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Insights from the draft genome into the pathogenicity of a clinical isolate of Elizabethkingia meningoseptica Em3

Standards in Genomic Sciences volume 12, Article number: 56 (2017) Cite this article

Abstract

Elizabethkingia meningoseptica is an emerging, healthcare-associated pathogen causing a high mortality rate in immunocompromised patients. We report the draft genome sequence of E. meningoseptica Em3, isolated from sputum from a patient with multiple underlying diseases. The genome has a length of 4,037,922 bp, a GC-content 36.4%, and 3673 predicted protein-coding sequences. Average nucleotide identity analysis (>95%) assigned the bacterium to the species E. meningoseptica. Genome analysis showed presence of the curli formation and assembly operon and a gene encoding hemagglutinins, indicating ability to form biofilm. In vitro biofilm assays demonstrated that E. meningoseptica Em3 formed more biofilm than E. anophelis Ag1 and E. miricola Emi3, both lacking the curli operon. A gene encoding thiol-activated cholesterol-dependent cytolysin in E. meningoseptica Em3 (potentially involved in lysing host immune cells) was also absent in E. anophelis Ag1 and E. miricola Emi3. Strain Em3 showed α-hemolysin activity on blood agar medium, congruent with presence of hemolysin and cytolysin genes. Furthermore, presence of heme uptake and utilization genes demonstrated adaptations for bloodstream infections. Strain Em3 contained 12 genes conferring resistance to β-lactams, including β-lactamases class A, class B, and metallo-β-lactamases. Results of comparative genomic analysis here provide insights into the evolution of E. meningoseptica Em3 as a pathogen.

Introduction

Elizabethkingia meningoseptica , a Gram-negative, aerobic bacillus, belongs to the family Flavobacteriaceae within the phylum Bacteroidaeota [1,2,3]. Among the three clinically important Elizabethkingia species (including E. meningoseptica , Elizabethkingia anophelis and Elizabethkingia miricola ), E. meningoseptica has been intensively investigated for its pathogenicity [4,5,6]. Most of the E. meningoseptica infections are nosocomial, often transmitted in intensive care units [1, 7]. This bacterium survives in tap water, in disinfection fluid, on wet surfaces of sinks, in ventilators, hemodialysis equipment, catheters, and other medical apparatus. E. meningoseptica infection causes neonatal meningitis, nosocomial pneumonia, bacteremia, osteomyelitis, endocarditis, and skin infections [1, 4, 8]. Moreover, older (age > 65) and immunocompromised patients are more susceptible to infection; case-fatality rates have reached 50% [9].

Infections by E. meningoseptica are difficult to treat with antimicrobial agents due to multiple drug resistance [4]. Tetracycline, chloramphenicol, and β-lactams have been used to treat patients [10], but increasingly clinical isolates lack susceptibility to these antibiotics [11]. Analysis of the resistome in the related bacterium E. miricola revealed multiple drug resistance genes [12]. Some antibiotics effective against Gram-positive bacteria such as vancomycin, quinolones, tigecycline, and rifampin have been used for treating E. meningoseptica -infected patients, though the mechanism of action remains unclear [12, 13]. Also, the effectiveness of these antibiotics varied; many patients resolved infection but isolates showed high MICs in vitro, thus the relationship between MICs and clinical response was obscure [14]. Further genome analyses will elucidate the breadth of antibiotic susceptibility and resistance mechanisms in Elizabethkingia spp.

Differentiation of Elizabethkingia species using routine morphological and biochemical tests is difficult in clinical laboratories [14]. Comparison of 16S rRNA identity does not provide sufficient resolution to identify and separate these closely-related Elizabethkingia species [2, 14]. Characterization of Elizabethkingia species by MALDI-TOF mass spectrometry would facilitate it if species reference spectra were added to the database [14]. A limitation is that MALDI-TOF mass spectrometry is not available in many smaller clinical microbiology laboratories. Whole genome analysis facilitates the development of molecular diagnosis tools (such as single nucleotide polymorphisms) that can be potentially useful for small laboratories. In this study, we sequenced, annotated and analyzed a clinical E. meningoseptica genome, with the aim of providing a better understanding of antibiotic resistance and pathogenesis mechanisms in this pathogen, and of unveiling useful biosystematic molecular markers.

