Stenotrophomonas maltophilia is a Gram-negative bacterium widely distributed in the environment and associated with nosocomial infections, pneumonia, and bacteremia in humans and other mammals. We have isolated and sequenced a new virus that lyses the S. maltophilia strain from a dog skin. The virus has a siphovirus-like morphology and a linear dsDNA genome 60,804 pb in length with terminal repeats, four tRNA genes, and 111 putative proteins. The annotated genes resemble the corresponding genes of some siphoviruses, but the unique genome arrangement and limited similarity of the encoded proteins suggest that this virus does not belong to any known genus. The virus uses zinc metallopeptidase for lysis of its host. This enzyme is active in the presence of Zn2+ or Mg2+ ions and maintains its bactericidal activity up to 50 °C. Both the virus itself and the endolysin specifically degrade only the host bacterial strain.

Institute of Plant Molecular Biology Department of Plant Virology Biology Centre of the Czech Academy of Sciences Branišovská 31 370 05 České Budějovice Czech Republic

Zobrazit více v PubMed

Juhnke ME, Mathre DE, Sands DC (1987) Identification of rhizosphere-competent bacteria of wheat. Appl Environ Microbiol 53:2793–2799. https://doi.org/10.1128/aem.53.12.2793-2799.1987 PubMed DOI PMC

Jeon YD, Jeong WY, Kim MH, Jung Y et al (2016) Risk factors for mortality in patients with Stenotrophomonas maltophilia bacteremia. Medicine 95:31. https://doi.org/10.1097/MD.0000000000004375 DOI

Senol E, DesJardin J, Stark PC et al (2022) Attributable mortality of Stenotrophomonas maltophilia bacteremia. Clin Infect Dis 34:1653–1656 DOI

Burdge DR, Noble MA, Campbell ME, Krell VL, Speert DP (1995) Xanthomonas maltophilia misidentified as Pseudomonas cepacia in cultures of sputum from patients with cystic fibrosis: a diagnostic pitfall with major clinical implications. Clin Infect Dis 20:445–448. https://doi.org/10.1093/clinids/20.2.445 PubMed DOI

Spencer RC (1995) The emergence of epidemic, multiple-antibiotic resistant Stenotrophomonas (Xanthomonas) maltophilia and Burkholderia (Pseudomonas) cepacia. J Hosp Infec 30:453–464. https://doi.org/10.1016/0195-6701(95)90049-7 DOI

Gales AC, Jones RN, Forward KR, Liñares J, Sader HS, Verhoef J (2001) Emerging importance of multidrug-resistant Acinetobacter species and Stenotrophomonas maltophilia as pathogens in seriously ill patients: geographic patterns, epidemiological features, and trends in the SENTRY antimicrobial surveillance program (1997–1999). Clin Infect Dis 32:S104–S113. https://doi.org/10.1086/320183 PubMed DOI

Nayyar C, Thakur P, Tak V, Saigal K (2016) Stenotrophomonas maltophilia: An emerging pathogen in paediatric population. J Clin Diagn Res 11:8–11

Albini S, Abril C, Franchira M, Hussy D, Filioussis G (2009) Stenotrophomonas maltophilia isolated from the airways of animals with chronic respiratory disease. Schweiz Arch Tierheilk 151:323–328. https://doi.org/10.1024/0036-7281.151.7.323 DOI

Winther L, Andersen RM, Baptiste KE, Aalbæk B, Guardabassi L (2010) Association of Stenotrophomonas maltophilia infection with lower airway disease in the horse: a retrospective case series. Vet J 186:358–363. https://doi.org/10.1016/j.tvjl.2009.08.026 PubMed DOI

Okazaki A, Avison MB (2008) Induction of L1 and L2 β-lactamase production in Stenotrophomonas maltophilia is dependent on an AmpR-type regulator. Antimicrob Agents Chemother 52:1525–1528. https://doi.org/10.1128/AAC.01485-07 PubMed DOI PMC

Gil-Gil T, Martínez JL, Blanco P (2020) Mechanisms of antimicrobial resistance in Stenotrophomonas maltophilia: a review of current knowledge. Expert Rev Anti Infect 18:335–347. https://doi.org/10.1080/14787210.2020.1730178 DOI

Chang HC, Chen CR, Lin JW, Shen GH, Chang KM, Tseng YH, Weng SF (2005) Isolation and characterization of novel giant Stenotrophomonas maltophilia phage phiSMA5. Appl Environ Microbiol 71:1387–1393. https://doi.org/10.1128/AEM.71.3.1387-1393.2005 PubMed DOI PMC

Peters DL, Lynch KH, Stothard P, Dennis JJ (2015) The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity. BMC Genomics 16:664. https://doi.org/10.1186/s12864-015-1848-y PubMed DOI PMC

McCutcheon JG, Lin A, Dennis JJ (2020) Isolation and characterization of the novel bacteriophage AXL3 against Stenotrophomonas maltophilia. Int J Mol Sci 21:6338. https://doi.org/10.3390/ijms21176338 PubMed DOI PMC

Li F, Li L, Zhang Y, Bai S, Sun L, Guan J, Zhang W, Cui X, Feng J, Tong Y (2022) Isolation and characterization of the novel bacteriophage vB_SmaS_BUCT626 against Stenotrophomonas maltophilia. Virus Genes 58:458–466. https://doi.org/10.1007/s11262-022-01917-5 PubMed DOI

