Rethinking Manure Application: Increase in Multidrug-Resistant Enterococcus spp. in Agricultural Soil Following Chicken Litter Application

Abstract

The current study investigated the impact of chicken litter application on the abundance of multidrug-resistant Enterococcus spp. in agricultural soil. Soil samples were collected from five different strategic places on a sugarcane farm before and after manure application for four months. Chicken litter samples were also collected. Enterococci were enumerated using the Enterolert®/Quanti-Tray 2000® system and confirm and differentiated into species using real-time PCR. The antibiotic susceptibility profile of the isolates was determined using the disk diffusion method following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The overall mean bacterial count was significantly higher (p < 0.05) in manure-amended soil (3.87 × 107 MPN/g) than unamended soil (2.89 × 107 MPN/g). Eight hundred and thirty-five enterococci (680 from soil and 155 from litter) were isolated, with E. casseliflavus being the most prevalent species (469; 56.2%) and E. gallinarum being the least (16; 1.2%). Approximately 56% of all the isolates were resistant to at least one antibiotic tested, with the highest resistance observed against tetracycline (33%) and the lowest against chloramphenicol (0.1%); 17% of E. faecium were resistant to quinupristin-dalfopristin. Additionally, 27.9% (130/466) of the isolates were multidrug-resistant, with litter-amended soil harbouring more multidrug-resistant (MDR) isolates (67.7%; 88/130) than unamended soil (10.0%; 13/130). All isolates were susceptible to tigecycline, linezolid and gentamicin. About 7% of the isolates had a multiple antimicrobial resistance index > 0.2, indicative of high antibiotic exposure. Although organic fertilizers are regarded as eco-friendly compared to chemical fertilizers for improving soil fertility, the application of untreated animal manure could promote the accumulation of antibiotics and their residues and antibiotic-resistant bacteria in the soil, creating an environmental reservoir of antimicrobial resistance, with potential human and environmental health risks.

Transmission of Antibiotic-Resistant Escherichia coli from Chicken Litter to Agricultural Soil

“…Additionally, Chen and others (2016b) observed a significant increase in the bacterial diversity and the abundance of tetracyclines genes in the soil following manure amendment in China. Fatoba et al (2021) also observed an increase in MDR Enterococcus spp. in agricultural soil following chicken litter application.…”

“…This study was carried out on a sugarcane field located in uMshwathi Local Municipality in uMgungundlovu District, KwaZulu-Natal, South Africa, fertilized with chicken litter. The study site and its surroundings have previously been described (Fatoba et al, 2021). The sample collection was carried out for one hundred and 16 days (October 2018 to February 2019).…”

“…However, several studies have reported on the relatively shorter duration of survival of E. coli in the environment compared with other organisms (Sengeløv et al, 2003a;Bolton et al, 2011;Abia et al, 2015b). In addition, a previous study showed that Enterococcus could be found in litter amended soils up to 105 days following manure application (Fatoba et al, 2021). Therefore, this study investigated the potential transmission of antibiotic-resistant E. coli from chicken litter to agricultural soil and sought to determine how long E. coli could be detected in litter amended soil following chicken litter application.…”

“…A growing concern about the application of untreated animal manure to agricultural soil is the possibility of contamination with pathogenic ARB and antibiotic resistance genes (ARGs), as animal manure is considered a significant reservoir of both enteric and pathogenic ARB and ARGs (Robins-Browne, 2005;Johnson et al, 2016). Previous studies that investigated the impact of animal manure on soil resistome demonstrated that fertilisation with animal manure resulted in the appearance or increased level and diversity of ARB and ARGs in soils (Jensen et al, 2013;Chen et al, 2016b;Fatoba et al, 2021;Sun et al, 2021). Jensen et al (2013) reported the appearance of E. coli in soil after the application of animal slurry to three Danish agricultural fields.…”

Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles

“…This is of concern, considering a recent study that detected E. faecium and E. faecalis in soil after litter amendment. Considering this data, we recommend targeting E. faecalis (especially vancomycin-resistant strains) in routine monitoring and source tracking experiments that evaluate transmission between BL, the environment and humans, through exposure to contaminated soil or consumption of poorly washed crops from manure fertilized farms [73] . While most of the identified staphylococci are not pathogenic, low abundances of the opportunistic pathogen S. aureus (an etiological agent of arthritis and gangrenous dermatitis in chickens and foodborne gastroenteritis in humans) were detected in the BL stockpile, especially at the later sampling times.…”