# Isolation and Characterization of Gardnerella Phage vB_Gva_AB1, a Bacteriophage Infecting a Clinical Strain of Gardnerella vaginalis

Alexia Bordigoni, Sonia Bouchard, Christelle Desnues

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Alexia Bordigoni, Sonia Bouchard, Christelle Desnues. Isolation and Characterization of Gardnerella Phage vB_Gva_AB1, a Bacteriophage Infecting a Clinical Strain of Gardnerella vaginalis. Microbiology Resource Announcements, 2021, 10 (12), 10.1128/MRA.00053-21. hal-03203911

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Submitted on 21 Apr 2021

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# Isolation and Characterization of *Gardnerella* Phage *vB_Gva_AB1*, a Bacteriophage Infecting a Clinical Strain of *Gardnerella vaginalis*

Alexia Bordigoni,ª Sonia Bouchard,ᵇ Christelle Desnuesª,ᵇ

**ABSTRACT** *Gardnerella vaginalis* is the presumed causative agent of bacterial vaginosis. Here, we describe the complete genome sequence of *Gardnerella* phage *vB_Gva_AB1*, induced from a vaginal bacterial strain from a woman suffering with bacterial vaginosis. The phage double-stranded DNA (dsDNA) genome is 50,268 bp long with a GC content of 39.55% and contains 62 predicted open reading frames.

*Gardnerella vaginalis* is an anaerobic bacterium considered one of the etiological agents of bacterial vaginosis (BV) (1, 2). Conventional treatment consists of clindamycin or metronidazole intake (3) with frequent relapses (4, 5). Probiotics are used to replace or complement traditional therapy (6), but their effects on BV are controversial (7-9). Phagotherapy could be another alternative treatment to restore vaginal flora (10). The genome of *Gardnerella vaginalis* strains contains a multitude of prophage sequences (11), but so far, none have been isolated.

*Gardnerella vaginalis* strain CSUR P680, isolated from a vaginal swab of a French woman suffering from BV (IHU Méditerranée Infection. Marseille, France), was used to induce prophages. The patient provided informed consent, and the study was authorized by the ethics committee of the Institut Federatif de Recherche 48 (number 09-022). The vaginal swab was treated as previously described (12), and the strain was cultured in brain-heart infusion (BHI; BD) broth medium, supplemented with yeast extract (0.5%; Fisher Scientific), glucose (0.25%; Euromedex), and fetal bovine serum (10%; Life Technologies) at 37°C, 5% CO₂ (BD), and agitation (200 rpm). Bacteriophage excision was induced by adding mitomycin C (10 µg/ml; MedChemExpress). The overnight culture was centrifuged (13,000 × g; 10 min), and the supernatant was filtered (0.22 µm; Dutscher). On a *Gardnerella vaginalis* P680 double-layer plaque assay (0.6% agar; Life Technologies), a large double turbid halo phage plaque, characteristic of temperate phages (Fig. 1A), was observed. Phage DNA extraction was performed on 1 ml of clarified and filtered induced culture supernatant by using a High Pure viral nucleic acid large-volume kit (Roche), randomly amplified using the GenomiPhi v3 DNA amplification kit (GE Healthcare), purified with a NucleoFast plate (Macherey-Nagel), and quantified using a Qubit double-stranded DNA (dsDNA) high-sensitivity assay kit (Life Technologies) and instrument (Invitrogen), all according to the manufacturer's protocols. Purified nucleic acids were used to construct a paired-end library with the Nextera XT library kit and sequenced with MiSeq technology (Illumina, Inc.). Raw paired reads (2,594,168) were imported, trimmed, and *de novo* assembled using the CLC Genomics Workbench v7.5 software. All tools were run with default parameters unless otherwise specified. This generated 1,916 contigs with a length ranging from 53 bp to 23,344 bp and a coverage of 1 × to 11,936 ×. Contigs with a length of

**Citation** Bordigoni A, Bouchard S, Desnues C. 2021. Isolation and characterization of *Gardnerella* phage *vB_Gva_AB1*, a bacteriophage infecting a clinical strain of *Gardnerella vaginalis*. Microbiol Resour Announc 10:e00053-21. https://doi.org/10.1128/MRA.00053-21.

**Editor** Catherine Putonti, Loyola University Chicago

**Copyright** © 2021 Bordigoni et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Christelle Desnues, christelle.desnues@univ-amu.fr.

