skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: A molecular portrait of maternal sepsis from Byzantine Troy

Abstract

Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While we excavated a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman’s remains. Scanning electron microscopy of the tissue revealed ‘ghost cells’, resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis.Gardnerella vaginalisandStaphylococcus saprophyticusdominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed thatG. vaginalisTroy fell within contemporary genetic diversity, whereasS. saprophyticusTroy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology ofS. saprophyticusinfection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. Our results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections.

Authors:
 [1]; ORCiD logo [2];  [3];  [4];  [5];  [6];  [7];  [8];  [8];  [9];  [10];  [10];  [11];  [11];  [12];  [12];  [13];  [14]; ORCiD logo [15];  [16] more »; ORCiD logo [17] « less
  1. McMaster Univ., Hamilton, ON (Canada). McMaster Ancient DNA Centre, Dept. of Anthropology; MYcroarray, Ann Arbor, MI (United States)
  2. Univ. of Wisconsin, Madison, WI (United States). Dept. of Medical Microbiology and Immunology, Microbiology Doctoral Training Program
  3. Univ. of Iowa, Iowa City, IA (United States). Dept. of Anthropology
  4. Tubingen Univ. (Germany). Inst. of Prehistory, Early History, and Medieval Archaeology
  5. McMaster Univ., Hamilton, ON (Canada). McMaster Ancient DNA Centre, Dept. of Anthropology; MYcroarray, Ann Arbor, MI (United States)
  6. McMaster Univ., Hamilton, ON (Canada). Dept. of Biology
  7. Univ. of California, Irvine, CA (United States). Earth Systems Science Dept.
  8. McMaster Univ., Hamilton, ON (Canada). McMaster Ancient DNA Centre, Dept. of Anthropology
  9. Univ. of Wisconsin, Madison, WI (United States). Molecular Archaeology Lab., Dept. of Classics and Ancient Near Eastern Studies
  10. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  11. McMaster Univ., Hamilton, ON (Canada). Michael G. DeGroote Inst. for Infectious Disease Research
  12. National Inst. of Infectious Diseases, Tokyo (Japan). Lab. of Bacterial Genomics
  13. Yale Univ., New Haven, CT (United States). Dept. of Geology and Geophysics
  14. Univ. of Pisa (Italy). Dept. of Translational Research on New Technologies in Medicine and Surgery
  15. Univ. of Sydney, NSW (Australia). Marie Bashir Inst. for Infectious Diseases and Biosecurity
  16. McMaster Univ., Hamilton, ON (Canada). McMaster Ancient DNA Centre, Dept. of Anthropology; McMaster Univ., Hamilton, ON (Canada). Dept. of Biology; McMaster Univ., Hamilton, ON (Canada). Michael G. DeGroote Inst. for Infectious Disease Research; Canadian Inst. for Advanced Research, Toronto, ON (Canada). Humans and the Microbiome Program
  17. Univ. of Wisconsin, Madison, WI (United States). Dept. of Medical Microbiology and Immunology, Molecular Archaeology Lab., Dept. of Medicine
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1395322
Grant/Contract Number:  
AC52-07NA27344; T32 GM07215; R01AI13287; DGE-1256259
Resource Type:
Accepted Manuscript
Journal Name:
eLife
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Devault, Alison M., Mortimer, Tatum D., Kitchen, Andrew, Kiesewetter, Henrike, Enk, Jacob M., Golding, G. Brian, Southon, John, Kuch, Melanie, Duggan, Ana T., Aylward, William, Gardner, Shea N., Allen, Jonathan E., King, Andrew M., Wright, Gerard, Kuroda, Makoto, Kato, Kengo, Briggs, Derek EG, Fornaciari, Gino, Holmes, Edward C., Poinar, Hendrik N., and Pepperell, Caitlin S. A molecular portrait of maternal sepsis from Byzantine Troy. United States: N. p., 2017. Web. doi:10.7554/eLife.20983.
Devault, Alison M., Mortimer, Tatum D., Kitchen, Andrew, Kiesewetter, Henrike, Enk, Jacob M., Golding, G. Brian, Southon, John, Kuch, Melanie, Duggan, Ana T., Aylward, William, Gardner, Shea N., Allen, Jonathan E., King, Andrew M., Wright, Gerard, Kuroda, Makoto, Kato, Kengo, Briggs, Derek EG, Fornaciari, Gino, Holmes, Edward C., Poinar, Hendrik N., & Pepperell, Caitlin S. A molecular portrait of maternal sepsis from Byzantine Troy. United States. doi:10.7554/eLife.20983.
Devault, Alison M., Mortimer, Tatum D., Kitchen, Andrew, Kiesewetter, Henrike, Enk, Jacob M., Golding, G. Brian, Southon, John, Kuch, Melanie, Duggan, Ana T., Aylward, William, Gardner, Shea N., Allen, Jonathan E., King, Andrew M., Wright, Gerard, Kuroda, Makoto, Kato, Kengo, Briggs, Derek EG, Fornaciari, Gino, Holmes, Edward C., Poinar, Hendrik N., and Pepperell, Caitlin S. Tue . "A molecular portrait of maternal sepsis from Byzantine Troy". United States. doi:10.7554/eLife.20983. https://www.osti.gov/servlets/purl/1395322.
@article{osti_1395322,
title = {A molecular portrait of maternal sepsis from Byzantine Troy},
author = {Devault, Alison M. and Mortimer, Tatum D. and Kitchen, Andrew and Kiesewetter, Henrike and Enk, Jacob M. and Golding, G. Brian and Southon, John and Kuch, Melanie and Duggan, Ana T. and Aylward, William and Gardner, Shea N. and Allen, Jonathan E. and King, Andrew M. and Wright, Gerard and Kuroda, Makoto and Kato, Kengo and Briggs, Derek EG and Fornaciari, Gino and Holmes, Edward C. and Poinar, Hendrik N. and Pepperell, Caitlin S.},
abstractNote = {Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While we excavated a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman’s remains. Scanning electron microscopy of the tissue revealed ‘ghost cells’, resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis.Gardnerella vaginalisandStaphylococcus saprophyticusdominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed thatG. vaginalisTroy fell within contemporary genetic diversity, whereasS. saprophyticusTroy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology ofS. saprophyticusinfection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. Our results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections.},
doi = {10.7554/eLife.20983},
journal = {eLife},
number = ,
volume = 6,
place = {United States},
year = {2017},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 8 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication
journal, May 2012