Organism information

Classification and features

E. meningoseptica Em3 (Fig. 1) was isolated from a sputum sample from a patient with multiple underlying diseases and on life support. E. meningoseptica Em3 is Gram-negative, non-motile and non-spore-forming (Fig. 1 and Table 1). A taxonomic analysis was performed by comparing the 16S rRNA gene sequence to those in the GenBank (Fig. 2). The phylogenetic tree based on the 16S rRNA gene sequences indicated that strain Em3 was clustered within a branch containing other E. meningoseptica and departing from the clusters E. anophelis and E. miricola in the genus Elizabethkingia (Fig. 2). We further calculated the ANI and DDH values among the representative Elizabethkingia (Table 2). Our results showed that strain Em3 belongs to E. meningoseptica because of the high ANI (>95%, cutoff for species differentiation) and DDH (>70%, cutoff for species differentiation) values between strain Em3 and E. meningoseptica ATCC 13253T [15].

Fig. 1
figure 1

Demonstration of cell growth, pigment production and micrograph. a Em3 growing on SBA medium; b Demonstration of Em3 grown on SBA medium (control, up part) and MacConkey agar (low part). c Pigment production in Em3 grown on TSA agar. d Scanning electron microscopy image of Em3

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Table 1 Classification and general features of E. meningoseptica Em3
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Fig. 2
figure 2

Phylogenetic tree displays the position of E. meningoseptica Em3 (shown in bold) relative to the other type strains of Elizabethkingia based on 16S rRNA. The phylogenetic tree was constructed by MEGA v. 7.0.14 using the Neighbor-Joining method [42]. The percentage of replicate trees where the associated taxa clustered together in the bootstrap test (500 replicates) is indicated next to the branches. The branch lengths are scaled to the same units as those of the evolutionary distances for inferring the phylogenetic tree. The accession numbers for 16 s rRNA sequences are listed in the parenthesis following selected bacteria: E. meningoseptica LMG 12279 (NR_115236), E. meningoseptica Che01 (KX774527), E. meningoseptica NBRC 12535 (NR_113592), E. meningoseptica ATCC 13253T (NR_115201), E. meningoseptica JL1 (JN201943), E. meningoseptica YMC R3259 (KP836320), E. meningoseptica Em3, E. meningoseptica 16H-201 M0546 (KX774526), E. miricola YMC R1459 (KP844567), E. miricola BM10T (CP011059), E. miricola EM_CHUV (CM003640), E. miricola YMC R1241 (KP836321), E. miricola ATCC 33958 (NZ_JRFN00000000), E. meningoseptica pp5b (GQ360070), E. anophelis NUHP1 (NUHP1_00209), E. anophelis PW2809 (NZ_CBYE010000032), E. anophelis 5.20 (EF426427), E. anophelis R26T (NR_116021), E. anophelis Endophthalmitis (JSAA01000000), Elizabethkingia endophytica JM-87T (NR_136481), Elizabethkingia endophytica F3201 (CP016374.1), E. anophelis B2D (NZ_JNCG00000000) and Riemerella anatipestifer ATCC 11845T (NC_017045)

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Table 2 Percentage of in silico DNA-DNA hybridization (DDH)a and average nucleotide identities (ANI)b among the selected Elizabethkingia genomes
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The motility was tested on semi-TSA. The cells of strain Em3 are straight and rods and have a diameter of 0.7 μm and length of 24.0 μm. Strain Em3 grew on TSA, producing yellow pigment (Fig. 1). This bacterium also grew well on SBA with greyish discoloration around the colonies, showing it had the α-hemolytic activity (Fig. 1). E. meningoseptica Em3 did not grow on MacConkey agar, a finding consistent with strain-dependent growth on this medium; e.g., E. meningoseptica CCUG 214T grew on MacConkey agar whereas other hospital-associated E. meningoseptica strains did not [2]. Of those strains growing on MacConkey agar, lactose was not utilized [2]. The optimal growth temperature for strain Em3 was 37 °C (Table 1). Carbon source, nitrogen source utilization and osmotic tolerance were assayed by incubating cells in Biolog GEN III microplates at 37 °C overnight (CA, USA). The results showed that E. meningoseptica Em3 did not tolerate 4% NaCl. E. meningoseptica Em3 utilized several carbon sources, including D-maltose, D-trehalose, D-gentibiose, D-melibiose, D-glucose, D-mammose, D-fructose, D-fucose, D-mannitol and D-glycerol. The ability to use D-melibiose can differentiate E. meningoseptica from E. anophelis and E. miricola [16]. The inability to grow on cellobiose or citrate was consistent with previous reports [16]. Moreover, E. meningoseptica Em3 utilized D-serine, L-alanine, L-aspartic acid, L-glutamic acid, L-histidine and L-serine when tested on Biolog GEN III microplates.

