Comparative genomic analysis of Mycoplasma related to cell culture for infB gene-based loop-mediated isothermal amplification.
Cell culture
Comparative genomics
Loop-mediated isothermal amplification
Mycoplasma contamination
infB gene
Journal
World journal of microbiology & biotechnology
ISSN: 1573-0972
Titre abrégé: World J Microbiol Biotechnol
Pays: Germany
ID NLM: 9012472
Informations de publication
Date de publication:
25 Oct 2023
25 Oct 2023
Historique:
received:
09
06
2023
accepted:
06
10
2023
medline:
26
10
2023
pubmed:
25
10
2023
entrez:
25
10
2023
Statut:
epublish
Résumé
Mycoplasma contamination in cell culture affects the properties of cell lines. Gold standard detection by microbiological culture takes days and requires specialists. The polymerase chain reaction and loop-mediated isothermal amplification (LAMP) are fast molecular options, but LAMP only requires one heating block for DNA amplification. This study presents a comparative genomic analysis of Mycoplasma species to identify common target genes different from the rrsA gene, which encodes 16 S rRNA. The aim is to implement a LAMP assay to detect Mycoplasma species, reducing the time and specialized equipment required for detection. We performed a comparative genomic analysis through Mauve software and the GView server and selected infB and clpB genes as target candidates for designing LAMP primers. We evaluated both genes by multiple sequence alignment (MSA). The infB gene presented the best score MSA assessment with lower odd-log values (5,480,281) than other genes. We selected the infB gene to design LAMP primers specific to Mycoplasma spp. We used these primers to implement LAMP at 63 °C for 30 min, which showed 100% positive amplifications for detecting Mycoplasma spp. In conclusion, we present a methodology utilizing the infB gene-based LAMP assay to detect three of the six most prevalent Mycoplasma species in cell culture.
Identifiants
pubmed: 37878143
doi: 10.1007/s11274-023-03794-y
pii: 10.1007/s11274-023-03794-y
doi:
Substances chimiques
DNA Primers
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
355Subventions
Organisme : Secretaría de Investigación y Posgrado (SIP-IPN)
ID : SIP:20221169
Organisme : Instituto de Ingeniería, Universidad Nacional Autónoma de México
ID : PAPIIT IT100922
Organisme : Consejo Nacional de Ciencia y Tecnología
ID : A1-S-21548
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature B.V.
Références
Akram A, Maley M, Gosbell I, Nguyen T, Chavada R (2017) Utility of 16S rRNA PCR performed on clinical specimens in patient management. Int J Infect Dis 57:144–149. https://doi.org/10.1016/j.ijid.2017.02.006
doi: 10.1016/j.ijid.2017.02.006
pubmed: 28216180
Altschul SF, Gish W (1996) Local alignment statistics. Methods Enzymol 266:460–480. https://doi.org/10.1016/S0076-6879(96)66029-7
doi: 10.1016/S0076-6879(96)66029-7
pubmed: 8743700
Arfaatabar M, Goodarzi NN, Afshar D, Memariani H, Azimi G, Masoorian E, Pourmand MR (2019) Rapid detection of Mycoplasma pneumoniae by loop-mediated isothermal amplification (LAMP) in clinical respiratory specimens. Iran J Public Health 48:917–924
pubmed: 31523649
pmcid: 6717426
Bertelli C, Laird MR, Williams KP, Simon Fraser University Research Computing Group, Lau BY, Hoad G, Brinkman FS (2017) IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 45:W30–W35. https://doi.org/10.1093/nar/gkx343
doi: 10.1093/nar/gkx343
pubmed: 28472413
pmcid: 5570257
