Extended-Spectrum Cephalosporin- and Colistin-Resistant E. coli in Tanzania: High Prevalence of Gut Colonization in Healthy People and Chicken Meat Contamination

Abstract

Background: Contamination of the food chain with extended-spectrum cephalosporin- (ESC-R) and colistin-resistant (COL-R) E. coli (Ec) may favor intestinal colonization of people in the community. Most surveys conducted to study this overall phenomenon have been performed in Europe/USA, while data from low-/middle-income countries are scarce. Here, we evaluated the prevalence of ESC-/COL-R-Ec in chicken meat and intestinal tract of healthy people in Zanzibar (Tanzania). Methods: The stools of 59 volunteers and 37 meat samples were collected during June-July 2018 and screened. Samples 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, rep-PCR, and Illumina WGS (interpreted using ResFinder, PlasmidFinder and MLST). Results: The overall gut colonization prevalence with ESC-R-Ec, COL-R-Ec, and mcr-1-positive Ec were 74.6%, 33.9%, and 18.6%, respectively. In total, we detected 49 ESC-R-Ec (3 also COL-R) and 17 non-ESC-R but COL-R-Ec. In particular, ESC-R-Ec carried CTX-M-15-like (51%), CTX-M-1-like (34.7%), CTX-M-9-like (14.3%) ESBLs and mcr-1 (2%), while 62.5% of non-ESC-R but COL-R-Ec carried mcr-1. The prevalence of meat samples contaminated with ESC-R-Ec and COL-R-Ec were 40.5% and 18.9%, respectively. In total, 17 ESC-R-Ec (none COL-R) and 7 non-ESC-R but COL-R-Ec were detected. In particular, ESC-R-Ec carried CTX-M-15-like (62.5%), CTX-M-32-, CTX-M-1-, or CTX-M-9-like (12.5% each), while all non-ESC-R but COL-R-Ec carried mcr-1. Preliminary analyses using rep-PCR and WGS indicate that ESC-R-Ec from both humans and meat mostly belong to heterogeneous clones and STs. In contrast, most mcr-1-positive Ec strains isolated from volunteers and meat belong to a unique clone. Conclusions: The prevalence of ESC-/COL-R-Ec colonizing the gut of healthy people in Tanzania is extremely high. This represents a tremendous challenge for the local health care system regarding the treatment of infections. More intriguingly is the finding that the same mcr-1-positive Ec found among people in community was also causing chicken meat contamination. Therefore, the food chain-human interface will be further investigated to understand the exchange dynamics of these life-threatening pathogens. Moreover, local animals and international travelers will be also examined.