Whole-genome sequencing of Listeria monocytogenes serotype 4b isolated from ready-to-eat lentil salad in Algiers, Algeria

Journal Pre-proof Whole genome sequencing of 1 Listeria monocytogenes serotype 4b isolated from ready to eat lentil salad in Algiers, Algeria R. Drali, A. Deriet, B. Verhaegen, S.C.J. De Keersmaecker, N. Botteldoorn, K. Vanneste, N.H.C. Roosens, F. Mouffok PII:

S2052-2975(19)30125-8

DOI:

https://doi.org/10.1016/j.nmni.2019.100628

Reference:

NMNI 100628

To appear in:

New Microbes and New Infections

Received Date: 5 November 2019 Accepted Date: 13 November 2019

Please cite this article as: Drali R, Deriet A, Verhaegen B, De Keersmaecker SCJ, Botteldoorn N, Vanneste K, Roosens NHC, Mouffok F, Whole genome sequencing of 1 Listeria monocytogenes serotype 4b isolated from ready to eat lentil salad in Algiers, Algeria, New Microbes and New Infections, https://doi.org/10.1016/j.nmni.2019.100628. This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. © 2019 Institut Pasteur d'Algérie. Published by Elsevier Ltd.

New Microbes and New Infections Whole genome sequencing of Listeria monocytogenes serotype 4b isolated from ready to eat lentil salad in Algiers, Algeria --Manuscript Draft-Manuscript Number: Article Type:

Taxonogenomics: genome of known organism

Keywords:

Whole genome sequencing, Listeria monocytogenes, ready to eat, Algeria.

Corresponding Author:

Rezak DRALI, Ph.D. Pasteur Institute of Algeria Algiers, ALGERIA

First Author:

Rezak DRALI, Ph.D.

Order of Authors:

Rezak DRALI, Ph.D. Abdelhamid Deriet Bavo Verhaegen Sigrid CJ DeKeersmaecker Nadine Botteldoorn Kevin Vanneste Nancy HC Roosens Fawzia Mouffok

Abstract:

Listeria monocytogenes is a Gram-positive foodborne pathogen causing a serious threat for public health. Here we announce the whole genome sequence (3,011,693 bp) of Listeria monocytogenes serotype 4b isolated from ready to eat lentil salad in Algiers and belonging to sequence type 2, lineage I and Clonal complex 2.

Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation

Cover Letter

Algiers, 04/11/2019

New Microbes & New Infections

Dear Editor, Please find enclosed the initial version of the manuscript entitled “Whole genome sequencing of Listeria monocytogenes serotype 4b isolated from ready to eat lentil salad in Algiers, Algeria.” Drali R, Deriet A, Verhaegen B, Vanneste K, De Keersmaecker SCJ, Botteldoorn N, Roosens NHC, Mouffok F., that we wish to submit to New Microbes & New Infections as Taxonogenomics: genome of known organism. We hope that the manuscript is quite convenient and adequate for publication in your journal.

Sincerely yours. Dr. Rezak DRALI

Manuscript (without author details)

1

Whole genome sequencing of Listeria monocytogenes serotype 4b

2

isolated from ready to eat lentil salad in Algiers, Algeria

3 4

Running title: WGS of Listeria monocytogenes from ready to eat in Algeria.

5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

Conflict of interest: none to declare

23

Abstract word count: 49

24

Text word count: 493

25

Keywords: Whole genome sequencing, Listeria monocytogenes, ready to eat, Algeria.

1

26

Abstract

27

Listeria monocytogenes is a Gram-positive foodborne pathogen causing a serious threat for

28

public health. Here we announce the whole genome sequence (3,011,693 bp) of Listeria

29

monocytogenes serotype 4b isolated from ready to eat lentil salad in Algiers and belonging to

30

sequence type 2, lineage I and Clonal complex 2.