  • Weinert, Lucy A.; Welch, John J.; Suchard, Marc A.
  • Biology Letters, Vol. 8, Issue 5
  • DOI: 10.1098/rsbl.2012.0290

T HE R OLE OF D ECAY AND M INERALIZATION IN THE P RESERVATION OF S OFT -B ODIED F OSSILS
journal, May 2003


Fibroblast involvement in soft connective tissue calcification
journal, January 2013


QUAST: quality assessment tool for genome assemblies
journal, February 2013


Prevalence ofStaphylococcus saprophyticus in patients in a venereal disease clinic
journal, June 1986

  • Ringertz, O.; Torssander, J.
  • European Journal of Clinical Microbiology, Vol. 5, Issue 3
  • DOI: 10.1007/BF02017800

Mechanism of Stone Formation
journal, February 1997


Parallel independent evolution of pathogenicity within the genus Yersinia
journal, April 2014

  • Reuter, S.; Connor, T. R.; Barquist, L.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 18
  • DOI: 10.1073/pnas.1317161111

Molecular Evolutionary Consequences of Niche Restriction in Francisella tularensis, a Facultative Intracellular Pathogen
journal, June 2009


An 8500-Year-Old Bladder Stone from uzzo cave (Trapani): Fourier Transform-Infrared Spectroscopy Analysis*
journal, February 2005


leeHom: adaptor trimming and merging for Illumina sequencing reads
journal, August 2014

  • Renaud, Gabriel; Stenzel, Udo; Kelso, Janet
  • Nucleic Acids Research, Vol. 42, Issue 18
  • DOI: 10.1093/nar/gku699

Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009


Ectocranial suture closure: A revised method for the determination of skeletal age at death based on the lateral-anterior sutures
journal, September 1985

