Abstract
Diphtheria is an infectious disease potentially fatal that constitutes a threat to global health security, with possible local and systemic manifestations that result mainly from the production of diphtheria toxin (DT). In the present work, we report a case of infection by Corynebacterium diphtheriae in a cutaneous lesion of a fully immunized individual and provided an analysis of the complete genome of the isolate. The clinical isolate was first identified by MALDI-TOF Mass Spectrometry. The commercial strip system and mPCR performed phenotypic and genotypic characterization, respectively. The antimicrobial susceptibility profile was determined by the disk diffusion method. Additionally, genomic DNA was sequenced and analyzed for species confirmation and sequence type (ST) determination. Detection of resistance and virulence genes was performed by comparisons against ResFinder and VFDB databases. The isolate was identified as a nontoxigenic C. diphtheriae biovar Gravis strain. Its genome presented a size of 2.46 Mbp and a G + C content of 53.5%. Ribosomal Multilocus Sequence Typing (rMLST) allowed the confirmation of species as C. diphtheriae with 100% identity. DDH in silico corroborated this identification. Moreover, MLST analyses revealed that the isolate belongs to ST-536. No resistance genes were predicted or mutations detected in antimicrobial-related genes. On the other hand, virulence genes, mostly involved in iron uptake and adherence, were found. Presently, we provided sufficient clinical data regarding the C. diphtheriae cutaneous infection in addition to the phenotypic and genomic data of the isolate. Our results indicate a possible circulation of ST-536 in Brazil, causing cutaneous infection. Considering that cases of C. diphtheriae infections, as well as diphtheria outbreaks, have still been reported in several regions of the world, studies focusing on taxonomic analyzes and predictions of resistance genes may help to improve the diagnosis and to monitor the propagation of resistant clones. In addition, they can contribute to understanding the association between variation in genetic factors and resistance to antimicrobials.
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References
Zumla A, Hui DSC (2019) Emerging and reemerging infectious diseases: global overview. Infect Dis Clin North Am 33:xiii–xix. https://doi.org/10.1016/j.idc.2019.09.001
Dazas M, Badell E, Carmi-Leroy A, Criscuolo A, Brisse S (2018) Taxonomic status of Corynebacterium diphtheriae biovar Belfanti and proposal of Corynebacterium belfantii sp. nov. Int J Syst Evol Microbiol 68:3826–3831. https://doi.org/10.1099/ijsem.0.003069
World Health Organization. Diphtheria - number of reported cases (2023) Diphtheria - number of reported cases. https://www.who.int/data/gho/data/indicators/indicator-details/GHO/diphtheria---number-of-reported-cases. Accessed 28 May 2023
Zasada AA (2014) Antimicrobial Susceptibility and Treatment. In: Burkovski A (ed) Corynebacterium diphtheriae and Related Toxigenic Species. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7624-1_12
Batista Araújo MR, Bernardes Sousa MÂ, Seabra LF, Caldeira LA, Faria CD, Bokermann S et al (2021) Cutaneous infection by non-diphtheria-toxin producing and penicillin-resistant Corynebacterium diphtheriae strain in a patient with diabetes mellitus. Access Microbiol 3:284. https://doi.org/10.1099/acmi.0.000284
Pereira GA, Pimenta FP, Dos Santos FRW, Damasco PV, Hirata R, Mattos-Guaraldi AL (2008) Antimicrobial resistance among Brazilian Corynebacterium diphtheriae strains. Mem Inst Oswaldo Cruz 103:507–510. https://doi.org/10.1590/S0074-02762008000500019
Fraz Z, Litt D, Duncan J, Mann G, Pike R, Chand M et al (2019) Molecular epidemiology and antimicrobial resistance of Corynebacterium diphtheriae and Corynebacterium ulcerans strains isolated in the UK between 2004–2017. Access Microbiol 1(1A):1. https://doi.org/10.1099/acmi.ac2019.po0110
Husada D, Soegianto SDP, Kurniawati IS, Hendrata AP, Irawan E, Kartina L et al (2019) First-line antibiotic susceptibility pattern of toxigenic Corynebacterium diphtheriae in Indonesia. BMC Infect Dis 19:1049. https://doi.org/10.1186/s12879-019-4675-y
