Published in PLOS One on 2026-07-24, this study is presented as an attributed evidence briefing. The excerpts below are the original researchers’ words, reproduced under their Creative Commons Attribution licence. Health Signal has selected the abstract and, where needed, opening background paragraphs; the complete methods, results, limitations and references remain in the linked paper.
Original authors: Richard M Machoka, Florence Ng’ong’a, Christabel Muhonja, Heshborne Tindih, Zachary Getenga, Sören Thiele-Bruhn, Mabel Kamweli Aworh
Source: PLOS One • DOI 10.1371/journal.pone.0337311
Read the complete primary study ↗ · Creative Commons Attribution licence
From the researchers
Abstract
The excessive and often unregulated use of antibiotics in livestock production and human health has led to the dissemination of antibiotic residues and antibiotic resistance genes (ARGs) posing a serious threat to the environment and public health. This study investigates the co-occurrence and spatial distribution of antibiotic residues and ARGs in livestock manure and agricultural soils from Machakos, Kiambu, and Kajiado counties in Kenya, regions characterized by intensive livestock farming. A total of 180 animal manure and soil samples from 30 farms across the three counties were collected and pooled into 18 samples. Antibiotic residues were extracted and quantified using high-performance liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Nine ARGs (aadA, ermB, sul1, tetQ, tetW, dfrA1, blaMOX, blaOXA and qnrB were quantified via absolute and relative qPCR, normalized to 16S rRNA gene copy numbers. Multivariate analyses, including PCoA and Spearman Correlation, were conducted to explore ARG structure and co-occurrence. Tetracycline, particularly oxytetracycline, was the most abundant antibiotic in manure (up to 1150 ng mL−1), especially in pig manure from Kiambu. Sulfadimethoxine was undetectable in nearly all samples except in soil mixed with pig manure from Kajiado county, which showed a concentration above 70 ng mL−1, the pig manure from the same county had levels below 2 ng mL−1. Sulfadimidine, sulfamethoxanole and erythromycin were not detected in any of the samples. A three-way ANOVA showed that animal source (cattle, pigs, poultry) and sample type (manure, soil) were generally not significant factors for antibiotic concentration. Only oxytetracycline (P = 0.0421, 0.0901) and sulfadimethoxine (P = 0.0904, 0.044, 0.054) showed marginal significance by sample type (P = 0.0785). Antibiotic resistance genes were widely distributed, with aadA, ermB and sul1 being the most prevalent, especially in soils from Kiambu and Machakos. The tetQ showed extremely high relative abundance, indicating intense selection pressure from tetracyclines. Strong positive correlations were observed between co-occurring ARGs, including tetQ and tetW as well as erm and sul1. The concurrent detection of persistent antibiotic residues and high ARG loads in both manure and soils underscores the urgent need for improved antibiotic stewardship, sustainable manure management, and environmental monitoring in Kenyan agroecosystems.
Background
Antibiotics are commonly used in the treatment of animal and human diseases; however, excessive usage of antibiotics has led to an increase in antibiotic-resistant microbes and antibiotic-resistance genes (ARGs), which has become a threat to human and animal health [1]. Thus, the World Health Organization (WHO) has listed antimicrobial resistance among the top ten public health threats facing humanity [2]. Globally, about 700,000 deaths result from infections caused by antimicrobial-resistant pathogens annually, with more deaths occurring in Sub-Saharan Africa [3]. This number may rise to about 10 million by 2050 if urgent action is not taken [4,5].
Reading this evidence
Use the full paper to check the study design, participant selection, comparator and outcome definitions before drawing a practical conclusion. An association does not by itself show cause and effect. A reported performance measure needs its denominator and uncertainty. A finding from a particular facility, sample or time period should retain that scope when it is discussed elsewhere.
This briefing makes the source accessible within the wider public health desk. It does not assess an individual patient or certify a product. When considering relevance to another health system, examine the original authors’ account of context and limitations, then seek local implementation evidence. The related reporting below provides other studies to read alongside this one; it is a topic connection, rather than a claim that their results are directly comparable.
© 2026 Richard M Machoka, Florence Ng’ong’a, Christabel Muhonja, Heshborne Tindih, Zachary Getenga, Sören Thiele-Bruhn, Mabel Kamweli Aworh. Excerpts reproduced under CC BY. Selection, formatting and contextual notes by Health Signal. The researchers are the authors of the source study, not members of Health Signal’s staff.
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