Trends in human intestinal carriage of ESBL- and carbapenemase-producing Enterobacterales among food handlers in Tunisia: emergence of C1-M27-ST131 subclades, blaOXA-48 and blaNDM.

Abstract

To determine the prevalence of community intestinal carriage of ESBL-producing Enterobacterales (ESBL-E), acquired-AmpC-producing Enterobacterales (aAmpC-E) and carbapenemase-producing Enterobacterales (CPE) in Tunisia. From November 2012 to September 2017, stool samples from food handlers in Sfax, Tunisia, were screened for ESBL-E, AmpC-E and CPE using antibiotic-containing media. The genes encoding these β-lactamases were characterized by PCR, sequencing, and transfer assays. ST131 clonal groups were detected by PCR and characterized for antibiotic resistance, virulence genes and PFGE patterns. Of 2135 participants, ESBL-E, aAmpC-E, and CPE carriage were detected in 419 (19.63%), 35 (1.63%) and 7 (0.33%) participants, respectively. CTX-M-15 (60%), CTX-M-1 (16.8%) and CTX-M-27 (12.8%) were the most common ESBL determinants. The ESBL-E carriage was significantly higher in summer (33%) and autumn (25.7%) than in winter (12.1%) and spring (11.4%). ST131 was detected in 50 (13.2%) of the 378 ESBL-producing Escherichia coli isolates; most of them (35; 70%) belonged to subclade C1 (cluster C1-M27: 23 isolates, 46%; cluster C1-non-M27: 12 isolates, 24%) followed by those belonging to subclade C2 (11; 22%). Although subclade C2 isolates, all harbouring blaCTX-M-15, had the highest resistance rates and virulence factor and addiction system scores, the subclade C1 isolates, mainly harbouring blaCTX-M-27 (94%), were predominant since 2015. The most frequently detected carbapenemase-encoding gene was blaOXA-48-like (85%) and acquired AmpC-encoding genes were blaDHA-1 (54%) and blaCMY-2 (46%). This is the first large Tunisian study to reveal a high faecal ESBL carriage rate, a low CPE carriage rate, and the predominance of CTX-M-27-producing subclade C1 among faecal ESBL-ST131 isolates in the Tunisian community.