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Thread: Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports

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    Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports

    https://www.cell.com/iscience/fullte...21)00989-5#%20

    SUMMARY

    Ancient pathogen genomics is an emerging field allowing reconstruction of past epidemics. The demise of post-contact American populations may, at least in part, have been caused by paratyphoid fever brought by Europeans. We retrieved genome-wide data from two Spanish soldiers who were besieging the city of Barcelona in 1652, during the Reapers’ War. Their ancestry derived from the Basque region and Sardinia, respectively, (at that time, this island belonged to the Spanish kingdom). Despite the proposed plague epidemic, we could not find solid evidence for the presence of the causative plague agent in these individuals. However, we retrieved from one individual a substantial fraction of the Salmonella enterica serovar Paratyphi C lineage linked to paratyphoid fever in colonial period Mexico. Our results support a growing body of evidence that Paratyphi Centeric fever was more prevalent in Europe and the Americas in the past than it is today.

    RESULTS

    Ancient DNA sequencing and characterization of La Sagrera soldiers Archaeological excavations at La Sagrera uncovered 576 skeletons of soldiers grouped in shallow graves. Most of these contained between one and ten individuals, but they also included two large pits with 69 and 79 individuals, respectively. Based on the archaeological context of the burials, the soldiers were hastily buried—sometimes still dressed and with boots on—without signs of war injuries and within a short period of time. Archaeologists tend to associate such burial procedures with disease outbreaks (Signoli et al., 2004; Raoult et al., 2006). In contemporaneous chronicles, it is mentioned that both the defenders—within the city—and the besiegers suffered a bout of ‘‘pestilence’’ that has been previously considered to be a plague outbreak (Parets, 1660; Luis and Moya, 1990).

    We sampled the teeth of two soldiers of the Spanish army, labeled F1691-1810 and F1364-1436, for ancient DNA sequencing (Figure 1A). From these samples, we obtained 246,473,297 and 99,018,404 DNA reads, respectively. The ends of the DNA reads obtained displayed typical ancient DNA (aDNA) damage patterns in a ratio consistent with the estimated age of the site (Figure S1). In both cases, the molecular sex was assigned to male (Table S1). Based on the presence of different mitochondrial DNA (mtDNA) haplogroups and on heterozygosity levels of the X chromosome, we found that one of the libraries was partially contaminated (around 9% of human reads). Therefore, we only considered the non-contaminated libraries for the subsequent human population genetics analysis. The mtDNA haplogroups were assigned as U5b1f1a and H2a5a for F1691-1810 (Sardinian) and F1364-1436(Basque), respectively (Table S2). Y chromosome haplogroups were assigned with differing degrees of resolution to R1 and R1b1a1b1 for F1691-1810 and F1364-1436, respectively."


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    I'm not sure if both samples are available for download, but if anyone wants to download and convert them (so that they can be used with the Global 25), I would be very interested.

    Thank you.

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    This is just F1364-1436. I am not sure which one of F1691-1810's samples is the shotgun mentioned in the paper.

    https://drive.google.com/drive/folde...ww?usp=sharing

    Code:
    Result (88.5% 115 -0 +15): R-Y3961
    R1b -> R-L754 -> R-L389 -> R-P297 -> R-M269 -> R-L23 -> R-L51 -> R-L52 -> R-L151 -> R-P312 -> R-U152 -> R-L2 -> R-Y3961 (ISOGG: )
    Extra: FGC64085 BY177908/Y157514 Y33053 Y726(H) Y33366/BY17177(H) M4072 Y21370 Z10267 FGC2504 PH865 Y173685 Y21865 BZ3597 FGC85694 Y147223

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    Quote Originally Posted by teepean47 View Post
    This is just F1364-1436. I am not sure which one of F1691-1810's samples is the shotgun mentioned in the paper.

    https://drive.google.com/drive/folde...ww?usp=sharing

    Code:
    Result (88.5% 115 -0 +15): R-Y3961
    R1b -> R-L754 -> R-L389 -> R-P297 -> R-M269 -> R-L23 -> R-L51 -> R-L52 -> R-L151 -> R-P312 -> R-U152 -> R-L2 -> R-Y3961 (ISOGG: )
    Extra: FGC64085 BY177908/Y157514 Y33053 Y726(H) Y33366/BY17177(H) M4072 Y21370 Z10267 FGC2504 PH865 Y173685 Y21865 BZ3597 FGC85694 Y147223

    Thanks!