Carrillo-Ávila JA, de la Fuente A, Aguilar-Quesada R, Ligero G, Río-Ortiz D, Catalina P (2023) Development and evaluation of a New qPCR assay for the detection of Mycoplasma in cell cultures. Curr Issues Mol Biol 45(8):6903–6915. https://doi.org/10.3390/cimb45080435
doi: 10.3390/cimb45080435
pubmed: 37623254
pmcid: 10453501
Christensen H, Kuhnert P, Olsen JE, Bisgaard M (2004) Comparative phylogenies of the housekeeping genes atpD, infB, and rpoB and the 16S rRNA gene within the Pasteurellaceae. Int J Syst Evol Microbiol 54:1601–1609. https://doi.org/10.1099/ijs.0.03018-0
doi: 10.1099/ijs.0.03018-0
pubmed: 15388716
Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14(6):1188–1190. https://doi.org/10.1101/gr.849004
doi: 10.1101/gr.849004
pubmed: 15173120
pmcid: 419797
D’Apolito D, D’Aiello L, Pasqua S, Pecoraro L, Barbera F, Douradinha B, Vitale A, Cancelliere R, Currò M, Mauro V, Pascale M, Schillaci O, Conaldi PG (2020) Strategy and validation of a consistent and reproducible nucleic acid technique for mycoplasma detection in advanced therapy medicinal products. Biologicals 64:49–57. https://doi.org/10.1016/j.biologicals.2020.01.001
doi: 10.1016/j.biologicals.2020.01.001
pubmed: 31980348
Darling AC, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394–1403. https://doi.org/10.1101/gr.2289704
doi: 10.1101/gr.2289704
pubmed: 15231754
pmcid: 442156
Dhama K, Karthik K, Chakraborty S, Tiwari R, Kapoor S, Kumar A, Thomas P (2014) Loop-mediated isothermal amplification of DNA (LAMP): a new diagnostic tool lights the world of diagnosis of animal and human pathogens: a review. Pak J Biol Sci 17:151–166. https://doi.org/10.3923/pjbs.2014.151.166
doi: 10.3923/pjbs.2014.151.166
pubmed: 24783797
Drexler HG, Uphoff CC (2002) Mycoplasma contamination of cell cultures: incidence, sources, effects, detection, elimination, prevention. Cytotechnol 39(2):75–90. https://doi.org/10.1023/A:1022913015916
doi: 10.1023/A:1022913015916
Edwards T, Burke P, Smalley HB, Gillies L, Longhurst D, Vipond B, Hobbs G (2015) Loop-mediated isothermal amplification (LAMP) for the rapid detection of Mycoplasma genitalium. Diagn Microbiol Infect Dis 83(1):13–17. https://doi.org/10.1016/j.diagmicrobio.2015.05.010
doi: 10.1016/j.diagmicrobio.2015.05.010
pubmed: 26072150
Falagan-Lotsch P, Lopes TS, Ferreira N, Balthazar N, Monteiro AM, Borojevic R, Granjeiro JM (2015) Performance of PCR-based and bioluminescent assays for mycoplasma detection. J Microbiol Methods 118:31–36. https://doi.org/10.1016/j.mimet.2015.08.010
doi: 10.1016/j.mimet.2015.08.010
pubmed: 26296900
Feng N, Huang X, Jia Y (2019) Mycoplasma contamination affects cell characteristics and decreases the sensitivity of BV2 microglia to LPS stimulation. Cytotechnology 71:623–634. https://doi.org/10.1007/s10616-019-00311-8
doi: 10.1007/s10616-019-00311-8
pubmed: 30945036
pmcid: 6465415
Fratz-Berilla EJ, Faison T, Kohnhorst CL, Velugula‐Yellela SR, Powers DN, Brorson K, Agarabi C (2019) Impacts of intentional mycoplasma contamination on CHO cell bioreactor cultures. Biotechnol Bioeng 116:3242–3252. https://doi.org/10.1002/bit.27161
doi: 10.1002/bit.27161
pubmed: 31478189
pmcid: 6900124
Gioia G, Werner B, Nydam DV, Moroni P (2016) Validation of a mycoplasma molecular diagnostic test and distribution of mycoplasma species in bovine milk among New York State dairy farms. J Dairy Sci 99:4668–4677. https://doi.org/10.3168/jds.2015-10724
doi: 10.3168/jds.2015-10724
pubmed: 27016831