Garcia P, Monjardín C, Martín R, Madera C, Soberón N, Garcia E, Meana Á, Suárez JE (2008) Isolation of new Stenotrophomonas bacteriophages and genomic characterization of temperate phage S1. Appl Env Microbiol 74:7552–7560. https://doi.org/10.1128/AEM.01709-08 DOI

Peters DL, Stothard P, Dennis JJ (2017) The isolation and characterization of Stenotrophomonas maltophilia T4-like bacteriophage DLP6. PLoS ONE 12:e0173341. https://doi.org/10.1371/journal.pone.0173341 PubMed DOI PMC

Fan H, Huang Y, Mi Z, Yin X, Wang L, Fan H, Zhang Z, An X, Chen J, Tong Y (2012) Complete genome sequence of IME13, a Stenotrophomonas maltophilia bacteriophage with large burst size and unique plaque polymorphism. J Virol 86:11392–11393. https://doi.org/10.1128/jvi.01908-12 PubMed DOI PMC

Vicary A, Newkirk H, Moreland R, Gonzales CF, Liu M, Ramsey J, Leavitt J (2020) Complete genome sequence of Stenotrophomonas myophage Moby. Microbiol Res Ann 9:e01422-e1519. https://doi.org/10.1128/MRA.01422-19 DOI

Chen CR, Lin CH, Lin JW, Chang CI, Tseng YH, Weng SF (2007) Characterization of a novel T4- type Stenotrophomonas maltophilia virulent phage Smp14. Arch Microbiol 188:191–197. https://doi.org/10.1007/s00203-007-0238-5 PubMed DOI

Huang Y, Fan H, Pei G, Fan H, Zhang Z, An X et al (2012) Complete genome sequence of IME15, the first T7-like bacteriophage lytic to pan-antibiotic-resistant Stenotrophomonas maltophilia. J Virol 86:13839–13840. https://doi.org/10.1128/JVI.02661-12 PubMed DOI PMC

Marquez A, Newkirk H, Moreland R, Gonzalez CF, Liu M, Ramsey J (2019) Complete genome sequence of Stenotrophomonas maltophilia podophage Ponderosa. Microbiol Res Ann 8:e01032-e1119. https://doi.org/10.1128/MRA.01032-19 DOI

Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD et al (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365. https://doi.org/10.1038/srep08365 PubMed DOI PMC

Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V (2018) A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J Mol Biol S0022–2836(17):30587–30589. https://doi.org/10.1016/j.jmb.2017.12.007 DOI

Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msv096 PubMed DOI PMC

Nishimura Y, Yoshida T, Kuronishi M, Uehara H, Ogata H, Goto S (2017) ViPTree: the viral proteomic tree server. Bioinformatics 33:2379–2380. https://doi.org/10.1093/bioinformatics/btx157 PubMed DOI

Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2012) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucl Acids Res 41:e1. https://doi.org/10.1093/nar/gks808 PubMed DOI PMC

Kaiser S, Biehler K, Jonas D (2009) A Stenotrophomonas maltophilia multilocus sequence typing scheme for inferring population structure. J Bacteriol 191:2934–2943. https://doi.org/10.1128/JB.00892-08 PubMed DOI PMC

Czajkowski R, Ozymko Z, Lojkowska E (2014) Isolation and characterization of novel soilborne lytic bacteriophages infecting Dickeya spp. biovar 3 (“D. solani”). Plant Pathol 63:758–772. https://doi.org/10.1111/ppa.12157 DOI

Korndörfer IP, Kanitz A, Danzer J, Zimmer M, Loessner MJ, Skerra A (2008) Structural analysis of the L-alanoyl-D-glutamate endopeptidase domain of Listeria bacteriophage endolysin Ply500 reveals a new member of the LAS peptidase family. Acta Cryst Sect D D64:644–650. https://doi.org/10.1107/S0907444908007890 DOI

Zheng W, Zhang C, Li Y, Pearce R, Bell EW, Zhang Y (2021) Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Rep Methods 1:100014. https://doi.org/10.1016/j.crmeth.2021.100014 PubMed DOI PMC

Owen RA, Fyfe PK, Lodge A, Biboy J, Vollmer W, Hunter WN, Sargent F (2018) Structure and activity of ChiX: a peptidoglycan hydrolase required for chitinase secretion by Serratia marcescens. Biochem J 475:415–428. https://doi.org/10.1042/BCJ20170633 PubMed DOI

Brooke JS (2012) Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clin Microbiol Rev 25:2–41. https://doi.org/10.1128/CMR.00019-11 PubMed DOI PMC

Flores-Treviño S, Bocanegra-Ibarias P, Camacho-Ortiz A, Morfín-Otero R, Salazar-Sesatty HA, Garza-González E (2019) Stenotrophomonas maltophilia biofilm: its role in infectious diseases. Expert Rev Anti Infect Therapy 17:877–893. https://doi.org/10.1080/14787210.2019.1685875 DOI

Turner D, Kropinski AM, Adriaenssens EM (2021) A roadmap for genome-based phage taxonomy. Viruses 13:506. https://doi.org/10.3390/v13030506 PubMed DOI PMC

New lytic and new temperate Staphylococcus hyicus phages