LETTERSwas the same genome type as and was highly homologouswith the H5N6 virus in Laos. The findings in this study arealso supported by the previous genetic characterization ofthese viruses by Wong et al. (11). However, the adaptation,host range, and virulence of this reassortant H5N6 virus arestill unclear and should be further investigated. Furthermore,the potential for infection, outbreaks, and pandemic in otherpoultry and mammals should be carefully monitored.This work was supported by the National Modern AgriculturalIndustry Technology System Project of China (CARS-41) andby the Technology Planning Project of Guangdong Province ofChina (grant nos. 2012B020306002 and 2012B091100078).References1. Chen H, Deng G, Li Z, Tian G, Li Y, Jiao P, et al. The evolutionof H5N1 influenza viruses in ducks in southern China. Proc NatlAcad Sci U S A. 2004;101:10452–7. http://dx.doi.org/10.1073/pnas.04032121012. García M, Suarez DL, Crawford JM, Latimer JW, Slemons RD,Swayne DE, et al. Evolution of H5 subtype avian influenza Aviruses in North America. Virus Res. 1997;51:115–24.http://dx.doi.org/10.1016/S0168-1702(97)00087-73. Zhao K, Gu M, Zhong L, Duan Z, Zhang Y, Zhu Y, et al.Characterization of three H5N5 and one H5N8 highly pathogenicavian influenza viruses in China. Vet Microbiol. 2013;163:351–7.http://dx.doi.org/10.1016/j.vetmic.2012.12.0254. Zhao G, Gu X, Lu X, Pan J, Duan Z, Zhao K, et al. Novelreassortant highly pathogenic H5N2 avian influenza viruses inpoultry in China. PLoS ONE. 2012;7:e46183. http://dx.doi.org/10.1371/journal.pone.00461835. Hoffmann E, Stech J, Guan Y, Webster RG, Perez DR.Universal primer set for the full-length amplification of allinfluenza A viruses. Arch Virol. 2001;146:2275–89.http://dx.doi.org/10.1007/s0070501700026. Gu M, Zhao G, Zhao K, Zhong L, Huang J, Wan H, et al.Novel variants of clade 2.3.4 highly pathogenic avian influenzaA(H5N1) viruses, China. Emerg Infect Dis. 2013;19:2021–4.http://dx.doi.org/10.3201/eid1912.1303407. Liu Z, Xu B, Chen Q, Chen Z. Complete genome sequence of amixed-subtype (H5N1 and H6N6) avian influenza virusisolated from a duck in Hunan Province, China. Genome Announc.2014;2:e00310-4. http://dx.doi.org/10.1128/genomeA.00310-148. Steinhauer DA. Role of hemagglutinin cleavage for thepathogenicity of influenza virus. Virology. 1999;258:1–20.http://dx.doi.org/10.1006/viro.1999.97169. Stevens J, Blixt O, Tumpey TM, Taubenberger JK, Paulson JC,Wilson IA. Structure and receptor specificity of the hemagglutininfrom an H5N1 influenza virus. Science. 2006;312:404–10.http://dx.doi.org/10.1126/science.112451310. Li Z, Chen H, Jiao P, Deng G, Tian G, Li Y, et al. Molecularbasis of replication of duck H5N1 influenza viruses in amammalian mouse model. J Virol. 2005;79:12058–64.http://dx.doi.org/10.1128/JVI.79.18.12058-12064.200511. Wong FYK, Phommachanh P, Kalpravidh W, Chanthavisouk C,Gilbert J, Bingham J, et al. Reassortant highly pathogenic influenzaA(H5N6) virus in Laos. Emerg Infect Dis. 2015;21:511–6.http://dx.doi.org/10.3201/eid2103.141488Address for correspondence: Qingmei Xie, College of Animal Science,South China Agricultural University, 483 Wushan St, Guangzhou510642, China; email: qmx@scau.edu.cnCharacterization of3 Megabase-SizedCircular Replicons fromVibrio choleraeKazuhisa Okada, Wirongrong Natakuathung,Mathukorn Na-Ubol, Amonrattana Roobthaisong,Warawan Wongboot, Fumito Maruyama,Ichiro Nakagawa, Siriporn Chantaroj,Shigeyuki HamadaAuthor affiliations: Thailand–Japan Research CollaborationCenter on Emerging and Re-emerging Infections, Nonthaburi,Thailand (K. Okada, W. Natakuathung, M. Na-Ubol,A. Roobthaisong, W. Wongboot, S. Hamada); Osaka University,Osaka, Japan (K. Okada, S. Hamada); Tokyo Medical andDental University, Tokyo, Japan (F. Maruyama, I. Nakagawa);National Institute of Health, Nonthaburi (S. Chantaroj)DOI: http://dx.doi.org/10.3201/eid2107.141055To the Editor: Prokaryotes typically have a single circularchromosome. However, some