Characterization of Carbapenem-resistant Enterobacterales in Nairobi River, Wastewater Treatment Plant, and Slaughterhouse Discharge in Nairobi County, Kenya

Abstract

Carbapenemase-producing Enterobacterales (CPE) present a significant global public health concern. CPE have been identified in humans, hospital environments, as well as communities. Sub-Saharan Africa bears a heavy burden of CPE with several studies reporting a prevalence of up to 60% in clinical isolates. Most studies on epidemiology of CPE have focused on clinical samples, with limited data on CPE in wastewater, their spread, and their potential clinical relevance. The purpose of this study was to characterize CPE in untreated water from the upstream, downstream 100 meters after final effluent, and way downstream of Nairobi River, the wastewater treatment plant, a slaughterhouse in Dagoretti, and the affluent neighbourhood of Karen in Nairobi County, Kenya. This was a longitudinal study in which wastewater was filtered through membrane filters of 0.45μm to capture bacteria. Swiffer samples from animal contact areas were also collected from slaughterhouse. The membrane filters and swiffer samples were then placed on whirl-pak bags containing MacConkey (MAC) broth modified with 0.5 μg/mL meropenem and 70 μg/mL of ZnSO4 and incubated overnight at 37°C. Up to four morphologically distinct colonies were tested for carbapenemase production using the Carba-NP test and identified using the Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS). The presence of blaNDM, blaOXA, blaVIM, blaGES, blaIMP, and blaKPC carbapenemase-encoding genes were examined by conventional PCR. Molecular characteristics of carbapenem-resistant isolates were further investigated by whole-genome sequencing (WGS) using Illumina Miseq2000 platforms to identify multidrug-resistant strains circulating in different environmental sampling locations. A total of 336 CRE were recovered from 336 (250 mL) wastewater and swiffer samples, with 230 of the samples (68.4%) producing one or more CRE. CRE were recovered most commonly from untreated sewage influent 10.7%, (36/336), treated effluent 29.8%, (100/336), fecal samples of livestock grazing at the WWTP 0.9%,.........................................