform bacteria in drinking water

“…This is concurrent with previous studies proposing a high level of horizontal gene transfer in the evolution of lacZ as well as the phylogeny presented here (Bej et al, 1991b(Bej et al, , 1990bFricker and Eldred, 2009;Fricker and Fricker, 1994;Horáková et al, 2006;Molina and Lowe, 2012;Zhang et al, 2015). Other studies have highlighted the same problem with other targets like tufA; gap; ompA; rpoB and infB (10,62). This emphasises false positives/negatives are a problem when analysing coliforms both in vitro or in vivo, and the group's lack of phenotypic and genotypic similarities make these only a group in terms of their ability to be cultured using specific growth media, often under stress.…”

Molecular detection of Escherichia coli in Wadi Hanifa, Saudi Arabia

“…The ISO 9308-1 was the technique of choice for us for the subsequent detection and enumeration of coliforms and E. coli in real samples of water, in the second part of the study. Our results are in accordance with those reported by Paradis et al [18] and Afnor [19] who reported that the membrane filtration technique is the method most widely used for the enumeration of coliforms in drinking water in Europe [20], have also demonstrated that PCR methods offer a higher level of specificity detection. Nevertheless, they have major limitations when applied to natural samples, including low amplification rates linked to the presence of inhibitor substances and the lack of information on the physiological activity of cells.…”

Identification of Bacteria Associated with Post-Operative Wounds of Patients with the Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Approach

“…The listed species of bacteria belong to the large Enterobacteriaceae family, and the results from the phyloproteomic tree correlate with their genetic background. This is confirmed, among other things, by the studies by Paradis et al [ 44 ]. No close relationship was found for the bacteria of the genus Staphylococcus triggered on the MH medium as they were divided into three groups based on species ( S. haemolyticus , S. aureus , and S. epidermidis ).…”

Design and testing of a PCR assay to quantify coliform bacteria in drinking water

“…This is concurrent with previous studies proposing a high level of horizontal gene transfer in the evolution of lacZ as well as the phylogeny presented here (Bej et al, 1991b(Bej et al, , 1990bFricker and Eldred, 2009;Fricker and Fricker, 1994;Horáková et al, 2006;Molina and Lowe, 2012;Zhang et al, 2015). Other studies have highlighted the same problem with other targets like tufA; gap; ompA; rpoB and infB (10,62). This emphasises false positives/negatives are a problem when analysing coliforms both in vitro or in vivo, and the group's lack of phenotypic and genotypic similarities make these only a group in terms of their ability to be cultured using specific growth media, often under stress.…”

Molecular detection of Escherichia coli in Wadi Hanifa, Saudi Arabia

“…The ISO 9308-1 was the technique of choice for us for the subsequent detection and enumeration of coliforms and E. coli in real samples of water, in the second part of the study. Our results are in accordance with those reported by Paradis et al [18] and Afnor [19] who reported that the membrane filtration technique is the method most widely used for the enumeration of coliforms in drinking water in Europe [20], have also demonstrated that PCR methods offer a higher level of specificity detection. Nevertheless, they have major limitations when applied to natural samples, including low amplification rates linked to the presence of inhibitor substances and the lack of information on the physiological activity of cells.…”

Identification of Bacteria Associated with Post-Operative Wounds of Patients with the Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Approach

“…The listed species of bacteria belong to the large Enterobacteriaceae family, and the results from the phyloproteomic tree correlate with their genetic background. This is confirmed, among other things, by the studies by Paradis et al [ 44 ]. No close relationship was found for the bacteria of the genus Staphylococcus triggered on the MH medium as they were divided into three groups based on species ( S. haemolyticus , S. aureus , and S. epidermidis ).…”

Design and testing of a PCR assay to quantify coliform bacteria in drinking water

“…This is concurrent with previous studies proposing a high level of horizontal gene transfer in the evolution of lacZ as well as the phylogeny presented here (Bej et al, 1991b(Bej et al, , 1990bFricker and Eldred, 2009;Fricker and Fricker, 1994;Horáková et al, 2006;Molina and Lowe, 2012;Zhang et al, 2015). Other studies have highlighted the same problem with other targets like tufA; gap; ompA; rpoB and infB (10,62). This emphasises false positives/negatives are a problem when analysing coliforms both in vitro or in vivo, and the group's lack of phenotypic and genotypic similarities make these only a group in terms of their ability to be cultured using specific growth media, often under stress.…”