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Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis.

Jin D, Chen C, Li L, Lu S, Li Z, Zhou Z, Jing H, Xu Y, Du P, Wang H, Xiong Y, Zheng H, Bai X, Sun H, Wang L, Ye C, Gottschalk M, Xu J - BMC Microbiol. (2013)

Bottom Line: Eight of nine children whom three consecutive fecal samples were collected had Streptococcus as the dominant fecal bacterial genus, including three in the Streptococcus bovis group and three Streptococcus sp., which was reduced during and after recovery.We sequenced the genome of S. lutetiensis and identified five antibiotic islands, two pathogenicity islands, and five unique genomic islands.The identified virulence genes included hemolytic toxin cylZ of Streptococcus agalactiae and sortase associated with colonization of pathogenic streptococci.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.

ABSTRACT

Background: The sequences of the 16S rRNA genes extracted from fecal samples provide insights into the dynamics of fecal microflora. This potentially gives valuable etiological information for patients whose conditions have been ascribed to unknown pathogens, which cannot be accomplished using routine culture methods. We studied 33 children with diarrhea who were admitted to the Children's Hospital in Shanxi Province during 2006.

Results: Nineteen of 33 children with diarrhea could not be etiologically diagnosed by routine culture and polymerase chain reaction methods. Eleven of 19 children with diarrhea of unknown etiology had Streptococcus as the most dominant fecal bacterial genus at admission. Eight of nine children whom three consecutive fecal samples were collected had Streptococcus as the dominant fecal bacterial genus, including three in the Streptococcus bovis group and three Streptococcus sp., which was reduced during and after recovery. We isolated strains that were possibly from the S. bovis group from feces sampled at admission, which were then identified as Streptococcus lutetiensis from one child and Streptococcus gallolyticus subsp. pasteurianus from two children. We sequenced the genome of S. lutetiensis and identified five antibiotic islands, two pathogenicity islands, and five unique genomic islands. The identified virulence genes included hemolytic toxin cylZ of Streptococcus agalactiae and sortase associated with colonization of pathogenic streptococci.

Conclusions: We identified S. lutetiensis and S. gallolyticus subsp. pasteurianus from children with diarrhea of unknown etiology, and found pathogenic islands and virulence genes in the genome of S. lutetiensis.

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Phylogenetic analysis of isolated strains of the S. bovis group and other major streptococcal species based on complete 16S rRNA gene sequences. The multiple sequence alignment of 16S rRNA genes was performed using ClustalW. The conserved tree was constructed using the neighbor-joining method. Bootstrap values are shown above each branch. All 16S rRNA gene sequences were derived from the NCBI and validated using genome sequences. The strains with complete genomes are marked with a star to the right of the species name. Staphylococcus aureus subsp. aureus MRSA252 was included as an out-group. The strains in red were isolated in this study.
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Figure 3: Phylogenetic analysis of isolated strains of the S. bovis group and other major streptococcal species based on complete 16S rRNA gene sequences. The multiple sequence alignment of 16S rRNA genes was performed using ClustalW. The conserved tree was constructed using the neighbor-joining method. Bootstrap values are shown above each branch. All 16S rRNA gene sequences were derived from the NCBI and validated using genome sequences. The strains with complete genomes are marked with a star to the right of the species name. Staphylococcus aureus subsp. aureus MRSA252 was included as an out-group. The strains in red were isolated in this study.

Mentions: Patient 017 had seven isolates belonging to the S. bovis group in the feces samples collected at admission, Patient 033 had 19, and Patient 035 had 10. According to the results of the MicroScan WalkAway SI 40 system, all isolates of the S. bovis group were identified as biotype II (mannitol fermentation negative). We then amplified, cloned, and sequenced the major portion of the 16S rRNA gene from each isolate. The strains isolated from Patient 033 were identified as S. lutetiensis and those from Patients 017 and 035 were S. gallolyticus subsp. pasteurianus. A dendrogram comparing representative 16S rRNA gene sequences of the isolated S. bovis group strains with other Streptococcus species mapped our isolates within the S. bovis group (FigureĀ 3).


Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis.

