Short-Sequence DNA Repeats in Prokaryotic Genomes

DNA polymorphisms amplified by arbitrary primers are useful as genetic markers

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The complete genome sequence of Escherichia coli K-12.

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Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd

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Life with 6000 Genes

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Hypervariable ‘minisatellite’ regions in human DNA

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Distribution of repetitive DNA sequences in eubacteria and application to finerpriting of bacterial enomes

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Microsatellite Instability in Cancer of the Proximal Colon

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Exon 1 of the HD gene with an expanded CAG repeat is sufficient to cause a progressive neurological phenotype in transgenic mice

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Applicability of rep‐PCR genomic fingerprinting to molecular discrimination of members of the genera Phaeoacremonium and Phaeomoniella

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Typing of Enterococcus faecium by polymerase chain reaction and pulsed field gel electrophoresis

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CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes

Uchiyama, I., Higuchi, T., & Kobayashi, I. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-472 · Cited by 23

Genetic Diversity: Frameshift Mechanisms Alter Coding of a Gene (Epstein-Barr Virus LF3 Gene) That Contains Multiple 102-Base-Pair Direct Sequence Repeats

Xue, S., Jones, M. D., Lu, Q., Middeldorp, J. M., & Griffin, B. E. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.6.2192-2201.2003 · Cited by 23

Sequence Analysis of dru Regions from Methicillin-Resistant Staphylococcus aureus and Coagulase-Negative Staphylococcal Isolates

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DNA‐Directed Mutations: Leading and Lagging Strand Specificity

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Microbial genomes

Pallen, M. J. (1999) · Molecular Microbiology · doi:10.1046/j.1365-2958.1999.01427.x · Cited by 23

Sequencing Independent Molecular Typing of Staphylococcus aureus Isolates: Approach for Infection Control and Clonal Characterization

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Variability of trinucleotide tandem repeats in the MgPa operon and its repetitive chromosomal elements in Mycoplasma genitalium

Ma, L., Jensen, J. S., Mancuso, M. M., Hamasuna, R., Jia, Q., McGowin, C. L., & Martin, D. H. (2011) · Journal of Medical Microbiology · doi:10.1099/jmm.0.030858-0 · Cited by 22

Molecular Diversity and Pathogenicity of Ralstonia solanacearum Species Complex Associated With Bacterial Wilt of Potato in Rwanda

Sharma, K., Kreuze, J. F., Abdurahman, A., Parker, M. L., Nduwayezu, A., & Rukundo, P. (2020) · Plant Disease · doi:10.1094/pdis-04-20-0851-re · Cited by 22

Validation of ‘Variable Number of Tandem Repeat’-Based Approach for Examination of ‘Candidatus Liberibacter asiaticus’ Diversity and Its Applications for the Analysis of the Pathogen Populations in the Areas of Recent Introduction

Matos, L. A., Hilf, M. E., Chen, J., & Folimonova, S. Y. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078994 · Cited by 22

Multiple-locus, variable number of tandem repeat analysis (MLVA) of the fish-pathogen Francisella noatunensis

Brevik, Ø. J., Ottem, K. F., & Nylund, A. (2011) · BMC Veterinary Research · doi:10.1186/1746-6148-7-5 · Cited by 22

Comparison of multiple typing methods for Aspergillus fumigatus

Vanhee, L. M. E., Symoens, F., Jacobsen, M. D., Nelis, H. J. C. F., & Coenye, T. (2009) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2009.02844.x · Cited by 22

Multiple-Locus Variable-Number Tandem-Repeat Analysis for Clonal Identification of Vibrio parahaemolyticus Isolates by Using Capillary Electrophoresis

Harth-Chú, É. N., Espejo, R. T., Christen, R., Guzmán, C. A., & Höfle, M. G. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.02729-08 · Cited by 22

Tandem repeats in complete bacterial genome sequences: sequence and structural analyses for comparative studies

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DNA sequence analysis linguistic tools: contrast vocabularies, compositional spectra and linguistic complexity.

