# How to cite

## Citing Pathogenwatch

### General notes

When citing Pathogenwatch, it is important to distinguish between the results from the tools incorporated into the system, and the web resource itself. Please ensure that individual analysis tools are acknowledged and supported.

{% hint style="info" %}
If a citation for a tool or resource is missing, please contact our support address <pathogenwatch@cgps.group> and we will rectify the documentation.
{% endhint %}

### Citing the website

The website URL <https://pathogen.watch> is the best reference for Pathogenwatch. We advise including the version (which can be found in the menu on the top left of the website) and the date.

However, if a peer-reviewed publication is needed, generally use the most recent of the individual species publications below. If citing results from one of these species, use the appropriate reference.

#### Core publications

* Bayliss SC, Verner-Jeffreys DW, Bartie KL, et al. The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens. *Front Microbiol*. 2017;8:121. Published 2017 Feb 3. doi:10.3389/fmicb.2017.00121 \[Note that Pathogenwatch was called "WGSA" at this point]
* Harris SR, Cole MJ, Spiteri G, et al. Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey. *Lancet Infect Dis*. 2018;18(7):758-768. doi:10.1016/S1473-3099(18)30225-1 \[Note that Pathogenwatch was called "WGSA" at this point]
* Sánchez-Busó L, Cole MJ, Spiteri G, et al. Europe-wide expansion and eradication of multidrug-resistant Neisseria gonorrhoeae lineages: a genomic surveillance study. *Lancet Microbe*. 2022;3(6):e452-e463. doi:10.1016/S2666-5247(22)00044-1
* Gladstone RA, Lo SW, Goater R, et al. Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates. *Microb Genom*. 2020;6(5):e000357. doi:10.1099/mgen.0.000357
* Mitchell C, Steward KF, Charbonneau ARL, et al. Globetrotting strangles: the unbridled national and international transmission of *Streptococcus equi* between horses. *Microb Genom*. 2021;7(3):mgen000528. doi:10.1099/mgen.0.000528
* Argimón S, Yeats CA, Goater RJ, et al. A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch. *Nat Commun*. 2021;12(1):2879. Published 2021 May 17. doi:10.1038/s41467-021-23091-2
* Li X, Muñoz JF, Gade L, et al. Comparing genomic variant identification protocols for *Candida auris*. *Microb Genom*. 2023;9(4):mgen000979. doi:10.1099/mgen.0.000979

### Citing individual tools

Each tool described in Technical Descriptions has a "How to cite" section at the bottom. If this is missing or incomplete, please [contact us](mailto:pathogenwatch@cgps.group).


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# Agent Instructions: Querying This Documentation

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Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://cgps.gitbook.io/pathogenwatch/how-to-cite.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.