One Health compartmental analysis of ESBL-producing Escherichia coli on Reunion Island reveals partitioning between humans and livestock

Abstract

Background: Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) is a major cause of infections worldwide. An understanding of the reservoirs and modes of transmission of these pathogens is essential, to tackle their increasing frequency.

Objectives: We investigated the contributions of various compartments (humans, animals, environment), to human colonization or infection with ESBL-Ec over a 3 year period, on an island.

Methods: The study was performed on Reunion Island (Southwest Indian Ocean). We collected ESBL-Ec isolates prospectively from humans, wastewater and livestock between April 2015 and December 2018. Human specimens were recovered from a regional surveillance system representative of the island's health facilities. These isolates were compared with those from livestock and urban/rural wastewater, by whole-genome sequencing.

Results: We collected 410 ESBL-Ec isolates: 161 from humans, 161 from wastewater and 88 from animals. Phylogenomic analysis demonstrated high diversity (100 STs), with different STs predominating among isolates from humans (ST131, ST38, ST10) and animals (ST57, ST156). The large majority (90%) of the STs, including ST131, were principally associated with a single compartment. The CTX-M-15, CTX-M-27 and CTX-M-14 enzymes were most common in humans/human wastewater, whereas CTX-M-1 predominated in animals. Isolates of human and animal origin had different plasmids carrying blaCTX-M genes, with the exception of a conserved IncI1-ST3 blaCTX-M-1 plasmid.

Conclusions: These molecular data suggest that, despite their high level of contamination, animals are not a major source of the ESBL-Ec found in humans living on this densely populated high-income island. Public health policies should therefore focus primarily on human-to-human transmission, to prevent human infections with ESBL-Ec.

Figure 1.

Map of Reunion Island, showing the locations from which the ESBL-producing E. coli-positive samples were obtained. (a) Map indicating the position of Reunion Island in the Southwest Indian Ocean. (b) Detailed map of Reunion Island showing the locations of the healthcare facilities (L, private laboratories; H, hospitals) at which the human ESBL-Ec isolates were obtained. The wastewater sampling sites are indicated by a teardrop shape; those in the north correspond to the sewage and wastewater treatment plant of Saint-Denis, the largest city on the island. The teardrop in the centre corresponds to the Camp Pierrot animal waste treatment plant in Grand Ilet. The animal symbols indicate the farms of the various livestock sectors. The symbols surrounded by a red circle represent farms with clonally related isolates, belonging to ST156, in common.

Figure 2.

Phylogenetic tree illustrating the relationship between ESBL-producing E. coli isolates from humans, animals and wastewater. Neighbour-joining phylogenetic tree of 410 ESBL-Ec based on cgMLST data. Clonally related isolates are shown in red on the dendrogram. The innermost coloured ring indicates the ecological origin of the isolates, whereas the outermost ring indicates the phylogroup. The symbols located between these two rings (round, triangle) represent the β-lactam resistance-encoding bla_BLSE genes. The main STs are represented by a specific colour on the dendrogram, as defined in the legend.

Figure 3.

Clonality network representing the healthcare facilities, farms and wastewater sources at which clonally related ESBL-producing E. coli isolates were detected. After phylogenetic analysis, each clonally related isolate was assigned to its sampling site. Farms (F), laboratories (L), hospitals (H), wastewater from sewage (WW), wastewater treatment plant (WWTP) and the animal waste treatment plant (AWTP) are symbolized by circles, whereas clonal links are indicated by the lines connecting the circles. The more clonal strains connecting two sites, the wider the line between the two sites.

Figure 4.

Bubble graph showing the proportion of bla_BLSE resistance genes common to ESBL-producing E. coli from humans and animals. Each bla_BLSE resistance gene is positioned according to its prevalence in the human and animal compartments. The size of each bubble represents the number of isolates in which the gene was identified. Bubbles are coloured according to the type of ESBL enzyme: blue for CTX-M, turquoise for SHV and purple for TEM enzymes. With the exception of the bla_TEM gene, bubbles are relatively close to the axes, with no bubble in a central position on the bisector. CTX-M Oth, bubble representing the other CTX-M variants.

Figure 5.

Dendrograms of mobile genetic elements identified for bla_CTX-M-1 and bla_CTX-M-15 genes. Strains containing bla_CTX-M-1 and bla_CTX-M-15 β-lactam resistance genes were clustered according to the presence/absence of mobile genes associated with these resistance genes. The isolate name is indicated in the first column on the left, the ecological origin of the isolate in the second column, the ST in the third and then the co-resistance genes most frequently shared by the selected isolates. We chose two triplets of isolates of interest on the basis of the inclusion of strains with the same co-resistances but from different STs. The analysis of these six isolates of interest enabled us to reconstitute the plasmids carrying these genes, which are illustrated schematically at the right of the figure. The plasmids carrying the bla_CTX-M-1 and bla_CTX-M-15 genes are represented in linear form. The resistance genes are indicated by triangles colour-coded as in the dendrogram, with β-lactam resistance genes indicated by red triangles.