Downloaded from www.microbiologyresearch.org by IP: 54.70.40.11 On: Sat, 15 Dec 2018 07:26:00 Oral cavities of healthy infants harbour high proportions of Streptococcus salivarius strains with phenotypic and genotypic resistance to multiple classes of antibiotics Thaís H. Palma, 1 Erika N. Harth-Chú, 1 Jodie Scott, 2 Rafael N. Stipp, 1 Heike Boisvert, 2 Mariana F. Salom~ ao, 3 J essica D. Theobaldo, 1 Rosana F. Possobon, 4 Leandro C. Nascimento, 5 Jonathan W. McCafferty, 2 Lina Faller, 2 Margaret J. Duncan 2 and Renata O. Mattos-Graner 1 Correspondence Renata O. Mattos-Graner rmgraner@fop.unicamp.br Received 7 June 2016 Accepted 22 October 2016 1 Department of Oral Diagnosis, University of Campinas, S~ ao Paulo, Brazil 2 Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA 3 Piracicaba Dental School, University of Campinas, S~ ao Paulo, Brazil 4 Cepae – Research and Dental Care Center for Special Needs Patients of Piracicaba Dental School, University of Campinas, S~ ao Paulo, Brazil 5 Laboratory of Genomics and Gene Expression (LGE), University of Campinas, S~ ao Paulo, Brazil Emerging antibiotic resistance in the oropharyngeal microbiota, of which Streptococcus salivarius is a prominent species, represents a challenge for treating paediatric populations. In this study, we investigated the role of Streptococcus salivarius as a reservoir for antibiotic resistance genes (ARG) in the oral microbiota by analysing 95 Streptococcus salivarius isolates from 22 healthy infants (2–16 months of age). MICs of penicillin G, amoxicillin, erythromycin, tetracycline, doxycycline and streptomycin were determined. ARG profiles were assessed in a subset of 21 strains by next- generation sequencing of genomes, followed by searches of assembled reads against the Comprehensive Antibiotic Resistance Database. Strains resistant to erythromycin, penicillins and tetracyclines were isolated from 83.3, 33.3 and 16.6 %, respectively, of infants aged 2 to 8 months with no prior antibiotic treatment. These percentages were100.0, 66.6 and 50.0 %, by 13 to 16 months of age. ARG or polymorphisms associated with antibiotic resistance were the most prevalent and involved genes for macrolide efflux (mel, mefA/E and macB), ribosomal protection [erm(B), tet(M) and tet(O)] and b-lactamase-like proteins. Phylogenetically related strains showing multidrug-resistant phenotypes harboured multidrug efflux ARG. Polymorphic genes associated with antibiotic resistance to drugs affecting DNA replication, folate synthesis, RNA/protein synthesis and regulators of antibiotic stress responses were detected. These data imply that Streptococcus salivarius strains established during maturation of the oral microbiota harbour a diverse array of functional ARG, even in the absence of antibiotic selective pressures, highlighting a potential role for this species in shaping antibiotic susceptibility profiles of oropharyngeal communities. Abbreviations: ARG, antibiotic resistance gene(s); CARD, Comprehensive Antibiotic Resistance Database; CLSI, Clinical and Laboratory Standards Insti- tute; MBC, minimum bactericidal concentration; MEGA, macrolide efflux genetic assembly. The GenBank/EMBL/DDBJ/ENA accession numbers of novel whole-genome sequences of Streptococcus salivarius strains are S1-LXMB00000000, S2- LXMC00000000, S3-LXZU00000000, S4-LXZV00000000, S5-LXZW00000000, S6-LXZX00000000, S7-LXIF00000000, S8-LXOR00000000, S9- LXIG00000000, S10-LXIH00000000, S12-LXII00000000, S13-LXIJ00000000, S14-LXOS00000000, S15-LXIK00000000, S16-LXIL00000000, S18- LXIM00000000, S20-LXIN00000000, S21-LXOT00000000, S22-LXIP00000000, S23-LXIO00000000 and S24-LXOU00000000. Journal of Medical Microbiology (2016), 65, 1456–1464 DOI 10.1099/jmm.0.000377 1456 000377 Printed in Great Britain