File Download
  Links for fulltext
     (May Require Subscription)
Supplementary

Article: Development of a multi-locus sequence typing scheme for Laribacter hongkongensis, a novel bacterium associated with freshwater fish-borne gastroenteritis and traveler's diarrhea

TitleDevelopment of a multi-locus sequence typing scheme for Laribacter hongkongensis, a novel bacterium associated with freshwater fish-borne gastroenteritis and traveler's diarrhea
Authors
Issue Date2009
PublisherBioMed Central Ltd.
Citation
BMC Microbiology, 2009, v. 9, article no. 21 How to Cite?
AbstractBACKGROUND: Laribacter hongkongensis is a newly discovered, facultative anaerobic, Gram-negative, motile, sea gull-shaped rod associated with freshwater fish borne gastroenteritis and traveler's diarrhea. A highly reproducible and discriminative typing system is essential for better understanding of the epidemiology of L. hongkongensis. In this study, a multilocus sequence typing (MLST) system was developed for L. hongkongensis. The system was used to characterize 146 L. hongkongensis isolates, including 39 from humans and 107 from fish. RESULTS: Fragments (362 to 504 bp) of seven housekeeping genes were amplified and sequenced. Among the 3068 bp of the seven loci, 332 polymorphic sites were observed. The median number of alleles at each locus was 34 [range 22 (ilvC) to 45 (thiC)]. All seven genes showed very low d(n)/d(s) ratios of < 0.04, indicating that no strong positive selective pressure is present. A total of 97 different sequence types (STs) were assigned to the 146 isolates, with 80 STs identified only once. The overall discriminatory power was 0.9861. eBURST grouped the isolates into 12 lineages, with six groups containing only isolates from fish and three groups only isolates from humans. Standardized index of association (I(S)(A)) measurement showed significant linkage disequilibrium in isolates from both humans and fish. The I(S)(A) for the isolates from humans and fish were 0.270 and 0.636, indicating the isolates from fish were more clonal than the isolates from humans. Only one interconnected network (acnB) was detected in the split graphs. The P-value (P = 0) of sum of the squares of condensed fragments in Sawyer's test showed evidence of intragenic recombination in the rho, acnB and thiC loci, but the P-value (P = 1) of maximum condensed fragment in these gene loci did not show evidence of intragenic recombination. Congruence analysis showed that all the pairwise comparisons of the 7 MLST loci were incongruent, indicating that recombination played a substantial role in the evolution of L. hongkongensis. A website for L. hongkongensis MLST was set up and can be accessed at http://mlstdb.hku.hk:14206/MLST_index.html. CONCLUSION: A highly reproducible and discriminative MLST system was developed for L. hongkongensis.
Persistent Identifierhttp://hdl.handle.net/10722/59396
ISSN
2015 Impact Factor: 2.581
2015 SCImago Journal Rankings: 1.391
PubMed Central ID
ISI Accession Number ID
Funding AgencyGrant Number
Control of Infectious Diseases of the Health
Welfare and Food Bureau of the Hong Kong SAR Government
Research Grant Council
HKU Special Research Achievement Award
Croucher Senior Medical Research Fellowship, The University of Hong Kong
Funding Information:

This work was partly supported by the Research Fund for the Control of Infectious Diseases of the Health, Welfare and Food Bureau of the Hong Kong SAR Government and Research Grant Council Grant, University Development Fund, Outstanding Young Researcher Award, HKU Special Research Achievement Award and The Croucher Senior Medical Research Fellowship, The University of Hong Kong.

References

 