Bolshoy, A. (2003) · PubMed · Cited by 22

A positive perspective on DNA methylation: regulatory functions of DNA methylation outside of host defense in Gram-positive bacteria

Nye, T. M., Fernandez, N. L., & Simmons, L. A. (2020) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2020.1828257 · Cited by 21

Mycobacterium avium subspecies paratuberculosis

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Alternate measure of information useful for DNA sequences

Bose, R., & Chouhan, S. (2011) · Physical Review E · doi:10.1103/physreve.83.051918 · Cited by 21

Variable-Number Tandem Repeats as Molecular Markers for Biotypes of Pasteuria ramosa in Daphnia spp

Mouton, L., Nong, G., Preston, J. F., & Ebert, D. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02398-06 · Cited by 21

Variable numbers of tandem repeat loci in genetically homogeneous Haemophilus influenzae strains alter during persistent colonisation of cystic fibrosis patients

Renders, N. H. M., Licciardello, L., IJsseldijk, C., Sijmons, M., van Alphen, L., Verbrugh, H. A., & van Belkum, A. (1999) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1999.tb13489.x · Cited by 21

Genomic Variability of Haemophilus influenzae Isolated from Mexican Children Determined by Using Enterobacterial Repetitive Intergenic Consensus Sequences and PCR

de León, P. G., Santos, J. I., Caballero, J., Gómez, D. T., Monteros, L. E. E. D. L., Moreno, I., Piñero, D., & Cravioto, A. (2000) · Journal of Clinical Microbiology · doi:10.1128/jcm.38.7.2504-2511.2000 · Cited by 21

Genetic variability of Trypanosoma evansi isolates detected by inter-simple sequence repeat anchored-PCR and microsatellite

Njiru, Z. K., Constantine, C. C., Gitonga, P. K., Thompson, R. C. A., & Reid, S. A. (2007) · Veterinary Parasitology · doi:10.1016/j.vetpar.2007.03.010 · Cited by 20

Variable-number tandem repeat 3690 polymorphism in Indian clinical isolates of Mycobacterium tuberculosis and its influence on transcription

Akhtar, P., Singh, S., Bifani, P. J., Kaur, S., Srivastava, B. S., & Srivastava, R. (2009) · Journal of Medical Microbiology · doi:10.1099/jmm.0.002550-0 · Cited by 20

Genomics of food-borne bacterial pathogens

Wells, J. M., & Bennik, M. H. J. (2003) · Nutrition Research Reviews · doi:10.1079/nrr200358 · Cited by 20

Tandem Repeat Deletion in the Alpha C Protein of Group B Streptococcus Is recA Independent

Puopolo, K. M., Hollingshead, S. K., Carey, V. J., & Madoff, L. C. (2001) · Infection and Immunity · doi:10.1128/iai.69.8.5037-5045.2001 · Cited by 20

Very small mobile repeated elements in cyanobacterial genomesPreprint

Elhai, J., Kato, M., Cousins, S., Lindblad, P. C., & Costa, J. L. (2008) · Genome Research · doi:10.1101/gr.074336.107 · Cited by 20

Molecular Typing and Global Epidemiology of Staphylococcus aureus

Kumar, S., Anwer, R., Yadav, M. K., Sehrawat, N., Singh, M. P., & Kumar, V. (2021) · Current Pharmacology Reports · doi:10.1007/s40495-021-00264-7 · Cited by 19

Multilocus variable-number of tandem-repeats analysis of Salmonella enterica serotype Gallinarum and comparison with pulsed-field gel electrophoresis genotyping

Bergamini, F., Iori, A., Massi, P., & Pongolini, S. (2010) · Veterinary Microbiology · doi:10.1016/j.vetmic.2010.12.002 · Cited by 19