**Received** 18 January 2021

**Accepted** 24 February 2021

**Published** 25 March 2021

<footnote>ªAix-Marseille Université, IRD 198, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Marseille, France</footnote>

<footnote>ᵇAix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography, UM 110, Marseille, France</footnote>
<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /><figcaption>**FIG 1** Double-layer plaque assay and circular genome representation of the *Gardnerella* phage vB_Gva_AB1. (A) Spot test showing large double turbid halo phage plaque, characteristic of temperate phages from induced culture (I), not-induced culture (NI), and control of culture (supplemented BHI [sBHI] medium only). (B) Genome organization with predicted ORF direction and annotation colored according to functional group of genes: yellow, lysogeny; orange, DNA packaging; green, DNA replication, transcription, and repair; pink, viral particle structure; light blue, phage virulence against host; purple, lysis; and gray, hypothetical protein. GC content is represented by the central dark-blue line. Genome visualization was obtained using Geneious software v2021.0.1.</figcaption></figure>

>1,000 bp and a coverage of >1,000× were manually concatenated according to their position on a bacterial reference genome (GenBank accession number CP019058.1) using BLASTn. Concatenation and circularization of the genome were verified, corrected, and validated by PCR performed with AmpliTaq Gold 360 master mix (Life Technologies) and Sanger sequencing using the BigDye Terminator v1.1 cycle sequencing kit (Life Technologies) and a 3500xL genetic analyzer capillary sequencer (Thermo Fisher) according to the manufacturers' recommendations.

The complete genome consisted of a circular double-stranded DNA molecule of 50,268 bp with a GC content of 39.55% (Fig. 1B). The closest viral homolog (76.42% identity and 3% query coverage) detected after a BLASTn search against the nonredundant (nr) database was *Streptococcus* phage Javan112 (GenBank accession number MK448843.1), which belongs to the *Siphoviridae* family. A total of 62 open reading frames (ORFs) were predicted with GeneMarkS v4.28 (13, 14). No tRNAs were detected using tRNAscan-SE 2.0 (15, 16). No CRISPR spacer arrays, identified within *G. vaginalis* complete genomes available in the NCBI genome database using CRISPRCasFinder (17), perfectly matched (100% query coverage and 100% identity) the *Gardnerella* phage vB_Gva_AB1 genome sequence. The genome was manually annotated using BLASTp against the nr database and InterPro. Putative function was assigned to the majority (64.5%) of predicted ORFs, whereas 35.5% matched hypothetical proteins or protein domains that had no characterized function. InterPro provided functional annotation for ORF33 (HK97 gp10 family phage protein) and ORF38 (phage tail tape measure protein). Predicted ORFs were categorized in 7 modules—lysogeny, DNA packaging, DNA replication/transcription/repair, viral particle structure, phage virulence against host, host lysis, and hypothetical protein (Fig. 1B, Table 1).

**Data availability.** The data set was deposited in the Sequence Read Archive (SRA) under the number SRX9776169 (BioProject number PRJNA687336). The complete and annotated genome sequence is available under GenBank accession number MW387018.1.
<figure><img src="image_5.png" /><figcaption>TABLE 1 Characteristics of *Gardnerella phage vB_gva_AB1* ORFs and predicted functions<sup>a</sup></figcaption></figure>

