We report here the draft genome sequence of a Staphylococcus lentus isolate, 050AP, collected in Tanzania from a swab of healthy bovine perineum. The draft genome sequence contained 2.72 Mbp and 2,750 coding sequences with a G+C content of 31.7%

Holmes, Mark A

Matee, Mecky

Mazigo, Humphrey

Mshana, Stephen E

Msigwa, Felician

Parkhill, Julian

Paterson, Gavin K

Seni, Jeremiah

English

PubMed

We report here the draft genome sequence of a Staphylococcus lentus isolate, 050AP, collected in Tanzania from a swab of healthy bovine perineum. The draft genome sequence contained 2.72 Mbp and 2,750 coding sequences with a G+C content of 31.7%.</p

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     Edinburgh Research Explorer                                      Draft Genome Sequence of a Multiresistant Bovine Isolate ofStaphylococcus lentus from TanzaniaCitation for published version:Seni, J, Mshana, SE, Msigwa, F, Matee, M, Mazigo, H, Parkhill, J, Holmes, MA & Paterson, GK 2016, 'DraftGenome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania' Genomeannouncements, vol. 4, no. 6, e01345-16. DOI: 10.1128/genomeA.01345-16Digital Object Identifier (DOI):10.1128/genomeA.01345-16Link:Link to publication record in Edinburgh Research ExplorerDocument Version:Publisher's PDF, also known as Version of recordPublished In:Genome announcementsPublisher Rights Statement:Copyright © 2016 Seni et al.This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 Internationallicense.General rightsCopyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s)and / or other copyright owners and it is a condition of accessing these publications that users recognise andabide by the legal requirements associated with these rights.Take down policyThe University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorercontent complies with UK legislation. If you believe that the public display of this file breaches copyright pleasecontact openaccess@ed.ac.uk providing details, and we will remove access to the work immediately andinvestigate your claim.Download date: 05. Apr. 2019Draft Genome Sequence of a Multiresistant Bovine Isolate ofStaphylococcus lentus from TanzaniaJeremiah Seni,a Stephen E. Mshana,a Felician Msigwa,a Mecky Matee,b Humphrey Mazigo,c Julian Parkhill,d Mark A. Holmes,eGavin K. PatersonfDepartment of Microbiology, Immunology, Weill Bugando School of Medicine, Tanzaniaa; Department of Microbiology, Immunology, School of Medicine, MuhimbiliUniversity of Health and Allied Sciences, Tanzaniab; Department of Parasitology and Entomology, Weill Bugando School of Medicine, Tanzaniac; The Wellcome TrustSanger Institute, Wellcome Trust, Genome Campus, Hinxton, United Kingdomd; Department of Veterinary Medicine, University of Cambridge, Cambridge, UnitedKingdome; Royal (Dick) School of Veterinary Studies and Roslin Institute, The University of Edinburgh, Easter Bush Campus, United KingdomfWe report here the draft genome sequence of a Staphylococcus lentus isolate, 050AP, collected in Tanzania from a swab of healthy bo-vine perineum. The draft genome sequence contained 2.72Mbp and 2,750 coding sequenceswith aGCcontent of 31.7%.Received 6 October 2016 Accepted 7 October 2016 Published 1 December 2016Citation Seni J, Mshana SE, Msigwa F, Matee M, Mazigo H, Parkhill J, Holmes MA, Paterson GK. 2016. Draft genome sequence of a multiresistant bovine isolate ofStaphylococcus lentus from Tanzania. Genome Announc 4(6):e01345-16. doi:10.1128/genomeA.01345-16.Copyright © 2016 Seni et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Gavin K. Paterson, gavin.paterson@ed.ac.uk.Staphylococcus lentus is a member of the Staphylococcus sciurigroup which also comprises S. sciuri, Staphylococcus vitulinus,Staphylococcus fleurettii, and Staphylococcus stepanovicii (1, 2).This group is part of the normal skin and mucosal flora in a widerange of animals, and while not frequently associated with disease,members of the S. sciuri group have been isolated from various hu-man and veterinary infections (1, 2). They have furthermore beenimplicated as a reservoir for virulence and resistance