Genomic Analysis of Bovine <named-content content-type="genus-species">Staphylococcus aureus</named-content> Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis

ABSTRACT Staphylococcus aureus causes persistent clinical and subclinical bovine intramammary infections (IMI) worldwide. However, there is a lack of comprehensive information regarding genetic diversity, the presence of antimicrobial resistance (AMR), and virulence genes for S. aureus in bovine mil...

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Autores principales:	Sohail Naushad, Diego B. Nobrega, S. Ali Naqvi, Herman W. Barkema, Jeroen De Buck
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	intramammary infection Staphylococcus aureus whole-genome sequencing virulence factors antimicrobial resistance genes sequence types Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/992a5bbd89994e72adb473d6c5560a89
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spelling	oai:doaj.org-article:992a5bbd89994e72adb473d6c5560a892021-12-02T19:46:20ZGenomic Analysis of Bovine <named-content content-type="genus-species">Staphylococcus aureus</named-content> Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis10.1128/mSystems.00063-202379-5077https://doaj.org/article/992a5bbd89994e72adb473d6c5560a892020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00063-20https://doaj.org/toc/2379-5077ABSTRACT Staphylococcus aureus causes persistent clinical and subclinical bovine intramammary infections (IMI) worldwide. However, there is a lack of comprehensive information regarding genetic diversity, the presence of antimicrobial resistance (AMR), and virulence genes for S. aureus in bovine milk in Canada. Here, we performed whole-genome sequencing (WGS) of 119 Canadian bovine milk S. aureus isolates and determined they belonged to 8 sequence types (ST151, ST352, ST351, ST2187, ST2270, ST126, ST133, and ST8), 5 clonal complexes (CC151, CC97, CC126, CC133, and CC8), and 18 distinct Spa types. Pan-, core, and accessory genomes were composed of 6,340, 1,279, and 2,431 genes, respectively. Based on phenotypic screening for AMR, resistance was common against beta-lactams (19% of isolates) and sulfonamides (7% of isolates), whereas resistance against pirlimycin, tetracycline, ceftiofur, and erythromycin and to the combination of penicillin and novobiocin was uncommon (3, 3, 3, 2, and 2% of all isolates, respectively). We also determined distributions of 191 virulence factors (VFs) in 119 S. aureus isolates after classifying them into 5 functional categories (adherence [n = 28], exoenzymes [n = 21], immune evasion [n = 20], iron metabolism [n = 29], and toxins [n = 93]). Additionally, we calculated the pathogenic potential of distinct CCs and STs and determined that CC151 (ST151 and ST351) had the highest pathogenic potential (calculated by subtracting core-VFs from total VFs), followed by CC97 (ST352 and ST2187) and CC126 (ST126 and ST2270), potentially linked to their higher prevalence in bovine IMI worldwide. However, there was no statistically significant link between the presence of VF genes and mastitis. IMPORTANCE Staphylococcus aureus is a major cause of bovine intramammary infections, leading to significant economic losses to dairy industry in Canada and worldwide. There is a lack of knowledge regarding genetic diversity, the presence of antimicrobial resistance (AMR), and virulence genes for S. aureus isolated from bovine milk in Canada. Based on whole-genome sequencing and genomic analysis, we have determined the phylogeny and diversity of S. aureus in bovine milk and concluded that it had a large accessory genome, limited distribution of AMR genes, variable VF gene profiles and sequence types (ST), and clonal complex (CC)-specific pathogenic potentials. Comprehensive information on the population structure, as well as the virulence and resistance characteristics of S. aureus from bovine milk, will allow for source attribution, risk assessment, and improved therapeutic approaches in cattle.Sohail NaushadDiego B. NobregaS. Ali NaqviHerman W. BarkemaJeroen De BuckAmerican Society for Microbiologyarticleintramammary infectionStaphylococcus aureuswhole-genome sequencingvirulence factorsantimicrobial resistance genessequence typesMicrobiologyQR1-502ENmSystems, Vol 5, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	intramammary infection Staphylococcus aureus whole-genome sequencing virulence factors antimicrobial resistance genes sequence types Microbiology QR1-502