  • Meindl, Richard S.; Lovejoy, C. Owen
  • American Journal of Physical Anthropology, Vol. 68, Issue 1
  • DOI: 10.1002/ajpa.1330680106

Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA
journal, October 1999

  • Andrews, Richard M.; Kubacka, Iwona; Chinnery, Patrick F.
  • Nature Genetics, Vol. 23, Issue 2
  • DOI: 10.1038/13779

SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011

  • Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
  • Nature Methods, Vol. 8, Issue 10
  • DOI: 10.1038/nmeth.1701

The mineralization of dinosaur soft tissue in the Lower Cretaceous of Las Hoyas, Spain
journal, July 1997

  • Briggs, Derek E. G.; Wilby, Philip R.; PÉRez-Moreno, Bernardino P.
  • Journal of the Geological Society, Vol. 154, Issue 4
  • DOI: 10.1144/gsjgs.154.4.0587

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
journal, October 2001

  • Parkhill, J.; Dougan, G.; James, K. D.
  • Nature, Vol. 413, Issue 6858
  • DOI: 10.1038/35101607

Mugsy: fast multiple alignment of closely related whole genomes
journal, December 2010


ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
journal, January 2013


Mineralization of soft-part anatomy and invading microbes in the horseshoe crab Mesolimulus from the Upper Jurassic Lagerstätte of Nusplingen, Germany
journal, March 2005

  • Briggs, Derek E. G.; Moore, Rachel A.; Shultz, Jeffrey W.
  • Proceedings of the Royal Society B: Biological Sciences, Vol. 272, Issue 1563
  • DOI: 10.1098/rspb.2004.3006

Magnesium Whitlockite, a Calcium Phosphate Crystal of Special Interest in Pathology
journal, January 2003


Melanosomes or Microbes: Testing an Alternative Hypothesis for the Origin of Microbodies in Fossil Feathers
journal, March 2014

  • Moyer, Alison E.; Zheng, Wenxia; Johnson, Elizabeth A.
  • Scientific Reports, Vol. 4, Issue 1
  • DOI: 10.1038/srep04233

Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock
journal, June 2009

  • Soares, Pedro; Ermini, Luca; Thomson, Noel
  • The American Journal of Human Genetics, Vol. 84, Issue 6
  • DOI: 10.1016/j.ajhg.2009.05.001

Accurate sex identification of ancient human remains using DNA shotgun sequencing
journal, December 2013

  • Skoglund, Pontus; Storå, Jan; Götherström, Anders
  • Journal of Archaeological Science, Vol. 40, Issue 12
  • DOI: 10.1016/j.jas.2013.07.004

Kraken: ultrafast metagenomic sequence classification using exact alignments
journal, January 2014


HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups
journal, November 2010

  • Kloss-Brandstätter, Anita; Pacher, Dominic; Schönherr, Sebastian
  • Human Mutation, Vol. 32, Issue 1
  • DOI: 10.1002/humu.21382

A framework for variation discovery and genotyping using next-generation DNA sequencing data
journal, April 2011

  • DePristo, Mark A.; Banks, Eric; Poplin, Ryan
  • Nature Genetics, Vol. 43, Issue 5
  • DOI: 10.1038/ng.806

Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing
journal, June 2010


RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014


Prokka: rapid prokaryotic genome annotation
journal, March 2014


SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012

  • Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
  • Journal of Computational Biology, Vol. 19, Issue 5
  • DOI: 10.1089/cmb.2012.0021

A medieval bladder stone from Norwich, Norfolk
journal, January 2003

  • Anderson, T.
  • International Journal of Osteoarchaeology, Vol. 13, Issue 3
  • DOI: 10.1002/oa.641

Automated ensemble assembly and validation of microbial genomes
journal, May 2014

  • Koren, Sergey; Treangen, Todd J.; Hill, Christopher M.
  • BMC Bioinformatics, Vol. 15, Issue 1
  • DOI: 10.1186/1471-2105-15-126

A new look at the statistical model identification
journal, December 1974


Microbial community assembly and metabolic function during mammalian corpse decomposition
journal, December 2015


A Case–Control Study of Chorioamnionic Infection and Histologic Chorioamnionitis in Prematurity
journal, October 1988