Extended feature descriptions

Phylogenetic analysis (Additional file 1: Figure S1) was further conducted by using 19 genomes with 1181 core genes per genome (22,439 in total). As expected, E. meningoseptica Em3 grouped together with the selected E. meningoseptica species and separated from the clusters E. anophelis , E. endophytica and E. miricola , a finding similar to the phylogenetic analysis based on 16 s rRNA sequences. Further, both trees (Fig. 1 and Additional file 1: Figure S1) show that species E. anophelis and E. endophytica are not separated well, which is consistent with previous reports [17].

Genome sequencing information

Genome project history

The genome of E. meningoseptica Em3 was selected for whole genome sequencing because of its association with pulmonary disease. Comparison of strain Em3 genome with other Elizabethkingia species may provide insights into the molecular basis of pathogenicity and metabolic features of this strain. The high-quality draft genome sequence was completed on August 1, 2016 and was deposited to GenBank as a Whole Genome Shotgun project under accession number MDTY00000000 and the Genome OnLine Database with ID Gp0172366 (Table 3).

Table 3 Project information
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Growth conditions and genomic DNA preparation

For genomic DNA isolation, E. meningoseptica Em3 (CL16–200185, Bureau of Laboratories, Michigan Department of Health and Human Services) culture was grown overnight in 25 mL LB medium at 37 °C with vigorous shaking. DNA was isolated using a Wizard Genomic DNA Purification Kit (Promega, Madison). The amount of genomic DNA was measured using a Nanodrop2000 UV-Vis Spectrophotometer (Thermo scientific) and Qubit DNA assay kit. DNA integrity was confirmed by agarose gel assay (1.5%, w/v).

Genome sequencing and assembly

NGS libraries were prepared using the Illumina TruSeq Nano DNA Library Preparation Kit. Completed libraries were evaluated using a combination of Qubit dsDNA HS, Caliper LabChipGX HS DNA and Kapa Illumina Library Quantification qPCR assays. Libraries were combined in a single pool for multiplex sequencing and the pool was loaded on one standard MiSeq flow cell (v2) and sequencing performed in a 2x250bp, paired end format using a v2, 500 cycle reagent cartridge. Base calling was done by Illumina Real Time Analysis [18] v1.18.54 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.8.4.

The Illumina data were assembled into contiguous sequences using SPAdes version 3.9.0 [19], then short contigs (<400 bp) were filtered out. The 11 contigs identified in this strain were therefore submitted to the NCBI database as a Whole Genome Shotgun project.

Genome annotation

Annotation of the 11 contigs was first done through the NCBI Prokaryotic Genome Automatic Annotation Pipeline [20]. The predicted CDSs were next translated and analyzed against the NCBI non-redundant database, iPfam, TIGRfam, InterPro, KEGG and COG. The RAST system was used to check the annotated sequences [21, 22]. Additional gene prediction and manual revision was performed by using the IMG/MER platform. E. meningoseptica Em3 genome is available in IMG (genome ID = 2,703,719,242).

Genome properties

The draft genome sequence is 4,037,922 bp long, 36.37% G + C rich and contains 11 scaffolds (Table 4). Of 3729 genes predicted, 3673 encoded proteins and 56 were RNAs. 2585 (69.32%) were assigned a putative function, while the other 1088 (30.68%) were designated as hypothetical proteins. The distribution of coding genes into general COG functional categories analyzed by IMG is listed in Table 5. Collectively, the genome features were similar to those in other sequenced E. meningoseptica (Additional file 2: Table S1).

Table 4 Genome statistics of E. meningoseptica Em3
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Table 5 Number of genes associated with general COG functional categories
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Insights from the genome sequence

