Patel Shriram, Vlasblom Abel A, Verstappen Koen M, Zomer Aldert L, Fluit Ad C, Rogers Malbert R C, Wagenaar Jaap A, Claesson Marcus J, Duim Birgitta
APC Microbiome Ireland, University College Corkgrid.7872.a, Cork, Ireland.
Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
mSystems. 2021 Aug 31;6(4):e0015221. doi: 10.1128/mSystems.00152-21. Epub 2021 Jul 20.
Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen and often colonizes pigs. To lower the risk of MRSA transmission to humans, a reduction of MRSA prevalence and/or load in pig farms is needed. The nasal microbiome contains commensal species that may protect against MRSA colonization and may be used to develop competitive exclusion strategies. To obtain a comprehensive understanding of the species that compete with MRSA in the developing porcine nasal microbiome, and the moment of MRSA colonization, we analyzed nasal swabs from piglets in two litters. The swabs were taken longitudinally, starting directly after birth until 6 weeks. Both 16S rRNA and gene sequencing data with different phylogenetic resolutions and complementary culture-based and quantitative real-time PCR (qPCR)-based MRSA quantification data were collected. We employed a compositionally aware bioinformatics approach (CoDaSeq + rmcorr) for analysis of longitudinal measurements of the nasal microbiota. The richness and diversity in the developing nasal microbiota increased over time, albeit with a reduction of and , and an increase of . Coabundant groups (CAGs) of species showing strong positive and negative correlation with colonization of MRSA and S. aureus were identified. Combining 16S rRNA and gene sequencing provided greater Staphylococcus species resolution, which is necessary to inform strategies with potential protective effects against MRSA colonization in pigs. The large reservoir of methicillin-resistant Staphylococcus aureus (MRSA) in pig farms imposes a significant zoonotic risk. An effective strategy to reduce MRSA colonization in pig farms is competitive exclusion whereby MRSA colonization can be reduced by the action of competing bacterial species. We complemented 16S rRNA gene sequencing with Staphylococcus-specific gene sequencing to identify species anticorrelating with MRSA colonization. This approach allowed us to elucidate microbiome dynamics and identify species that are negatively and positively associated with MRSA, potentially suggesting a route for its competitive exclusion.
耐甲氧西林金黄色葡萄球菌（MRSA）是一种重要的人类病原体，且常定植于猪体内。为降低MRSA传播给人类的风险，需要降低猪场中MRSA的流行率和/或载量。鼻腔微生物群包含一些共生菌，它们可能预防MRSA定植，可用于制定竞争性排斥策略。为全面了解在发育中的猪鼻腔微生物群中与MRSA竞争的物种以及MRSA定植的时间，我们分析了两窝仔猪的鼻拭子。从出生后立即开始直至6周，纵向采集鼻拭子。收集了具有不同系统发育分辨率的16S rRNA和基因测序数据，以及基于培养和定量实时PCR（qPCR）的MRSA定量数据作为补充。我们采用了一种考虑成分的生物信息学方法（CoDaSeq + rmcorr）来分析鼻腔微生物群的纵向测量数据。发育中的鼻腔微生物群的丰富度和多样性随时间增加，尽管和有所减少，而有所增加。鉴定出了与MRSA和金黄色葡萄球菌定植呈强正相关和负相关的物种共丰度组（CAGs）。结合16S rRNA和基因测序可提供更高的葡萄球菌物种分辨率，这对于制定可能对猪的MRSA定植具有保护作用的策略至关重要。猪场中大量耐甲氧西林金黄色葡萄球菌（MRSA）构成了重大的人畜共患病风险。减少猪场中MRSA定植的有效策略是竞争性排斥，即通过竞争性细菌物种的作用减少MRSA定植。我们用葡萄球菌特异性基因测序对16S rRNA基因测序进行补充，以鉴定与MRSA定植呈反相关的物种。这种方法使我们能够阐明微生物群动态，并鉴定出与MRSA呈负相关和正相关的物种，这可能为其竞争性排斥提供一条途径。
