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Brangsch H, Sandalakis V, Babetsa M, Boukouvala E, Ntoula A, Makridaki E, Christidou A, Psaroulaki A, Akar K, Gürbilek SE, Jamil T, Melzer F, Neubauer H, Wareth G. Genotype diversity of brucellosis agents isolated from humans and animals in Greece based on whole-genome sequencing. BMC Infect Dis 2023; 23:529. [PMID: 37580676 PMCID: PMC10426126 DOI: 10.1186/s12879-023-08518-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 08/07/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Brucellosis is a zoonotic disease whose causative agent, Brucella spp., is endemic in many countries of the Mediterranean basin, including Greece. Although the occurrence of brucellosis must be reported to the authorities, it is believed that the disease is under-reported in Greece, and knowledge about the genomic diversity of brucellae is lacking. METHODS Thus, 44 Brucella isolates, primarily B. melitensis, collected between 1999 and 2009 from humans and small ruminants in Greece were subjected to whole genome sequencing using short-read technology. The raw reads and assembled genomes were used for in silico genotyping based on single nucleotide substitutions and alleles. Further, specific genomic regions encoding putative virulence genes were screened for characteristic nucleotide changes, which arose in different genotype lineages. RESULTS In silico genotyping revealed that the isolates belonged to three of the known sublineages of the East Mediterranean genotype. In addition, a novel subgenotype was identified that was basal to the other East Mediterranean sublineages, comprising two Greek strains. The majority of the isolates can be assumed to be of endemic origin, as they were clustered with strains from the Western Balkans or Turkey, whereas one strain of human origin could be associated with travel to another endemic region, e.g. Portugal. Further, nucleotide substitutions in the housekeeping gene rpoB and virulence-associated genes were detected, which were characteristic of the different subgenotypes. One of the isolates originating from an aborted bovine foetus was identified as B. abortus vaccine strain RB51. CONCLUSION The results demonstrate the existence of several distinct persistent Brucella sp. foci in Greece. To detect these and for tracing infection chains, extensive sampling initiatives are required.
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Affiliation(s)
- Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Fredrich-Loeffler-Institut - Federal Research Institute for Animal Health (FLI), 07743, Jena, Germany.
| | - Vassilios Sandalakis
- Laboratory of Clinical Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, Heraklion, Crete, 71500, Greece
| | - Maria Babetsa
- Veterinary Research Institute, ELGO-DIMITRA, Campus of Thermi, Thermi, 57001, Thessaloniki, Greece
| | - Evridiki Boukouvala
- Veterinary Research Institute, ELGO-DIMITRA, Campus of Thermi, Thermi, 57001, Thessaloniki, Greece
| | - Artemisia Ntoula
- Laboratory of Clinical Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, Heraklion, Crete, 71500, Greece
| | - Eirini Makridaki
- Laboratory of Clinical Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, Heraklion, Crete, 71500, Greece
| | - Athanasia Christidou
- Laboratory of Clinical Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, Heraklion, Crete, 71500, Greece
| | - Anna Psaroulaki
- Laboratory of Clinical Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, Heraklion, Crete, 71500, Greece
| | - Kadir Akar
- Faculty of Veterinary Medicine, Van Yuzuncu Yıl University, Van, 65090, Turkey
| | - Sevil Erdenlig Gürbilek
- Microbiology Department, Faculty of Veterinary Medicine, Harran University, Şanlıurfa, 63200, Turkey
| | - Tariq Jamil
- Institute of Bacterial Infections and Zoonoses, Fredrich-Loeffler-Institut - Federal Research Institute for Animal Health (FLI), 07743, Jena, Germany
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Fredrich-Loeffler-Institut - Federal Research Institute for Animal Health (FLI), 07743, Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Fredrich-Loeffler-Institut - Federal Research Institute for Animal Health (FLI), 07743, Jena, Germany
| | - Gamal Wareth
- Institute of Bacterial Infections and Zoonoses, Fredrich-Loeffler-Institut - Federal Research Institute for Animal Health (FLI), 07743, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, 07747, Jena, Germany
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Craddock HA, Motro Y, Zilberman B, Khalfin B, Bardenstein S, Moran-Gilad J. Long-Read Sequencing and Hybrid Assembly for Genomic Analysis of Clinical Brucella melitensis Isolates. Microorganisms 2022; 10:619. [PMID: 35336193 PMCID: PMC8955392 DOI: 10.3390/microorganisms10030619] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 01/27/2023] Open
Abstract
Brucella melitensis is a key etiological agent of brucellosis and has been increasingly subject to characterization using sequencing methodologies. This study aimed to investigate and compare short-read, long-read, and hybrid assemblies of B. melitensis. Eighteen B. melitensis isolates from Southern Israel were sequenced using Illumina and the Oxford Nanopore (ONP) MinION, and hybrid assemblies were generated with ONP long reads scaffolded on Illumina short reads. Short reads were assembled with INNUca with SPADes, long reads and hybrid with dragonflye. Abricate with the virulence factor database (VFDB) and in silico PCR (for the genes BetB, BPE275, BSPB, manA, mviN, omp19, perA, PrpA, VceC, and ureI) were used for identifying virulence genes, and a total of 61 virulence genes were identified in short-read, long-read, and hybrid assemblies of all 18 isolates. The phylogenetic analysis using long-read assemblies revealed several inconsistencies in cluster assignment as compared to using hybrid and short-read assemblies. Overall, hybrid assembly provided the most comprehensive data, and stand-alone short-read sequencing provided comparable data to stand-alone long-read sequencing regarding virulence genes. For genomic epidemiology studies, stand-alone ONP sequencing may require further refinement in order to be useful in endemic settings.
