Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing

Abstract

BackgroundStaphylococci are a major constituent of the nasal microbiome and a frequent cause of hospital-acquired infection. Antibiotic surgical prophylaxis is administered prior to surgery to reduce a patient’s risk of postoperative infection. The impact of surgical prophylaxis on the nasal staphylococcal microbiome is largely unknown. Here, we report the species present in the nasal staphylococcal microbiome and the impact of surgical prophylaxis revealed by a novel culture independent technique. Daily nasal samples from 18 hospitalised patients, six of whom received no antibiotics and 12 of whom received antibiotic surgical prophylaxis (flucloxacillin and gentamicin or teicoplanin +/− gentamicin), were analysed by tuf gene fragment amplicon sequencing.ResultsOn admission to hospital, the species diversity of the nasal staphylococcal microbiome varied from patient to patient ranging from 4 to 10 species. Administration of surgical prophylaxis did not substantially alter the diversity of the staphylococcal species present in the nose; however, surgical prophylaxis did impact on the relative abundance of the staphylococcal species present. The dominant staphylococcal species present in all patients on admission was Staphylococcus epidermidis, and antibiotic administration resulted in an increase in species relative abundance. Following surgical prophylaxis, a reduction in the abundance of Staphylococcus aureus was observed in carriers, but not a complete eradication.ConclusionsUtilising the tuf gene fragment has enabled a detailed study of the staphylococcal microbiome in the nose and highlights that although there is no change in the heterogeneity of species present, there are changes in abundance. The sensitivity of the methodology has revealed that the abundance of S. aureus is reduced to a low level by surgical prophylaxis and therefore reduces the potential risk of infection following surgery but also highlights that S. aureus does persist.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0210-1) contains supplementary material, which is available to authorized users.

Development and Evaluation of a Sensitive Bacteriophage-Based MRSA Diagnostic Screen

“…The control condition is not required or utilized for MRSA determination but was included to demonstrate the effectiveness of selection. A positive result was anticipated in most control wells due to the high nasal colonization rates of staphylococcal species and the cross-reactivity previously described with the phage cocktail [ 47 , 48 ]. In agreement with expectations, 36 of 40 (90%) samples were positive in the control well.…”

Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice

“…Sequence processing and the definition of ASVs were performed as describe above. Representative ASV sequences were aligned to a Staphylococcus tuf gene database, which includes 36 sequences and 1 sub-species used in McMurray et al [55], and with a sequence from the closest genus to Staphylococcus [56] i.e., Macrococcus canis (accession number: KM45013) as an outgroup (See Supplementary Methods and Supplementary Table 10). Negative extraction controls were included and treated in the same manner as for the 16S rRNA gene sequencing.…”

Amplicon-Based High-Throughput Sequencing Method Capable of Species-Level Identification of Coagulase-Negative Staphylococci in Diverse Communities

“…However, the 16S rRNA gene has little discriminatory power within the Staphylococcus genus [21,22]. To circumvent this, it is necessary to use other phylogenetic marker genes that have a sufficient level of discriminatory power, such as the gap, hsp60, or tuf genes, when studying complex communities of staphylococcal species [22,23]. Previously, a method has been developed for species-level analysis of staphylococci in the nasal microbiome based on partial sequences of the rpoB gene [24].…”

“…Previously, a method has been developed for species-level analysis of staphylococci in the nasal microbiome based on partial sequences of the rpoB gene [24]. Similarly, a previous study applying primers targeting the tuf gene and using only clinical isolates has shown that partial tuf gene amplicon sequencing can be used to unravel staphylococcal communities in the nasal microbiome [23]. Furthermore, the tuf gene has also been used successfully for the identification of CNS species present on the teat apices of dairy cows, albeit using PCR-DGGE [25].…”