808
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Genomic characters of Anaplasma bovis and genetic diversity in China

, , , , , , , , , , , & show all
Article: 2323153 | Received 27 Dec 2023, Accepted 20 Feb 2024, Published online: 05 Mar 2024

References

  • Atif FA. Alpha proteobacteria of genus Anaplasma (Rickettsiales: Anaplasmataceae): epidemiology and characteristics of Anaplasma species related to veterinary and public health importance. Parasitology. 2016;143(6):659–685. doi:10.1017/S0031182016000238
  • Dumler JS, Barbet AF, Bekker CP, et al. Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehirlichia with Anaplasma, Cowdria with Ehilichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and ‘HGE agent’ as subjective synonyms of Ehrlichia phagocytophila. Int J Syst Evol Microbiol. 2001;51(Pt 6):2145–2165. doi:10.1099/00207713-51-6-2145
  • Li H, Zheng YC, Ma L, et al. Human infection with a novel tick-borne Anaplasma species in China: a surveillance study. Lancet Infect Dis. 2015;15(6):663–670. doi:10.1016/S1473-3099(15)70051-4
  • Tate CM, Howerth EW, Mead DG, et al. Anaplasma odocoilei sp. nov. (family Anaplasmataceae) from white-tailed deer (Odocoileus virginianus). Ticks Tick Borne Dis. 2013;4(1-2):110–119. doi:10.1016/j.ttbdis.2012.09.005
  • Rar V, Tkachev S, Tikunova N. Genetic diversity of Anaplasma bacteria: twenty years later. Infect Genet Evol. 2021;91:104833. doi:10.1016/j.meegid.2021.104833
  • Ben Said M, Belkahia H, Messadi L. Anaplasma spp. in North Africa: a review on molecular epidemiology, associated risk factors and genetic characteristics. Ticks Tick Borne Dis. 2018;9(3):543–555. doi:10.1016/j.ttbdis.2018.01.003
  • Guo WP, Tie WF, Meng S, et al. Extensive genetic diversity of Anaplasma bovis in ruminants in Xi'an, China. Ticks Tick Borne Dis. 2020;11(5):101477. doi:10.1016/j.ttbdis.2020.101477
  • Masuzawa T, Uchishima Y, Fukui T, et al. Detection of Anaplasma phagocytophilum and Anaplasma bovis in small wild mammals from Taichung and Kinmen Island, Taiwan. Jpn J Infect Dis. 2014;67(2):111–114. doi:10.7883/yoken.67.111
  • Sashika M, Abe G, Matsumoto K, et al. Molecular survey of Anaplasma and Ehrlichia infections of feral raccoons (Procyon lotor) in Hokkaido, Japan. Vector Borne Zoonotic Dis. 2011;11(4):349–354. doi:10.1089/vbz.2010.0052
  • Li Y, Chen Z, Liu Z, et al. First report of Theileria and Anaplasma in the Mongolian gazelle, Procapra gutturosa. Parasite Vectors. 2014;7:614.
  • Oliveira AC, Luz MF, Granada S, et al. Molecular detection of Anaplasma bovis, Ehrlichia canis and Hepatozoon felis in cats from Luanda, Angola. Parasite Vectors. 2018;11(1):167. doi:10.1186/s13071-018-2767-y
  • Tay ST, Koh FX, Kho KL, et al. Rickettsial infections in monkeys, Malaysia. Emerg Infect Dis. 2015;21(3):545–547. doi:10.3201/eid2103.141457
  • Lu M, Li F, Liao Y, et al. Epidemiology and diversity of Rickettsiales bacteria in humans and animals in Jiangsu and Jiangxi provinces, China. Sci Rep. 2019;9(1):13176. doi:10.1038/s41598-019-49059-3
  • Lu M, Chen Q, Qin X, et al. Anaplasma bovis infection in fever and thrombocytopenia patients - Anhui Province, China, 2021. China CDC Wkly. 2022;4(12):249–253. doi:10.46234/ccdcw2022.053
  • Karpathy SE, Kingry L, Pritt BS, et al. Anaplasma bovis -like infections in humans, United States, 2015-2017. Emerg Infect Dis. 2023;29(9):1904–1907. doi:10.3201/eid2909.230559
  • Brayton KA, Kappmeyer LS, Herndon DR, et al. Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins. Proc Natl Acad Sci USA. 2005;102(3):844–849. doi:10.1073/pnas.0406656102
  • Dall'Agnol B, Webster A, Souza UA, et al. Genomic analysis on Brazilian strains of Anaplasma marginale. Rev Bras Parasitol Vet. 2021;30(2):e000421.
