Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924).
Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol. 72, 259–268 (1972).
Grimont, P. A. D., Grimont, F. & Dulong de Rosnay, H. L. C. Taxonomy of the genus Serratia. J. Gen. Microbiol. 98, 39–66 (1977).
Grimont, F., Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Characterization of Serratia marcescens, S. liquefaciens, S. plymuthica and S. marinorubra by electrophoresis of their proteinases. J. Gen. Microbiol. 99, 301–310 (1977).
Grimont, P. A. D. et al. Deoxyribonucleic acid relatedness between Serratia plymuthica and other Serratia species, with a description of Serratia odorifera sp. nov. (Type strain: ICPB 3995). Int. J. System. Bacteriol. 28, 453–463 (1978).
Grimont, P. A. D., Grimont, F. & Starr, M. P. Serratia ficaria sp. nov., a bacterial species associated with Smyrna figs and the fig wasp Blastophaga psenes. Curr. Microbiol. 2, 277–282 (1979).
Gavini, F. et al. Serratia fonticola, a new species from water. Int. J. System. Bacteriol. 29, 92–101 (1979).
Holmes, B. Proposal to conserve the specific epithet liquefaciens over the specific epithet proteamaculans in the name of the organism currently known as Serratia liquefaciens (Grimes and Hennerty 1931) Bascomb et al. 1971. Request for an opinion. Int. J. Systemic Bacteriol. 30, 220–222 (1980).
Grimont, P. A. D., Grimont, F. & Starr, M. P. Serratia species isolated from plants. Curr. Microbiol. 5, 317–322 (1981).
Grimont, P. A. D., Grimont, F. & Irino, K. Biochemical characterization of Serratia liquefaciens sensu stricto, Serratia proteamaculans, and Serratia grimesii sp. nov. Curr. Microbiol. 7, 69–74 (1982).
Grimont, P. A. D., Irino, K. & Grimont, F. The Serratia liquefaciens–S. proteamaculans–S. grimesii complex: DNA relatedness. Curr. Microbiol. 7, 63–67 (1982).
Grimont, P. A. D., Jackson, T. A., Ageron, E. & Noonan, M. J. Serratia entomophila sp. nov. associated with amber disease in the New Zealand Grass Grub Costelytra zealandica. Int. J. Syst. Bacteriol. 38, 1–6 (1988).
Murdoch, S. L. et al. The opportunistic pathogen Serratia marcescens utilizes Type VI secretion to target bacterial competitors. J. Bacteriol. 193, 6057–6069 (2011).
Williamson, N. R., Fineran, P. C., Ogawa, W., Woodley, L. R. & Salmond, G. P. C. Integrated regulation involving quorum sensing, a two-component system, a GGDEF/EAL domain protein and a post-transcriptional regulator controls swarming and RhlA-dependent surfactant biosynthesis in Serratia. Environ. Microbiol. 10, 1202–1217 (2008).
Kurz, C. L. et al. Virulence factors of the human opportunistic pathogen Serratia marcescens identified by in vivo screening. EMBO J. 22, 1451–1460 (2003).
Khanna, A., Khanna, M. & Aggarwal, A. Serratia marcescens—a rare opportunistic nosocomial pathogen and measures to limit its spread in hospitalized patients. J. Clin. Diagn. Res. 7, 243–246 (2013).
Mahlen, S. D. Serratia infections: from military experiments to current practice. Clin. Microbiol. Rev. 24, 755–791 (2011).
Moradigaravand, D., Boinett, C. J., Martin, V., Peacock, S. J. & Parkhill, J. Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland. Genome Res. 26, 1101–1109 (2016).
Karkey, A. et al. Outbreaks of Serratia marcescens and Serratia rubidaea bacteremia in a central Kathmandu hospital following the 2015 earthquakes. Trans. R. Soc. Trop. Med. Hyg. 112, 467–472 (2018).
Dubouix, A. et al. Epidemiological investigation of a Serratia liquefaciens outbreak in a neurosurgery department. J. Hosp. Infect. 60, 8–13 (2005).
Grimont, F. & Grimont, P. A. D. The Genus Serratia. in Prokaryotes (eds. Martin Dworkin, Stanley Falkow, Eugene Rosenberg, Karl-Heinz Schleifer & Erko Stackebrandt), Volume 6, 219–244 (Springer-Verlag, 2006).
Hurst, M. R. H., Glare, T. R., Jackson, T. A. & Ronson, C. W. Plasmid-located pathogenicity determinants of Serratia entomophila, the causal agent of amber disease of grass grub, show similarity to the insecticidal toxins of Photorhabdus luminescens. J. Bacteriol. 182, 5127–5138 (2000).
Hurst, M. R. H., Glare, T. R. & Jackson, T. A. Cloning Serratia entomophila antifeeding genes—a putative defective prophage active against the grass grub Costelytra zealandica. J. Bacteriol. 186, 5116–5128 (2004).