gene exchangewith other staphylococci (2). In this study an isolate of S. lentus,050AP, collected from a perineum swab of a healthy Friesian-Jerseymixed breed dairy cow in Nyakato, Tanzania in April 2014 was ge-nome sequenced using an Illumina HiSeq 2000. To our knowledgethis is the first veterinary S. lentus genome to be reported.Genome assembly was performed using Velvet software (3), andresulted in an assembly consisting of 37 contigs with a N50 of119,892bpwhichwas automatically annotatedusingProkka (4).Theresultant 050APdraft genomewas 2,719,515 bpwith aGC contentof 31.7% and contained 2,750 predicted protein-coding sequences.The macrolide resistance gene mph(C) and tetracycline resistancegene tet(K)were identifiedbyResFinder version2.1 (5). In the case ofmph(C) (locus tag: SAMEA3109314_01885) the best full lengthBLASTmatch in the nucleotide collection is a 91.9% identify matchto mph(C) in Staphylococcus aureus (CP017097.1). Thus, 050AP ap-pears to encode a novel mph(C) variant which may be the same orrelated to a variant reported as partial coding sequences in S. lentusfrom free-living small mammals in Poland (6). A single nucleotidedeletion causes a frameshiftmutation in tet(K) leading to a predictedprotein of at least 419 amino acids versus the typical 296 amino acids.However, with the gene located at the end of a contig the exact size oftet(K) in 050AP is uncertain from these sequence data. Phenotypi-cally 050AP was resistant to erythromycin, clindamycin, tetracy-cline, ciprofloxacin, fusidic acid, oxacillin, and trimethoprim asassessed by Vitek-2 using card AST-P620 (bioMérieux, Basing-stoke, United Kingdom) but susceptible to cefoxitin (screen),chloramphenicol, daptomycin, gentamicin, linezolid, mupirocin,penicillin, teicoplanin, tigecycline, and vancomycin. The avail-ability of this genome for comparative analysis with other staph-ylococcal genomes will provide insights into the biology of theS. sciuri group and their role as commensals and pathogens.Accession number(s). This whole-genome shotgun projecthas been deposited in DDBJ/EMBL/GenBank under the accessionnumber FMRW01000000. The version described in this paper isthe first version, FMRW01000000.1.ACKNOWLEDGMENTSWe thank the Tanzania Veterinary Laboratory Agency Mwanza Branch fortheir technical assistance. The help of the core sequencing and informaticsteam at theWellcome Trust Sanger Institute is gratefully acknowledged.FUNDING INFORMATIONThis work, including the efforts of Stephen E. Mshana, HumphreyMazigo, Mark A. Holmes, and Gavin K. Paterson, was funded byCambridge-Africa Alborada Trust (RG71098). This work, including theefforts of Julian Parkhill, was funded by Wellcome Trust (098051). Thiswork, including the efforts of Mark A. Holmes and Gavin K. Paterson,was funded by Medical Research Council (MRC) (G1001787/1).REFERENCES1. Becker K, Heilmann C, Peters G. 2014. Coagulase-negative staphylococci.ClinMicrobiol Rev 27:870–926. http://dx.doi.org/10.1128/CMR.00109-13.2. Nemeghaire S, Argudín MA, Feßler AT, Hauschild T, Schwarz S, ButayeP. 2014. The ecological importance of the Staphylococcus sciuri speciesgroup as a reservoir for resistance and virulence genes. Vet Microbiol 171:342–356. http://dx.doi.org/10.1016/j.vetmic.2014.02.005.3. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short readassembly using de Bruijn graphs. Genome Res 18:821– 829. http://dx.doi.org/10.1101/gr.074492.107.4. SeemannT. 2014. Prokka: rapid prokaryotic genome annotation. Bioinfor-matics 30:2068–2069. http://dx.doi.org/10.1093/bioinformatics/btu153.5. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, LundO, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicro-bial resistance genes. J Antimicrob Chemother 67:2640–2644. http://dx.doi.org/10.1093/jac/dks261.6. Hauschild T, Schwarz S. 2010. Macrolide resistance in Staphylococcus spp.from free-living small mammals. Vet Microbiol 144:530–531. http://dx.doi.org/10.1016/j.vetmic.2010.06.017.crossmarkGenome AnnouncementsNovember/December 2016 Volume 4 Issue 6 e01345-16 genomea.asm.org 1 on December 2, 2016 by guesthttp://genomea.asm.org/Downloaded from 

Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania

ABSTRACT
          
            We report here the draft genome sequence of a
            Staphylococcus lentus
            isolate, 050AP, collected in Tanzania from a swab of healthy bovine perineum. The draft genome sequence contained 2.72 Mbp and 2,750 coding sequences with a G+C content of 31.7%.
          </jats:p

Jeremiah Seni

Stephen E. Mshana

Felician Msigwa

Mecky Matee

Humphrey Mazigo

Julian Parkhill

Mark A. Holmes

Gavin K. Paterson

Crossref

Genome Announcements

Apollo (Cambridge)

Draft Genome Sequence of a Multiresistant Bovine Isolate ofStaphylococcus lentus from TanzaniaJeremiah Seni,a Stephen E. Mshana,a Felician Msigwa,a Mecky Matee,b Humphrey Mazigo,c Julian Parkhill,d Mark A. Holmes,eGavin K. PatersonfDepartment of Microbiology, Immunology, Weill Bugando School of Medicine, Tanzaniaa; Department of Microbiology, Immunology, School of Medicine, MuhimbiliUniversity of Health and Allied Sciences, Tanzaniab; Department of Parasitology and Entomology, Weill Bugando School of Medicine, Tanzaniac; The Wellcome TrustSanger Institute, Wellcome Trust, Genome Campus, Hinxton, United Kingdomd; Department of Veterinary Medicine, University of Cambridge, Cambridge, UnitedKingdome; Royal (Dick) School of Veterinary Studies and Roslin Institute, The University of Edinburgh, Easter Bush Campus, United KingdomfWe report here the draft genome sequence of a Staphylococcus lentus isolate, 050AP, collected in Tanzania from a swab of healthy bo-vine perineum. The draft genome sequence contained 2.72Mbp and 2,750 coding sequenceswith aGCcontent of 31.7%.Received 6 October 2016 Accepted 7 October 2016 Published 1 December 2016Citation Seni J, Mshana SE, Msigwa F, Matee M, Mazigo H, Parkhill J, Holmes MA, Paterson GK. 2016. Draft genome sequence of a multiresistant bovine isolate ofStaphylococcus lentus from Tanzania. Genome Announc 4(6):e01345-16. doi:10.1128/genomeA.01345-16.Copyright © 2016 Seni et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Gavin K. Paterson, gavin.paterson@ed.ac.uk.Staphylococcus lentus is a member of the Staphylococcus sciurigroup which also comprises S. sciuri, Staphylococcus vitulinus,Staphylococcus fleurettii, and Staphylococcus stepanovicii (1, 2).This group is part of the normal skin and mucosal flora in a widerange of animals, and while not frequently associated with disease,members of the S. sciuri group have been isolated from various hu-man and veterinary infections (1, 2). They have furthermore beenimplicated as a reservoir for virulence and resistance gene exchangewith other staphylococci (2). In this study an isolate of S. lentus,050AP, collected from a perineum swab of a healthy Friesian-Jerseymixed breed dairy cow in Nyakato, Tanzania in April 2014 was ge-nome sequenced using an Illumina HiSeq 2000. To our knowledgethis is the first veterinary S. lentus genome to be reported.Genome assembly was performed using Velvet software (3), andresulted in an assembly consisting of 37 contigs with a N50 of119,892bpwhichwas automatically annotatedusingProkka (4).Theresultant 050APdraft genomewas 2,719,515 bpwith aGC contentof 31.7% and contained 2,750 predicted protein-coding sequences.The macrolide resistance gene mph(C) and tetracycline resistancegene tet(K)were identifiedbyResFinder version2.1 (5). In the case ofmph(C) (locus tag: SAMEA3109314_01885) the best full lengthBLASTmatch in