High prevalence of gut colonization with extended-spectrum cephalosporin- and colistin-resistant Enterobacteriaceae in healthy people in Zanzibar, Tanzania

Büdel, Thomas; Kuenzli, Esther; Clément, Mathieu; Bernasconi, Odette Joëlle; Fehr, Jan; Mohammed, Ali Haji; Hassan, Nadir Khatib; Zinsstag, Jakob; Hatz, Christoph; Endimiani, Andrea (14 April 2019). High prevalence of gut colonization with extended-spectrum cephalosporin- and colistin-resistant Enterobacteriaceae in healthy people in Zanzibar, Tanzania (Unpublished). In: 29th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID). Amsterdam. 13-16 April, 2019.

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Background: Intestinal colonization with extended-spectrum cephalosporin- (ESC-R) and colistin-resistant (COL-R) Enterobacteriaceae (Ent) contributes to the spread of these pathogens. Most surveys conducted to study this phenomenon in the community have been performed in Europe/USA, while data from low-/middle-income countries are scarce. Here, we evaluated the prevalence of ESC-/COL-R-Ent gut colonization in healthy people in Zanzibar and characterized the strains.
Material/methods: During June-July 2018, 59 volunteers were enrolled. Rectal swabs were enriched in LB broth with cefuroxime or COL and plated on ChromID ESBL/Carba and CHROMagar Orientation plus COL. Species ID was achieved using the MALDI-TOF MS. Microdilution plates were implemented for ASTs. Strains were characterized with: CT103XL microarray, multiplex PCRs for mcr-1/-5 genes, rep-PCR, and Illumina WGS (interpreted using ResFinder, PlasmidFinder and MLST).
Results: The overall colonization prevalence with ESC-R-Ent, COL-R-Ent, and mcr-1-positive E. coli were 91.5%, 66.1%, and 18.6%, respectively (on average 1.85 resistant clones for each volunteer). In total, we detected 49 ESC-R-E. coli (4 also COL-R), 32 ESC-R-K. pneumoniae (1 also COL-R), 16 non-ESC-R but COL-R-E. coli, and 21 non-ESC-R but COL-R-K. pneumoniae. No carbapenemase producers were detected. The following main resistance mechanisms were found: ESC-R-E. coli (ESBLs CTX-M-15-like, 51%; CTX-M-1-like, 34.7%; CTX-M-9-like, 14.3%; 2% carried mcr-1), ESC-R-K. pneumoniae (CTX-M-9-like, 46.9%; CTX-M-15-like, 28.1%; DHA pAmpC, 15.6%; none carried mcr genes), non-ESC-R but COL-R-E. coli (62.5% carried mcr-1), non-ESC-R but COL-R-K. pneumoniae (none carried mcr genes). Preliminary analyses using rep-PCR and WGS indicate that both ESC-R-E. coli and -K. pneumoniae strains mostly belong to heterogeneous clones and STs, whereas mcr-1-positive E. coli isolates belong to a unique clone.
Conclusions: Our results emphasize that the prevalence of ESC-/COL-R-Ent colonizing the gut of healthy people in Tanzania is extremely high. For the local health system this high resistance rates pose a tremendous challenge regarding the treatment of infections due to Enterobacteriaceae. Therefore, research in the ecology of ESC-/COL-R-Ent in the local environment and in livestock production is warranted. Furthermore, as Zanzibar is a frequent holiday destination, attention should be paid to the risk of international travelers becoming colonized and thereby spreading these life-threatening pathogens in their low prevalence countries.

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