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Genome Sequences for a Cluster of Human Isolates of Listeria monocytogenes Identified in South Africa in 2015 Anthony M. Smith,a,b Preneshni Naicker,c Colleen Bamford,c Liliwe Shuping,d Kerrigan M. McCarthy,d Arvinda Sooka,a Shannon L. Smouse,a Nomsa Tau,a,b Karen H. Keddya,b Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africaa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africab; National Health Laboratory Service (Groote Schuur Hospital), Cape Town, South Africac; Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africad
Listeria monocytogenes is a Gram-positive bacterium with a ubiquitous presence in the environment. There is growing concern about the increasing prevalence of L. monocytogenes associated with food-borne outbreaks. Here we report genome sequences for a cluster of human isolates of L. monocytogenes identified in South Africa in 2015. Received 12 February 2016 Accepted 24 February 2016 Published 7 April 2016 Citation Smith AM, Naicker P, Bamford C, Shuping L, McCarthy KM, Sooka A, Smouse SL, Tau N, Keddy KH. 2016. Genome sequences for a cluster of human isolates of Listeria monocytogenes identified in South Africa in 2015. Genome Announc 4(2):e00200-16. doi:10.1128/genomeA.00200-16. Copyright © 2016 Smith et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Anthony M. Smith, [email protected].
L
isteria monocytogenes is a Gram-positive bacterium causing the disease listeriosis. The bacterium has a ubiquitous presence in the environment. Although listeriosis is relatively rare, infections can have fatality rates as high as 30% (1). L. monocytogenes is an opportunistic pathogen. Acquisition of the pathogen occurs mainly by consumption of contaminated food. Infections with Listeria can result in mild febrile gastroenteritis in healthy individuals; however, invasive disease characterized by bacteremia, meningitis, pneumonia, endocarditis, and sepsis can occur in high risk groups (2). The pathogen most commonly affects immunocompromised individuals, pregnant women, neonates, and the elderly. There is growing concern about the increasing prevalence of L. monocytogenes associated with food-borne outbreaks (3, 4). Reports, publications and data concerning the prevalence and epidemiology L. monocytogenes in South Africa are lacking. To prevent, investigate, and control outbreaks of disease, it is vital to have information about the molecular epidemiology of the disease. In particular, genomic sequence data can be used to investigate the population structure and evolution of pathogens (5). In the present study, we describe genomic sequence data which will greatly contribute to the current limited epidemiological data that exists for L. monocytogenes in South Africa. During September 2015, an increased number of human cases of L. monocytogenes were isolated from hospitals in the Western Cape Province of South Africa. Among the cases were 3 isolates of L. monocytogenes, all recovered from blood culture specimens. One patient was a pregnant woman (24 years old), while the two other patients were neonates (1 day old). All L. monocytogenes isolates were later determined to belong to multilocus sequence typing (MLST) subtype ST6, a subtype commonly associated with unfavorable outcomes in patients (6). Whole-genome sequencing analysis of the bacterial isolates was completed at the Centre for Enteric Diseases of the National Institute for Communicable Diseases. Genomic DNA was isolated from bacteria using the Qiagen QIAamp DNA minikit (Qiagen,
March/April 2016 Volume 4 Issue 2 e00200-16
Hilden, Germany). DNA libraries were prepared using a Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA), followed by a 2 ⫻ 300 paired-end sequencing runs with 100⫻ coverage using Illumina MiSeq equipment. Raw data generated on the MiSeq was further analyzed using tools available in the CLC Genomics Workbench Software, version 8.5 (Qiagen). Using the “Trim Sequences Tool,” sequence reads were trimmed to include quality trimming and ambiguity trimming, and length trimming to discard reads below a length of 100 bases. Trimmed reads were assembled using the “De novo Assembly Tool”; the assembly algorithm works by using de Bruijn graphs to produce contiguous (contig) sequences (minimum contig length was set at 500 bases). For the assemblies, final contig numbers ranged from 48 to 85, with N50 contig values ranging from 150,269 to 184,970. Contig measurements estimated genomes sizes of ~3 Mb with G⫹C nucleotide content of 38%. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers LROO00000000, LROP00000000, and LROQ00000000. The versions described in this paper are the first versions, LROO01000000, LROP01000000, and LROQ01000000. FUNDING INFORMATION This work, including the efforts of Anthony Marius Smith, was funded by HHS | Centers for Disease Control and Prevention (CDC) (5U19GH000571-02).