  • Hillier, Sharon L.; Martius, Joachim; Krohn, Marijane
  • New England Journal of Medicine, Vol. 319, Issue 15
  • DOI: 10.1056/NEJM198810133191503

Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty
journal, May 2008


Detection of recombination events in bacterial genomes from large population samples
journal, November 2011

  • Marttinen, Pekka; Hanage, William P.; Croucher, Nicholas J.
  • Nucleic Acids Research, Vol. 40, Issue 1
  • DOI: 10.1093/nar/gkr928

The MaSuRCA genome assembler
journal, August 2013


The Origin of Staphylococcus saprophyticus from Cattle and Pigs
journal, January 1993

  • Hedman, Per; Ringertz, Olof; Lindström, Monica
  • Scandinavian Journal of Infectious Diseases, Vol. 25, Issue 1
  • DOI: 10.1080/00365549309169670

Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis
journal, April 2014


MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Zika Virus Associated with Microcephaly
journal, March 2016

  • Mlakar, Jernej; Korva, Misa; Tul, Nataša
  • New England Journal of Medicine, Vol. 374, Issue 10
  • DOI: 10.1056/NEJMoa1600651

Placental Calcification a Study of 3,025 Singleton and Multiple Pregnancies
journal, June 1965


Rates of Vaccine Evolution Show Strong Effects of Latency: Implications for Varicella Zoster Virus Epidemiology
journal, January 2015

  • Weinert, Lucy A.; Depledge, Daniel P.; Kundu, Samit
  • Molecular Biology and Evolution, Vol. 32, Issue 4
  • DOI: 10.1093/molbev/msu406

Diversity and biofilm-forming capability of bacteria recovered from stainless steel pipes of a milk-processing dairy plant
journal, May 2015

  • Cherif-Antar, Asma; Moussa–Boudjemâa, Boumediene; Didouh, Nassima
  • Dairy Science & Technology, Vol. 96, Issue 1
  • DOI: 10.1007/s13594-015-0235-4

Renal Calculosis of Pandolfo III Malatesta (1370-1427)
journal, December 2011


Ectopic Calcification
journal, March 1999


mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
journal, April 2013


REAPR: a universal tool for genome assembly evaluation
journal, January 2013


Cutadapt removes adapter sequences from high-throughput sequencing reads
journal, May 2011


Urolithiasis Through the Ages: Data on More Than 200,000 Urinary Stone Analyses
journal, April 2011


The role of the calcium carbonate-calcium phosphate switch in the mineralization of soft-bodied fossils
journal, September 1996

  • Briggs, Derek E. G.; Wilby, Philip R.
  • Journal of the Geological Society, Vol. 153, Issue 5
  • DOI: 10.1144/gsjgs.153.5.0665

Staphylococcus saprophyticus as the Cause of Infected Urinary Calculus
journal, March 1985


Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
journal, October 2011

  • Kircher, Martin; Sawyer, Susanna; Meyer, Matthias
  • Nucleic Acids Research, Vol. 40, Issue 1
  • DOI: 10.1093/nar/gkr771

Livestock-associated Staphylococcus aureus: origin, evolution and public health threat
journal, April 2012


Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies
journal, June 2010


Circos: An information aesthetic for comparative genomics
journal, June 2009


Methicillin-Resistant Staphylococcus saprophyticus Isolates Carrying Staphylococcal Cassette Chromosome mec Have Emerged in Urogenital Tract Infections
journal, March 2008

  • Higashide, M.; Kuroda, M.; Omura, C. T. N.
  • Antimicrobial Agents and Chemotherapy, Vol. 52, Issue 6
  • DOI: 10.1128/AAC.01150-07

The 5300-year-old Helicobacter pylori genome of the Iceman
journal, January 2016


Bayesian Phylogenetics with BEAUti and the BEAST 1.7
journal, February 2012

  • Drummond, Alexei J.; Suchard, Marc A.; Xie, Dong
  • Molecular Biology and Evolution, Vol. 29, Issue 8
  • DOI: 10.1093/molbev/mss075

Finding of a bladder stone from the Avar period in southeast Hungary
journal, June 1987

  • Szalai, F.; Jávor, É.
  • International Urology and Nephrology, Vol. 19, Issue 2
  • DOI: 10.1007/BF02550466