<table><thead><tr><th>ORF</th><th>Strand</th><th>ORF start (bp)</th><th>ORF end (bp)</th><th>aa length</th><th>Description (best BLASTn hit)</th><th>Maximum score</th><th>Total score</th><th>Query coverage (%)</th><th>E value</th><th>Identity (%)</th><th>GenBank accession no.</th><th>Functional group</th></tr></thead><tbody><tr><td>1</td><td>-</td><td>1</td><td>162</td><td>53</td><td>IS3 family transposase</td><td>107</td><td>107</td><td>100</td><td>6.00e-29</td><td>92.45</td><td>WP_116431825.1</td><td>Lysogeny</td></tr><tr><td>2</td><td>-</td><td>256</td><td>666</td><td>136</td><td>IS3 family transposase</td><td>276</td><td>276</td><td>100</td><td>7.00e-93</td><td>97.79</td><td>WP_103014070.1</td><td>Lysogeny</td></tr><tr><td>3</td><td>+</td><td>1433</td><td>2065</td><td>210</td><td>RNA polymerase subunit sigma-24</td><td>421</td><td>421</td><td>100</td><td>9.00e-149</td><td>97.14</td><td>RFT26841.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>4</td><td>+</td><td>2126</td><td>2347</td><td>73</td><td>Hypothetical protein</td><td>151</td><td>151</td><td>100</td><td>3.00e-46</td><td>100.00</td><td>WP_016815920.1</td><td>Hypothetical protein</td></tr><tr><td>5</td><td>+</td><td>2360</td><td>2662</td><td>100</td><td>Hypothetical protein</td><td>195</td><td>195</td><td>100</td><td>8.00e-63</td><td>99.00</td><td>WP_014554450.1</td><td>Hypothetical protein</td></tr><tr><td>6</td><td>+</td><td>2655</td><td>3785</td><td>376</td><td>DUF2800 domain-containing protein</td><td>752</td><td>752</td><td>99</td><td>0</td><td>96.53</td><td>WP_014554451.1</td><td>Hypothetical protein</td></tr><tr><td>7</td><td>+</td><td>3787</td><td>4335</td><td>182</td><td>DUF2815 family protein</td><td>370</td><td>370</td><td>100</td><td>2.00e-129</td><td>98.35</td><td>WP_018645384.1</td><td>Hypothetical protein</td></tr><tr><td>8</td><td>+</td><td>4349</td><td>4459</td><td>36</td><td>Hypothetical protein</td><td>70.5</td><td>70.5</td><td>100</td><td>4.00e-15</td><td>97.22</td><td>OKY54901.1</td><td>Hypothetical protein</td></tr><tr><td>9</td><td>+</td><td>4521</td><td>7424</td><td>967</td><td>DNA polymerase</td><td>1,983</td><td>1,983</td><td>100</td><td>0</td><td>98.55</td><td>WP_048730082.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>10</td><td>+</td><td>7578</td><td>7952</td><td>124</td><td>Hypothetical protein</td><td>255</td><td>255</td><td>100</td><td>1.00e-85</td><td>95.97</td><td>RFT36085.1</td><td>Hypothetical protein</td></tr><tr><td>11</td><td>+</td><td>7945</td><td>10278</td><td>777</td><td>Hypothetical protein</td><td>1,594</td><td>1,594</td><td>100</td><td>0</td><td>98.07</td><td>WP_116440744.1</td><td>Hypothetical protein</td></tr><tr><td>12</td><td>+</td><td>10507</td><td>10842</td><td>111</td><td>Hypothetical protein</td><td>224</td><td>224</td><td>100</td><td>1.00e-73</td><td>98.20</td><td>WP_004117127.1</td><td>Hypothetical protein</td></tr><tr><td>13</td><td>+</td><td>10814</td><td>10975</td><td>53</td><td>VRR-NUC domain-containing protein</td><td>90.9</td><td>90.9</td><td>84</td><td>3.00e-22</td><td>100.00</td><td>WP_076002715.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>14</td><td>+</td><td>10981</td><td>11073</td><td>30</td><td>VRR-NUC domain-containing protein</td><td>61.2</td><td>61.2</td><td>100</td><td>6.00e-11</td><td>100.00</td><td>WP_102155316.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>15</td><td>+</td><td>11054</td><td>12493</td><td>479</td><td>DEAD/DEAH box helicase</td><td>984</td><td>984</td><td>100</td><td>0</td><td>99.16</td><td>WP_103014033.