Mainda Geoffrey, Lupolova Nadejda, Sikakwa Linda, Richardson Emily, Bessell Paul R, Malama Sydney K, Kwenda Geoffrey, Stevens Mark P, Bronsvoort Barend M deC, Muma John B, Gally David L
Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.
Department of Veterinary Services, Ministry of Fisheries and Livestock, Lusaka, Zambia.
Front Microbiol. 2019 May 31;10:1114. doi: 10.3389/fmicb.2019.01114. eCollection 2019.
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 isolated from both dairy cattle and human patients in central Zambia. Whole genome sequences of isolates from dairy cattle ( = 224) and from patients at a local hospital ( = 73) were compared for the presence of acquired AMR genes. In addition we analyzed the publicly available genomes of 317 human isolates from over the wider African continent. Both acquired antibiotic resistance genes and phylogroups were identified from assemblies and SNP based phylogenetic analyses were used to visualize the distribution of resistance genes in isolates from the two hosts. Greater acquired AMR gene diversity was detected in human compared to bovine isolates across multiple classes of antibiotics with particular resistance genes for extended-spectrum beta lactamases (ESBL), quinolones, macrolides and fosfomycin only detected in 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.
对患病奶牛进行抗生素治疗对于这种生产系统的可持续性至关重要，而这种生产系统在许多低收入和中等收入国家对粮食安全和社会繁荣至关重要。鉴于全球抗生素耐药性水平日益升高及其给细菌感染治疗带来的挑战，本着“同一健康”的理念，强烈建议在人和动物中合理使用抗生素。本研究的目的是从赞比亚中部奶牛和人类患者分离出的全基因组序列中，鉴定抗菌药物耐药性（AMR）基因及其频率。比较了奶牛（n = 224）和当地一家医院患者（n = 73）分离株的全基因组序列中获得性AMR基因的存在情况。此外，我们分析了来自非洲大陆更广泛地区的317株人类分离株的公开可用基因组。从组装序列中鉴定出获得性抗生素耐药基因和系统发育群，并使用基于单核苷酸多态性（SNP）的系统发育分析来可视化两个宿主分离株中耐药基因的分布。与牛分离株相比，在人类分离株中检测到更多类别的抗生素具有更高的获得性AMR基因多样性，其中仅在人类来源的基因组中检测到超广谱β-内酰胺酶（ESBL）、喹诺酮类、大环内酯类和磷霉素的特定耐药基因。显著的差异在于，与赞比亚奶牛分离株相比，赞比亚或更广泛非洲地区的人类分离株更有可能拥有多个获得性AMR基因。赞比亚牛群中耐药基因的中位数为0（四分位间距为0 - 1），而在赞比亚人类群体和更广泛的非洲群体中，中位数和四分位间距分别为6（4 - 9）和6（0 - 8）。奶牛分离株中获得性AMR基因的较低频率和多样性降低与我们在该地区记录的相对有限的抗生素使用情况一致，特别是在小农户中。两个宿主群体中相对不同的耐药谱也表明菌株或基因的共享有限。