González N, Rodríguez N, Torres W, De Jesús R (2011) Protocolo sencillo para la extracción de ADN genómico de tejido de oreja del ratón y la rata, usando la enzima bromelina. Rev Cient 21:233–238
Gotoh K, Nishimura N, Ohshima Y, Arakawa Y, Hosono H, Yamamoto Y, Ozaki T, Iwata Y, Nakane K, Funahashi K, Funahashi K (2012) Detection of Mycoplasma pneumoniae by loop-mediated isothermal amplification (LAMP) assay and serology in pediatric community-acquired pneumonia. J Infect Chemother 18(5):662–667. https://doi.org/10.1007/s10156-012-0388-5
doi: 10.1007/s10156-012-0388-5
pubmed: 22370920
Hardinge P, Murray JA (2019) Reduced false positives and improved reporting of loop-mediated isothermal amplification using quenched fluorescent primers. Sci Rep 9:1–13. https://doi.org/10.1038/s41598-019-43817-z
doi: 10.1038/s41598-019-43817-z
He L, Xu HS (2011) Development of a multiplex loop-mediated isothermal amplification (mLAMP) method for the simultaneous detection of white spot syndrome virus and infectious hypodermal and hematopoietic necrosis virus in penaeid shrimp. Aquaculture 311:94–99. https://doi.org/10.1016/j.aquaculture.2010.11.051
doi: 10.1016/j.aquaculture.2010.11.051
Huang X, Tang G, Ismail N, Wang X (2022) Developing RT-LAMP assays for rapid diagnosis of SARS-CoV-2 in saliva. E Bio Medicine 75:103736. https://doi.org/10.1016/j. ebiom.2021.103736
doi: 10.1016/j.ebiom.2021.103736
Ji Y, Karbaschi M, Cooke MS (2019) Mycoplasma infection of cultured cells induces oxidative stress and attenuates cellular base excision repair activity. Mutat Res Genet Toxicol Environ Mutagen 845:1–5. https://doi.org/10.1016/j.mrgentox.2019.05.010
doi: 10.1016/j.mrgentox.2019.05.010
Jia B, Li X, Liu W, Lu C, Lu X, Ma L, Ma Y, Shi C, Wang L, Wu D, Yang X, Yu J, Zhang X, Zhao J, Wei C (2019) GLAPD: whole genome-based LAMP primer design for a set of target genomes. Front Microbiol 10:2860. https://doi.org/10.3389/fmicb.2019.02860
doi: 10.3389/fmicb.2019.02860
pubmed: 31921040
pmcid: 6923652
Kaur N, Thota N, Toley BJ (2020) A stoichiometric and pseudo kinetic model of loop-mediated isothermal amplification. Comput Struct Biotechnol J 18:2336–2346. https://doi.org/10.1016/j.csbj.2020.08.020
doi: 10.1016/j.csbj.2020.08.020
pubmed: 32994892
pmcid: 7493047
Kazemiha VM, Azari S, Habibi-Anbouhi M, Amanzadeh A, Bonakdar S, Shokrgozar MA, Mahdian R (2018) Effectiveness of Plasmocure™ in eliminating Mycoplasma species from contaminated cell cultures: a comparative study versus other antibiotics. Cell J 21:143–149. https://doi.org/10.22074/cellj.2019.5996
doi: 10.22074/cellj.2019.5996
Krzysztoń-Russjan J, Chudziak J, Bednarek M, Anuszewska EL (2021) Development of new PCR assay with SYBR green I for detection of Mycoplasma, Acholeplasma, and Ureaplasma sp. in cell cultures. Diagnostics 11(5):876. https://doi.org/10.3390/diagnostics11050876
doi: 10.3390/diagnostics11050876
pubmed: 34068904
pmcid: 8156504
Kursa O, Woźniakowski G, Tomczyk G, Sawicka A, Minta Z (2015) Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification. Arch Microbiol 197:319–325. https://doi.org/10.1007/s00203-014-1063-2
doi: 10.1007/s00203-014-1063-2
pubmed: 25413672
Lai M, Iacono E, Spezia PG, Lottini G, La Rocca V, Quaranta P, Pistello M, Freer G (2022) A low-cost simple test for weekly detection of Mycoplasma hyorhinis and Mycoplasma arginini contaminations in cell cultures and viral preparations. J Virol Methods 299:114327. https://doi.org/10.1016/j.jviromet.2021.114327
doi: 10.1016/j.jviromet.2021.114327
pubmed: 34644588