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>16</td><td>+</td><td>12453</td><td>12881</td><td>142</td><td>RNA polymerase subunit sigma-70</td><td>287</td><td>287</td><td>100</td><td>5.00e-98</td><td>100.00</td><td>WP_101887643.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>17</td><td>+</td><td>13034</td><td>13366</td><td>110</td><td>HNH endonuclease</td><td>227</td><td>227</td><td>100</td><td>4.00e-75</td><td>98.18</td><td>WP_020760705.1</td><td>DNA packaging</td></tr><tr><td>18</td><td>+</td><td>13555</td><td>14106</td><td>183</td><td>Terminase</td><td>377</td><td>377</td><td>100</td><td>4.00e-132</td><td>99.45</td><td>WP_032842293.1</td><td>DNA packaging</td></tr><tr><td>19</td><td>+</td><td>14119</td><td>14904</td><td>261</td><td>S-Adenosylmethionine synthetase</td><td>533</td><td>533</td><td>100</td><td>0</td><td>100.00</td><td>WP_014554462.1</td><td>Phage virulence against host</td></tr><tr><td>20</td><td>+</td><td>14919</td><td>16154</td><td>411</td><td>DNA modification methylase</td><td>852</td><td>852</td><td>100</td><td>0</td><td>99.51</td><td>RIY23021.1</td><td>Phage virulence against host</td></tr><tr><td>21</td><td>+</td><td>16253</td><td>16903</td><td>216</td><td>Virulence protein</td><td>440</td><td>440</td><td>100</td><td>9.00e-156</td><td>100.00</td><td>WP_112928563.1</td><td>Phage virulence against host</td></tr><tr><td>22</td><td>+</td><td>16887</td><td>17051</td><td>54</td><td>Hypothetical protein</td><td>100</td><td>100</td><td>100</td><td>2.00e-26</td><td>92.59</td><td>WP_165847508.1</td><td>Hypothetical protein</td></tr><tr><td>23</td><td>+</td><td>17217</td><td>17501</td><td>94</td><td>Transcriptional regulator</td><td>189</td><td>189</td><td>100</td><td>2.00e-60</td><td>98.94</td><td>WP_076002844.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>24</td><td>+</td><td>17651</td><td>17875</td><td>74</td><td>Hypothetical protein</td><td>154</td><td>154</td><td>100</td><td>3.00e-47</td><td>100.00</td><td>WP_112928565.1</td><td>Hypothetical protein</td></tr><tr><td>25</td><td>+</td><td>18000</td><td>19592</td><td>530</td><td>Terminase large subunit</td><td>1,101</td><td>1,101</td><td>100</td><td>0</td><td>98.87</td><td>WP_116691915.1</td><td>DNA packaging</td></tr><tr><td>26</td><td>+</td><td>19602</td><td>20774</td><td>390</td><td>Phage portal protein</td><td>782</td><td>782</td><td>97</td><td>0</td><td>97.64</td><td>WP_076002846.1</td><td>DNA packaging</td></tr><tr><td>27</td><td>+</td><td>20765</td><td>20848</td><td>27</td><td>Portal protein</td><td>56.2</td><td>56.2</td><td>100</td><td>2.00e-09</td><td>100.00</td><td>RIY25730.1</td><td>DNA packaging</td></tr><tr><td>28</td><td>+</td><td>21078</td><td>21845</td><td>255</td><td>Hypothetical protein</td><td>513</td><td>513</td><td>100</td><td>0</td><td>98.04</td><td>WP_004104990.1</td><td>Hypothetical protein</td></tr><tr><td>29</td><td>+</td><td>21962</td><td>22705</td><td>247</td><td>ATP-dependent Clp protease</td><td>511</td><td>511</td><td>100</td><td>0</td><td>100.00</td><td>WP_192382072.1</td><td>DNA packaging</td></tr><tr><td>30</td><td>+</td><td>22708</td><td>23892</td><td>394</td><td>Phage major capsid protein</td><td>803</td><td>803</td><td>100</td><td>0</td><td>99.49</td><td>RIY23012.1</td><td>Viral particle structure</td></tr><tr><td>31</td><td>+</td><td>23918</td><td>24196</td><td>92</td><td>Phage gp6-like head-tail connector protein</td><td>188</td><td>188</td><td>100</td><td>4.00e-60</td><td>100.00</td><td>WP_004125785.1</td><td>Viral particle structure</td></tr><tr><td>32</td><td>+</td><td>24197</td><td>24529</td><td>110</td><td>Phage head closure protein</td><td>224</td><td>224</td><td>100</td><td>6.00e-74</td><td>98.18</td><td>WP_076002725.1</td><td>Viral particle structure</td></tr></tbody></table>

