Nguyen Anna T, Ratnasiri Kalani, Barratt Heitmann Gabriella, Tazin Sumaiya, Anderson Claire, Hanif Suhi, Yeamin Afsana, Shoab Abul Kasham, Shanta Ireen Sultana, Jahan Farjana, Hossain Md Sakib, Mahmud Zahid Hayat, Jubair Mohammad, Rahman Mustafizur, Rahman Mahbubur, Ercumen Ayse, Benjamin-Chung Jade
Department of Epidemiology & Population Health, Stanford University, Stanford, California, USA.
Stanford Immunology Program, Stanford University School of Medicine, Stanford, California, USA.
Appl Environ Microbiol. 2025 Jun 18;91(6):e0066925. doi: 10.1128/aem.00669-25. Epub 2025 May 27.
In low- and middle-income countries, living in homes with soil floors and animal cohabitation may expose children to fecal organisms, increasing the risk of enteric and antimicrobial-resistant infections. Our objective was to understand whether cow cohabitation in homes with soil floors in rural Bangladesh contributed to the presence and diversity of potential pathogens and antimicrobial resistance genes (ARGs) in the home. In 10 randomly selected households in rural Sirajganj District, we sampled floor soil and cow dung, which is commonly used as sealant in soil floors. We extracted DNA and performed shotgun metagenomic sequencing to explore potential pathogens and ARGs in each sample type. We detected 7 potential pathogens in soil only, 38 pathogens in cow dung only, and 182 pathogens in both soil and cow dung. Cow dung exhibited modestly higher potential pathogen genus richness compared to soil floors (Wilcoxon signed-rank test, = 0.002). Using Bray-Curtis dissimilarity, potential pathogen species community composition differed between floors and cow dung (permutational multivariate analysis of variance, < 0.001). All soil floor and cow dung samples contained ARGs; detected ARGs confer resistance to antibiotic classes including sulfonamides, rifamycin, aminoglycosides, lincosamides, and tetracycline. Paired floor and cow dung samples shared ARGs against rifamycin and glycopeptides, but otherwise, there was little overlap in resistomes between sample types. Our findings contribute to the growing literature on household soil and domestic animals as potentially important contributors to disease transmission and as reservoirs of antimicrobial resistance in low-income country settings.IMPORTANCEIn low-income countries, inadequate housing materials and animal cohabitation can lead to fecal contamination of rural homes. Contaminated soil floors are difficult to clean and may harbor organisms causing illness and antibiotic resistance, especially in young children, who frequently ingest soil. We sequenced soil floor and cow dung samples from households in Sirajganj district, Bangladesh, and identified potential pathogens and antibiotic resistance genes. We detected 182 potential pathogens in both soil and cow dung; organisms present in both sample types at the highest relative abundances were , , and . Antibiotic resistance genes were found in all samples. In cow dung, the most common genes conferred resistance to the antibiotics lincosamide, rifamycin, cephamycin, tetracycline, and multiple antibiotics. In soil floors, the most common genes conferred resistance to rifamycin, sulfonamides, and multiple antibiotics. Household soil and cow dung may be important reservoirs of pathogens and antimicrobial resistance in low-income country settings with high levels of animal cohabitation compared to settings with finished household floors and minimal animal cohabitation.
在低收入和中等收入国家，生活在泥土地面的房屋中且与动物共同居住可能会使儿童接触到粪便中的微生物，从而增加肠道感染和抗微生物药物耐药性感染的风险。我们的目标是了解在孟加拉国农村泥土地面的房屋中与牛共同居住是否会导致家中潜在病原体和抗微生物药物耐药基因（ARGs）的存在及多样性。在锡拉杰甘杰区农村随机选取的10户家庭中，我们采集了地面土壤和牛粪样本，牛粪通常用作泥土地面的密封剂。我们提取了DNA并进行鸟枪法宏基因组测序，以探究每种样本类型中的潜在病原体和ARGs。我们仅在土壤中检测到7种潜在病原体，仅在牛粪中检测到38种病原体，在土壤和牛粪中均检测到182种病原体。与泥土地面相比，牛粪中潜在病原体属的丰富度略高（Wilcoxon符号秩检验，P = 0.002）。使用Bray-Curtis差异法，泥土地面和牛粪中潜在病原体物种群落组成不同（置换多变量方差分析，P < 0.001）。所有泥土地面和牛粪样本均含有ARGs；检测到的ARGs对包括磺胺类、利福霉素、氨基糖苷类、林可酰胺类和四环素类等抗生素类别具有耐药性。配对的地面和牛粪样本共享对利福霉素和糖肽类的ARGs，但除此之外，不同样本类型的耐药组之间几乎没有重叠。我们的研究结果为关于家庭土壤和家畜作为低收入国家环境中疾病传播的潜在重要促成因素以及抗微生物药物耐药性储存库的文献不断增加做出了贡献。
重要性
在低收入国家，住房材料不足和与动物共同居住会导致农村家庭受到粪便污染。受污染的泥土地面难以清洁，可能藏有致病微生物和抗生素耐药菌，尤其是在经常摄入土壤的幼儿中。我们对孟加拉国锡拉杰甘杰区家庭的泥土地面和牛粪样本进行了测序，确定了潜在病原体和抗生素耐药基因。我们在土壤和牛粪中均检测到182种潜在病原体；在两种样本类型中相对丰度最高的微生物是大肠杆菌、肺炎克雷伯菌和粪肠球菌。在所有样本中均发现了抗生素耐药基因。在牛粪中，最常见的基因对林可酰胺类、利福霉素、头孢霉素、四环素类和多种抗生素具有耐药性。在泥土地面中，最常见的基因对利福霉素、磺胺类和多种抗生素具有耐药性。与家庭地面完善且动物共同居住极少的环境相比，在动物共同居住程度高的低收入国家环境中，家庭土壤和牛粪可能是病原体和抗微生物药物耐药性的重要储存库。