REFERENCES 1. Lomonaco S, Nucera D, Filipello V. 2015. The evolution and epidemiology of Listeria monocytogenes in Europe and the United States. Infect Genet Evol 35:172–183. http://dx.doi.org/10.1016/j.meegid.2015.08.008. 2. Ferreira V, Wiedmann M, Teixeira P, Stasiewicz MJ. 2014. Listeria monocytogenes persistence in food-associated environments: epidemiology, strain characteristics, and implications for public health. J Food Protect 77:150 –170. http://dx.doi.org/10.4315/0362-028X.JFP-13-150. 3. Newell DG, Koopmans M, Verhoef L, Duizer E, Aidara-Kane A, Sprong H, Opsteegh M, Langelaar M, Threfall J, Scheutz F, van der
Genome Announcements
genomea.asm.org 1
Smith et al.
Giessen J, Kruse H. 2010. Food-borne diseases—the challenges of 20years ago still persist while new ones continue to emerge. Int J Food Microbiol 139:S3–S15. http://dx.doi.org/10.1016/ j.ijfoodmicro.2010.01.021. 4. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, Griffin PM. 2011. Foodborne illness acquired in the United States—major pathogens. Emerg Infect Dis 17:7–15. http://dx.doi.org/ 10.3201/eid1701.P11101. 5. Schmid D, Allerberger F, Huhulescu S, Pietzka A, Amar C, Kleta S,
2 genomea.asm.org
Prager R, Preussel K, Aichinger E, Mellmann A. 2014. Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011–2013. Clin Microbiol Infect 20:431– 436. http://dx.doi.org/10.1111/1469-0691.12638. 6. Koopmans MM, Brouwer MC, Bijlsma MW, Bovenkerk S, Keijzers W, van der Ende A, van de Beek D. 2013. Listeria monocytogenes sequence type 6 and increased rate of unfavorable outcome in meningitis: epidemiologic cohort study. Clin Infect Dis 57:247–253. http://dx.doi.org/10.1093/ cid/cit250.
Genome Announcements
March/April 2016 Volume 4 Issue 2 e00200-16
Genome Sequences for a Cluster of Human Isolates of Listeria monocytogenes Identified in South Africa in 2015 Anthony M. Smith,a,b Preneshni Naicker,c Colleen Bamford,c Liliwe Shuping,d Kerrigan M. McCarthy,d Arvinda Sooka,a Shannon L. Smouse,a Nomsa Tau,a,b Karen H. Keddya,b Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africaa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africab; National Health Laboratory Service (Groote Schuur Hospital), Cape Town, South Africac; Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africad
Listeria monocytogenes is a Gram-positive bacterium with a ubiquitous presence in the environment. There is growing concern about the increasing prevalence of L. monocytogenes associated with food-borne outbreaks. Here we report genome sequences for a cluster of human isolates of L. monocytogenes identified in South Africa in 2015. Received 12 February 2016 Accepted 24 February 2016 Published 7 April 2016 Citation Smith AM, Naicker P, Bamford C, Shuping L, McCarthy KM, Sooka A, Smouse SL, Tau N, Keddy KH. 2016. Genome sequences for a cluster of human isolates of Listeria monocytogenes identified in South Africa in 2015. Genome Announc 4(2):e00200-16. doi:10.1128/genomeA.00200-16. Copyright © 2016 Smith et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Anthony M. Smith, [email protected].