Why do species vary in their rate of molecular evolution?
journal, February 2009


A Simple and Robust Statistical Test for Detecting the Presence of Recombination
journal, February 2006


The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults
journal, January 2013

  • Lewis, Debbie A.; Brown, Richard; Williams, Jon
  • Frontiers in Cellular and Infection Microbiology, Vol. 3
  • DOI: 10.3389/fcimb.2013.00041

Reconsidering obstetric death and female fertility in Anglo-Saxon England
journal, June 2013


BEAST: Bayesian evolutionary analysis by sampling trees
journal, January 2007


A Practical Synthesis of Nitrocefin
journal, January 2005

  • Lee, Mijoon; Hesek, Dusan; Mobashery, Shahriar
  • The Journal of Organic Chemistry, Vol. 70, Issue 1
  • DOI: 10.1021/jo0487395

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003


Staphylococcus saprophyticus urinary tract infections: epidemiological data from Western Australia
journal, February 1996

  • Schneider, Paul F.; Riley, Thomas V.
  • European Journal of Epidemiology, Vol. 12, Issue 1
  • DOI: 10.1007/BF00144428

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
journal, April 2010

  • Abascal, Federico; Zardoya, Rafael; Telford, Maximilian J.
  • Nucleic Acids Research, Vol. 38, Issue suppl_2
  • DOI: 10.1093/nar/gkq291

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Application of Phylogenetic Networks in Evolutionary Studies
journal, October 2005

  • Huson, Daniel H.; Bryant, David
  • Molecular Biology and Evolution, Vol. 23, Issue 2
  • DOI: 10.1093/molbev/msj030

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe
journal, March 2016


Analyzing the mosaic structure of genes
journal, February 1992

  • Smith, JohnMaynard
  • Journal of Molecular Evolution, Vol. 34, Issue 2
  • DOI: 10.1007/BF00182389

Extensive characterizations of bacteria isolated from catheterized urine and stone matrices in patients with nephrolithiasis
journal, March 2012

  • Tavichakorntrakool, R.; Prasongwattana, V.; Sungkeeree, S.
  • Nephrology Dialysis Transplantation, Vol. 27, Issue 11
  • DOI: 10.1093/ndt/gfs057

Fossilization of Soft Tissue in the Laboratory
journal, March 1993


Intrinsic Novobiocin Resistance in Staphylococcus saprophyticus
journal, September 2007

  • Vickers, A. A.; Chopra, I.; O'Neill, A. J.
  • Antimicrobial Agents and Chemotherapy, Vol. 51, Issue 12
  • DOI: 10.1128/AAC.00708-07

Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation
journal, February 2009

  • van Oven, Mannis; Kayser, Manfred
  • Human Mutation, Vol. 30, Issue 2
  • DOI: 10.1002/humu.20921

Scalable metagenomic taxonomy classification using a reference genome database
journal, July 2013


The incidence of placental calcification in normal pregnancies.
journal, March 1982


The colour of fossil feathers
journal, July 2008

  • Vinther, Jakob; Briggs, Derek E. G.; Prum, Richard O.
  • Biology Letters, Vol. 4, Issue 5
  • DOI: 10.1098/rsbl.2008.0302

A method for visual determination of sex, using the human hip bone
journal, January 2002

  • Bruzek, Jaroslav
  • American Journal of Physical Anthropology, Vol. 117, Issue 2
  • DOI: 10.1002/ajpa.10012

CGAL: computing genome assembly likelihoods
journal, January 2013


Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
journal, January 2016

  • Rambaut, Andrew; Lam, Tommy T.; Max Carvalho, Luiz
  • Virus Evolution, Vol. 2, Issue 1
  • DOI: 10.1093/ve/vew007

Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA
journal, October 2015


Fast gapped-read alignment with Bowtie 2
journal, March 2012

  • Langmead, Ben; Salzberg, Steven L.
  • Nature Methods, Vol. 9, Issue 4
  • DOI: 10.1038/nmeth.1923

BEDTools: a flexible suite of utilities for comparing genomic features
journal, January 2010


Molecular Epidemiology of Staphylococcus saprophyticus Isolated from Women with Uncomplicated Community-Acquired Urinary Tract Infection
journal, March 2007