Lin Y, Zhang RR (2011) Putative essential and core-essential genes in Mycoplasma genomes. Sci Rep 1(1):1–7. https://doi.org/10.1038/srep00053
doi: 10.1038/srep00053
Ludwig KU, Schmithausen RM, Li D, Jacobs ML, Hollstein R, Blumenstock, Liebging J, Słabicki M, Ben-Shmuel A, Israeli O, Weiss S, Ebert TS, Paran N, Rüdiger W, Wilbring G, Feldman D, Lippke B, Ishorst N, Hochfeld LM, Beins EC, Kaltheuner IH, Schmitz M, Wöhler A, Döhla M, Sib E, Jentzsch M, Moench EM, Borrajo JD, Strecker J, Reinhardt J, Cleary B, Geyer M, Hölzel M, Macrae R, Nöthen MM, Hoffmann P, Exner M, Regev A, Zhang F, Schmid-Burgk JL (2021) LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding. Nat Biotechnol 39(12):1556–1562. https://doi.org/10.1038/s41587-021-00966-9
doi: 10.1038/s41587-021-00966-9
pubmed: 34188222
pmcid: 8678193
Ma P, He LL, Pironti A, Laibinis HH, Ernst CM, Manson AL, Bhattacharyya RP, Earl AM, Livny J, Hung DT (2021) Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics. Elife 19(10):e67310. https://doi.org/10.7554/ELIFE.67310
doi: 10.7554/ELIFE.67310
Mbelo S, Gay V, Blanchard S, Abachin E, Falque S, Lechenet J, de Saint-Vis B (2018) Development of a highly sensitive PCR/DNA chip method to detect mycoplasmas in a veterinary modified live vaccine. Biologicals 54:22–27. https://doi.org/10.1016/j.biologicals.2018.05.002
doi: 10.1016/j.biologicals.2018.05.002
pubmed: 29753589
Molla Kazemiha V, Amanzadeh A, Memarnejadian A, Azari S, Shokrgozar MA, Mahdian R, Bonakdar S (2014) Sensitivity of biochemical test in comparison with other methods for the detection of mycoplasma contamination in human and animal cell lines stored in the National Cell Bank of Iran. Cytotechnology 66:861–873. https://doi.org/10.1007/s10616-013-9640-9
doi: 10.1007/s10616-013-9640-9
pubmed: 24493067
pmcid: 4158010
Nicholas KB, Nicholas HJ (1997) GeneDoc: a tool for editing and annotating multiple sequence alignments. Distributed by the authors. http://www.psc.edu/biomed/genedoc Accessed 07 Dec 2018
Okonechnikov K, Golosova O, Fursov M, Ugene Team (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinf 28:1166–1167. https://doi.org/10.1093/bioinformatics/bts091
doi: 10.1093/bioinformatics/bts091
Patel A, Harris KA, Fitzgerald F (2017) What is broad-range 16S rDNA PCR? Arch Dis Child Educ Pract 102(5):261–264. https://doi.org/10.1136/archdischild-2016-312049
doi: 10.1136/archdischild-2016-312049
Petkau A, Stuart-Edwards M, Stothard P, Van Domselaar G (2010) Interactive microbial genome visualization with GView. Bioinf 26:3125–3126. https://doi.org/10.1093/bioinformatics/btq588
doi: 10.1093/bioinformatics/btq588
Rice P, Longden I, Bleasby A (2000) EMBOSS: the european molecular biology open software suite. Trends Genet 16:276–277. https://doi.org/10.1016/s0168-9525(00)02024-2
doi: 10.1016/s0168-9525(00)02024-2
pubmed: 10827456
Shi W, Wei M, Wang Q, Wang H, Ma C, Shi C (2019) Rapid diagnosis of Mycoplasma pneumonia infection by denaturation bubble-mediated strand exchange amplification: comparison with LAMP and real-time PCR. Sci Rep 9(1):896. https://doi.org/10.1038/s41598-018-36751-z
doi: 10.1038/s41598-018-36751-z
pubmed: 30696841
pmcid: 6351683
Soheily Z, Soleimani M, Majidzadeh-Ardebili K (2019) Detection of Mycoplasma contamination of cell culture by a loop-mediated isothermal amplification method. Cell J 21:43–48. https://doi.org/10.22074/cellj.2019.5624
doi: 10.22074/cellj.2019.5624
pubmed: 30507087