A novel multilocus variable number tandem repeat analysis typing scheme for African phylotype III strains of theRalstonia solanacearumspecies complex

Ravelomanantsoa, S., Robène-Soustrade, I., Chiroleu, F., Guérin, F., Poussier, S., Pruvost, O., & Prior, P. (2016) · PeerJ · doi:10.7717/peerj.1949 · Cited by 19

Genetic Characterization and Comparative Genome Analysis ofBrucella melitensisIsolates from India

Azam, S., Rao, S. B., Jakka, P., NarasimhaRao, V., Bhargavi, B., Gupta, V. K., & Radhakrishnan, G. (2016) · International Journal of Genomics · doi:10.1155/2016/3034756 · Cited by 19

Analysis of Conserved Non-rRNA Genes of Tropheryma whipplei

Maiwald, M., Lepp, P. W., & Relman, D. A. (2003) · Systematic and Applied Microbiology · doi:10.1078/072320203322337254 · Cited by 19

Identification and characterization of simple sequence repeats in the genomes of Shigella species

Yang, J., Wang, J., Chen, L., Yu, J., Dong, J., Yao, Z.-J., Shen, Y., Jin, Q., & Chen, R. (2003) · Gene · doi:10.1016/j.gene.2003.09.017 · Cited by 19

In vitro effects of diazabicyclooctane β-lactamase inhibitors relebactam and nacubactam against three subspecies of Mycobacterium abscessus complex

Misawa, K., Nishimura, T., Kashimura, S., Enoki, Y., Taguchi, K., Uno, S., Uwamino, Y., Matsumoto, K., & Hasegawa, N. (2022) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2022.106669 · Cited by 18

We are doing it wrong: Putting homology before phylogeny in cyanobacterial taxonomy

Villanueva, C. D., Bohunická, M., & Johansen, J. R. (2024) · Journal of Phycology · doi:10.1111/jpy.13491 · Cited by 18

Highly discriminatory typing method for Listeria monocytogenes using polymorphic tandem repeat regions

Miya, S., Takahashi, H., Kamimura, C., Nakagawa, M., Kuda, T., & Kimura, B. (2012) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2012.05.023 · Cited by 18

Molecular typing for epidemiological evaluation of Brucella abortus and Brucella canis isolated in Korea

Kang, S., Her, M., Heo, E. J., Nam, H. M., Jung, S. C., & Cho, D. (2009) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2009.05.009 · Cited by 18

Molecular characterization of phosphorylcholine expression on the lipooligosaccharide of Histophilus somni

Elswaifi, S. F., Michael, F. S., Sreenivas, A., Cox, A. D., Carman, G. M., & Inzana, T. J. (2009) · Microbial Pathogenesis · doi:10.1016/j.micpath.2009.08.001 · Cited by 18

Isolation and characterization of microsatellite loci from the barley scald pathogen, Rhynchosporium secalis

Linde, C. C., Zala, M., & McDonald, B. A. (2005) · Molecular Ecology Notes · doi:10.1111/j.1471-8286.2005.00983.x · Cited by 18

Evaluation of three molecular methods of repetitive element loci for differentiation of Mycobacterium avium subsp. paratuberculosis (MAP)

El-Sayed, A., Hassan, A. A., Natour, S., Abdulmawjood, A. A., Bülte, M., Wolter, W., & Zschöck, M. (2009) · The Journal of Microbiology · doi:10.1007/s12275-008-0257-1 · Cited by 17

Identification and characterization of variable-number tandem-repeat markers for the molecular epidemiological analysis ofMycoplasma mycoidessubspeciesmycoidesSC

McAuliffe, L., Ayling, R. D., & Nicholas, R. A. J. (2007) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2007.00936.x · Cited by 17

What can be learned from genotyping of fungi?