Elizabethkingia bacteria cause sepsis, bacteremia, meningitis or respiratory tract infections in hospitalized patients, indicating that they have the ability to colonize host tissues, suppress the host immune response, and disrupt erythrocytes to obtain nutrients and propagate in the host bloodstream [1, 13, 14]. Genome analysis showed that E. meningoseptica Em3 carried a gene (BFF93_RS1398) encoding a hemagglutinin protein. Hemagglutinins as adhesins are required for virulence in bacterial pathogens [23]. Hemagglutins facilitate infection via adherence to epithelial cell lines from the human respiratory tract in Bordetella pertussis [24]. Darvish et al. showed that filamentous hemagglutinin adhesins were crucial for bacterial attachment and subsequent cell accumulation on target substrates [25]. An in vitro biofilm assay showed that, compared to the mosquito isolate E. anophelis Ag1, clinical isolates E. meningoseptica Em3 and E. miricola Emi3 formed a higher amount of biofilm (Fig. 3). Furthermore, E. meningoseptica Em3 had better ability to form biofilm than did E. miricola Emi3. The capacity for strain Em3 to form biofilm was further exemplified by discovery of an operon involved in curli biosynthesis and assembly (BFF93_RS03755, BFF93_RS03760, BFF93_RS03765, BFF93_03725 and BFF93_RS03775). In vitro studies demonstrated that curli fibers participated in bacterial adhesion to target cell surfaces, cell aggregation, as well as biofilm formation [26, 27]. Moreover, some studies showed that curli mediated host cell attachment and invasion in vivo [28]. Curli were involved in inducing the host inflammatory response [29]. It should be noted that this curli synthesis operon is present in E. meningoseptica while it is absent in E. miricola . Further experiments are warranted to test if the curli gene cluster contributed to biofilm formation in strain Em3 because biofilm formation may involve other genes.

Fig. 3
figure 3

In vitro biofilm assay in the selected Elizabethkingia sp. The cells were first cultured by shaking in TSB at 37 °C overnight. The cell density was adjusted to the same OD at 600 nm (0.1). 200 μl of cells were placed on 96-well plates for 24 h. The biofilm assay was carried out using crystal blue staining [49]. Values are mean values for single measurements from eight independent cultures. The error bars are standard deviations. The statistical test was the Student’s t-test. The asterisk indicates a significant difference compared to biofilm formation in E. anophelis Ag1 (p < 0.05).

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A cytolysin encoding gene (BFF93_RS16990) was found in the strain Em3 genome, whose product belonged to a thiol-activated, CDC family [30]. CDC as a virulence factor is widely distributed among Gram-positive, opportunistic pathogens [31]. For example, Streptococcus pyogenes utilized pore-forming CDC to translocate a protein into eukaryotic cells [32]. Disruption of expression of a hemolysin (CDC) gene in the intracellular pathogen Listeria monocytogenes reduced virulence in mice, showing that CDC was critical for full virulence [33]. Furthermore, perfringolysin, a CDC toxin, has cytotoxicity and leukostasis activities, allowing the cells to escape from macrophage phagosomes during Clostridium perfringens gas gangrene [34]. Only a few CDCs have been found in Gram-negative bacteria [31], and this is the first report of CDC genes in E. meningoseptica . It should also be noted that this cytolysin gene is located immediately downstream of hmuY, which together comprise part of an iron metabolism gene cluster. Such gene organization was only seen in E. meningoseptica . This CDC protein sequence in strain Em3 shared 87%, 83% and 81% identity to that in E. meningoseptica ATCC 13253, E. meningoseptica B2D and E. meningoseptica NBRC 12535, respectively. It is interesting that it did not have close identity to that in E. meningoseptica FMS-007 (48%) and E. meningoseptica 502 (48%); it was absent in an E. meningoseptica strain associated with endophthalmitis [35]. Similarly, it was not conserved in E. anophelis (identity ranging from 0 to 50%) and absent in all E. miricola species. Such observations may stress that a diverse pathogenesis process exists in various E. meningoseptica and other Elizabethkingia species.

Besides a CDC gene in strain Em3 genome, we found that there was a gene encoding the hemolysin with a CBS domain (BFF93_RS14485). Hemolysin can be possibly secreted and involved in lysis of the erythrocytes [35]. The predicted amino acid sequence was conserved in most E. meningoseptica strains (> 90%). Further examination of hemin-degrading/transporter/utilization proteins led to a discovery of the gene cluster including SAM-dependent methyltransferases (BFF93_RS02055), iron ABC transporter (BFF93_RS02045), hemin-degrading protein (hmuS, BFF93_RS02060), hemin importer ATP-binding protein (BFF93_RS02050) and iron-regulated protein (BFF93_RS02065). Furthermore, there was a gene encoding a hemin receptor (BFF93_RS03140).

