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Announcement
13 July 2017

Draft Genome Sequences of Seven Streptococcus agalactiae Strains Isolated from Camelus dromedarius at the Horn of Africa

ABSTRACT

We present draft whole-genome sequences of seven Streptococcus agalactiae strains isolated from Camelus dromedarius in Kenya and Somalia. These data are an extension to the group B Streptococcus (GBS) pangenome and might provide more insight into the underlying mechanisms of pathogenicity and antibiotic resistance of camel GBS.

GENOME ANNOUNCEMENT

The natural colonizer of human gastrointestinal and genitourinary tracts Streptococcus agalactiae, also known as Lancefield’s group B Streptococcus (GBS), is an emerging pathogen of serious clinical concern (1). As a main causative agent of meningitis, sepsis, and respiratory diseases in neonates, GBS is strongly linked to child mortality and morbidity (2). S. agalactiae has also been isolated from both healthy and diseased camels in countries from the Horn of Africa (37). Given the fundamental role of camels for human nutrition and financial safety in these regions, GBS-associated diseases, such as mastitis or udder abscesses resulting in significant losses in milk production, can have a devastating impact (5). Here, we report the whole-genome sequences of seven GBS strains, isolated from Kenyan and Somalian camels (Camelus dromedarius). Previous genomic analysis of these isolates by multilocus sequence typing (MLST) indicated a detached phylogenetic relationship compared to GBS strains of human or bovine origin (5). The three isolates ILRI025, ILRI030, and ILRI067 were isolated from healthy camels, while ILRI037 (causing gingivitis), ILRI054 (causing wound infection), ILRI120 (causing chronic cough), and ILRI127 (causing periarthricular abscess) were associated with disease.
Genomic DNA was extracted from a single bacterial colony cultivated on Columbia sheep blood agar using the QIAamp DSP DNA minikit (Qiagen, Hilden, Germany). DNA was fragmented by ultrasonication using the Covaris S2 instrument (Covaris, Inc., Woburn, MA, USA). Barcoded libraries were generated with the Ion fragment library kit and Ion Xpress DNA barcode adaptors (Life Technologies, Inc., Carlsbad, CA, USA). Sequencing was performed on an Ion Torrent Personal Genome Machine (PGM) system, with the Ion PGM sequencing 400 kit and the Ion 318 Chip version 2 (Life Technologies, Inc.). After sequencing, single processing and base calling were performed using Torrent Suite 3.6 (Life Technologies, Inc.), and barcode-separated FASTQ files were generated. For de novo assemblies, we used MIRA version 4.0 (8). Contigs were sorted along the already published (9) GBS genomes of ILRI112 (accession no. HF952106) and ILRI005 (accession no. HF952105) (only for isolate ILRI067) using the Move Contigs function in Mauve version 2.3.1 (10). SeqMan Pro from the Lasergene genomics package version 12.1.0 (DNAStar, Madison, WI) was used to check and manually close gaps between contigs. Genome annotation was added using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The seven genomes displayed an overall size between 1,973,342 and 2,049,911 bp, with 1,812 to 1,954 proteins detected (Table 1).
TABLE 1
TABLE 1 List of Streptococcus agalactiae draft whole genomes released to GenBank
StrainGenBank accession no.Multilocus STaSerotypeGenome size (bp)No. of proteins
ILRI025NDGG00000000610VI2,013,3841,876
ILRI030NDGF00000000617VI1,999,6261,883
ILRI037NDGE00000000612Ia2,020,0021,895
ILRI054NDGD00000000615II2,021,0311,867
ILRI067NDGC00000000614V1,980,4691,812
ILRI120NDGB00000000618Ia2,049,9111,954
ILRI127NDGA00000000613Ia1,973,3421,875
a
ST, sequence type.
The draft genome sequences of cameloid GBS isolates presented here are a valuable addition to the pangenome of S. agalactiae (11). These genomic data provide a basis for the investigation of adaptive factors in GBS host colonization as well as underlying mechanisms of antibiotic resistance development and pathogenicity of camel S. agalactiae.

Accession number(s).

The annotated draft whole-genome sequences of the seven S. agalactiae isolates were deposited in GenBank under BioProject no. PRJNA382326. The accession numbers for each isolate are shown in Table 1.

ACKNOWLEDGMENTS

This work was supported by funding from the Swiss Tropical and Public Health Institute and Mabritec AG.

REFERENCES

1.
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Schrag SJ, McGee L, and Verani J. 2010. Prevention of perinatal group B streptococcal disease—revised guidelines from CDC. MMWR Morb Mortal Wkly Rep59:1–32.
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Edelstein RM and Pegram RG. 1974. Contagious skin necrosis of Somali camels associated with Streptococcus agalactiae. Trop Anim Health Prod6:255–256.
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Bekele T and Molla B. 2001. Mastitis in lactating camels (Camelus dromedarius) in Afar Region, north-eastern Ethiopia. Berl Münch Tierarztl Wochenschr114:169–172.
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Fischer A, Liljander A, Kaspar H, Muriuki C, Fuxelius HH, Bongcam-Rudloff E, de Villiers EP, Huber CA, Frey J, Daubenberger C, Bishop R, Younan M, and Jores J. 2013. Camel Streptococcus agalactiae populations are associated with specific disease complexes and acquired the tetracycline resistance gene tetM via a Tn916-like element. Vet Res44:86.
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Younan M and Bornstein S. 2007. Lancefield group B and C streptococci in East African camels (Camelus dromedarius). Vet Rec160:330–335.
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Abera M, Abdi O, Abunna F, and Megersa B. 2010. Udder health problems and major bacterial causes of camel mastitis in Jijiga, Eastern Ethiopia: implication for impacting food security. Trop Anim Health Prod42:341–347.
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Zubair S, de Villiers EP, Younan M, Andersson G, Tettelin H, Riley DR, Jores J, Bongcam-Rudloff E, and Bishop RP. 2013. Genome sequences of two pathogenic Streptococcus agalactiae isolates from the one-humped camel Camelus dromedarius. Genome Announc1(4):e00515-13.
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Darling ACE, Mau B, Blattner FR, and Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res14:1394–1403.
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Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O’Connor KJ, Smith S, Utterback TR, White O, Rubens CE, and Grandi G. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome.”Proc Natl Acad Sci U S A102:13950–13955.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 5Number 2813 July 2017
eLocator: 10.1128/genomea.00525-17

History

Received: 22 May 2017
Accepted: 25 May 2017
Published online: 13 July 2017

Contributors

Authors

Julian Rothen
Swiss Tropical and Public Health Institute, Basel, Switzerland
University of Basel, Basel, Switzerland
Tobias Schindler
Swiss Tropical and Public Health Institute, Basel, Switzerland
University of Basel, Basel, Switzerland
Joël F. Pothier
Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
Mario Younan
Food and Agriculture Organization of the United Nations, Gaziantep, Turkey
Ulrich Certa
Roche Pharmaceutical Research and Early Development, Department of Pharmaceutical Sciences, Translational Technologies and Bioinformatics, Roche Innovation Center Basel, Basel, Switzerland
Claudia Daubenberger
Swiss Tropical and Public Health Institute, Basel, Switzerland
University of Basel, Basel, Switzerland
Valentin Pflüger
Mabritec AG, Riehen, Switzerland
Joerg Jores
International Livestock Research Institute, Nairobi, Kenya
Vetsuisse-Fakultät Universität Bern, Institut für Veterinär-Bakteriologie, Bern, Switzerland

Notes

Address correspondence to Julian Rothen, [email protected].

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