(Continued on next page)
<figure><img src="image_6.png" /><figcaption>TABLE 1 (Continued)</figcaption></figure>

<table><thead><tr><th>ORF</th><th>Strand</th><th>ORF start (bp)</th><th>ORF end (bp)</th><th>aa length</th><th>Description (best BLASTn hit)</th><th>Maximum score</th><th>Total score</th><th>Query coverage (%)</th><th>E value</th><th>Identity (%)</th><th>GenBank accession no.</th><th>Functional group</th></tr></thead><tbody><tr><td>33</td><td>+</td><td>24526</td><td>24906</td><td>126</td><td>Hypothetical protein</td><td>241</td><td>241</td><td>100</td><td>2.00e-80</td><td>98.41</td><td>RFT26873.1</td><td>Viral particle structure</td></tr><tr><td>34</td><td>+</td><td>24899</td><td>25228</td><td>109</td><td>Hypothetical protein</td><td>222</td><td>222</td><td>100</td><td>4.00e-73</td><td>99.08</td><td>WP_103014101.1</td><td>Hypothetical protein</td></tr><tr><td>35</td><td>+</td><td>25221</td><td>25793</td><td>190</td><td>Tail protein</td><td>386</td><td>386</td><td>100</td><td>2.00e-135</td><td>100.00</td><td>WP_014554473.1</td><td>Viral particle structure</td></tr><tr><td>36</td><td>+</td><td>25811</td><td>26176</td><td>121</td><td>Hypothetical protein</td><td>244</td><td>244</td><td>100</td><td>2.00e-81</td><td>99.17</td><td>WP_014554474.1</td><td>Viral particle structure</td></tr><tr><td>37</td><td>+</td><td>26173</td><td>26337</td><td>54</td><td>Hypothetical protein</td><td>111</td><td>111</td><td>100</td><td>9.00e-31</td><td>100.00</td><td>AEF31840.1</td><td>Hypothetical protein</td></tr><tr><td>38</td><td>+</td><td>26419</td><td>28986</td><td>855</td><td>Hypothetical protein</td><td>1,704</td><td>1,704</td><td>100</td><td>0</td><td>99.77</td><td>WP_004125799.1</td><td>Viral particle structure</td></tr><tr><td>39</td><td>+</td><td>28989</td><td>29651</td><td>220</td><td>Phage tail component protein</td><td>453</td><td>453</td><td>100</td><td>7.00e-161</td><td>98.64</td><td>EPI45861.1</td><td>Viral particle structure</td></tr><tr><td>40</td><td>+</td><td>29652</td><td>32471</td><td>939</td><td>Phage tail protein</td><td>1,927</td><td>1,927</td><td>99</td><td>0</td><td>99.04</td><td>WP_076002853.1</td><td>Hypothetical protein</td></tr><tr><td>41</td><td>+</td><td>32517</td><td>32681</td><td>54</td><td>Hypothetical protein</td><td>106</td><td>106</td><td>100</td><td>1.00e-28</td><td>100.00</td><td>EPI54250.1</td><td>Hypothetical protein</td></tr><tr><td>42</td><td>+</td><td>32684</td><td>33043</td><td>119</td><td>Hypothetical protein</td><td>223</td><td>223</td><td>100</td><td>3.00e-73</td><td>96.64</td><td>EIK79881.1</td><td>Hypothetical protein</td></tr><tr><td>43</td><td>+</td><td>33206</td><td>33625</td><td>139</td><td>Phage holin family protein</td><td>283</td><td>283</td><td>100</td><td>3.00e-96</td><td>100.00</td><td>WP_032812430.1</td><td>Lysis</td></tr><tr><td>44</td><td>+</td><td>33618</td><td>34538</td><td>306</td><td>1,4-beta-N-Acetylmuramidase</td><td>606</td><td>606</td><td>100</td><td>0</td><td>95.75</td><td>WP_065189413.1</td><td>Lysis</td></tr><tr><td>45</td><td>+</td><td>34688</td><td>35095</td><td>135</td><td>RNA polymerase subunit sigma-70</td><td>276</td><td>276</td><td>100</td><td>9.00e-94</td><td>99.26</td><td>WP_103014084.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>46</td><td>+</td><td>35082</td><td>35294</td><td>70</td><td>Hypothetical protein</td><td>142</td><td>142</td><td>100</td><td>1.00e-42</td><td>98.57</td><td>WP_111822612.1</td><td>Hypothetical protein</td></tr><tr><td>47</td><td>+</td><td>35356</td><td>36924</td><td>522</td><td>Recombinase family protein</td><td>1,050</td><td>1,050</td><td>100</td><td>0</td><td>97.32</td><td>WP_019260895.