Tracking the Source of Human Q Fever from a Southern French Village: Sentinel Animals and Environmental Reservoir

1. Introduction

2. Software

3. Data

5. Citation

Introduction

Coxiella burnetii, also known as the causal agent of Q fever, is a zoonotic pathogen infecting 15 humans and several animal species. Here, we investigated the epidemiological context of C. burnetii 16 from an area in the Hérault department in southern France, using the One Health paradigm. Multi-spacer typing based on dual barcoding nanopore sequencing highlighted the occur- 23 rence of new genotype of C. burnetii.

Softwares

1. [Sequence Demultipling:[nanoMLST] (https://github.com/jade-nhri/nanoMLST)]
2. [Adaptator Trimming:qcat]
3. [Sequence Alignement: MAFFT]
4. [Sequence Concatenation: SeaView]
5. [ML Phylogeny: Iqtree2]
6. [Tree Editing: iTOL-v5]
7. [Chat: Gitter]

Data

MS-Sequences.fasta: Fasta Files of the Multi-spacer Sequences of C. burnetti genotype. MST-02-maffted.fasta: Aligned Fasta Sequences used to generate the ML Tree. MS_Profil.pdf: MS Blast Results from [Blast: MST_Db] Treefeatures.txt: iqtree output file

• Final Tree is Available as Pre-edited Tree [Cb_Tree: MST_ML]

** Files used to annotate the tree

Labels.txt: Sequence Names and Info.

Origin.txt: Isolated Source of Cb. strains

Tag.txt: Highliting Cb Strain from Our Study

Citation

The original paper is freely downloadable from:

[Laidoudi et al., 2023: Tracking the Source of Human Q Fever from a Southern French 2 Village: Sentinel Animals and Environmental Reservoir]