2

31

Listeria monocytogenes (Lm) is a facultative anaerobe Gram positive bacterium that causes

32

two forms of listeriosis: gastroenteritis and invasive infection [1]. Lm is ubiquitously present

33

in the environment. It is often associated with food such as ready-to-eat deli meats and

34

unpasteurized dairy products. Its ability to grow at low temperatures favors its persistence in

35

manufactured food products [2]. The transmission via the fecal-oral route or by ingesting

36

contaminated food turns Lm into a major concern for food safety and public health. Several

37

historical Lm-related foodborne outbreaks around the world showed a high mortality rate,

38

particularly in elderly, pregnant women and immunocompromised individuals [3]. Listeriosis

39

can cause severe symptoms including septicemia, meningitis, stillbirths and even death [4].

40

There are 13 recognized serotypes for Lm worldwide, however only four of them are of

41

significant concern to human health: 1/2c, 1/2a, 1/2b, and 4b, the latter three serotypes are

42

responsible for more than 95% of invasive listeriosis cases [1,5,6]. Historically, the majority

43

of the clinical cases and outbreaks are associated with serotype 4b strains [1,7]. The strain

44

analyzed in this study was isolated in 2010 from a ready to eat lentil salad according to ISO

45

method 11290 [8,9]. Fraser broth was used for enrichments and Palcam agar for strain

46

isolation. Biochemical identification was then performed using the API Listeria test

47

(Biomerieux) and subsequently, the strain was serotyped using a multiplex polymerase chain

48

reaction [10]. Genomic DNA was extracted using genomic Tip 20/G (Qiagen) following the

49

manufacturer’s instructions. A paired-end 2x250 bp sequencing run was performed using an

50

Illumina MiSeq system. The Nextera XT DNA library Preparation kit was used to construct

51

libraries from the extracted DNA. Raw sequence reads were trimmed by Trimmomatic

52

v0.36.4 with following options: trailing: 10, leading: 10, slidingwindow: 4:20, minlen: 40

53

[11]. Assembly was carried out using Spades v1.3.1 with default settings [12]. Annotation of

54

assembly was done using Prokka Rapid prokaryotic genome annotation v1.11 with default

55

settings [13]. Antimicrobial resistance (AMR) gene occurrence was investigated with

3

56

Resfinder v3.1 with default settings (https://cge.cbs.dtu.dk/services/ResFinder/). Virulence,

57

Multilocus sequence typing (MLST) and PCR-serogroup was investigated using The BIGSdb

58

database for Listeria (http://bigsdb.pasteur.fr/listeria).

59

A total of 263,240 reads of 250 bp were obtained. The genome has a length of 3,011,693 bp,

60

with an average coverage depth of 17x, N50 of 272,618, contains 22 contigs > 1000 bp and

61

has a GC% of 38. Annotation revealed 2974 coding sequences (CDS), 58 tRNA and 2880

62

hypothetical proteins. This strain was found to belong to PCR-serogroup: IVb (3), sequence

63

type: 2, lineage: I and Clonal complex: CC2. The antimicrobial resistance gene fosX was

64

found in addition to 55 virulence genes. None of the known prfA alleles corresponds to our

65

prfA, the closest one was prfA with 99% identity [4].

66

In best of our knowledge this is the first genome of Listeria spp reported in Algeria. This

67

whole genome has been deposited at GenBank under accession number GCA_006348975.1

68

and its raw reads at Sequence Read Archive under accession number SRR9099607.

4

69

Funding section

70

This research was financed by Institut Pasteur d'Algérie and by Enabel - Agence belge de

71

développement.

72 73

Transparency declarations

74

There is no potential conflict of interest or financial disclosure for all authors.

75 76

Conflict of interest

77

None to declare.