bacteria have >1 chromosome.Vibrio bacteria, for example, have 2 circular chromosomes:1 (Ch1) and 2 (Ch2) (1–3). Most recognizablegenes responsible for essential cell functions and pathogenicityare located on Ch1. Ch2 is also thought to encodesome genes essential for normal cell function and thoseassociated with virulence. Both chromosomes are controlledcoordinately in their replication and segregation (4).Evidence suggests that Ch2 was originally a mega-plasmidcaptured by an ancestral Vibrio species (2,5). We report thecharacterization of recent isolates of V. cholerae O1 fromThailand that carry a novel gigantic replicon (Rep.3) in additionto Ch1 and Ch2.Cholera outbreaks occurred in Tak Province, Thailand,during March–December 2010. We obtained 118 isolates ofV. cholerae O1 and subjected their NotI digests to pulsedfieldgel electrophoresis (PFGE), which differentiated theisolates into 8 different patterns (6). The profile of PFGE typeA6 was identical to that of PFGE type A4, except that a largeDNA band existed in type A6. The PFGE profile of the intact(undigested) DNA of the type A6 isolates exhibited a uniquegenome structure consisting of 3 large replicons (Figure,http://wwwnc.cdc.gov/EID/article/21/7/14-1055-F1.htm).Three isolates of PFGE type A6 (TSY216, TSY241,and TSY421) were obtained during June 3–July 5, 2010,from 3 unrelated residents of a village near the Thailand–Myanmar border. The isolates were classified as multilocusvariable-number tandem-repeat analysis type 16, suggestingthat they are of clonal origin (6). Next, we performedwhole-genome sequencing of TSY216, as a representativeof PFGE type A6 isolates, by using the GS FLX Titanium1262 Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 21, No. 7, July 2015
LETTERSsystem (8 kb–span paired-end library; Roche, Indianapolis,IN, USA). Using Newbler <strong>version</strong> 2.6, the Roche 454GS De Novo Assembler software (454 Life Sciences,Branford, CT, USA), we assembled 424,273 reads into 3large scaffolds comprising 119 contigs at 18.3-fold coverage.The gaps between contigs were closed by PCR, andthe PCR products were then sequenced. Illumina sequencedata (Illumina, Inc., San Diego, CA, USA) were used toimprove low-quality regions. The whole-genome sequenceof TSY216 was completed and deposited in GenBank (accessionnos. CP007653–55).Full-genome sequencing revealed that V. choleraeO1 El Tor TSY216 consists of 3 circular replicons, Ch1(3,053,204 bp), Ch2 (1,051,284 bp), and Rep.3 (896,006 bp),with an average G+C content of 47.7%, 47.0%, and 37.3%,respectively. In total, 4,579 coding sequences were detectedand annotated by using the National Center for BiotechnologyInformation Prokaryotic Genome Annotation Pipeline(http://www.ncbi.nlm.nih.gov/genome/annotation_prok/).The whole-genome comparison between 2010EL-1786(an outbreak isolate from Haiti) (7) and TSY216 revealedthat Ch1 and Ch2 shared nearly identical gene content andshowed conserved synteny, but integrative and conjugativeelements were distinguishable. Strain TSY216 carriesCTX-3, whereas strain 2010EL-1786 possesses CTX-3b.These CTXs represent wave 3 of the seventh cholera pandemic(8). Rep.3 of TSY216 did not share a conserved regionwith Ch1 and Ch2. Thus, this replicon may have beengained fairly recently through horizontal gene transfer fromunknown organisms.Rep.3 encodes 999 coding sequences and 66 transferRNAs, among which 39 have been assigned putative functionsand 960 encode hypothetical proteins and proteins ofunknown function. The origin of the replicon could not betraced from the coding sequences in the public databases.Of note, Rep.3 encodes a specific transfer RNA for eachamino acid, for a total of 20 amino acids. In addition, Rep.3carries 2 genes encoding the histone-like nucleoid-structuringprotein. In this regard, a 165-kb plasmid, pSf-R27, inShigella flexneri encodes a histone-like nucleoid-structuringprotein that was claimed to be