1887

Journal of Medical Microbiology logo

Volume 70, Issue 11

Molecular characterization of O1 isolates obtained from outbreaks in the Philippines, 2015–2016 No Access

Abstract

The Philippines, comprising three island groups, namely, Luzon, Visayas and Mindanao, experienced an increase in cholera outbreaks in 2016. Previous studies have shown that isolates obtained from the Philippines are novel hybrid El Tor strains that have evolved in the country and are clearly distinct from those found in Mozambique and Cameroon.

The characterization of the strains isolated from outbreaks has been limited to phenotypic characteristics, such as biochemical and serological characteristics, in most previous studies.

We performed multilocus variable-number tandem repeat (VNTR) analysis (MLVA) for isolates obtained from 2015 to 2016 to further characterize and understand the emergence and dissemination of the strains in the Philippines.

A total of 139 . O1 Ogawa biotype El Tor isolates were obtained from the Philippines during diarrhoeal outbreaks in 18 provinces between 2015 and 2016. VNTR data were analysed to classify the MLVA profiles where the large-chromosome types (LCTs) were applied for grouping.

We identified 50 MLVA types among 139 isolates originating from 18 provinces, and 14 LCTs. The distribution of the LCTs was variable, and a few were located in specific areas or even in specific provinces. Based on eBURST analysis, 99 isolates with 7 LCTs and 32 MLVA types belonged to 1 group, suggesting that they were related to each other. LCT A was predominant (=67) and was isolated from Luzon and Visayas. LCT A had 14 MLVA types; however, it mostly emerged during a single quarter of a year. Eight clusters were identified, each of which involved specific MLVA type(s). The largest cluster involved 23 isolates showing 3 MLVA types, 21 of which were MLVA type A-14 isolated from Negros Occidental during quarter 4 of 2016. Comparative analysis showed that almost all isolates from the Philippines were distinct from those in other countries.

The genotypic relationship of the isolates obtained during outbreaks in the Philippines was studied, and their emergence and dissemination were elucidated. MLVA revealed the short-term dynamics of genotypes in the Philippines.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): eBURST grouping , large-chromosome types , molecular epidemiology , multilocus variable-number tandem repeat analysis , Philippines and V. cholerae O1
Funding
This study was supported by the:
  • Japan Agency for Medical Research and Development (Award JP19fm0108013)
    • Principle Award Recipient: HitoshiOshitani
  • Ministry of Health, Labour and Welfare (Award H30- Shinkogyosei -Ippan-001, 21HA1001)
    • Principle Award Recipient: HidemasaIzumiya
  • Japan Agency for Medical Research and Development (Award JP20fk0108139, JP21fk0108139)
    • Principle Award Recipient: MakotoOhnishi
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.001443
2021-11-24
2024-04-19
Loading full text...

Full text loading...