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Affiliation(s)
- Hillary A. Craddock
- Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (H.A.C.); (Y.M.); (B.Z.); (B.K.)
| | - Yair Motro
- Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (H.A.C.); (Y.M.); (B.Z.); (B.K.)
| | - Bar Zilberman
- Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (H.A.C.); (Y.M.); (B.Z.); (B.K.)
| | - Boris Khalfin
- Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (H.A.C.); (Y.M.); (B.Z.); (B.K.)
| | | | - Jacob Moran-Gilad
- Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (H.A.C.); (Y.M.); (B.Z.); (B.K.)
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Zilberman B, Motro Y, Sagi O, Kornspan D, Ben-Shimol S, Gdalevich M, Yagel Y, Davidovitch N, Khalfin B, Rabinowitz P, Nesher L, Grotto I, Bardenstein S, Moran-Gilad J. Genomic Epidemiology of Clinical Brucella melitensis Isolates from Southern Israel. Microorganisms 2022; 10:microorganisms10020238. [PMID: 35208693 PMCID: PMC8878301 DOI: 10.3390/microorganisms10020238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 12/16/2022] Open
Abstract
Brucellosis, a zoonosis mainly transmitted by consumption of unpasteurized dairy products, is endemic in Southern Israel, mainly among the Bedouin Arab population. However, the genomic epidemiology of B. melitensis in this region has not yet been elucidated. A cohort of brucellosis cases (n = 118) diagnosed between 2017–2019 was studied using whole-genome sequencing (WGS). Phylogenetic analyses utilized core genome MLST (cgMLST) for all local isolates and core genome SNPs for 347 human-associated B. melitensis genomes, including Israeli and publicly available sequences. Israeli isolates formed two main clusters, presenting a notable diversity, with no clear dominance of a specific strain. On a global scale, the Israeli genomes clustered according to their geographical location, in proximity to genomes originating from the Middle East, and formed the largest cluster in the tree, suggesting relatively high conservation. Our study unveils the genomic epidemiology of B. melitensis in Southern Israel, implicating that rather than a common source, the transmission pattern of brucellosis among Bedouin communities is complex, predominantly local, and household-based. Further, genomic surveillance of B. melitensis is expected to inform future public health and veterinary interventions and clinical care.
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Affiliation(s)
- Bar Zilberman
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
| | - Yair Motro
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
| | - Orli Sagi
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
- Soroka University Medical Center, Beer Sheva 84101, Israel
| | - David Kornspan
- Brucellosis Lab, OIE, FAO Reference Laboratory, Kimron Veterinary Institute, Bet Dagan 50250, Israel; (D.K.); (S.B.)
| | - Shalom Ben-Shimol
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
- Soroka University Medical Center, Beer Sheva 84101, Israel
| | - Michael Gdalevich
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
- Southern District Health Office, Ministry of Health, Beer Sheva 84104, Israel
| | - Yael Yagel
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
- Soroka University Medical Center, Beer Sheva 84101, Israel
| | - Nadav Davidovitch
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
| | - Boris Khalfin
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
| | - Peter Rabinowitz
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA 98195, USA;
| | - Lior Nesher
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
- Soroka University Medical Center, Beer Sheva 84101, Israel
| | - Itamar Grotto
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
| | - Svetlana Bardenstein
- Brucellosis Lab, OIE, FAO Reference Laboratory, Kimron Veterinary Institute, Bet Dagan 50250, Israel; (D.K.); (S.B.)
| | - Jacob Moran-Gilad
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; (B.Z.); (Y.M.); (O.S.); (S.B.-S.); (M.G.); (Y.Y.); (N.D.); (B.K.); (L.N.); (I.G.)
- Soroka University Medical Center, Beer Sheva 84101, Israel
- Correspondence:
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