    After downloading, how could I convert the files to be compatible with the Global 25?

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    Quote Originally Posted by teepean47 View Post
    This is just F1364-1436. I am not sure which one of F1691-1810's samples is the shotgun mentioned in the paper.

    https://drive.google.com/drive/folde...ww?usp=sharing

    Code:
    Result (88.5% 115 -0 +15): R-Y3961
    R1b -> R-L754 -> R-L389 -> R-P297 -> R-M269 -> R-L23 -> R-L51 -> R-L52 -> R-L151 -> R-P312 -> R-U152 -> R-L2 -> R-Y3961 (ISOGG: )
    Extra: FGC64085 BY177908/Y157514 Y33053 Y726(H) Y33366/BY17177(H) M4072 Y21370 Z10267 FGC2504 PH865 Y173685 Y21865 BZ3597 FGC85694 Y147223
    According Lucy Van Dorp

    "Thank you for your interest in our study.

    Toni (cc’d) has quickly checked this. The ftp file for the Basque starts with L017 and there are multiple files for the Sardinian starting with L014 (October and April). Please note if you use the column selection and select Sample_alias and/or Sample_title, the name of each sample will be displayed.

    I hope that helps.

    All the best,

    Lucy"


    I asked her which one should I download, because there are a lot of files labeled as L014.
    Last edited by Olymp; 09-14-2021 at 02:42 PM.

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    Quote Originally Posted by Olymp View Post
    Thanks!

    After downloading, how could I convert the files to be compatible with the Global 25?
    Email to [email protected] and ask nicely if you could get G25 coordinates and the data can be downloaded from the Google drive link from above. You should receive results in day or two.

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    I got a response from another person who took part in the study:

    "Hello,

    The original files of the Sardinian individual were splitted because of logistics reasons, but all of them (L014) are from the same individuals.

    Regards,

    Toni'

    So, i should maybe trying to download the most recent file.


    Quote Originally Posted by teepean47 View Post
    Email to [email protected] and ask nicely if you could get G25 coordinates and the data can be downloaded from the Google drive link from above. You should receive results in day or two.
    He has already replied to me, he is not available at the moment to do it, so I am trying to do it myself.

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    Quote Originally Posted by teepean47 View Post
    This is just F1364-1436. I am not sure which one of F1691-1810's samples is the shotgun mentioned in the paper.

    https://drive.google.com/drive/folde...ww?usp=sharing

    Code:
    Result (88.5% 115 -0 +15): R-Y3961
    R1b -> R-L754 -> R-L389 -> R-P297 -> R-M269 -> R-L23 -> R-L51 -> R-L52 -> R-L151 -> R-P312 -> R-U152 -> R-L2 -> R-Y3961 (ISOGG: )
    Extra: FGC64085 BY177908/Y157514 Y33053 Y726(H) Y33366/BY17177(H) M4072 Y21370 Z10267 FGC2504 PH865 Y173685 Y21865 BZ3597 FGC85694 Y147223

    Ok, so here the "final" answer:

    "Hi again,

    no no, you should download all libraries April and October. Most salmonella sequences are in the April library, while most non contaminated human sequences are in the October library (the April one contains a bit of contaminant that can be filtered out with PMDtools).

    Kind regards,

    Toni"


    But the files are too large, it would take a long time to download

    So I'm waiting for someone to do it, with a better connection than mine ...

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    Quote Originally Posted by Olymp View Post
    Ok, so here the "final" answer:

    "Hi again,

    no no, you should download all libraries April and October. Most salmonella sequences are in the April library, while most non contaminated human sequences are in the October library (the April one contains a bit of contaminant that can be filtered out with PMDtools).

    Kind regards,

    Toni"


    But the files are too large, it would take a long time to download

    So I'm waiting for someone to do it, with a better connection than mine ...
    I am already downloading so can do the rest of the work as well.

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    Quote Originally Posted by teepean47 View Post
    I am already downloading so can do the rest of the work as well.
    Thank you.

    I wish I could, but I can't because i have a really bad connection.

    Thanks again to you.

    You will tell me how it goes. If you can convert the files (both samples, but several files) for Global 25.

    I had already converted BAM files (some files, I had to wait a long time to complete the download) for Gedmatch calculters, but for Global 25 it seems more complex.

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