a transcriptional repressorof the plasmid (9). Rep.3 may have a stealth strategysimilar to that of pSf-R27.We assessed the stability of the Rep.3 of the 3 A6 isolates.In total, 96 colonies for the 3 isolates were subculturedeach day for 30 consecutive days. Then, using PCRand PFGE, we determined whether Rep.3 remained in the96 subcultures. The Rep.3-specific primer set (Rep3hns-F: 5′-TTCAATGCGTCCAGCGTTGC-3′ and Rep3hns-R:5′-TCGCACCTCTATCAATAGCC-3′) for PCR was designedfor detection of the histone-like nucleoid-structuringprotein gene encoded on the third replicon. All subculturesmaintained Rep.3 in an unchanged state. However, whenthe organisms were cultured at 42°C, ≈70% of the subcultureslost Rep.3. The growth rates of the organisms withand without Rep.3 showed no substantial difference whenthe organisms were cultured in Luria-Bertani mediumat 37°C.The appearance of V. cholerae O1 variants with additionalcircular replicons may contribute to evolution of thebacteria in unexpected manners. Clones from the seventhcholera pandemic, which began in 1961, share nearly identicalgene content (8,10). However, some clones, such asTSY216, can gain a replicon of megabase class and maintainit stably. Eventually, epidemic V. cholerae O1 may gainthe ability to incorporate genes that change properties suchas antigenicity or pathogenicity. The function of Rep.3 remainsunder investigation.References1. Kolstø AB. Time for a fresh look at the bacterial chromosome.Trends Microbiol. 1999;7:223–6. http://dx.doi.org/10.1016/S0966-842X(99)01519-X2. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML,Dodson RJ, et al. DNA sequence of both chromosomes of thecholera pathogen Vibrio cholerae. Nature. 2000;406:477–83.http://dx.doi.org/10.1038/350200003. Yamaichi Y, Iida T, Park KS, Yamamoto K, Honda T. Physical andgenetic map of the genome of Vibrio parahaemolyticus: presenceof two chromosomes in Vibrio species. Mol Microbiol. 1999;31:1513–21. http://dx.doi.org/10.1046/j.1365-2958.1999.01296.x4. Yamaichi Y, Gerding MA, Davis BM, Waldor MK. Regulatorycross-talk links Vibrio cholerae chromosome II replication andsegregation. PLoS Genet. 2011;7:e1002189. http://dx.doi.org/10.1371/journal.pgen.10021895. Okada K, Iida T, Kita-Tsukamoto K, Honda T. Vibrios commonlypossess two chromosomes. J Bacteriol. 2005;187:752–7.http://dx.doi.org/10.1128/JB.187.2.752-757.20056. Okada K, Roobthaisong A, Nakagawa I, Hamada S, Chantaroj S.Genotypic and PFGE/MLVA analyses of Vibrio cholerae O1:geographical spread and temporal changes during the 2007–2010cholera outbreaks in Thailand. PLoS ONE. 2012;7:e30863.http://dx.doi.org/10.1371/journal.pone.00308637. Reimer AR, Van Domselaar G, Stroika S, Walker M, Kent H, TarrC, et al. Comparative genomics of Vibrio cholerae from Haiti,Asia, and Africa. Emerg Infect Dis. 2011;17:2113–21. http://dx.doi.org/10.3201/eid1711.1107948. Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH,Kariuki S, et al. Evidence for several waves of global transmissionin the seventh cholera pandemic. Nature. 2011;477:462–5.http://dx.doi.org/10.1038/nature103929. Doyle M, Fookes M, Ivens A, Mangan MW, Wain J, Dorman CJ.An H-NS-like stealth protein aids horizontal DNA transmission inbacteria. Science. 2007;315:251–2. http://dx.doi.org/10.1126/science.113755010. Chun J, Grim CJ, Hasan NA, Lee JH, Choi SY, Haley BJ, et al.Comparative genomics reveals mechanism for short-term andlong-term clonal transitions in pandemic Vibrio cholerae. ProcNatl Acad Sci U S A. 2009;106:15442–7. http://dx.doi.org/10.1073/pnas.0907787106Address for correspondence: Kazuhisa Okada, Thailand-JapanRCC-ERI, DMSc, Ministry of Public Health, Tiwanon Rd, Muang,Nonthaburi 11000, Thailand; email: kazuhisa@biken.osaka-u.ac.jpEmerging Infectious Diseases • www.cdc.gov/eid • Vol. 21, No. 7, July 2015 1263
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1240 Gastroenteritis OutbreaksCause
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