crossmark Whole-Genome Sequencing of Two Bartonella bacilliformis Strains Yolanda Guillen,a Maria Casadellà,a,b Ruth García-de-la-Guarda,c Abraham Espinoza-Culupú,c Roger Paredes,a,b,d,e Joaquim Ruiz,f Marc Noguera-Juliana,d irsiCaixa AIDS Research Institute, Badalona, Catalonia, Spaina; Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spainb; Laboratorio de Microbiología Molecular y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peruc; Universitat de Vic–Universitat Central de Catalunya, Vic, Catalonia, Spaind; Unitat VIH, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spaine; ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic, Universitat de Barcelona, Barcelona, Spainf Bartonella bacilliformis is the causative agent of Carrion’s disease, a highly endemic human bartonellosis in Peru. We performed a whole-genome assembly of two B. bacilliformis strains isolated from the blood of infected patients in the acute phase of Carri- on’s disease from the Cusco and Piura regions in Peru. Received 18 May 2016 Accepted 19 May 2016 Published 7 July 2016 Citation Guillen Y, Casadellà M, García-de-la-Guarda R, Espinoza-Culupú A, Paredes R, Ruiz J, Noguera-Julian M. 2016. Whole-genome sequencing of two Bartonella bacilliformis strains. Genome Announc 4(4):e00659-16. doi:10.1128/genomeA.00659-16. Copyright © 2016 Guillen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Marc Noguera-Julian, mnoguera@irsicaixa.es. C arrion’s disease is a vector-borne neglected illness restricted to Andean valleys in Peru, Ecuador, and Colombia (1), where it remains endemic. The causal agent of Carrion’s disease is Barto- mans Trias i Pujol Research Institute using an Illumina MiSeq sequencer with a paired-end 300-bp sequencing kit. Using Trimmomatic (7), low-quality reads were filtered out and nella bacilliformis, an intracellular, nonfermentative, pleomor- adapter sequences were trimmed. Quality-controlled sequence phic, Gram-negative microorganism, with Lutzomyia verrucarum reads were assembled using A5-miseq (8) small genome assem- being the main illness vector. bly software (8). Protein-coding genes were predicted using the This illness has two different phases. In the acute phase, NCBI Prokaryote Genome Annotation Pipeline (PGAP) (9). called Oroya fever, the intense destruction of erythrocytes leads The functions of the predicted protein-coding genes were an- to a severe hemolytic anemia and temporal immunosuppres- notated with the Clusters of Orthologous Groups (COG) (10) sion, which facilitates both the reactivation of silent illnesses, database using the WebMGA (11) interface with standard pa- such as tuberculosis or histoplasmosis, and the growth of op- rameters. For strains USM-LMMB-006 and USM-LMMB-007, portunistic infections that may be fatal, such as bloodstream assemblies produced 15 and 11 scaffolds with median depths of Salmonella infections (1, 2). In fact, in the preantibiotic era, coverage of 72⫻ and 77⫻, total sizes of 1,401,011 and Oroya fever was considered one of the most lethal infections, 1,405,613 bp, and GC contents of 38.0% and 38.0%, respec- having a mortality rate of up to 85% (3); at present, a 10% tively. The draft genomes of B. bacilliformis strains USM- mortality rate is reported in reference hospitals, even with cor- LMMB-006 and USM-LMMB-007 contained 1,136/1,135 cod- rect antibiotic treatments (1). ing sequences, 3/3 rRNAs, and 39/39tRNAs, respectively. The chronic phase is considered to take place months after Using COG functional assignment, the 996 (88%) and 998 Oroya fever, due to the development of partial immunity, but it (88%) predicted proteins of strains USM-LMMB-006 and may also be present even without a previous acute diagnosis. This phase is characterized by the proliferation of verrucous USM-LMMB-007, respectively, could be classified into 868 lesions, so-called verruga peruana. In this phase, the most se- COG families and 21 COG classes. The most abundant COG rious complication is the presence of verrucous lesion bleed- classes in both strains were related to translation, ribosomal ing, which in extreme cases may require blood transfusions (4). structure, and biogenesis, including 135 predicted proteins in Often, a clinical cure does not result in microbiological both strains. The abundant classes in USM-LMMB-006 and clearance, leading to asymptomatic carriers, with persistent USM-LMMB-007 were general function (92/92); replication, B. bacilliformis bacteremia serving as a source for human-to- recombination, and repair (76/74); amino acid transport and human transmissions (1). Nonetheless, their real number re- metabolism (76/76); and energy production and conversion mains uncertain due to the lack of enough sensitive diagnosis (72/72); 88/86 had unknown function. tools (5); additional genomic data may help close these gaps. Nucleotide sequence accession numbers. This whole-genome Sequencing of the two B. bacilliformis strains, USM-LMMB- shotgun project has been deposited at NCBI GenBank under the 006 and USM-LMMB-007, collected in 2011 in southern (La sequence accession numbers LQWW00000000 (LQWW01000001 to Convención, Cusco) and northern Peru (Huancabamba, LQWW01000015) and LQXX00000000 (LQXX01000001 to Piura), respectively, and identified as causal agents of Oroya LQXX01000011) for strains USM-LMMB-006 and USM-LMMB- fever (6), was carried out at the genomics platform of the Ger- 007, respectively. July/August 2016 Volume 4 Issue 4 e00659-16 Genome Announcements genomea.asm.org 1 Guillen et al. FUNDING INFORMATION 4. Pachas P. (2000). Epidemiología de la Bartonelosis en el Perú. Oficina This work, including the efforts of Joaquim Ruiz, was funded by General de Epidemiología – Instituto Nacional de Salud. Lima (Peru). MINECO | Instituto de Salud Carlos III (ISCIII) (CES11/012). This 5. Gomes C, Martinez-Puchol S, Pons MJ, Bazán J, Tinco C, Del Valle J, Ruiz J. 2016. Evaluation of PCR approaches for detection of Bartonella work, including the efforts of Ruth García-de-la-Guarda and bacilliformis in blood samples. PLoS Negl Trop Dis 10:e0004529. http:// Abraham Espinoza-Culupú, was funded by Consejo Nacional de dx.doi.org/10.1371/journal.pntd.0004529. Ciencia, Tecnologia e Innovación Tecnológica (CONCYTEC) under 6. Espinoza-Culupú A, Quispe-Gaspar R, Jaramillo M, Icho M, Eca A, grant number 323-2010-CONCYTEC-OAJ. This work, including the Ramírez P, Alvarado D, Guerrero JC, Vargas-Vásquez F, Córdova O, efforts of Ruth García-de-la-Guarda and Abraham Espinoza-Culupú, García-de-la-Guarda R. 2014. Caracterización molecular de la región de- was funded by Universidad Nacional Mayor de San Marcos, Perú) terminante de resistencia a quinolonas (QRDR) de la topoisomerasa IV de (UNMSM) (111001032, 111001141, and 131001101). Bartonella bacilliformis en aislados clínicos. 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