5

78

Reference List

79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118

1. Burall LS, Grim CJ, Mammel MK, Datta AR (2017). A Comprehensive Evaluation of the Genetic Relatedness of Listeria monocytogenes Serotype 4b Variant Strains. Front Public Health 5: 241. 10.3389/fpubh.2017.00241 [doi]. 2. Kathariou S. (2002). Listeria monocytogenes virulence and pathogenicity, a food safety perspective. J Food Prot 65: 1811-1829. 3. Jordan K, McAuliffe O. (2018). Listeria monocytogenes in Foods. Adv Food Nutr Res 86: 181-213. S1043-4526(18)30022-6 [pii];10.1016/bs.afnr.2018.02.006 [doi]. 4. Charlier C, Perrodeau E, Leclercq A, Cazenave B, Pilmis B, Henry B, Lopes A, Maury MM, Moura A, Goffinet F, Dieye HB, Thouvenot P, Ungeheuer MN, Tourdjman M, Goulet V, de VH, Lortholary O, Ravaud P, Lecuit M. (2017). Clinical features and prognostic factors of listeriosis: the MONALISA national prospective cohort study. Lancet Infect Dis 17: 510-519. S1473-3099(16)30521-7 [pii];10.1016/S1473-3099(16)30521-7 [doi]. 5. Leclercq A, Chenal-Francisque V, Dieye H, Cantinelli T, Drali R, Brisse S, Lecuit M. (2011). Characterization of the novel Listeria monocytogenes PCR serogrouping profile IVb-v1. Int J Food Microbiol 147: 74-77. S0168-1605(11)00165-6 [pii];10.1016/j.ijfoodmicro.2011.03.010 [doi]. 6. Liu, D. (2008). Handbook of Listeria monocytogenes. CRC press. 7. Laksanalamai P, Huang B, Sabo J, Burall LS, Zhao S, Bates J, Datta AR. (2014). Genomic characterization of novel Listeria monocytogenes serotype 4b variant strains. PLoS One 9: e89024. 10.1371/journal.pone.0089024 [doi];PONE-D-13-44873 [pii]. 8. Scotter SL, Langton S, Lombard B, Schulten S, Nagelkerke N, Rollier P, Lahellec C. (2001). Validation of ISO method 11290: part 1. Detection of Listeria monocytogenes in foods. International Journal of Food Microbiology, 64(3), 295-306. 9. Scotter SL, Langton S, Lombard B, Lahellec C, Schulten S, Nagelkerke N, Rollier P. (2001). Validation of ISO method 11290: Part 2. Enumeration of Listeria monocytogenes in foods. International journal of food microbiology, 70(1-2), 121-129. 10. Doumith M, Buchrieser C, Glaser P, Jacquet C, Martin P (2004). Differentiation of the major Listeria monocytogenes serovars by multiplex PCR. J Clin Microbiol 42: 38193822. 10.1128/JCM.42.8.3819-3822.2004 [doi];42/8/3819 [pii].

6

119 120 121 122 123 124 125 126 127 128 129

11. Bolger AM, Lohse M, Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30, 2114-2120. 12. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. 13. Cuccuru G, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, Uva P, Zanetti G, Fotia G. (2014). Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics. 30, 1928-1929.

7

Title Page (with author details)

Whole genome sequencing of Listeria monocytogenes serotype 4b isolated from ready to eat lentil salad in Algiers, Algeria

R. Drali1*, A. Deriet2, B. Verhaegen3, S.C.J. De Keersmaecker4, N. Botteldoorn3, K. Vanneste4, N.H.C. Roosens4, F. Mouffok2

1

Plateforme Génomique - Bioinformatique, Institut Pasteur d'Algérie, Alger, Algérie.

2

Laboratoire de Bactériologie des Aliments, Eaux et Environnement, Institut Pasteur d'Algérie, Alger, Algérie. 3

Sciensano, Service Food Borne Pathogens, Brussels, Belgium.

4

Sciensano, Transversal Activities in Applied Genomics, Brussels, Belgium.

Address correspondence to R. Drali, [email protected] Tel/Fax: 213 23 36 74 00

Conflict of Interest Form