Weill et al (2019): Genomic insights into the 2016-2017 cholera epidemic in Yemen

 I have been reading the paper by Weill et al (2019): "Genomic insights into the 2016-2017 cholera epidemic in Yemen".

In this paper, the authors (which include my group leader Nick Thomson) sequenced the genomes of 42 isolates from 2016-2017 from the Yemen cholera epidemic, as well as 74 additional isolates from South Asia, the Middle East, and Eastern and Central Africa (116 isolates sequenced in total). 

Epidemiology

They showed that the Yemeni isolates belonged to a single sublineage of the current pandemic lineage (7PET lineage), and that this sublineage, named "T13", had originated in South Asia and caused outbreaks in East Africa (e.g. Kenya, Tanzania, Uganda) in 2015-2016 before appearing in Yemen. They point out that prior to the Yemen epidemic, there were large cholera outbreaks across the Horn of Afria, which serves as a major hub of migration into Yemen.

 The Yemeni isolates were different from those that had been previously circulating in the Middle East, such as those from Iraq in 2007 and 2015, and from Iran in 2012 and 2015. Those previous isolates were independently imported from South Asia on two separate occasions. 

Antibiotic resistance

The Yemeni isolates had a narrow lab. phenotype of antimicrobial drug resistance to nalidixic acid, the vibriostatic agent O/129 and nitrofurantoin. Resistance to O/129 is due to the gene dfrA1, which is part of an integratic conjugative element ICEVchInd5/ICEVchBan5 in the Yemeni isolates.

The authors found that the Yemeni isolates were susceptible to polymyxin B, resistance to which is used as a marker of the El Tor biotype (which is a common phenotype in the 7PET lineage).

Cholera toxin subtype

The Yemeni isolates had the cholera toxin subunit B gene variant ctxB7. The ctxB7 allele was first detected in India in 2006, and has been exported outside Asia on three separate occasions: to West Africa in 2008 ("T12 sublineage"), Haiti in 2010, and East Africa around 2013-2014 ("T13 sublineage").

Pathogenwatch

I have added a "collection" of the genomes sequenced by Weill et al to Pathogenwatch, which you can see here (116 genomes).