Song Q, Wang L, Fang R, Khan MK, Zhou Y, Zhao J (2012) Detection of Mycoplasma wenyonii in cattle and transmission vectors by the loop-mediated isothermal amplification (LAMP) assay. Trop Animl Health Prod 45:247–250. https://doi.org/10.1007/s11250-012-0197-y
doi: 10.1007/s11250-012-0197-y
Soudy AF (2019) Prophylactic control of Mycoplasma contamination in starting biological materials used in viral vaccine production. J Appl Vet Sci 4:30–34. https://doi.org/10.21608/JAVS.2019.62673
doi: 10.21608/JAVS.2019.62673
Suleman E, Mtshali MS, Lane E (2016) Investigation of false positives associated with loop-mediated isothermal amplification assays for detection of Toxoplasma gondii in archived tissue samples of captive felids. J Vet Diagn Invest 28:536–542. https://doi.org/10.1177/1040638716659864
doi: 10.1177/1040638716659864
pubmed: 27449130
Sung J, Hawkins JR (2020) A highly sensitive internally-controlled real-time PCR assay for mycoplasma detection in cell cultures. Biologicals 64:58–72. https://doi.org/10.1016/j.biologicals.2019.12.007
doi: 10.1016/j.biologicals.2019.12.007
pubmed: 31956000
Tang J, Hu M, Lee S, Roblin R (2000) A polymerase chain reaction based method for detecting Mycoplasma /Acholeplasma contaminants in cell culture. J Microbiol J Methods 39(2):121–126. https://doi.org/10.1016/s0167-7012(99)00107-4
doi: 10.1016/s0167-7012(99)00107-4
Uphoff CC, Denkmann SA, Drexler HG (2012) Treatment of mycoplasma contamination in cell cultures with plasmocin. J Biomed Biotechnol. https://doi.org/10.1155/2012/267678
doi: 10.1155/2012/267678
pubmed: 23091342
pmcid: 3470117
Wan L, Chen T, Gao J, Dong C, Wong AHH, Jia Y, Martins RP (2017) A digital microfluidic system for loop-mediated isothermal amplification and sequence specific pathogen detection. Sci Rep 7:14586. https://doi.org/10.1038/s41598-017-14698-x
doi: 10.1038/s41598-017-14698-x
pubmed: 29109452
pmcid: 5673945
Warneford-Thomson R, Shah PP, Lundgren P, Lerner J, Morgan J, Davila A, Timp W, Wu Y, Lu S, Deikus G, Chen S, Hultquist JF, Bonasio R (2022) A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva. Elife 11:e69949. https://doi.org/10.7554/eLife.69949
doi: 10.7554/eLife.69949
pubmed: 35532013
pmcid: 9084890
Xia Q, Cheng L, Zhang H, Sun S, Liu F, Li H, Diao Y (2016) Identification of vaginal bacteria diversity and its association with clinically diagnosed bacterial vaginosis by denaturing gradient gel electrophoresis and correspondence analysis. Infect Genet Evol 44:479–486. https://doi.org/10.1016/j.meegid.2016.08.001
doi: 10.1016/j.meegid.2016.08.001
pubmed: 27503595
Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL (2012) Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinf 13:1–13. https://doi.org/10.1186/1471-2105-13-134
doi: 10.1186/1471-2105-13-134
Young L, Sung J, Stacey G, Masters JR (2010) Detection of Mycoplasma in cell cultures. Nat Protoc 5:929. https://doi.org/10.1038/nprot.2010.43
doi: 10.1038/nprot.2010.43
pubmed: 20431538
Zhang J, Cao J, Zhu M, Xu M (2019a) Loop-mediated isothermal amplification-lateral-flow dipstick (LAMP-LFD) to detect Mycoplasma ovipneumoniae. World J Microbiol Biotechnol 35:31. https://doi.org/10.1007/s11274-019-2601-5
doi: 10.1007/s11274-019-2601-5
pubmed: 30701329
pmcid: 6353813
Zhang TT, Liu MZ, Yin RH, Yao LQ, Liu BS, Chen ZL (2019b) Rapid and simple detection of Glaesserella parasuis in synovial fluid by recombinase polymerase amplification and lateral flow strip. BMC Vet Res 15(1):1–7. https://doi.org/10.1186/s12917-019-2039-x
doi: 10.1186/s12917-019-2039-x