Whole Genome Sequence Analysis Reveals Lower Diversity and Frequency of Acquired Antimicrobial Resistance (AMR) Genes in E. coli From Dairy Herds Compared With Human Isolates From the Same Region of Central Zambia
Whole Genome Sequence Analysis Reveals Lower Diversity and Frequency of Acquired Antimicrobial Resistance (AMR) Genes in E. coli From Dairy Herds Compared With Human Isolates From the Same Region of Central Zambia
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DOI：
10.3389/fmicb.2019.01114
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发表时间：
2019-05-31
影响因子：
5.2
通讯作者：
Gally, David L.
中科院分区：
文献类型：
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作者：
Mainda, Geoffrey;Lupolova, Nadejda;Gally, David L.
对患病奶牛进行抗生素治疗对于该生产系统的可持续性至关重要，而这对于许多低收入和中等收入国家的粮食安全和社会繁荣至关重要。鉴于全球范围内抗生素耐药性水平日益升高，以及这给细菌感染治疗带来的挑战，本着“同一个健康”方法的精神，强烈建议人类和动物合理使用抗生素。本研究的目的是从赞比亚中部的奶牛和人类患者中分离出的大肠杆菌的全基因组序列中表征抗菌素耐药性 (AMR) 基因及其频率。对来自奶牛 (n = 224) 和当地医院患者 (n = 73) 的大肠杆菌分离株的全基因组序列进行了比较，以确定是否存在获得性 AMR 基因。此外，我们还分析了来自更广泛的非洲大陆的 317 种人类大肠杆菌分离株的公开基因组。两种获得性抗生素抗性基因和系统群都是从从头组装中鉴定出来的，并且使用基于 SNP 的系统发育分析来可视化来自两个宿主的大肠杆菌分离株中抗性基因的分布。与跨多类抗生素的牛大肠杆菌分离株相比，在人类中检测到了更大的获得性 AMR 基因多样性，并且仅在人类来源的大肠杆菌基因组中检测到了超广谱 β 内酰胺酶 (ESBL)、喹诺酮类、大环内酯类和磷霉素的特定抗性基因。显着的差异是，与赞比亚奶牛分离株相比，赞比亚或更广泛的非洲人类分离株更可能拥有多个获得性 AMR 基因。赞比亚牛队列中的抗性基因中位数为 0（四分位距为 0-1），而赞比亚人和更广泛的非洲队列中的中位数和四分位距分别为 6（4-9）和 6（0-8）。奶牛分离株中获得性 AMR 基因的频率较低且多样性降低，这与我们在该地区（尤其是小农户）记录的相对有限的抗生素使用相一致。两个宿主群体中相对不同的抗性特征也表明菌株或基因的共享有限。
Antibiotic treatment of sick dairy cattle is critical for the sustainability of this production system which is vital for food security and societal prosperity in many low and middle-income countries. Given the increasingly high levels of antibiotic resistance worldwide and the challenge this presents for the treatment of bacterial infections, the rational use of antibiotics in humans and animals has been emphatically recommended in the spirit of a "One Health" approach. The aim of this study was to characterize antimicrobial resistance (AMR) genes and their frequencies from whole genome sequences of Escherichia coli isolated from both dairy cattle and human patients in central Zambia. Whole genome sequences of E. coli isolates from dairy cattle (n = 224) and from patients at a local hospital (n = 73) were compared for the presence of acquired AMR genes. In addition we analyzed the publicly available genomes of 317 human E. coli isolates from over the wider African continent. Both acquired antibiotic resistance genes and phylogroups were identified from de novo assemblies and SNP based phylogenetic analyses were used to visualize the distribution of resistance genes in E. coli isolates from the two hosts. Greater acquired AMR gene diversity was detected in human compared to bovine E. coli isolates across multiple classes of antibiotics with particular resistance genes for extended-spectrum beta lactamases (ESBL), quinolones, macrolides and fosfomycin only detected in E. coli genomes of human origin. The striking difference was that the Zambian or wider African human isolates were significantly more likely to possess multiple acquired AMR genes compared to the Zambian dairy cattle isolates. The median number of resistance genes in the Zambian cattle cohort was 0 (0-1 interquartile range), while in the Zambian human and wider African cohorts the medians and interquartile ranges were 6 (4-9) and 6 (0-8), respectively. The lower frequency and reduced diversity of acquired AMR genes in the dairy cattle isolates is concordant with relatively limited antibiotic use that we have documented in this region, especially among smallholder farmers. The relatively distinct resistant profiles in the two host populations also indicates limited sharing of strains or genes.