Nuñez-Valdez, M. E. et al. Identification of a putative Mexican strain of Serratia entomophila pathogenic against root-damaging larvae of Scarabaeidae (Coleoptera). Appl. Environ. Microbiol. 74, 802–810 (2008).
Rodríguez-Segura, Z., Chen, J., Villalobos, F. J., Gill, S. & Nuñez-Valdez, M. E. The lipopolysaccharide biosynthesis core of the Mexican pathogenic strain Serratia entomophila is associated with toxicity to larvae of Phyllophaga blanchardi. J. Invertebr. Pathol. 110, 24–32 (2012).
Hurst, M. R. H. et al. Serratia proteamaculans strain AGR96X encodes an antifeeding prophage (Tailocin) with activity against Grass Grub (Costelytra giveni) and Manuka Beetle (Pyronota Species) larvae. Appl. Environ. Microbiol. 84, e02739-17 (2018).
Flyg, C., Kenne, K. & Boman, H. G. Insect pathogenic properties of Serratia marcescens: phage-resistant mutants with a decreased resistance to Cecropia immunity and a decreased virulence to Drosophila. Microbiology 120, 173–181 (1980).
Ishii, K., Adachi, T., Hara, T., Hamamoto, H. & Sekimizu, K. Identification of a Serratia marcescens virulence factor that promotes hemolymph bleeding in the silkworm, Bombyx mori. J. Invertebr. Pathol. 117, 61–67 (2014).
Raymann, K., Coon, K. L., Shaffer, Z., Salisbury, S. & Moran, N. A. Pathogenicity of Serratia marcescens strains in honey bees. mBio 9, e01649–18 (2018).
Ashelford, K. E., Fry, J. C., Bailey, M. J. & Day, M. J. Characterization of Serratia isolates from soil, ecological implications and transfer of Serratia proteamaculans subsp. quinovora Grimont et al. 1983 to Serratia quinivorans corrig., sp. nov. Int. J. Syst. Evolut. Microbiol. 52, 2281–2289 (2002).
Lim, Y.-L. L. et al. Complete genome sequence of Serratia fonticola DSM 4576T, a potential plant growth promoting bacterium. J. Biotechnol. 214, 43–44 (2015).
Abebe-Akele, F. et al. Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae. BMC Genom. 16, 531 (2015).
Petersen, L. M. & Tisa, L. S. Friend or foe? A review of the mechanisms that drive Serratia towards diverse lifestyles. Can. J. Microbiol. 59, 627–640 (2013).
Cheng, T. H. et al. Genome sequence of Serratia marcescens subsp. sakuensis strain K27, a marine bacterium isolated from sponge (Haliclona amboinensis). Genome Announc. 6, e00022–18 (2018).
Matilla, M. A., Udaondo, Z. & Salmond, G. P. C. Genome sequence of the Oocydin A-producing rhizobacterium Serratia plymuthica 4Rx5. Microbiol. Resour. Announcements 7, e00997–18 (2018).
Chen, S., Blom, J. & Walker, E. D. Genomic, physiologic, and symbiotic characterization of Serratia marcescens strains isolated from the mosquito Anopheles stephensi. Front. Microbiol. 8, 1483 (2017).
Ward, D. V. et al. Metagenomic sequencing with strain-level resolution implicates uropathogenic E. coli in necrotizing enterocolitis and mortality in preterm infants. Cell Rep. 14, 2912–2924 (2016).
Roach, D. J. et al. A year of infection in the intensive care unit: prospective whole genome sequencing of bacterial clinical isolates reveals cryptic transmissions and novel microbiota. PLOS Genet. 11, e1005413 (2015).
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).
Grimont, F. & Grimont, P. A. D. Genus XXXIV, Serratia. In Bergey’s Manual of Systematic Bacteriology, Volume 2 Part B (eds. George Garrity, Don Brenner, Nole Kreig & James Staley) 799–810 (Springer, 2005).
Horesh, G. et al. Different evolutionary trends form the twilight zone of the bacterial pan-genome. Microb. Genom. 7, 000670 (2021).
Karp, P. D. et al. Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology. Brief. Bioinform. 22, 109 (2021).
Foerstner, K. U., von Mering, C., Hooper, S. D. & Bork, P. Environments shape the nucleotide composition of genomes. EMBO Rep. 6, 1208–1213 (2005).
Palidwor, G. A., Perkins, T. J. & Xia, X. A general model of codon bias due to GC mutational bias. PLOS ONE 5, e13431 (2010).
Reuter, S. et al. Parallel independent evolution of pathogenicity within the genus Yersinia. Proc. Natl Acad. Sci. USA 111, 6768–6773 (2014).
Ondov, B. D. et al. Mash: Fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).