DC FieldValueLanguage
dc.contributor.authorWoo, PCYen_HK
dc.contributor.authorTeng, JLLen_HK
dc.contributor.authorTsang, AKLen_HK
dc.contributor.authorTse, Hen_HK
dc.contributor.authorTsang, VYMen_HK
dc.contributor.authorChan, KMen_HK
dc.contributor.authorLee, EKYen_HK
dc.contributor.authorChan, JKHen_HK
dc.contributor.authorMa, SSLen_HK
dc.contributor.authorTam, DMWen_HK
dc.contributor.authorChung, LMWen_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2010-05-31T03:49:15Z-
dc.date.available2010-05-31T03:49:15Z-
dc.date.issued2009en_HK
dc.identifier.citationBMC Microbiology, 2009, v. 9, article no. 21en_HK
dc.identifier.issn1471-2180en_HK
dc.identifier.urihttp://hdl.handle.net/10722/59396-
dc.description.abstractBACKGROUND: Laribacter hongkongensis is a newly discovered, facultative anaerobic, Gram-negative, motile, sea gull-shaped rod associated with freshwater fish borne gastroenteritis and traveler's diarrhea. A highly reproducible and discriminative typing system is essential for better understanding of the epidemiology of L. hongkongensis. In this study, a multilocus sequence typing (MLST) system was developed for L. hongkongensis. The system was used to characterize 146 L. hongkongensis isolates, including 39 from humans and 107 from fish. RESULTS: Fragments (362 to 504 bp) of seven housekeeping genes were amplified and sequenced. Among the 3068 bp of the seven loci, 332 polymorphic sites were observed. The median number of alleles at each locus was 34 [range 22 (ilvC) to 45 (thiC)]. All seven genes showed very low d(n)/d(s) ratios of < 0.04, indicating that no strong positive selective pressure is present. A total of 97 different sequence types (STs) were assigned to the 146 isolates, with 80 STs identified only once. The overall discriminatory power was 0.9861. eBURST grouped the isolates into 12 lineages, with six groups containing only isolates from fish and three groups only isolates from humans. Standardized index of association (I(S)(A)) measurement showed significant linkage disequilibrium in isolates from both humans and fish. The I(S)(A) for the isolates from humans and fish were 0.270 and 0.636, indicating the isolates from fish were more clonal than the isolates from humans. Only one interconnected network (acnB) was detected in the split graphs. The P-value (P = 0) of sum of the squares of condensed fragments in Sawyer's test showed evidence of intragenic recombination in the rho, acnB and thiC loci, but the P-value (P = 1) of maximum condensed fragment in these gene loci did not show evidence of intragenic recombination. Congruence analysis showed that all the pairwise comparisons of the 7 MLST loci were incongruent, indicating that recombination played a substantial role in the evolution of L. hongkongensis. A website for L. hongkongensis MLST was set up and can be accessed at http://mlstdb.hku.hk:14206/MLST_index.html. CONCLUSION: A highly reproducible and discriminative MLST system was developed for L. hongkongensis.en_HK
dc.languageengen_HK
dc.publisherBioMed Central Ltd.en_HK
dc.relation.ispartofBMC Microbiologyen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong Licenseen_HK
dc.subject.meshBacterial Proteins - genetics-
dc.subject.meshDiarrhea - microbiology-
dc.subject.meshFish Diseases - microbiology-
dc.subject.meshGastroenteritis - microbiology-
dc.subject.meshNeisseriaceae - classification - genetics - isolation and purification-
dc.titleDevelopment of a multi-locus sequence typing scheme for Laribacter hongkongensis, a novel bacterium associated with freshwater fish-borne gastroenteritis and traveler's diarrheaen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1471-2180&volume=9&spage=21&epage=&date=2009&atitle=Development+of+a+multi-locus+sequence+typing+scheme+for+Laribacter+hongkongensis,+a+novel+bacterium+associated+with+freshwater+fish-borne+gastroenteritis+and+traveler%27s+diarrheaen_HK
dc.identifier.emailWoo, PCY: pcywoo@hkucc.hku.hken_HK
dc.identifier.emailTeng, JLL: llteng@hku.hken_HK
dc.identifier.emailTsang, AKL: h0365593@hku.hken_HK
dc.identifier.emailTse, H: htse@hkucc.hku.hken_HK
dc.identifier.emailTsang, VYM: h0294402@hku.hken_HK
dc.identifier.emailChan, KM: kmanchan@hku.hk-
dc.identifier.emailLee, EKY: ekylee02@hotmail.com-
dc.identifier.emailChan, JKH: jimchan8@hku.hk-
dc.identifier.emailMa, SSL: slmhku@graduate.hku.hk-
dc.identifier.emailTam, DMW: dmwtam@graduate.hku.hk-
dc.identifier.emailChung, LMW: lilt28@gmail.com-
dc.identifier.emailLau, SKP: skplau@hkucc.hku.hk-
dc.identifier.emailYuen, KY: kyyuen@hkucc.hku.hk, hkumicro@hkucc.hku.hk-
dc.identifier.authorityWoo, PCY=rp00430en_HK
dc.identifier.authorityTeng, JLL=rp00277en_HK
dc.identifier.authorityTse, H=rp00519en_HK
dc.identifier.authorityLau, SKP=rp00486en_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/1471-2180-9-21en_HK
dc.identifier.pmid19178751-
dc.identifier.pmcidPMC2644701-
dc.identifier.scopuseid_2-s2.0-60649108647en_HK
dc.identifier.hkuros160602en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-60649108647&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume9, article no. 21en_HK
dc.identifier.isiWOS:000264159000001-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridChung, LMW=15847898900en_HK
dc.identifier.scopusauthoridTam, DMW=7006053712en_HK
dc.identifier.scopusauthoridMa, SSL=26424668200en_HK
dc.identifier.scopusauthoridChan, JKH=35236330300en_HK
dc.identifier.scopusauthoridLee, EKY=37030374300en_HK
dc.identifier.scopusauthoridChan, KM=26324790600en_HK
dc.identifier.scopusauthoridTsang, VYM=35914196600en_HK
dc.identifier.scopusauthoridTse, H=7006070596en_HK
dc.identifier.scopusauthoridTsang, AKL=7006979247en_HK
dc.identifier.scopusauthoridTeng, JLL=7202560229en_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK
dc.identifier.citeulike3982334-

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats