Whole-Genome Sequencing for Tracing the Genetic Diversity of <em>Brucella abortus</em> and <em>Brucella melitensis</em> Isolated from Livestock in Egypt
Aman Ullah Khan,
Falk Melzer,
Ashraf E. Sayour,
Waleed S. Shell,
Jörg Linde,
Mostafa Abdel-Glil,
Sherif A. G. E. El-Soally,
Mandy C. Elschner,
Hossam E. M. Sayour,
Eman Shawkat Ramadan,
Shereen Aziz Mohamed,
Ashraf Hendam,
Rania I. Ismail,
Lubna F. Farahat,
Uwe Roesler,
Heinrich Neubauer,
Hosny El-Adawy
Affiliations
Aman Ullah Khan
Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany
Falk Melzer
Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany
Ashraf E. Sayour
Department of Brucellosis, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt
Waleed S. Shell
Central Laboratory for Evaluation of Veterinary Biologics, Agricultural Research Center, Abbassia, Cairo 11517, Egypt
Jörg Linde
Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany
Mostafa Abdel-Glil
Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany
Sherif A. G. E. El-Soally
Veterinary Service Department, Armed Forces Logistics Authority, Egyptian Armed Forces, Nasr City, Cairo 11765, Egypt
Mandy C. Elschner
Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany
Hossam E. M. Sayour
Biomedical Chemistry Unit, Department of Chemistry and Nutritional Deficiency Disorders, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt
Eman Shawkat Ramadan
Animal Reproduction Research Institute, Agricultural Research Center, Al Ahram, Giza 12556, Egypt
Shereen Aziz Mohamed
Veterinary Serum and Vaccine Research Institute, Agricultural Research Center, Abbassia, Cairo 11517, Egypt
Ashraf Hendam
Climate Change Information Center, Renewable Energy and Expert Systems (CCICREES), Agricultural Research Center, 9 Algamaa Street, Giza 12619, Egypt
Rania I. Ismail
Department of Brucellosis, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt
Lubna F. Farahat
Veterinary Serum and Vaccine Research Institute, Agricultural Research Center, Abbassia, Cairo 11517, Egypt
Uwe Roesler
Institute for Animal Hygiene and Environmental Health, Free University of Berlin, 14163 Berlin, Germany
Heinrich Neubauer
Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany
Hosny El-Adawy
Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany
Brucellosis is a highly contagious zoonosis that occurs worldwide. Whole-genome sequencing (WGS) has become a widely accepted molecular typing method for outbreak tracing and genomic epidemiology of brucellosis. Twenty-nine Brucella spp. (eight B. abortus biovar 1 and 21 B. melitensis biovar 3) were isolated from lymph nodes, milk, and fetal abomasal contents of infected cattle, buffaloes, sheep, and goats originating from nine districts in Egypt. The isolates were identified by microbiological methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Differentiation and genotyping were confirmed using multiplex PCR. Illumina MiSeq® was used to sequence the 29 Brucella isolates. Using MLST typing, ST11 and ST1 were identified among B. melitensis and B. abortus, respectively. Brucella abortus and B. melitensis isolates were divided into two main clusters (clusters 1 and 2) containing two and nine distinct genotypes by core-genome SNP analysis, respectively. The genotypes were irregularly distributed over time and space in the study area. Both Egyptian B. abortus and B. melitensis isolates proved to be genomically unique upon comparison with publicly available sequencing from strains of neighboring Mediterranean, African, and Asian countries. The antimicrobial resistance mechanism caused by mutations in rpoB, gyrA, and gyrB genes associated with rifampicin and ciprofloxacin resistance were identified. To the best of our knowledge, this is the first study investigating the epidemiology of Brucella isolates from livestock belonging to different localities in Egypt based on whole genome analysis.