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>48</td><td>+</td><td>36921</td><td>37331</td><td>136</td><td>Hypothetical protein</td><td>274</td><td>274</td><td>100</td><td>6.00e-93</td><td>99.26</td><td>WP_020760681.1</td><td>Hypothetical protein</td></tr><tr><td>49</td><td>+</td><td>37333</td><td>38910</td><td>525</td><td>Recombinase family protein</td><td>1,076</td><td>1,076</td><td>100</td><td>0</td><td>99.05</td><td>WP_004125822.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>50</td><td>+</td><td>38932</td><td>39072</td><td>46</td><td>Hypothetical protein</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>Hypothetical protein</td></tr><tr><td>51</td><td>+</td><td>39227</td><td>40171</td><td>314</td><td>Recombinase family protein</td><td>638</td><td>638</td><td>100</td><td>0</td><td>99.36</td><td>WP_119675718.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>52</td><td>+</td><td>40191</td><td>40829</td><td>212</td><td>Hypothetical protein</td><td>434</td><td>434</td><td>100</td><td>8.00e-154</td><td>100.00</td><td>WP_119675717.1</td><td>Hypothetical protein</td></tr><tr><td>53</td><td>+</td><td>41857</td><td>43866</td><td>669</td><td>ATP-binding cassette domain-containing protein</td><td>1,352</td><td>1,352</td><td>100</td><td>0</td><td>100.00</td><td>WP_014554440.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>54</td><td>+</td><td>43863</td><td>44255</td><td>130</td><td>Hypothetical protein</td><td>258</td><td>258</td><td>100</td><td>1.00e-86</td><td>100.00</td><td>WP_004114689.1</td><td>Hypothetical protein</td></tr><tr><td>55</td><td>+</td><td>44242</td><td>45132</td><td>296</td><td>Lantibiotic transport ATP-binding protein</td><td>582</td><td>582</td><td>100</td><td>0</td><td>98.65</td><td>EIK77256.1</td><td>Lysogeny</td></tr><tr><td>56</td><td>+</td><td>45101</td><td>45751</td><td>216</td><td>Hypothetical protein</td><td>420</td><td>420</td><td>100</td><td>5.00e-148</td><td>100.00</td><td>AEF31611.1</td><td>Hypothetical protein</td></tr><tr><td>57</td><td>+</td><td>45755</td><td>46144</td><td>129</td><td>Thioredoxin family protein</td><td>267</td><td>267</td><td>100</td><td>2.00e-90</td><td>100.00</td><td>WP_004125685.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>58</td><td>+</td><td>46150</td><td>46623</td><td>157</td><td>Thioredoxin family protein</td><td>319</td><td>319</td><td>100</td><td>5.00e-110</td><td>99.36</td><td>WP_004125686.1</td><td>DNA replication/ transcription/repair</td></tr><tr><td>59</td><td>+</td><td>47265</td><td>47828</td><td>187</td><td>Hypothetical protein</td><td>380</td><td>380</td><td>100</td><td>2.00e-133</td><td>100.00</td><td>WP_004114700.1</td><td>Hypothetical protein</td></tr><tr><td>60</td><td>+</td><td>47842</td><td>48066</td><td>74</td><td>Hypothetical protein</td><td>149</td><td>149</td><td>100</td><td>6.00e-45</td><td>100.00</td><td>EPI41518.1</td><td>Hypothetical protein</td></tr><tr><td>61</td><td>+</td><td>48651</td><td>49661</td><td>336</td><td>Amidase domain-containing protein</td><td>703</td><td>703</td><td>100</td><td>0</td><td>100.00</td><td>WP_048730094.1</td><td>Lysis</td></tr><tr><td>62</td><td>+</td><td>49648</td><td>50052</td><td>134</td><td>Hypothetical protein</td><td>261</td><td>261</td><td>100</td><td>8.00e-88</td><td>100.00</td><td>WP_048730092.1</td><td>Hypothetical protein</td></tr></tbody></table>

<footnote>a NA, not applicable; +, positive; -, negative; bp, base pair; aa, amino acid.</footnote>
<figure><img src="image_7.png" /></figure>

## ACKNOWLEDGMENTS

This work was supported by the French government under the "Investissements d'Avenir" (Investments for the Future) program managed by the Agence Nationale de la Recherche (ANR; National Agency for Research), grant 10-IAHU-03. This work was supported by Région Provence Alpes Côte d'Azur and European funding FEDER PRIMI.

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