Elizabethkiniga infections can be fatal in immune-compromised patients if appropriate antibiotic therapy is delayed or the antimicrobial treatment is not properly provided [9, 14]. However, Elizabethkiniga spp. are multi-drug resistant [4, 13]. The prediction results by CARD and RAST (Table 6) showed that there are at least 31 genes involved in antibiotic resistance including antibiotic inactivation enzymes and related efflux pumps in E. meningoseptica Em3. Many of them are possibly involved in mupirocin, vancomycin, β-lactam, aminocoumarin, elfamycin, isoniazid, tetracycline and fluoroquinolone resistance (Table 6). Several drugs used to treat Elizabethkiniga-infected patients in the past are not effective anymore [4], which agrees with recent resistome assays in clinical E. meningoseptica isolates [12]. Genes associated with resistance to β-lactams, aminoglycosides, tetracycline, vancomycin, and chloramphenicol, reported here in strain Em3, are present in most of the studied Elizabethkingia spp. (Table 6). Remarkably, at least 12 β-lactam resistance genes encoding MBL fold metallo-hydrolases, metallo-β-lactamases and β-lactamases (class A and B) were found in E. meningoseptica Em3 genome (Table 6). Alternatively, antibiotics such as ciprofloxacin, minocycline, trimethoprim-sulfamethoxazole, rifampin and novobiocin may remain effective due to absence of relevant antibiotic resistance genes in Elizabethkingia sp. [36]. Therefore, a combination of antimicrobial tests and resistome analysis, combined with rapid identification of infections, will contribute to efficient management for E. meningoseptica infections in the future.

Table 6 Antibiotic genes prediction
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Conclusions

The draft genome sequence of E. meningoseptica Em3 isolated from a sputum sample in a patient was sequenced, annotated and described. We found that E. meningoseptica Em3 had novel genes encoding thiol-activated cholesterol-dependent cytolysin, curli and heme metabolism related proteins, showing that E. meningoseptica Em3 may be a causative agent. Our results also indicated that E. meningoseptica might be resistant to β-lactam antibiotics due to the production of diverse MBLs and β-lactamases. Furthermore, these β-lactamase encoding genes were also found in other Elizabethkingia species, indicating that Elizabethkingia species were important reservoirs of novel β-lactamase genes. Comparative genomics is a crucial approach in the discovery of novel virulence determinants in Elizabethkingia species. Genome-based approaches contribute to develop novel genetic markers for future molecular diagnosis of Elizabethkingia infections.

Abbreviations

ANI:

Average nucleotide identities

CDC:

Cholesterol-dependent cytolysin

IMG/MER:

Integrated Microbial Genomes and Microbiome Samples Expert Review

MALDI-TOF:

Matrix assisted laser desorption-ionisation time-of-flight

MBL:

Metallo-β-lactamase

MIC:

Minimum inhibitory concentration

SBA:

Sheep blood agar

TSA:

Solid trypticase soy agar

References

  1. Jean SS, Lee WS, Chen FL, Ou TY, Hsueh PR. Elizabethkingia meningoseptica: an important emerging pathogen causing healthcare-associated infections. J Hosp Infect. 2014;86:244–9.

    Article  CAS  PubMed  Google Scholar 

  2. Kim KK, Kim MK, Lim JH, Park HY, Lee ST. Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. Nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov. Int J Syst Evol Microbiol. 2005;55:1287–93.

    Article  CAS  PubMed  Google Scholar 

  3. Oren A, da Costa MS, Garrity GM, Rainey FA, Rosselló-Móra R, Schink B, Sutcliffe I, Trujillo ME, Whitman WB. Proposal to include the rank of phylum in the international code of nomenclature of prokaryotes. Int J Syst Evol Microbiol. 2015;65:4284–7.

    Article  CAS  PubMed  Google Scholar 

  4. Hsu M-S, Liao C-H, Huang Y-T, Liu C-Y, Yang C-J, Kao K-L, Hsueh P-R. Clinical features, antimicrobial susceptibilities, and outcomes of Elizabethkingia meningoseptica (Chryseobacterium meningosepticum) bacteremia at a medical center in Taiwan, 1999–2006. Eur J Clin Microbiol Infect Dis. 2011;30:1271–8.

    Article  CAS  PubMed  Google Scholar 

  5. Teo J, Tan SY-Y, Liu Y, Tay M, Ding Y, Li Y, Kjelleberg S, Givskov M, Lin RTP, Yang L. Comparative genomic analysis of malaria mosquito vector associated novel pathogen Elizabethkingia anophelis. Genome Biol Evol. 2014; doi: 10.1093/gbe/evu1094.

  6. Ceyhan M, Celik M. Elizabethkingia meningosepticum (Chryseobacterium meningosepticum) infections in children. Int J Pediatr. 2011;2011:1–7.