  • Widerstrom, M.; Wistrom, J.; Ferry, S.
  • Journal of Clinical Microbiology, Vol. 45, Issue 5
  • DOI: 10.1128/JCM.02071-06

Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection
journal, August 2005

  • Kuroda, M.; Yamashita, A.; Hirakawa, H.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 37
  • DOI: 10.1073/pnas.0502950102

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
journal, April 2016

  • Page, Andrew J.; Taylor, Ben; Delaney, Aidan J.
  • Microbial Genomics, Vol. 2, Issue 4
  • DOI: 10.1099/mgen.0.000056

Detection of a microbial biofilm in intraamniotic infection
journal, January 2008

  • Romero, Roberto; Schaudinn, Christoph; Kusanovic, Juan Pedro
  • American Journal of Obstetrics and Gynecology, Vol. 198, Issue 1
  • DOI: 10.1016/j.ajog.2007.11.026

Decay and Mineralization of Shrimps
journal, October 1994

  • Briggs, Derek E. G.; Kear, Amanda J.
  • PALAIOS, Vol. 9, Issue 5
  • DOI: 10.2307/3515135

Coagulase-negative staphylococci: update on the molecular epidemiology and clinical presentation, with a focus on Staphylococcus epidermidis and Staphylococcus saprophyticus
journal, May 2011

  • Widerström, M.; Wiström, J.; Sjöstedt, A.
  • European Journal of Clinical Microbiology & Infectious Diseases, Vol. 31, Issue 1
  • DOI: 10.1007/s10096-011-1270-6

A Case of Ancient Bladder Stones from Oluz Höyük, Amasya, Turkey: The Oluz Höyük Bladder Stone
journal, October 2013

  • Özdemir, K.; Akyol, A. A.; Erdal, Y. S.
  • International Journal of Osteoarchaeology, Vol. 25, Issue 6
  • DOI: 10.1002/oa.2349

Informed and automated k-mer size selection for genome assembly
journal, June 2013


De novo likelihood-based measures for comparing genome assemblies
journal, January 2013

  • Ghodsi, Mohammadreza; Hill, Christopher M.; Astrovskaya, Irina
  • BMC Research Notes, Vol. 6, Issue 1
  • DOI: 10.1186/1756-0500-6-334

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
journal, January 2013

  • Treangen, Todd J.; Koren, Sergey; Sommer, Daniel D.
  • Genome Biology, Vol. 14, Issue 1
  • DOI: 10.1186/gb-2013-14-1-r2

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology
journal, December 1971


Bone preparation at the KCCAMS laboratory
journal, April 2010

  • Beaumont, Will; Beverly, Robert; Southon, John
  • Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Vol. 268, Issue 7-8
  • DOI: 10.1016/j.nimb.2009.10.061

Giant Bladder Stone in a Natural Mummy of the Early 19th Century
journal, October 2008


Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
journal, November 2014


The Sequence Alignment/Map format and SAMtools
journal, June 2009


Staphylococcus saprophyticus as a Common Cause of Urinary Tract Infections
journal, May 1984


jModelTest 2: more models, new heuristics and parallel computing
journal, July 2012

  • Darriba, Diego; Taboada, Guillermo L.; Doallo, Ramón
  • Nature Methods, Vol. 9, Issue 8
  • DOI: 10.1038/nmeth.2109

Historical Zoonoses and Other Changes in Host Tropism of Staphylococcus aureus, Identified by Phylogenetic Analysis of a Population Dataset
journal, May 2013


    Works referencing / citing this record:

    Ancient pathogen genomics as an emerging tool for infectious disease research
    journal, April 2019

    • Spyrou, Maria A.; Bos, Kirsten I.; Herbig, Alexander
    • Nature Reviews Genetics, Vol. 20, Issue 6
    • DOI: 10.1038/s41576-019-0119-1

    Ancient pathogen genomics as an emerging tool for infectious disease research
    journal, April 2019

    • Spyrou, Maria A.; Bos, Kirsten I.; Herbig, Alexander
    • Nature Reviews Genetics, Vol. 20, Issue 6
    • DOI: 10.1038/s41576-019-0119-1