Jin D, Chen C, Li L, Lu S, Li Z, Zhou Z, Jing H, Xu Y, Du P, Wang H, Xiong Y, Zheng H, Bai X, Sun H, Wang L, Ye C, Gottschalk M, Xu J - BMC Microbiol. (2013)

Phylogenetic analysis of isolated strains of the S. bovis group and other major streptococcal species based on complete 16S rRNA gene sequences. The multiple sequence alignment of 16S rRNA genes was performed using ClustalW. The conserved tree was constructed using the neighbor-joining method. Bootstrap values are shown above each branch. All 16S rRNA gene sequences were derived from the NCBI and validated using genome sequences. The strains with complete genomes are marked with a star to the right of the species name. Staphylococcus aureus subsp. aureus MRSA252 was included as an out-group. The strains in red were isolated in this study.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3716944&req=5

Figure 3: Phylogenetic analysis of isolated strains of the S. bovis group and other major streptococcal species based on complete 16S rRNA gene sequences. The multiple sequence alignment of 16S rRNA genes was performed using ClustalW. The conserved tree was constructed using the neighbor-joining method. Bootstrap values are shown above each branch. All 16S rRNA gene sequences were derived from the NCBI and validated using genome sequences. The strains with complete genomes are marked with a star to the right of the species name. Staphylococcus aureus subsp. aureus MRSA252 was included as an out-group. The strains in red were isolated in this study.
Mentions: Patient 017 had seven isolates belonging to the S. bovis group in the feces samples collected at admission, Patient 033 had 19, and Patient 035 had 10. According to the results of the MicroScan WalkAway SI 40 system, all isolates of the S. bovis group were identified as biotype II (mannitol fermentation negative). We then amplified, cloned, and sequenced the major portion of the 16S rRNA gene from each isolate. The strains isolated from Patient 033 were identified as S. lutetiensis and those from Patients 017 and 035 were S. gallolyticus subsp. pasteurianus. A dendrogram comparing representative 16S rRNA gene sequences of the isolated S. bovis group strains with other Streptococcus species mapped our isolates within the S. bovis group (FigureĀ 3).

Bottom Line: Eight of nine children whom three consecutive fecal samples were collected had Streptococcus as the dominant fecal bacterial genus, including three in the Streptococcus bovis group and three Streptococcus sp., which was reduced during and after recovery.We sequenced the genome of S. lutetiensis and identified five antibiotic islands, two pathogenicity islands, and five unique genomic islands.The identified virulence genes included hemolytic toxin cylZ of Streptococcus agalactiae and sortase associated with colonization of pathogenic streptococci.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.

ABSTRACT

Background: The sequences of the 16S rRNA genes extracted from fecal samples provide insights into the dynamics of fecal microflora. This potentially gives valuable etiological information for patients whose conditions have been ascribed to unknown pathogens, which cannot be accomplished using routine culture methods. We studied 33 children with diarrhea who were admitted to the Children's Hospital in Shanxi Province during 2006.

Results: Nineteen of 33 children with diarrhea could not be etiologically diagnosed by routine culture and polymerase chain reaction methods. Eleven of 19 children with diarrhea of unknown etiology had Streptococcus as the most dominant fecal bacterial genus at admission. Eight of nine children whom three consecutive fecal samples were collected had Streptococcus as the dominant fecal bacterial genus, including three in the Streptococcus bovis group and three Streptococcus sp., which was reduced during and after recovery. We isolated strains that were possibly from the S. bovis group from feces sampled at admission, which were then identified as Streptococcus lutetiensis from one child and Streptococcus gallolyticus subsp. pasteurianus from two children. We sequenced the genome of S. lutetiensis and identified five antibiotic islands, two pathogenicity islands, and five unique genomic islands. The identified virulence genes included hemolytic toxin cylZ of Streptococcus agalactiae and sortase associated with colonization of pathogenic streptococci.

Conclusions: We identified S. lutetiensis and S. gallolyticus subsp. pasteurianus from children with diarrhea of unknown etiology, and found pathogenic islands and virulence genes in the genome of S. lutetiensis.

Show MeSH
Related in: MedlinePlus