Vanhee, L. M. E., Nelis, H. J. C. F., & Coenye, T. (2010) · Medical Mycology · doi:10.3109/13693786.2010.484816 · Cited by 17

Analysis of tandem repeats in the genome of Chinese shrimp Fenneropenaeus chinensis

Kong, J. (2005) · Chinese Science Bulletin · doi:10.1360/982005-270 · Cited by 17

Comparison of Multilocus Variable-Number Tandem-Repeat Analysis and Multilocus Sequence Typing for Differentiation of Hemolytic-Uremic Syndrome-Associated Escherichia coli (HUSEC) Collection Strains

Jenke, C., Lindstedt, B.-A., Harmsen, D., Karch, H., Brandal, L. T., & Mellmann, A. (2011) · Journal of Clinical Microbiology · doi:10.1128/jcm.05035-11 · Cited by 17

Clonal isolates of Treponema pallidum subsp. pallidum Nichols provide evidence for the occurrence of microevolution during experimental rabbit infection and in vitro culture

Edmondson, D. G., DeLay, B. D., Hanson, B., Kowis, L. E., & Norris, S. J. (2023) · PLoS ONE · doi:10.1371/journal.pone.0281187 · Cited by 15

Biodiversity of Enterococcus faecalis based on genomic typing

Buhnik‐Rosenblau, K., Efimov, V., Danin‐Poleg, Y., Franz, C. M. A. P., Klein, G., & Kashi, Y. (2013) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2013.04.009 · Cited by 17

Simple Sequence Repeats and Mucoid Conversion: Biased mucA Mutagenesis in Mismatch Repair-Deficient Pseudomonas aeruginosa

Moyano, A. J., & Smania, A. M. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008203 · Cited by 17

Development and characterization of simple sequence repeat (SSR) markers based on a full-length cDNA library of Scutellaria baicalensis

Yuan, Y., Long, P., Jiang, C., Li, M., & Huang, L. (2014) · Genomics · doi:10.1016/j.ygeno.2014.10.009 · Cited by 17

Interplay Between Virulence and Variability Factors as a Potential Driver of Invasive Meningococcal Disease

Siena, E., Bodini, M., & Medini, D. (2018) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2018.02.002 · Cited by 17

Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)

Sammeth, M., Weniger, T., Harmsen, D., & Stoye, J. (2005) · Lecture notes in computer science · doi:10.1007/11557067_23 · Cited by 17

Genetic populations ofBacillus anthracisisolates from Korea

Jung, K. H., Kim, S. H., Kim, S. K., Cho, S. Y., Chai, J. C., Lee, Y. S., Kim, J. C., Kim, S. J., Oh, H., & Chai, Y. G. (2012) · Journal of Veterinary Science · doi:10.4142/jvs.2012.13.4.385 · Cited by 17

Impact of Compounding Error on Strategies for Subtyping Pathogenic Bacteria

Call, D. R., Orfe, L. H., Davis, M. A., LaFrentz, S. A., & Kang, M.-S. (2008) · Foodborne Pathogens and Disease · doi:10.1089/fpd.2008.0097 · Cited by 17

Longstanding Taxonomic Enigmas within the ‘Bacillus cereusgroup’ are on the Verge of being Resolved by Far‒reaching Molecular Developments: forecasts on the possible outcome by anad hocteam

Turnbull, P. C. B., Jackson, P. J., Hill, K. K., Keim, P., Kolstø, A., & Beecher, D. J. (2002) · doi:10.1002/9780470696743.ch3 · Cited by 17

Comparison of PCR ribotyping and multilocus variable-number tandem-repeat analysis (MLVA) for improved detection of Clostridium difficile

Wei, H.-L., Kao, C. W., Wei, S. H., Tzen, J. T. C., & Chiou, C. (2011) · BMC Microbiology · doi:10.1186/1471-2180-11-217 · Cited by 16

Molecular Epidemiology of Ralstonia pseudosolanacearum Phylotype I Strains in the Southwest Indian Ocean Region and Their Relatedness to African Strains