  • Dunning Hotopp JC, Lin M, Madupu R, et al. Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet. 2006;2(2):e21. doi:10.1371/journal.pgen.0020021
  • Barbet AF, Al-Khedery B, Stuen S, et al. An emerging tick-borne disease of humans is caused by a subset of strains with conserved genome structure. Pathogens. 2013;2(3):544–555. doi:10.3390/pathogens2030544
  • Liu Z, Peasley AM, Yang J, et al. The Anaplasma ovis genome reveals a high proportion of pseudogenes. BMC Genomics. 2019;20(1):69. doi:10.1186/s12864-018-5374-6
  • Lin ZT, Du LF, Zhang MZ, et al. Genomic characteristics of emerging intraerythrocytic Anaplasma capra and high prevalence in goats, China. Emerg Infect Dis. 2023;29(9):1780–1788.
  • Herndon DR, Palmer GH, Shkap V, et al. Complete genome sequence of Anaplasma marginale subsp. centrale. J Bacteriol. 2010;192(1):379–380. doi:10.1128/JB.01330-09
  • Llanes A, Rajeev S. First whole genome sequence of Anaplasma platys, an obligate intracellular rickettsial pathogen of dogs. Pathogens. 2020;9(4):277. doi:10.3390/pathogens9040277
  • Wen B, Jian R, Zhang Y, et al. Simultaneous detection of Anaplasma marginale and a new Ehrlichia species closely related to Ehrlichia chaffeensis by sequence analyses of 16S ribosomal DNA in Boophilus microplus ticks from Tibet. J Clin Microbiol. 2002;40(9):3286–3290. doi:10.1128/JCM.40.9.3286-3290.2002
  • Aung A, Kaewlamun W, Narapakdeesakul D, et al. Molecular detection and characterization of tick-borne parasites in goats and ticks from Thailand. Ticks Tick Borne Dis. 2022;13(3):101938. doi:10.1016/j.ttbdis.2022.101938
  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359. doi:10.1038/nmeth.1923
  • Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2). doi:10.1093/gigascience/giab008
  • Nurk S, Meleshko D, Korobeynikov A, et al. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27(5):824–834. doi:10.1101/gr.213959.116
  • Kang DD, Froula J, Egan R, et al. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165. doi:10.7717/peerj.1165
  • Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–2069. doi:10.1093/bioinformatics/btu153
  • Parks DH, Imelfort M, Skennerton CT, et al. Checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043–1055. doi:10.1101/gr.186072.114
  • Emms DM, Kelly S. Orthofinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20(1):238. doi:10.1186/s13059-019-1832-y
  • Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780. doi:10.1093/molbev/mst010
  • Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17(4):540–552. doi:10.1093/oxfordjournals.molbev.a026334
  • Minh BQ, Schmidt HA, Chernomor O, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37(5):1530–1534. doi:10.1093/molbev/msaa015
  • Conway JR, Lex A, Gehlenborg N. Upsetr: an R package for the visualization of intersecting sets and their properties. Bioinformatics. 2017;33(18):2938–2940. doi:10.1093/bioinformatics/btx364
  • Aramaki T, Blanc-Mathieu R, Endo H, et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2020;36(7):2251–2252. doi:10.1093/bioinformatics/btz859
  • Cantalapiedra CP, Hernández-Plaza A, Letunic I, et al. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38(12):5825–5829. doi:10.1093/molbev/msab293
  • Pebesma E. Simple features for R: standardized support for spatial vector data. R J. 2018;10(1):439–446. doi:10.32614/RJ-2018-009
  • Yu G. Using ggtree to visualize data on tree-like structures. Curr Protoc Bioinformatics. 2020;69(1):e96. doi:10.1002/cpbi.96
  • Mann S, Chen YP. Bacterial genomic G + C composition-eliciting environmental adaptation. Genomics. 2010;95(1):7–15. doi:10.1016/j.ygeno.2009.09.002
  • Frutos R, Viari A, Ferraz C, et al. Comparative genomic analysis of three strains of Ehrlichia ruminantium reveals an active process of genome size plasticity. J Bacteriol. 2006;188(7):2533–2542. doi:10.1128/JB.188.7.2533-2542.2006
  • Li G, Xie F, Zhang Y, et al. Role of (p)ppGpp in viability and biofilm formation of Actinobacillus pleuropneumoniae S8. PLoS One. 2015;10(10):e0141501.