the nucleotide collection is a 91.9% identify matchto mph(C) in Staphylococcus aureus (CP017097.1). Thus, 050AP ap-pears to encode a novel mph(C) variant which may be the same orrelated to a variant reported as partial coding sequences in S. lentusfrom free-living small mammals in Poland (6). A single nucleotidedeletion causes a frameshiftmutation in tet(K) leading to a predictedprotein of at least 419 amino acids versus the typical 296 amino acids.However, with the gene located at the end of a contig the exact size oftet(K) in 050AP is uncertain from these sequence data. Phenotypi-cally 050AP was resistant to erythromycin, clindamycin, tetracy-cline, ciprofloxacin, fusidic acid, oxacillin, and trimethoprim asassessed by Vitek-2 using card AST-P620 (bioMérieux, Basing-stoke, United Kingdom) but susceptible to cefoxitin (screen),chloramphenicol, daptomycin, gentamicin, linezolid, mupirocin,penicillin, teicoplanin, tigecycline, and vancomycin. The avail-ability of this genome for comparative analysis with other staph-ylococcal genomes will provide insights into the biology of theS. sciuri group and their role as commensals and pathogens.Accession number(s). This whole-genome shotgun projecthas been deposited in DDBJ/EMBL/GenBank under the accessionnumber FMRW01000000. The version described in this paper isthe first version, FMRW01000000.1.ACKNOWLEDGMENTSWe thank the Tanzania Veterinary Laboratory Agency Mwanza Branch fortheir technical assistance. The help of the core sequencing and informaticsteam at theWellcome Trust Sanger Institute is gratefully acknowledged.FUNDING INFORMATIONThis work, including the efforts of Stephen E. Mshana, HumphreyMazigo, Mark A. Holmes, and Gavin K. Paterson, was funded byCambridge-Africa Alborada Trust (RG71098). This work, including theefforts of Julian Parkhill, was funded by Wellcome Trust (098051). Thiswork, including the efforts of Mark A. Holmes and Gavin K. Paterson,was funded by Medical Research Council (MRC) (G1001787/1).REFERENCES1. Becker K, Heilmann C, Peters G. 2014. Coagulase-negative staphylococci.ClinMicrobiol Rev 27:870–926. http://dx.doi.org/10.1128/CMR.00109-13.2. Nemeghaire S, Argudín MA, Feßler AT, Hauschild T, Schwarz S, ButayeP. 2014. The ecological importance of the Staphylococcus sciuri speciesgroup as a reservoir for resistance and virulence genes. Vet Microbiol 171:342–356. http://dx.doi.org/10.1016/j.vetmic.2014.02.005.3. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short readassembly using de Bruijn graphs. Genome Res 18:821– 829. http://dx.doi.org/10.1101/gr.074492.107.4. SeemannT. 2014. Prokka: rapid prokaryotic genome annotation. Bioinfor-matics 30:2068–2069. http://dx.doi.org/10.1093/bioinformatics/btu153.5. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, LundO, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicro-bial resistance genes. J Antimicrob Chemother 67:2640–2644. http://dx.doi.org/10.1093/jac/dks261.6. Hauschild T, Schwarz S. 2010. Macrolide resistance in Staphylococcus spp.from free-living small mammals. Vet Microbiol 144:530–531. http://dx.doi.org/10.1016/j.vetmic.2010.06.017.crossmarkGenome AnnouncementsNovember/December 2016 Volume 4 Issue 6 e01345-16 genomea.asm.org 1

Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania.

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Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania.

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