    Article  Google Scholar 

  7. Balm MND, Salmon S, Jureen R, Teo C, Mahdi R, Seetoh T, Teo JTW, Lin RTP, Fisher DA. Bad design, bad practices, bad bugs: frustrations in controlling an outbreak of Elizabethkingia meningoseptica in intensive care units. J Hosp Infect. 2013;85:134–40.

    Article  CAS  PubMed  Google Scholar 

  8. Luke SPM, Daniel SO, Annette J, Jane FT, Simon A, Hugo D, Alison HH. Waterborne Elizabethkingia meningoseptica in adult critical care. Emerg Infect Dis. 2016;22(1):9–17.

    Article  Google Scholar 

  9. Pereira GH, Garcia DO, Abboud CS, Barbosa VLB, da PSL S. Nosocomial infections caused by Elizabethkingia meningoseptica: an emergent pathogen. Braz J Infect Dis. 2013;17:606–9.

    Article  PubMed  Google Scholar 

  10. Neuner EA, Ahrens CL, Groszek JJ, Isada C, Vogelbaum MA, Fissell WH, Bhimraj A. Use of therapeutic drug monitoring to treat Elizabethkingia meningoseptica meningitis and bacteraemia in an adult. J Antimicrob Chemother. 2012;67:1558–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Kirby JT, Sader HS, Walsh TR, Jones RN. Antimicrobial susceptibility and epidemiology of a worldwide collection of Chryseobacterium spp.: report from the SENTRY antimicrobial surveillance program (1997-2001). J Clin Microbiol. 2004;42:445–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Opota O, Diene SM, Bertelli C, Prod'hom G, Eckert P, Greub G. Genome of the carbapenemase-producing clinical isolate Elizabethkingia miricola EM_CHUV and comparative genomics with Elizabethkingia meningoseptica and Elizabethkingia anophelis: evidence for intrinsic multidrug resistance trait of emerging pathogens. Int J Antimicrob Agents. 2017;49:93–7.

    Article  CAS  PubMed  Google Scholar 

  13. Breurec S, Criscuolo A, Diancourt L, Rendueles O, Vandenbogaert M, Passet V, Caro V, Rocha EPC, Touchon M, Brisse S. Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis. Sci Rep. 2016;6:30379.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Lau SKP, Chow W-N, Foo C-H, Curreem SOT, Lo GC-S, Teng JLL, Chen JHK, Ng RHY, Wu AKL, Cheung IYY, et al. Elizabethkingia anophelis bacteremia is associated with clinically significant infections and high mortality. Sci Rep. 2016;6:26045.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A. 2009;106:19126–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kämpfer P, Busse H-J, McInroy JA, Glaeser SP. Elizabethkingia endophytica sp. nov., isolated from Zea Mays and emended description of Elizabethkingia anophelis Kämpfer et al. 2011. Int J Syst Evol Microbiol. 2015;65:2187–93.

    Article  PubMed  Google Scholar 

  17. Doijad S, Ghosh H, Glaeser S, Kämpfer P, Chakraborty T. Taxonomic reassessment of the genus Elizabethkingia using whole-genome sequencing: Elizabethkingia endophytica Kämpfer et al. 2015 is a later subjective synonym of Elizabethkingia anophelis Kämpfer et al. 2011. Int J Syst Evol Microbiol. 2016;66:4555–9.

    Article  PubMed  Google Scholar 

  18. Klein CC, Alves JMP, Serrano MG, Buck GA, Vasconcelos ATR, Sagot M-F, Teixeira MMG, Camargo EP, Motta MCM. Biosynthesis of vitamins and cofactors in bacterium-harbouring Trypanosomatids depends on the symbiotic association as revealed by genomic analyses. PLoS One. 2013;8:e79786.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comp Biol. 2012;19:455–77.

    Article  CAS  Google Scholar 

  20. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M. The RAST server: rapid annotations using subsystems technology. BMC Genet. 2008;9 doi:10.1186/1471-2164-9-75.

  22. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 2014;42:D206–14.

    Article  CAS  PubMed  Google Scholar 

  23. Song H, Bélanger M, Whitlock J, Kozarov E, Progulske-Fox A. Hemagglutinin B is involved in the adherence of Porphyromonas gingivalis to human coronary artery endothelial cells. Infect Immun. 2005;73:7267–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. van den Berg BM, Beekhuizen H, Willems RJL, Mooi FR, van Furth R. Role of Bordetella pertussis virulence factors in adherence to epithelial cell lines derived from the human respiratory tract. Infect Immun. 1999;67:1056–62.

