<em>Yersinia pestis</em>: New Evidence for an Old Infection

<div><p>The successful reconstruction of an ancient bacterial genome from archaeological material presents an important methodological advancement for infectious disease research. The reliability of evolutionary histories inferred by the incorporation of ancient data, however, are highly contingent upon the level of genetic diversity represented in modern genomic sequences that are publicly accessible, and the paucity of available complete genomes restricts the level of phylogenetic resolution that can be obtained. Here we add to our original analysis of the <em>Yersinia pestis</em> strain implicated in the Black Death by consolidating our dataset for 18 modern genomes with single nucleotide polymorphism (SNP) data for an additional 289 strains at over 600 positions. The inclusion of this additional data reveals a cluster of <em>Y. pestis</em> strains that diverge at a time significantly in advance of the Black Death, with divergence dates roughly coincident with the Plague of Justinian (6^th to 8^th century AD). In addition, the analysis reveals further clues regarding potential radiation events that occurred immediately preceding the Black Death, and the legacy it may have left in modern <em>Y. pestis</em> populations. This work reiterates the need for more publicly available complete genomes, both modern and ancient, to achieve an accurate understanding of the history of this bacterium.</p> </div

Additional file 11: Figure S6. of Next-generation sequencing diagnostics of bacteremia in septic patients

Time course of patient S11. A 62-year-old male patient presented with a multilocular hepatocellular carcinoma with the need for a left-sided hemihepatectomy. Following the surgical procedure the patient suffered from septic shock due to severe pneumonia with Klebsiella pneumoniae as the dominant organism in blood cultures as well as tracheal secretions. Empiric antibiotic therapy was performed with imipenem, which was then switched to moxifloxacin based on the susceptibility findings. In the further course of the disease, K. pneumoniae was shown to be multidrug resistant. Although antibiotic therapy was adapted according to the findings of susceptibility testing, the pulmonary septic focus could not be removed sufficiently. In the end, the patient died from ongoing septic shock due to pneumonia with K. pneumonia 2 months after study inclusion. In addition, septic disease was shown to be accompanied by a reactivation of herpes simplex virus type 1 (HSV1) as well as cytomegalovirus (CMV) in different secretions as assessed by a PCR-based diagnostic procedure. These findings were in good agreement with next generation sequencing (NGS) of plasma. In this figure, the antibiotic treatment regime, SIQ scores for species identified via NGS, and cfDNA concentrations of the respective plasma samples are plotted over the timeline of the trial period for patient S11. Pertinent (clinical microbiology) laboratory results are marked using arrows to indicate the day the clinical specimen was obtained. Abbreviations: BC blood culture, CVC central venous catheter, TS tracheal secretion, GNST Gram-negative staphylococci, HSV1 herpes simplex virus 1, IPM imipenem, VAN vancomycin, MXF moxiflocaxin, CIP ciprofloxacin, TGC tigecycline, CAZ ceftazidime. Antibacterial antibiotics are displayed in light grey. The relative amount of bacteria found by conventional clinical microbiology is indicated with plenty (p), medium (m), or scarce (s). (For a detailed list of the anti-infective abbreviations, see Additional file 9: Table S5) (PDF 16 kb

Additional file 9: Table S5. of Next-generation sequencing diagnostics of bacteremia in septic patients

Anti-infective abbreviations. (XLSX 9 kb

Lonicera affinis Hook. et Arn.

原著和名: ハマニンドウ イヌニンドウ科名: スイカズラ科 = Caprifoliaceae採集地: 鹿児島県 肝属郡 佐多町 大中尾 (大隅 肝属郡 佐多町 大中尾)採集日: 1965/10/30採集者: 萩庭丈壽整理番号: JH042503国立科学博物館整理番号: TNS-VS-99250

Additional file 6: Table S2. of Next-generation sequencing diagnostics of bacteremia in septic patients

List of contaminant species identified from water controls. (XLSX 10 kb

Additional file 6: Table ST3. of Dual transcriptome of the immediate neutrophil and Candida albicans interplay

Most altered DEGs in neutrophils infected with C. albicans. Up- and down-regulated DEGs of neutrophils infected with C. albicans yeast and hyphae were sorted by their respective fold change of expression. Positive numbers indicate the ranking amongst up-regulated DEGs; negative numbers indicate the ranking amongst the down-regulated numbers (XLSX 4327 kb

Additional file 5: Figure S3. of Next-generation sequencing diagnostics of bacteremia in septic patients

Distribution of species-specific normalized read counts in septic patients and controls for potential contaminant species. Red, septic patients; blue, controls (elective surgery (timepoint T0) and healthy volunteers). (PDF 18 kb

Additional file 1: Table S1. of Next-generation sequencing diagnostics of bacteremia in septic patients

List of fungal reference genomes included in the kraken database to identify microbial reads in non-human reads. (XLSX 11 kb

Additional file 10: Table ST5. of Dual transcriptome of the immediate neutrophil and Candida albicans interplay

Differential regulation of arginine metabolism genes in C. albicans. DEGs involved in arginine metabolism of yeast and hypha C. albicans infecting neutrophils and NETs are displayed. The transcript level is indicated by fold change (log2). (XLS 41 kb

Additional file 2: Table ST1. of Dual transcriptome of the immediate neutrophil and Candida albicans interplay

Mapping results. Mapping statistics of neutrophil and Candida reads using NextGenMap. (XLSX 19149 kb