FitzGerald RP, Rosser AJ, Perera DN (2015) Non-toxigenic penicillin-resistant cutaneous C. diphtheriae infection: a case report and review of the literature. J Infect Public Health 8:98–100. https://doi.org/10.1016/j.jiph.2014.05.006
von Hunolstein C (2002) Penicillin tolerance amongst non-toxigenic Corynebacterium diphtheriae isolated from cases of pharyngitis. J Antimicrob Chemother 50:125–128. https://doi.org/10.1093/jac/dkf107
Benamrouche N, Hasnaoui S, Badell E, Guettou B, Lazri M, Guiso N et al (2016) Microbiological and molecular characterization of Corynebacterium diphtheriae isolated in Algeria between 1992 and 2015. Clin Microbiol Infect 22:1005.e1-1005.e7. https://doi.org/10.1016/j.cmi.2016.08.013
Paveenkittiporn W, Sripakdee S, Koobkratok O, Sangkitporn S, Kerdsin A (2019) Molecular epidemiology and antimicrobial susceptibility of outbreak-associated Corynebacterium diphtheriae in Thailand, 2012. Infect Genet Evol 75:104007. https://doi.org/10.1016/j.meegid.2019.104007
Bernard K, Pacheco AL (2015) In Vitro Activity of 22 Antimicrobial Agents against Corynebacterium and Microbacterium Species Referred to the Canadian National Microbiology Laboratory. Clin Microbiol Newsl 37:187–198. https://doi.org/10.1016/j.clinmicnews.2015.11.003
Schiller J, Groman N, Coyle M (1980) Plasmids in Corynebacterium diphtheriae and diphtheroids mediating erythromycin resistance. Antimicrob Agents Chemother 18:814–821. https://doi.org/10.1128/AAC.18.5.814
Jellard CH, Lipinski AE (1973) Corynebacterium diphtheriae resistant to erytromicin and lincomycin. Lancet 301:156. https://doi.org/10.1016/S0140-6736(73)90236-5
Patey O, Bimet F, Emond JP, Estrangin E, Riegel Ph, Halioua B et al (1995) Antibiotic susceptibilities of 38 non-toxigenic strains of Corynebacterium diphtheriae. J Antimicrob Chemother 36:1108–1110. https://doi.org/10.1093/jac/36.6.1108
Sharma NC, Efstratiou A, Mokrousov I, Mutreja A, Das B, Ramamurthy T (2019) Diphtheria. Nat Rev Dis Primers 5. https://doi.org/10.1038/s41572-019-0131-y
Santos LS, Sant’Anna LO, Ramos JN, Ladeira EM, Stavracakis-Peixoto R, Borges LLG et al (2015) Diphtheria outbreak in Maranhão, Brazil: microbiological, clinical and epidemiological aspects. Epidemiol Infect 143:791–798. https://doi.org/10.1017/S0950268814001241
Truelove SA, Keegan LT, Moss WJ, Chaisson LH, Macher E, Azman AS et al (2020) Clinical and epidemiological aspects of diphtheria: a systematic review and pooled analysis. Clin Infect Dis 71:89–97. https://doi.org/10.1093/cid/ciz808
Möller J, Kraner M, Sonnewald U, Sangal V, Tittlbach H, Winkler J et al (2019) Proteomics of diphtheria toxoid vaccines reveals multiple proteins that are immunogenic and may contribute to protection of humans against Corynebacterium diphtheriae. Vaccine 37:3061–3070. https://doi.org/10.1016/j.vaccine.2019.04.059
Pimenta FP, Hirata R, Rosa ACP, Milagres LG, Mattos-Guaraldi AL (2008) A multiplex PCR assay for simultaneous detection of Corynebacterium diphtheriae and differentiation between non-toxigenic and toxigenic isolates. J Med Microbiol 57:1438–1439. https://doi.org/10.1099/jmm.0.2008/000414-0
Brazilian Committee on Antimicrobial Susceptibility Testing (BrCAST) (2021) Método de Disco-Difusão para Teste de Sensibilidade aos Antimicrobianos. https://brcast.org.br/wp-content/uploads/2022/09/06-Método-de-Disco-Difusão-BrCAST-24-6-2021.pdf. Accessed 26 May 2023
Brazilian Committee on Antimicrobial Susceptibility Testing (BrCAST) (2023) Tabelas de pontos de corte para interpretação de CIMs e diâmetros de halos. https://brcast.org.br/wp-content/uploads/2022/09/Tabela-pontos-de-corte-BrCAST-15-03-2023.pdf. Accessed 26 May 2023
Afgan E, Nekrutenko A, Grüning BA, Blankenberg D, Goecks J, Schatz MC et al (2022) The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res 50:W345–W351. https://doi.org/10.1093/nar/gkac247
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA et al (2008) The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75
Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM et al (2012) Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology (N Y) 158:1005–1015. https://doi.org/10.1099/mic.0.055459-0
Lee I, Ouk Kim Y, Park S-C, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760
Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V et al (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75:3491–3500. https://doi.org/10.1093/jac/dkaa345
Liu B, Zheng D, Zhou S, Chen L, Yang J (2022) VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res 50:D912–D917. https://doi.org/10.1093/nar/gkab1107
Zhou X, Wang X, Wu H, Huang M, Wang S, Wang X et al (2022) Bacteremia complicated with pneumonia caused by Corynebacterium diphtheriae. Infect Med 1:276–280. https://doi.org/10.1016/j.imj.2022.11.002
Peixoto RS, Hacker E, Antunes CA, Weerasekera D, de Souza de Oliveira Dias AA, Martins CA et al (2016) Pathogenic properties of a Corynebacterium diphtheriae strain isolated from a case of osteomyelitis. J Med Microbiol 65:1311–1321. https://doi.org/10.1099/jmm.0.000362
de Santis A, Siciliano RF, Sampaio RO, Akamine M, Veronese ET, de Almeida Magalhaes FM et al (2020) Non-toxigenic Corynebacterium diphtheriae infective endocarditis with embolic events: a case report. BMC Infect Dis 20:907. https://doi.org/10.1186/s12879-020-05652-w
Lowe CF, Bernard KA, Romney MG (2011) Cutaneous diphtheria in the urban poor population of Vancouver, British Columbia, Canada: a 10-year review. J Clin Microbiol 49:2664–2666. https://doi.org/10.1128/JCM.00362-11
Orouji A, Kiewert A, Filser T, Goerdt S, Peitsch WK (2012) Cutaneous diphtheria in a German man with travel history. Acta Derm Venereol 92:179–180. https://doi.org/10.2340/00015555-1216
Levi LI, Barbut F, Chopin D, Rondeau P, Lalande V, Jolivet S et al (2021) Cutaneous diphtheria: three case-reports to discuss determinants of re-emergence in resource-rich settings. Emerg Microbes Infect 10:2300–2302. https://doi.org/10.1080/22221751.2021.2008774
Kates O, Starr K, Bourassa L (2020) The brief case: nontoxigenic Corynebacterium diphtheriae in a nonhealing wound. J Clin Microbiol 58(12):e00506-20. https://doi.org/10.1128/JCM.00506-20
Berih A (1995) Cutaneous Corynebacterium diphtheriae: a traveller’s disease? Can J Infect Dis 6:150–152. https://doi.org/10.1155/1995/646325
Cockcroft WH, Boyko WJ, Allen DE (1973) Cutaneous infections due to Corynebacterium diphtheriae. Can Med Assoc J 108:329–331
Rahman KM, Khan HM, Haq JA (1983) Incidence of cutaneous diphtheria in Bangladesh. Bangladesh Med Res Counc Bull 9:49–53
Zasada AA (2013) Nontoxigenic highly pathogenic clone of Corynebacterium diphtheriae, Poland, 2004–2012. Emerg Infect Dis 19(11):1870–1872. https://doi.org/10.3201/eid1911.130297
Wojewoda CM, Koval CE, Wilson DA, Chakos MH, Harrington SM (2012) Bloodstream infection caused by nontoxigenic Corynebacterium diphtheriae in an immunocompromised host in the United States. J Clin Microbiol 50:2170–2172. https://doi.org/10.1128/JCM.00237-12
Pappenheimer AM, Murphy JR (1983) Studies on the molecular epidemiology of diphtheria. Lancet 322:923–926. https://doi.org/10.1016/S0140-6736(83)90449-X
Koopman JS, Campbell J (1975) The role of cutaneous diphtheria infections in a diphtheria epidemic. J Infect Dis 131:239–244. https://doi.org/10.1093/infdis/131.3.239
De Benoist AC, White JM, Efstratiou A, Kelly C, Mann G, Nazareth B et al (2004) Imported cutaneous diphtheria, United Kingdom. Emerg Infect Dis 10:511–513. https://doi.org/10.3201/eid1003.030524
Setiawaty V, Puspandari N, Saraswati RD, Febriyana D, Febrianti T, Rukminiati Y et al (2022) Whole-genome sequencing data of Corynebacterium diphtheriae isolated from diphtheria outbreaks in Indonesia. Data Brief 43:108460. https://doi.org/10.1016/j.dib.2022.108460
Chorlton SD, Ritchie G, Lawson T, Romney MG, Lowe CF (2020) Whole-genome sequencing of Corynebacterium diphtheriae isolates recovered from an inner-city population demonstrates the predominance of a single molecular strain. J Clin Microbiol 58(2):e01651-19. https://doi.org/10.1128/JCM.01651-19
Berger A, Dangel A, Schober T, Schmidbauer B, Konrad R, Marosevic D et al (2019) Whole genome sequencing suggests transmission of Corynebacterium diphtheriae-caused cutaneous diphtheria in two siblings, Germany, 2018. Euro Surveill 24:1800683. https://doi.org/10.2807/1560-7917.ES.2019.24.2.1800683