    PubMed  PubMed Central  Google Scholar 

  25. Darvish Alipour Astaneh S, Rasooli I, Mousavi Gargari SL. The role of filamentous hemagglutinin adhesin in adherence and biofilm formation in Acinetobacter baumannii ATCC19606T. Microb Pathog. 2014;74:42–9.

    Article  CAS  PubMed  Google Scholar 

  26. Kline KA, Fälker S, Dahlberg S, Normark S, Henriques-Normark B. Bacterial adhesins in host-microbe interactions. Cell Host Microbe. 2009;5:580–92.

    Article  CAS  PubMed  Google Scholar 

  27. Yaron S, Römling U. Biofilm formation by enteric pathogens and its role in plant colonization and persistence. Microb Biotechnol. 2014;7(6):496–516.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Garcia MC, Lipke PN, Klotz SA. Pathogenic microbial amyloids: their function and the host response. OA microbial. 2013;1:2.

    Google Scholar 

  29. Telford JL, Barocchi MA, Margarit I, Rappuoli R, Grandi G. Pili in gram-positive pathogens. Nat Rev Micro. 2006;4:509–19.

    Article  CAS  Google Scholar 

  30. Tweten RK. Cholesterol-dependent cytolysins, a family of versatile pore-forming toxins. Infect Immun. 2005;73:6199–209.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Hotze EM, Le HM, Sieber JR, Bruxvoort C, McInerney MJ, Tweten RK. Identification and characterization of the first cholesterol-dependent cytolysins from gram-negative bacteria. Infect Immun. 2013;81:216–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Madden JC, Ruiz N, Caparon M. Cytolysin-mediated translocation (CMT). Cell. 104:143–52.

  33. Portnoy DA, Jacks PS, Hinrichs DJ. Role of hemolysin for the intracellular growth of Listeria monocytogenes. J Exp Med. 1988;167:1459–71.

    Article  CAS  PubMed  Google Scholar 

  34. O'Brien DK, Melville SB. Effects of Clostridium perfringens Alpha-toxin (PLC) and perfringolysin O (PFO) on cytotoxicity to macrophages, on escape from the phagosomes of macrophages, and on persistence of C. perfringens in host tissues. Infect Immun. 2004;72:5204–15.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Pradeep BE, Mahalingam N, Manivannan B, Padmanabhan K, Nilawe P, Gurung G, Chhabra A, Nagaraja V. Draft genome sequence of Elizabethkingia meningoseptica, isolated from a postoperative endophthalmitis patient. Genome Announc. 2014;2:e01335–14.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Lin P-Y, Chu C, Su L-H, Huang C-T, Chang W-Y, Chiu C-H. Clinical and microbiological analysis of bloodstream infections caused by Chryseobacterium meningosepticum in nonneonatal patients. J Clin Microbiol. 2004;42:3353–5.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Bernardet J-F. Class II. Flavobacteriia class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, WWWB L, editors. Bergey’s Manual of systematic bacteriology. 2nd ed. New York: Springer; 2010. p. 106–314.

    Google Scholar 

  39. Bernardet JF, Order I. Flavobacteriales ord. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB, editors. Bergey’s Manual of systematic bacteriology. 2nd ed. New York: Springer; 2011. p. 105–329.

    Google Scholar 

  40. Bernardet, Nakagawa and Holmes 2002, 1057. In: Bergey's Manual of Systematic Bacteriology, vol. 4. 2nd ed. New York: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Spring; 2011. p. 106–314.

  41. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 For bigger datasets. Mol Biol Evol. 2016;33:1870–4.

    Article  CAS  PubMed  Google Scholar 

  43. Kukutla P, Lindberg BG, Pei D, Rayl M, Yu W, Steritz M, Faye I, Xu J. Draft genome sequences of Elizabethkingia anophelis strains R26T and Ag1 from the midgut of the malaria mosquito Anopheles gambiae. Genome Announc. 2013;1(6):e01030–13.

  44. Matyi SA, Hoyt PR, Hosoyama A, Yamazoe A, Fujita N, Gustafson JE. Draft genome sequences of Elizabethkingia meningoseptica. Genome Announc. 2013;1(4):e00444–13.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Lee D, Kim Y-K, Kim Y-S, Kim T-J. Complete genome sequence of Elizabethkingia sp. Bm10, a symbiotic bacterium of the wood-feeding termite Reticulitermes speratus KMT1. Genome Announc. 2015;3(5):e01181–15.