References

  1. Sack DA, Sack RB, Nair GB, Siddique A. Cholera. Lancet 2004; 363:223–233 [View Article]
     [Google Scholar]
  2. Ali M, Nelson AR, Lopez AL, Sack DA. Updated global burden of cholera in endemic countries. PLoS Negl Trop Dis 2015; 9:e0003832 [View Article]
     [Google Scholar]
  3. Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 2011; 477:462–465 [View Article]
     [Google Scholar]
  4. Domman D, Quilici M-L, Dorman MJ, Njamkepo E, Mutreja A et al. Integrated view of Vibrio cholerae in the Americas. Science 2017; 358:789–793 [View Article]
     [Google Scholar]
  5. Weill F-X, Domman D, Njamkepo E, Tarr C, Rauzier J et al. Genomic history of the seventh pandemic of cholera in Africa. Science 2017; 358:785–789 [View Article]
     [Google Scholar]
  6. Weill F-X, Domman D, Njamkepo E, Almesbahi AA, Naji M et al. Genomic insights into the 2016-2017 Yemeni cholera epidemic. Nature 2019; 565:230–233 [View Article]
     [Google Scholar]
  7. Lopez AL, Macasaet LY, Ylade M, Tayag EA, Ali M. Epidemiology of cholera in the Philippines. PLoS Negl Trop Dis 2015; 9:e3440 [View Article]
     [Google Scholar]
  8. Klinzing DC, Choi SY, Hasan NA, Matias RR, Tayag E et al. Hybrid Vibrio cholerae El Tor lacking SXT identified as the cause of a cholera outbreak in the Philippines. mBio 2015; 6:e00047-15 [View Article]
     [Google Scholar]
  9. Debes AK, Ateudjieu J, Guenou E, Lopez AL, Bugayong MP et al. Evaluation in Cameroon of a novel, simplified methodology to assist molecular microbiological analysis of V. cholerae in resource-limited settings. PLoS Negl Trop Dis 2016; 10:e0004307 [View Article]
     [Google Scholar]
  10. Lam C, Octavia S, Reeves PR, Lan R. Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae. BMC Microbiol 2012; 12:82 [View Article]
     [Google Scholar]
  11. Moore S, Miwanda B, Sadji AY, Thefenne H, Jeddi F et al. Relationship between distinct African cholera epidemics revealed via MLVA haplotyping of 337 Vibrio cholerae isolates. PLoS Negl Trop Dis 2015; 9:e0003817 [View Article]
     [Google Scholar]
  12. Danin-Poleg Y, Cohen LA, Gancz H, Broza YY, Goldshmidt H et al. Vibrio cholerae strain typing and phylogeny study based on simple sequence repeats. J Clin Microbiol 2007; 45:736–746 [View Article]
     [Google Scholar]
  13. Morita M, Ohnishi M, Arakawa E, Yamamoto S, Nair GB et al. Emergence and genetic diversity of El Tor Vibrio cholerae O1 that possess classical biotype ctxB among travel-associated cases of cholera in Japan. J Med Microbiol 2010; 59:708–712 [View Article]
     [Google Scholar]
  14. Hyytiä-Trees E, Smole SC, Fields PA, Swaminathan B, Ribot EM. Second generation subtyping: a proposed PulseNet protocol for multiple-locus variable-number tandem repeat analysis of Shiga toxin–producing Escherichia coli O157 (STEC O157). Foodborne Pathog Dis 2006; 3:118–131 [View Article]
     [Google Scholar]
  15. Nadon CA, Trees E, LK N, Møller Nielsen E, Reimer A et al. Development and application of MLVA methods as a tool for inter-laboratory surveillance. Euro Surveill 2013; 18:20565 [View Article]
     [Google Scholar]
  16. Grundmann H, Hori S, Tanner G. Determining confidence intervals when measuring genetic diversity and the discriminatory abilities of typing methods for microorganisms. J Clin Microbiol 2001; 39:4190–4192 [View Article]
     [Google Scholar]
  17. Choi SY, Lee JH, Jeon Y-S, Lee HR, Kim EJ et al. Multilocus variable-number tandem repeat analysis of Vibrio cholerae O1 El Tor strains harbouring classical toxin B. J Med Microbiol 2010; 59:763–769 [View Article]
     [Google Scholar]
  18. Nguyen DT, Ngo TC, Le TH, Nguyen HT, Morita M et al. Molecular epidemiology of Vibrio cholerae O1 in northern Vietnam (2007–2009), using multilocus variable-number tandem repeat analysis. J Med Microbiol 2016; 65:1007–1012 [View Article]
     [Google Scholar]
  19. Vogler AJ, Keys C, Nemoto Y, Colman RE, Jay Z et al. Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7. J Bacteriol 2006; 188:4253–4263 [View Article]
     [Google Scholar]
  20. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 2000; 406:477–483 [View Article]
     [Google Scholar]
  21. Hendriksen RS, Price LB, Schupp JM, Gillece JD, Kaas RS et al. Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak. mBio 2011; 2: [View Article]
     [Google Scholar]
  22. Katz LS, Petkau A, Beaulaurier J, Tyler S, Antonova ES et al. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. mBio 2013; 4: [View Article]
     [Google Scholar]
  23. Kiiru J, Mutreja A, Mohamed AA, Kimani RW, Mwituria J et al. A Study on the geophylogeny of clinical and environmental Vibrio cholerae in Kenya. PLoS One 2013; 8:e74829 [View Article]
     [Google Scholar]
  24. Abd El Ghany M, Chander J, Mutreja A, Rashid M, Hill-Cawthorne GA et al. The population structure of Vibrio cholerae from the Chandigarh region of northern India. PLoS Negl Trop Dis 2014; 8: [View Article]
     [Google Scholar]
  25. Shah MA, Mutreja A, Thomson N, Baker S, Parkhill J et al. Genomic epidemiology of Vibrio cholerae O1 associated with floods, Pakistan, 2010. Emerg Infect Dis 2014; 20:13–20 [View Article]
     [Google Scholar]
  26. Didelot X, Pang B, Zhou Z, McCann A, Ni P et al. The role of China in the global spread of the current cholera pandemic. PLOS Genet 2015; 11:e1005072 [View Article]
     [Google Scholar]
  27. Morita M, Okada K, Yamashiro T, Sekizuka T, Roobthaisong A et al. Phylogenetic analysis revealed the dissemination of closely related epidemic Vibrio cholerae O1 isolates in Laos, Thailand, and Vietnam. Open Forum Infect Dis 2020; 7: [View Article]
     [Google Scholar]
  28. Sithivong N, Morita-Ishihara T, Vongdouangchanh A, Phouthavane T, Chomlasak K et al. Molecular subtyping in cholera outbreak, Laos, 2010. Emerg Infect Dis 2011; 17:2060–2062 [View Article]
     [Google Scholar]
  29. Nguyen VH, Pham HT, Diep TT, Phan CDH, Nguyen TQ et al. Vibrio cholerae O1 El Tor from southern Vietnam in 2010 was molecularly distinct from that present from 1999 to 2004. Epidemiol Infect 2016; 144:1241–1247 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.001443
Loading
Molecular characterization of Vibrio cholerae O1 isolates obtained from outbreaks in the Philippines, 2015–2016
J. Med. Microbiol. 70, 001443 (2021); https://doi.org/10.1099/jmm.0.001443
/content/journal/jmm/10.1099/jmm.0.001443
/content/journal/jmm/10.1099/jmm.0.001443
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error