Cellier, G., Nordey, T., Cortada, L., Gauche, M., Rasoamanana, H., Yahiaoui, N., Rébert, E., Prior, P., Chéron, J. J., Poussier, S., et al. (2022) · Phytopathology · doi:10.1094/phyto-09-22-0355-r · Cited by 16

ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections

Chindelevitch, L., Colijn, C., Moodley, P., Wilson, D., & Cohen, T. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004475 · Cited by 16

A new Multi Locus Variable Number of Tandem Repeat Analysis Scheme for epidemiological surveillance of Xanthomonas vasicola pv. musacearum, the plant pathogen causing bacterial wilt on banana and enset

Nakato, G. V., Rojas, J. L. F., Verniere, C., Blondin, L., Coutinho, T. A., Mahuku, G., & Wicker, E. (2019) · PLoS ONE · doi:10.1371/journal.pone.0215090 · Cited by 16

Characterisation of human outbreaks of brucellosis and sporadic cases by the use of hyper-variable octameric oligonucleotide fingerprint (HOOF) variable number tandem repeats

Valdezate, S., Cervera, I., Hernandez, P., Navarro, A., & Nieto, J. A. S. (2007) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2007.01768.x · Cited by 16

Microbial Systematics: Background and Uses

Goodfellow, M. (2000) · Springer eBooks · doi:10.1007/978-94-011-4020-1_1 · Cited by 16

Distribution of a family of Haemophilus influenzae genes containing CCAA nucleotide repeating units

Morton, D. J., & Stull, T. L. (1999) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1999.tb13583.x · Cited by 16

Synthetic strategy for the production of electrically polarized polyvinylidene fluoride‐trifluoroethylene—co‐polymer osseo‐functionalized with hydroxyapatite scaffold

Swain, S., Lenka, R., & Rautray, T. R. (2024) · Journal of Biomedical Materials Research Part A · doi:10.1002/jbm.a.37720 · Cited by 15

Survey and analysis of simple sequence repeats in the Ustilaginoidea virens genome and the development of microsatellite markers

Yu, M., Yu, J., Li, H., Wang, Y.-H., Yin, X., Bo, H., Ding, H., Zhou, Y., & Liu, Y. (2016) · Gene · doi:10.1016/j.gene.2016.03.016 · Cited by 15

Improved Short-Sequence-Repeat Genotyping of Mycobacterium avium subsp. paratuberculosis by Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

Ahlstrom, C. A., Barkema, H. W., & Buck, J. D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.03212-13 · Cited by 15

Variable-Number-of-Tandem-Repeats Analysis of Genetic Diversity in Pasteuria ramosa

Mouton, L., & Ebert, D. (2008) · Current Microbiology · doi:10.1007/s00284-008-9104-1 · Cited by 15

Evaluation of growth and gene expression of Mycoplasma hyopneumoniae and Mycoplasma hyorhinis in defined medium

Beier, L. S., Siqueira, F. M., & Schrank, I. S. (2018) · Molecular Biology Reports · doi:10.1007/s11033-018-4413-3 · Cited by 15

Nucleic Acid-Based Methods to Identify, Detect and Type Pathogenic Bacteria Occurring in Milk and Dairy Products

Fusco, V., & Marina, G. (2012) · InTech eBooks · doi:10.5772/49937 · Cited by 17

Genome sequence of the temperate bacteriophage PH10 from Streptococcus oralis

van der Ploeg, J. R. (2010) · Virus Genes · doi:10.1007/s11262-010-0525-0 · Cited by 15

Genome analysis technologies: Towards species identification by genotype

Naimuddin, M. (2003) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/1.4.356 · Cited by 15

Genomic Analysis Reveals Mycoplasma pneumoniae Repetitive Element 1-Mediated Recombination in a Clinical Isolate

Musatovova, O., Kannan, T. R., & Baseman, J. B. (2008) · Infection and Immunity · doi:10.1128/iai.01621-07 · Cited by 15

Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation

Ramamoorthy, S., Garapati, H. S., & Mishra, R. K. (2014) · Gene · doi:10.1016/j.gene.2014.08.052 · Cited by 14

Using unique ORFan genes as strain-specific identifiers for Escherichia coli

Ferrandis-Vila, M., Tiwari, S. K., Mamerow, S., Semmler, T., Ferrandis-Vila, M., Tiwari, S. K., van der Putten, B. C. L., Trung, N. V., Oldenkamp, R., Bootsma, M., et al. (2022) · BMC Microbiology · doi:10.1186/s12866-022-02508-y · Cited by 14

Breaking the Ice: A Review of Phages in Polar Ecosystems

Heinrichs, M. E., Piedade, G. J., Popa, O., Sommers, P. N., Trubl, G., Weißenbach, J., & Rahlff, J. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3549-0_3 · Cited by 14

Genetic relationships between sympatric populations of Bacillus cereus and Bacillus thuringiensis, as revealed by rep-PCR genomic fingerprinting

Peruca, A. P. S., Vilas-Bôas, G. T., & Arantes, O. M. N. (2008) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/s0074-02762008000500016 · Cited by 14

Molecular typing of methicillin-resistant and methicillin-susceptible Staphylococcus aureus isolates from Shiraz teaching hospitals by PCR-RFLP of coagulase gene.

Khoshkharam-Roodmajani, H., Sarvari, J., Bazargani, A., Kandekar-Ghahraman, M. R., Nazari-Alam, A., & Motamedifar, M. (2014) · Europe PMC (PubMed Central) · Cited by 14

A UspA2H-Negative Variant of Moraxella catarrhalis Strain O46E Has a Deletion in a Homopolymeric Nucleotide Repeat Common to uspA2H Genes

Wang, W., Pearson, M. M., Attia, A. S., Blick, R. J., & Hansen, E. J. (2007) · Infection and Immunity · doi:10.1128/iai.00609-06 · Cited by 14

Characterization of Salmonella Typhimurium isolates from domestically acquired infections in Finland by phage typing, antimicrobial susceptibility testing, PFGE and MLVA

Lienemann, T., Kyyhkynen, A., Halkilahti, J., Haukka, K., & Siitonen, A. (2015) · BMC Microbiology · doi:10.1186/s12866-015-0467-8 · Cited by 14

The Excess of Small Inverted Repeats in Prokaryotes

Ladoukakis, E. D., & Eyre‐Walker, A. (2008) · Journal of Molecular Evolution · doi:10.1007/s00239-008-9151-z · Cited by 14

Intraspecies variability ofDesulfovibrio desulfuricansstrains determined by the genetic profiles

ewicz, Z. D. ⁄., Szczerba, J., Wȩglarz, L., Świa̧tkowska, L., Jasinska, D., & Wilczok, T. (2003) · FEMS Microbiology Letters · doi:10.1016/s0378-1097(02)01199-0 · Cited by 14

The Future of Microbial Source Tracking Studies

Sadowsky, M. J., Call, D. R., & Domingo, J. W. S. (2014) · ASM Press eBooks · doi:10.1128/9781555815769.ch8 · Cited by 14

Assessment of Molecular Diversity in Chickpea (Cicer arietinum L.) Rhizobia and Structural Analysis of 16S rDNA Sequences from Mesorhizobium ciceri

Yadav, A., Singh, A. L., RAI, G. K., & Singh, M. (2013) · Polish Journal of Microbiology · doi:10.33073/pjm-2013-033 · Cited by 14

Promoter analysis of macrophage- and tick cell-specific differentially expressed Ehrlichia chaffeensis p28-Omp genes

Peddireddi, L., Cheng, C., & Ganta, R. R. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-99 · Cited by 14

Selection on the genic location of disruptive elements

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Molecular typing of environmental isolates

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