Irenge et al (2020): Genomic analysis of pathogenic isolates of Vibrio cholerae from easter Democratic Republic of the Congo (2014-2017)

I have been reading the paper by Irenge et al (2020): "Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017)". 

Epidemiology

In this paper, they carried out whole genome sequencing of 78 clinical isolates of V. cholerae associated cholera in eastern DRC between 2014 and 2017. They found that most isolates (73/78) were V. cholerae O1 biotype El Tor with CTX-3 type prophage, and belonged to current pandemic lineage (7PET lineage). Furthermore, they belonged to the T10 sublineage of 7PET found in East Africa, and comprised two sub-clades corresponding to MLST sequence types ST69 and ST515. The isolates had the a large deletion in the VSP-II genomic island; this deletion had previously been seen in several East African isolates.

 Antimicrobial resistance

All V. cholerae isolates displayed resistance in laboratory tests to trimethoprim-sulfamethoxazole and nalidixic acid. Nine V. cholerae O1 isolates displayed decreased susceptibility to ciprofloxacin, whereas 9 O1 and 2 non-O1 isolates were resistant to ampicillin. 

From genome sequencing, they found that all DRC 01 isolates had the SXT/R391 integrative conjugative element ICEVchBan5. Another very interesting finding was that while V. cholerae in Yemen with mutations gyrA(S83I) and parC(S85L) had decreased susceptibility to ciprofloxacin in laboratory tests, relatively few DRC isolates with this combination of mutations showed decreased susceptibility to ciprofloxacin.