    PubMed  PubMed Central  Google Scholar 

  46. Nicholson AC, Humrighouse BW, Graziano JC, Emery B, McQuiston JR. Draft genome sequences of strains representing each of the Elizabethkingia Genomospecies previously determined by DNA-DNA hybridization. Genome Announc. 2016;4(2):e00045–16.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci. 2010;2(1):117–34.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y, Seo H, Chun J. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017;67:1613–7.

    Article  PubMed  PubMed Central  Google Scholar 

  49. Kwasny SM, Opperman TJ. Static biofilm cultures of Gram-positive pathogens grown in a microtiter format used for anti-biofilm drug discovery. Current protocols in pharmacology / editorial board, SJ Enna (editor-in-chief). 2010, 50:13A.18.11-13A.18.23.

  50. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C, Ernst C, Goesmann A. EDGAR 2.0: An enhanced software platform for comparative gene content analyses. Nucleic Acids Res. 2016; doi:10.1093/nar/gkw255.

  51. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Felsenstein J. PHYLIP - phylogeny inference package (version 3.2). Cladistics. 1989;5:164–6.

    Google Scholar 

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Acknowledgements

We acknowledge Dr. Jiannong Xu at the New Mexico State University for the provision of E. anophelis Ag1.

Funding

This project was funded by NIH grant R37 AI21884.

Author information

Authors and Affiliations

  1. Department of Microbiology and Molecular Genetics, Michigan State University, 2215 Biomedical and Physical Sciences Building, 567 Wilson Road, East Lansing, MI, 48824-4320, USA

    Shicheng Chen & Edward D. Walker

  2. Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, 48906, USA

    Marty Soehnlen

  3. Biomedical Laboratory Diagnostics Program, Michigan State University, East Lansing, MI, 48824, USA

    Frances P. Downes

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  1. Shicheng Chen
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Contributions

SC assembled the genome sequence, analyzed the genome data in public databases for genes of interest and wrote the manuscript. MS performed the experiments and acquired the data. FD wrote and revised the manuscript. EW analyzed the data and wrote the manuscript. All authors read approved final the manuscript.

Corresponding author

Correspondence to Shicheng Chen.

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Additional files

Additional file 1: Figure S1.

Phylogenetic tree of the Elizabethkingia genus. The core genome computed by EDGAR 2.0 [50] was extracted to infer a phylogeny for the 18 Elizabethkingia genomes. The amino acid sequences of the core genome were aligned using MUSCLE v3.8.31 [51], and then used to construct a phylogenetic tree using the neighbor-joining method as implemented in the PHYLIP package [52]. The accession numbers for genome sequences are listed in the parenthesis following selected bacteria: E. anophelis R26T (NZ_ANIW01000066), E. anophelis Ag1 (AHHG00000000), E. endophytica CSID 3000516978 (NZ_MAHJ01000016), E. endophytica F3201 (NZ_MAHU01000055), E. endophytica JM-87T (NZ_CP016372), E. anophelis NUHP1 (NZ_CP007547), E. anophelis CSID 3015183678 (NZ_CP014805), E. anophelis FMS007 (NZ_CP006576), E. miricola BM10T (NZ_CP011059), E. miricola CSID_3000517120 (NZ_MAGX01000009), E. miricola GTC862 (NZ_LSGQ01000033), E. meningoseptica ATCC 13253T (NZ_ASAN01000115), E. meningoseptica G4076 (NZ_CP016376), E. meningoseptica CSID_3000515919 (NZ_MAGZ01000024), E. meningoseptica EM1 (NZ_MCJH01000010), E. meningoseptica EM3 (NZ_MDTY01000011), E. meningoseptica EM2 (NZ_MDTZ01000014), E. meningoseptica G4120 (NZ_CP016378), Riemerella anatipestifer ATCC 11845T (NC_017045). (PDF 172 kb)

Additional file 2: Table S1.

Genome features for the selected Elizabethkingia. Seven genomes from E. meningoseptica were provided for comparison of size, gene count, CRISPR, GC and coding count. (XLS 21 kb)

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Chen, S., Soehnlen, M., Downes, F.P. et al. Insights from the draft genome into the pathogenicity of a clinical isolate of Elizabethkingia meningoseptica Em3. Stand in Genomic Sci 12, 56 (2017). https://doi.org/10.1186/s40793-017-0269-8

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Keywords

Environmental Microbiome

ISSN: 2524-6372