title: First insight into the genetic population structure of Mycobacterium tuberculosis isolated from pulmonary tuberculosis patients in Egypt.
abstract: The present study aimed to assess the population structure of Mycobacterium tuberculosis (MTB) isolates from Egypt. A total of 230 MTB isolates were analysed using spoligotyping, large sequence polymorphism (LSPs), mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and multi-locus sequence typing (MLST). The majority of isolates (93.0%) belonged to lineage 4, including 44.3, 13.4 and 10.8% of the ill-defined T clade, LAM and Haarlem families, respectively, and lineage 3 was identified in 7.0% of the isolates. MIRU-VNTRs typing allowed efficient discrimination of the spoligotype-defined clusters, including spoligo-international types (SIT) 53, 34, and 4, into 56 patterns, including 13 clusters and 43 unique patterns. A new SNP at position 311614 was identified in all six isolates to form the biggest MIRU-VNTR cluster, which suggested a recent clonal expansion. This SNP could possibly be used as a genetic marker for robust discriminations of Egyptian MTB isolates belonging to SIT53. The combination of spoligotyping, 12 MIRU-VNTRs loci and MLST provided insight into the genetic diversity and transmission dynamics of the Egyptian MTB genotypes and could be a key to implementation of effective control measures by public health authorities.
authors.affiliation: Department of Animal Hygiene, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.
authors.forename: Hassan Mahmoud
authors.initials: HM
authors.lastname: Diab
authors.affiliation: Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan.
authors.forename: Chie
authors.initials: C
authors.lastname: Nakajima
authors.affiliation: Department of Animal Hygiene, Faculty of Veterinary Medicine, Assiut University, Egypt.
authors.forename: Saber A
authors.initials: SA
authors.lastname: Kotb
authors.affiliation: National Tuberculosis Control Program, Ministry of Health and Population, Egypt.
authors.forename: Alaa
authors.initials: A
authors.lastname: Mokhtar
authors.affiliation: TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt.
authors.forename: Nagwa F M
authors.initials: NF
authors.lastname: Khder
authors.affiliation: TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt.
authors.forename: Ahmed S A
authors.initials: AS
authors.lastname: Abdelaal
authors.affiliation: TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt.
authors.forename: Azza
authors.initials: A
authors.lastname: Hegazy
authors.affiliation: Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.
authors.forename: Ajay
authors.initials: A
authors.lastname: Poudel
authors.affiliation: Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.
authors.forename: Yogendra
authors.initials: Y
authors.lastname: Shah
authors.affiliation: Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan. Electronic address: suzuki@czc.hokudai.ac.jp.
authors.forename: Yasuhiko
authors.initials: Y
authors.lastname: Suzuki
mesh_terms: D001431:Bacteriological Techniques; D004269:DNA, Bacterial / Q000235:genetics*; D004534:Egypt / Q000453:epidemiology; D019143:Evolution, Molecular; D005838:Genotype; D006801:Humans; D020071:Interspersed Repetitive Sequences; D018598:Minisatellite Repeats; D017720:Molecular Epidemiology; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013183:Sputum / Q000382:microbiology; D014397:Tuberculosis, Pulmonary / Q000453:epidemiology / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial
keywords: Egypt; Genotyping; MTB lineages