L
isteria monocytogenes is a Gram-positive bacterium causing the disease listeriosis. The bacterium has a ubiquitous presence in the environment. Although listeriosis is relatively rare, infections can have fatality rates as high as 30% (1). L. monocytogenes is an opportunistic pathogen. Acquisition of the pathogen occurs mainly by consumption of contaminated food. Infections with Listeria can result in mild febrile gastroenteritis in healthy individuals; however, invasive disease characterized by bacteremia, meningitis, pneumonia, endocarditis, and sepsis can occur in high risk groups (2). The pathogen most commonly affects immunocompromised individuals, pregnant women, neonates, and the elderly. There is growing concern about the increasing prevalence of L. monocytogenes associated with food-borne outbreaks (3, 4). Reports, publications and data concerning the prevalence and epidemiology L. monocytogenes in South Africa are lacking. To prevent, investigate, and control outbreaks of disease, it is vital to have information about the molecular epidemiology of the disease. In particular, genomic sequence data can be used to investigate the population structure and evolution of pathogens (5). In the present study, we describe genomic sequence data which will greatly contribute to the current limited epidemiological data that exists for L. monocytogenes in South Africa. During September 2015, an increased number of human cases of L. monocytogenes were isolated from hospitals in the Western Cape Province of South Africa. Among the cases were 3 isolates of L. monocytogenes, all recovered from blood culture specimens. One patient was a pregnant woman (24 years old), while the two other patients were neonates (1 day old). All L. monocytogenes isolates were later determined to belong to multilocus sequence typing (MLST) subtype ST6, a subtype commonly associated with unfavorable outcomes in patients (6). Whole-genome sequencing analysis of the bacterial isolates was completed at the Centre for Enteric Diseases of the National Institute for Communicable Diseases. Genomic DNA was isolated from bacteria using the Qiagen QIAamp DNA minikit (Qiagen,
March/April 2016 Volume 4 Issue 2 e00200-16
Hilden, Germany). DNA libraries were prepared using a Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA), followed by a 2 ⫻ 300 paired-end sequencing runs with 100⫻ coverage using Illumina MiSeq equipment. Raw data generated on the MiSeq was further analyzed using tools available in the CLC Genomics Workbench Software, version 8.5 (Qiagen). Using the “Trim Sequences Tool,” sequence reads were trimmed to include quality trimming and ambiguity trimming, and length trimming to discard reads below a length of 100 bases. Trimmed reads were assembled using the “De novo Assembly Tool”; the assembly algorithm works by using de Bruijn graphs to produce contiguous (contig) sequences (minimum contig length was set at 500 bases). For the assemblies, final contig numbers ranged from 48 to 85, with N50 contig values ranging from 150,269 to 184,970. Contig measurements estimated genomes sizes of ~3 Mb with G⫹C nucleotide content of 38%. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers LROO00000000, LROP00000000, and LROQ00000000. The versions described in this paper are the first versions, LROO01000000, LROP01000000, and LROQ01000000. FUNDING INFORMATION This work, including the efforts of Anthony Marius Smith, was funded by HHS | Centers for Disease Control and Prevention (CDC) (5U19GH000571-02).
REFERENCES 1. Lomonaco S, Nucera D, Filipello V. 2015. The evolution and epidemiology of Listeria monocytogenes in Europe and the United States. Infect Genet Evol 35:172–183. http://dx.doi.org/10.1016/j.meegid.2015.08.008. 2. Ferreira V, Wiedmann M, Teixeira P, Stasiewicz MJ. 2014. Listeria monocytogenes persistence in food-associated environments: epidemiology, strain characteristics, and implications for public health. J Food Protect 77:150 –170. http://dx.doi.org/10.4315/0362-028X.JFP-13-150. 3. Newell DG, Koopmans M, Verhoef L, Duizer E, Aidara-Kane A, Sprong H, Opsteegh M, Langelaar M, Threfall J, Scheutz F, van der
Genome Announcements
genomea.asm.org 1
Smith et al.
Giessen J, Kruse H. 2010. Food-borne diseases—the challenges of 20years ago still persist while new ones continue to emerge. Int J Food Microbiol 139:S3–S15. http://dx.doi.org/10.1016/ j.ijfoodmicro.2010.01.021. 4. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, Griffin PM. 2011. Foodborne illness acquired in the United States—major pathogens. Emerg Infect Dis 17:7–15. http://dx.doi.org/ 10.3201/eid1701.P11101. 5. Schmid D, Allerberger F, Huhulescu S, Pietzka A, Amar C, Kleta S,
2 genomea.asm.org
Prager R, Preussel K, Aichinger E, Mellmann A. 2014. Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011–2013. Clin Microbiol Infect 20:431– 436. http://dx.doi.org/10.1111/1469-0691.12638. 6. Koopmans MM, Brouwer MC, Bijlsma MW, Bovenkerk S, Keijzers W, van der Ende A, van de Beek D. 2013. Listeria monocytogenes sequence type 6 and increased rate of unfavorable outcome in meningitis: epidemiologic cohort study. Clin Infect Dis 57:247–253. http://dx.doi.org/10.1093/ cid/cit250.
Genome Announcements
March/April 2016 Volume 4 Issue 2 e00200-16