Harris, A. K. P. et al. The Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species- and strain-dependent genome context variation. Microbiology 150, 3547–3560 (2004).
Kwak, Y., Khan, A. R. & Shin, J.-H. Genome sequence of Serratia nematodiphila DSM 21420T, a symbiotic bacterium from entomopathogenic nematode. J. Biotechnol. 193, 1–2 (2015).
Matilla, M. A., Udaondo, Z., Krell, T. & Salmond, G. P. C. Genome sequence of Serratia marcescens MSU97, a plant-associated bacterium that makes multiple antibiotics. Genome Announc. 5, (2017).
Cristina, M. L., Sartini, M. & Spagnolo, A. M. Serratia marcescens infections in neonatal intensive care units (NICUs). Int. J. Environ. Res. Public Health 16, (2019).
Daoudi, A., Benaoui, F., el Idrissi Slitine, N., Soraa, N. & Rabou Maoulainine, F. M. An outbreak of Serratia marcescens in a Moroccan neonatal intensive care unit. Adv. Med. 2018, 1–4 (2018).
Moles, L. et al. Serratia marcescens colonization in preterm neonates during their neonatal intensive care unit stay. Antimicrob. Resistance Infect. Control 8, 135 (2019).
Martineau, C. et al. Serratia marcescens outbreak in a neonatal intensive care unit: New insights from next-generation sequencing applications. J. Clin. Microbiol. 56, 148–154 (2018).
Escribano, E. et al. Influence of a Serratia marcescens outbreak on the gut microbiota establishment process in low-weight preterm neonates. PLOS ONE 14, e0216581 (2019).
Montagnani, C. et al. Serratia marcescens outbreak in a neonatal intensive care unit: Crucial role of implementing hand hygiene among external consultants. BMC Infect. Dis. 15, 11 (2015).
Hurst, M. R. H., Becher, S. A. & O’Callaghan, M. Nucleotide sequence of the Serratia entomophila plasmid pADAP and the Serratia proteamaculans pU143 plasmid virulence-associated region. Plasmid 65, 32–41 (2011).
Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, 1–12 (2014).
Lu, J., Breitwieser, F. P., Thielen, P. & Salzberg, S. L. Bracken: estimating species abundance in metagenomics data. PeerJ Comput. Sci. 2017, e104 (2017).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).
Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008).
Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D. & Pirovano, W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27, 578–579 (2011).
Boetzer, M. & Pirovano, W. Toward almost closed genomes with GapFiller. Genome Biol. 13, 1–9 (2012).
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput. Biol. 13, e1005595 (2017).
Koren, S. et al. Canu: Scalable and accurate long-read assembly via adaptive κ-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).
Hunt, M. et al. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 16, 294 (2015).
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Tonkin-Hill, G. et al. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol. 21, 1–21 (2020).
Dixon, P. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927–930 (2003).
Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691–3693 (2015).
Page, A. J. et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb. Genom. 2, e000056 (2016).
Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evolution 32, 268 (2015).
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 2018 9:1 9, 1–8 (2018).
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
Tonkin-Hill, G., Lees, J. A., Bentley, S. D., Frost, S. D. W. & Corander, J. Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Res. 47, 5539 (2019).
Belcour, A. et al. Inferring biochemical reactions and metabolite structures to understand metabolic pathway drift. iScience 23, 100849 (2020).
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).
Robertson, J., Bessonov, K., Schonfeld, J. & Nash, J. H. E. Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance. Microb. Genom. 6, 1–12 (2020).
Wickham, Hadley. Ggplot2: Elegant Graphics for Data Analysis. (Springer, 2009).
Morris, J. H. et al. ClusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinform. 12, 1–14 (2011).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Eddy, S. R. Accelerated profile HMM searches. PLOS Comput. Biol. 7, e1002195 (2011).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).
Guy, L., Kultima, J. R., Andersson, S. G. E. & Quackenbush, J. GenoPlotR: comparative gene and genome visualization in R. Bioinformatics 27, 2334–2335 (2011).
Arndt, D. et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44, W16 (2016).
Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T.-Y. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8, 28–36 (2017).
Conway, J. R., Lex, A. & Gehlenborg, N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics 33, 2938–2940 (2017).
Williams, D. W. et al. The genus Serratia revisited by genomics. Figshare doi.org/10.6084/m9.figshare.18051824 (2022).
David Williams. djw533/hamburger: Initial release. (2022) doi.org/10.5281/zenodo.6981393
David Williams. djw533/micro.gen.extra:. (2022) doi.org/10.5281/zenodo.6981456.
David Williams. djw533/pathwaytools_gff2gbk:. (2022) doi.org/10.5281/zenodo.6981411.
Wickham, H. et al. Welcome to the Tidyverse. J. Open Source Softw. 4, 1686 (2019).
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