spellingShingle	intramammary infection Staphylococcus aureus whole-genome sequencing virulence factors antimicrobial resistance genes sequence types Microbiology QR1-502 Sohail Naushad Diego B. Nobrega S. Ali Naqvi Herman W. Barkema Jeroen De Buck Genomic Analysis of Bovine <named-content content-type="genus-species">Staphylococcus aureus</named-content> Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis
description	ABSTRACT Staphylococcus aureus causes persistent clinical and subclinical bovine intramammary infections (IMI) worldwide. However, there is a lack of comprehensive information regarding genetic diversity, the presence of antimicrobial resistance (AMR), and virulence genes for S. aureus in bovine milk in Canada. Here, we performed whole-genome sequencing (WGS) of 119 Canadian bovine milk S. aureus isolates and determined they belonged to 8 sequence types (ST151, ST352, ST351, ST2187, ST2270, ST126, ST133, and ST8), 5 clonal complexes (CC151, CC97, CC126, CC133, and CC8), and 18 distinct Spa types. Pan-, core, and accessory genomes were composed of 6,340, 1,279, and 2,431 genes, respectively. Based on phenotypic screening for AMR, resistance was common against beta-lactams (19% of isolates) and sulfonamides (7% of isolates), whereas resistance against pirlimycin, tetracycline, ceftiofur, and erythromycin and to the combination of penicillin and novobiocin was uncommon (3, 3, 3, 2, and 2% of all isolates, respectively). We also determined distributions of 191 virulence factors (VFs) in 119 S. aureus isolates after classifying them into 5 functional categories (adherence [n = 28], exoenzymes [n = 21], immune evasion [n = 20], iron metabolism [n = 29], and toxins [n = 93]). Additionally, we calculated the pathogenic potential of distinct CCs and STs and determined that CC151 (ST151 and ST351) had the highest pathogenic potential (calculated by subtracting core-VFs from total VFs), followed by CC97 (ST352 and ST2187) and CC126 (ST126 and ST2270), potentially linked to their higher prevalence in bovine IMI worldwide. However, there was no statistically significant link between the presence of VF genes and mastitis. IMPORTANCE Staphylococcus aureus is a major cause of bovine intramammary infections, leading to significant economic losses to dairy industry in Canada and worldwide. There is a lack of knowledge regarding genetic diversity, the presence of antimicrobial resistance (AMR), and virulence genes for S. aureus isolated from bovine milk in Canada. Based on whole-genome sequencing and genomic analysis, we have determined the phylogeny and diversity of S. aureus in bovine milk and concluded that it had a large accessory genome, limited distribution of AMR genes, variable VF gene profiles and sequence types (ST), and clonal complex (CC)-specific pathogenic potentials. Comprehensive information on the population structure, as well as the virulence and resistance characteristics of S. aureus from bovine milk, will allow for source attribution, risk assessment, and improved therapeutic approaches in cattle.
format	article
author	Sohail Naushad Diego B. Nobrega S. Ali Naqvi Herman W. Barkema Jeroen De Buck
author_facet	Sohail Naushad Diego B. Nobrega S. Ali Naqvi Herman W. Barkema Jeroen De Buck
author_sort	Sohail Naushad
title	Genomic Analysis of Bovine <named-content content-type="genus-species">Staphylococcus aureus</named-content> Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis
title_short	Genomic Analysis of Bovine <named-content content-type="genus-species">Staphylococcus aureus</named-content> Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis
title_full	Genomic Analysis of Bovine <named-content content-type="genus-species">Staphylococcus aureus</named-content> Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis
title_fullStr	Genomic Analysis of Bovine <named-content content-type="genus-species">Staphylococcus aureus</named-content> Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis
title_full_unstemmed	Genomic Analysis of Bovine <named-content content-type="genus-species">Staphylococcus aureus</named-content> Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis
title_sort	genomic analysis of bovine <named-content content-type="genus-species">staphylococcus aureus</named-content> isolates from milk to elucidate diversity and determine the distributions of antimicrobial and virulence genes and their association with mastitis
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/992a5bbd89994e72adb473d6c5560a89
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Genomic Analysis of Bovine <named-content content-type="genus-species">Staphylococcus aureus</named-content> Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis

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