Hoefer A, Pampaka D, Herrera-León S, Peiró S, Varona S, López-Perea N et al (2021) Molecular and epidemiological characterization of toxigenic and nontoxigenic Corynebacterium diphtheriae, Corynebacterium belfantii, Corynebacterium rouxii, and Corynebacterium ulcerans isolates identified in Spain from 2014 to 2019. J Clin Microbiol 59(3):e02410-20. https://doi.org/10.1128/JCM.02410-20
Hennart M, Panunzi LG, Rodrigues C, Gaday Q, Baines SL, Barros-Pinkelnig M et al (2020) Population genomics and antimicrobial resistance in Corynebacterium diphtheriae. Genome Med 12:107. https://doi.org/10.1186/s13073-020-00805-7
Lyman LR, Peng ED, Schmitt MP (2018) Corynebacterium diphtheriae iron-regulated surface protein HbpA is involved in the utilization of the hemoglobin-haptoglobin complex as an iron source. J Bacteriol 200(7):e00676-17. https://doi.org/10.1128/JB.00676-17
Drazek ES, Hammack CA, Schmitt MP (2000) Corynebacterium diphtheriae genes required for acquisition of iron from haemin and haemoglobin are homologous to ABC haemin transporters. Mol Microbiol 36:68–84. https://doi.org/10.1046/j.1365-2958.2000.01818.x
Billington SJ, Esmay PA, Songer JG, Jost BH (2002) Identification and role in virulence of putative iron acquisition genes from Corynebacterium pseudotuberculosis. FEMS Microbiol Lett 208:41–45. https://doi.org/10.1111/j.1574-6968.2002.tb11058.x
Qian Y, Lee JH, Holmes RK (2002) Identification of a DtxR-regulated operon that is essential for siderophore-dependent iron uptake in Corynebacterium diphtheriae. J Bacteriol 184:4846–4856. https://doi.org/10.1128/JB.184.17.4846-4856.2002
Kunkle CA, Schmitt MP (2005) Analysis of a DtxR-regulated iron transport and siderophore biosynthesis gene cluster in Corynebacterium diphtheriae. J Bacteriol 187:422–433. https://doi.org/10.1128/JB.187.2.422-433.2005
Broadway MM, Rogers EA, Chang C, Huang IH, Dwivedi P, Yildirim S et al (2013) Pilus gene pool variation and the virulence of Corynebacterium diphtheriae clinical isolates during infection of a nematode. J Bacteriol 195:3774–3783. https://doi.org/10.1128/JB.00500-13
Antunes CA, Sanches dos Santos L, Ott L, Hirata R, de Luna M das G, Burkovski A et al (2015) Characterization of DIP0733, a multi-functional virulence factor of Corynebacterium diphtheriae. Microbiology (N Y) 161:639–647. https://doi.org/10.1099/mic.0.000020
Ott L, Höller M, Gerlach RG, Hensel M, Rheinlaender J, Schäffer TE et al (2010) Corynebacterium diphtheriae invasion-associated protein (DIP1281) is involved in cell surface organization, adhesion and internalization in epithelial cells. BMC Microbiol 10:2. https://doi.org/10.1186/1471-2180-10-2
Kolodkina V, Denisevich T, Titov L (2011) Identification of Corynebacterium diphtheriae gene involved in adherence to epithelial cells. Infect Genet Evol 11:518–521. https://doi.org/10.1016/j.meegid.2010.11.004
Reardon-Robinson ME, Osipiuk J, Jooya N, Chang C, Joachimiak A, Das A et al (2015) A thiol-disulfide oxidoreductase of the Gram-positive pathogen Corynebacterium diphtheriae is essential for viability, pilus assembly, toxin production and virulence. Mol Microbiol 98:1037–1050. https://doi.org/10.1111/mmi.13172
Funding
This study was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico—CNPq (309948/2018–5) and Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro—FAPERJ (E26/211.554/2019; E-26/202.087/2020; E- 26/205.900/2022).
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Araújo MRB et al. – Corynebacterium diphtheriae in an immunized individual.
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Araújo, M.R.B., Ramos, J.N., de Oliveira Sant’Anna, L. et al. Phenotypic and molecular characterization and complete genome sequence of a Corynebacterium diphtheriae strain isolated from cutaneous infection in an immunized individual. Braz J Microbiol 54, 1325–1334 (2023). https://doi.org/10.1007/s42770-023-01086-z
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DOI: https://doi.org/10.1007/s42770-023-01086-z