  • Liang J, Liu J, Wang X, et al. Genomic analysis reveals adaptation of Vibrio campbellii to the hadal ocean. Appl Environ Microbiol. 2022;88(16):e0057522. doi:10.1128/aem.00575-22
  • Mandal RK, Kwon YM. Global screening of Salmonella enterica serovar Typhimurium genes for desiccation survival. Front Microbiol. 2017;8:1723. doi:10.3389/fmicb.2017.01723
  • Chen L, Yang J, Yu J, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005;33:D325–D328. doi:10.1093/nar/gki008
  • Liu B, Zheng D, Zhou S, et al. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 2022;50(D1):D912–d917. doi:10.1093/nar/gkab1107
  • Crosby FL, Munderloh UG, Nelson CM, et al. Disruption of VirB6 paralogs in Anaplasma phagocytophilum attenuates its growth. J Bacteriol. 2020;202(23):e00301-20. doi:10.1128/JB.00301-20
  • Matos AL, Curto P, Simões I. Moonlighting in Rickettsiales: expanding virulence landscape. Trop Med Infect Dis. 2022;7(2):32. doi:10.3390/tropicalmed7020032
  • Park J, Kim KJ, Choi KS, et al. Anaplasma phagocytophilum AnkA binds to granulocyte DNA and nuclear proteins. Cell Microbiol. 2004;6(8):743–751. doi:10.1111/j.1462-5822.2004.00400.x
  • IJdo JW, Carlson AC, Kennedy EL. Anaplasma phagocytophilum AnkA is tyrosine-phosphorylated at EPIYA motifs and recruits SHP-1 during early infection. Cell Microbiol. 2007;9(5):1284–1296. doi:10.1111/j.1462-5822.2006.00871.x
  • Hebert KS, Seidman D, Oki AT, et al. Anaplasma marginale outer membrane protein A is an Adhesin that recognizes sialylated and fucosylated glycans and functionally depends on an essential binding domain. Infect Immun. 2017;85(3). doi:10.1128/IAI.00968-16
  • Ojogun N, Kahlon A, Ragland SA, et al. Anaplasma phagocytophilum outer membrane protein A interacts with sialylated glycoproteins to promote infection of mammalian host cells. Infect Immun. 2012;80(11):3748–3760. doi:10.1128/IAI.00654-12
  • Niu H, Kozjak-Pavlovic V, Rudel T, et al. Anaplasma phagocytophilum Ats-1 is imported into host cell mitochondria and interferes with apoptosis induction. PLoS Pathog. 2010;6(2):e1000774. doi:10.1371/journal.ppat.1000774
  • Niu H, Rikihisa Y. Ats-1: a novel bacterial molecule that links autophagy to bacterial nutrition. Autophagy. 2013;9(5):787–788. doi:10.4161/auto.23693
  • Ge Y, Yin H, Rikihisa Y, et al. Molecular detection of tick-borne Rickettsiales in goats and sheep from southeastern China. Vector Borne Zoonotic Dis. 2016;16(5):309–316. doi:10.1089/vbz.2015.1884
  • Lu M, Tian J, Zhao H, et al. Molecular survey of vector-borne pathogens in ticks, sheep keds, and domestic animals from Ngawa, Southwest China. Pathogens. 2022;11(5):606. doi:10.3390/pathogens11050606.