Highly Resistant Cholera Outbreak Strain in Zimbabwe

To the Editor:

From September 4, 2018, to March 12, 2019, Zimbabwe experienced a large cholera outbreak, with 10,730 suspected cases of cholera and 69 deaths (Fig. S1 in the Supplementary Appendix, available with the full text of this letter at NEJM.org). Antimicrobial-susceptibility data that were available for 65.0% of the confirmed cases (241 of 371 cases) showed that the Vibrio cholerae O1 serotype Ogawa isolates were multidrug-resistant, with an unexpectedly high-level resistance to ciprofloxacin (96.7% [233 of 241 cases]) and ceftriaxone (99.6% [240 of 241 cases]). We sequenced the whole genomes of 13 V. cholerae O1 isolates — including 10 that had been obtained during the cholera outbreak in Zimbabwe, 1 that had been obtained from a South African patient who had a history of travel to Zimbabwe, and 2 that had been obtained in Zimbabwe in 2015 (Table S1 and Fig. S1) — to investigate the determinants of antimicrobial resistance as well as the phylogenetic relationships of the isolates to 1200 global seventh pandemic V. cholerae El Tor (7PET) genomes.^1,2 Details of the methods are provided in the Supplementary Appendix.

Figure 1. Figure 1. Phylogenetic Relatedness of the Vibrio cholerae O1 El Tor Isolates from the 2018–2019 Outbreak in Zimbabwe.

Panel A shows the phylogenetic analysis of 1213 seventh pandemic V. cholerae El Tor (7PET) genomic sequences according to maximum likelihood. A6 was used as an outgroup (i.e., a more distantly related group serving as a reference). The scale bar indicates substitutions per variable site. Branches are colored according to geographic location, which was inferred by stochastic mapping of the geographic origin of each isolate onto the tree. The inferred introduction events into Africa are indicated by the letter “T.” One branch was artificially shortened (hash mark). Panel B shows the maximum clade credibility tree produced with the use of BEAST (Bayesian Evolutionary Analysis Sampling Trees) software for a subset of 92 representative isolates of the distal part of genomic wave 3 (i.e., those with the ctxB7 allele). The geographic locations of the isolates are indicated in the same colors as in Panel A. Selected nodes that were supported by bootstrap values of at least 0.95 are shown. Acquisition of the IncA/C2 multidrug-resistant plasmid is indicated by the arrow. Panel C indicates the geographic distribution of selected 7PET sublineages T10 through T13. Date ranges shown for the introductions are the 95% credible interval estimate of the most recent common ancestor in years. The curved arrows and dashed lines with arrows do not represent the routes of transmission precisely.

Genomic analyses showed that the 11 isolates obtained during the 2018 cholera outbreak in Zimbabwe belonged to sublineage T13 of the 7PET lineage (Figure 1A and 1B and Table S2). Sublineage T13 was recently introduced from South Asia into East Africa and from there to Yemen (Figure 1B and 1C).² The T13 isolates were previously shown to have a narrow antimicrobial-resistance pattern, mostly owing to an approximate 10-kb deletion in the SXT/R391 genomic island (called ICEVchInd5), which resulted in the loss of four antimicrobial-resistance genes.² However, the 2018 Zimbabwean outbreak isolates differed from previous T13 isolates by having 14 additional antimicrobial-resistance genes carried on an approximately 160-kb IncA/C2 plasmid, leading to a broader resistance profile (Fig. S2 and Tables S3 and S4). In particular, the isolates were intermediately resistant or resistant to tetracycline (presence of the tet[A] gene) and ciprofloxacin (mutations of the gyrA and parC genes and presence of the aac[6′]-Ib-cr gene) and produced the extended-spectrum beta-lactamase CTX-M-15.

Antibiotic agents such as tetracyclines, macrolides, and fluoroquinolones are commonly used in the treatment of moderate-to-severe cases of cholera, as an adjunct to rehydration therapy, in order to shorten the duration and volume of diarrhea and thereby limit bacterial transmission.³ However, beta-lactams are not commonly used in this context. Resistance to extended-spectrum cephalosporins is uncommon in 7PET isolates, and only extended-spectrum cephalosporin–resistant 7PET isolates from sporadic or small-outbreak cases had been observed in Africa before 2018.¹ It is noteworthy that a large typhoid outbreak (>3000 suspected cases) that was caused by a ciprofloxacin-resistant strain — and that led to the use of extended-spectrum cephalosporins — occurred in Harare, Zimbabwe, between October 2017 and February 2018.^4,5 This situation might have contributed to the extended-spectrum cephalosporin–resistant patterns that were seen among the cholera outbreak strain several months later.

The 2018 Zimbabwean isolates were susceptible to azithromycin, which was consequently used to treat severe cases of cholera during the outbreak. However, azithromycin-resistance genes, such as mph(A) or mph(E), were sporadically identified in CTX-M-15–producing 7PET isolates obtained in Zimbabwe (Table S4), the Democratic Republic of Congo,¹ and Kenya² from 2010 through 2015. The acquisition by this T13 7PET strain of an IncA/C2 plasmid with both the mph and tet genes would jeopardize the oral antibiotic treatment of cholera.

We emphasize the need for cross-border collaboration and continued laboratory surveillance to stem this highly drug-resistant T13 cholera strain in Africa.

Tapfumanei Mashe, M.Sc.
Ministry of Health and Child Care, Harare, Zimbabwe

Daryl Domman, Ph.D.
University of New Mexico Health Sciences Center, Albuquerque, NM

Andrew Tarupiwa, M.Sc.
Portia Manangazira, M.D., M.P.H.
Isaac Phiri, M.D., M.P.H.
Ministry of Health and Child Care, Harare, Zimbabwe

Kudzai Masunda, M.D., M.P.H.
Prosper Chonzi, M.D., M.P.H.
Beatrice Road Infectious Diseases Hospital, Harare, Zimbabwe

Elisabeth Njamkepo, Ph.D.
Institut Pasteur, Paris, France

Masindi Ramudzulu, B.Sc.
National Institute for Communicable Diseases, Johannesburg, South Africa

Sekesai Mtapuri-Zinyowera, Ph.D.
Ministry of Health and Child Care, Harare, Zimbabwe

Anthony M. Smith, Ph.D.
National Institute for Communicable Diseases, Johannesburg, South Africa

François-Xavier Weill, M.D., Ph.D.
Institut Pasteur, Paris, France
[email protected]