Cerebral Autoregulation Assessment Using the Near Infrared Spectroscopy 'NIRS-Only' High Frequency Methodology in Critically Ill Patients:A Prospective Cross-Sectional Study

Impairments in cerebral autoregulation (CA) are related to poor clinical outcome. Near infrared spectroscopy (NIRS) is a non-invasive technique applied to estimate CA. Our general purpose was to study the clinical feasibility of a previously published 'NIRS-only' CA methodology in a critically ill intensive care unit (ICU) population and determine its relationship with clinical outcome. Bilateral NIRS measurements were performed for 1-2 h. Data segments of ten-minutes were used to calculate transfer function analyses (TFA) CA estimates between high frequency oxyhemoglobin (oxyHb) and deoxyhemoglobin (deoxyHb) signals. The phase shift was corrected for serial time shifts. Criteria were defined to select TFA phase plot segments (segments) with 'high-pass filter' characteristics. In 54 patients, 490 out of 729 segments were automatically selected (67%). In 34 primary neurology patients the median (q1-q3) low frequency (LF) phase shift was higher in 19 survivors compared to 15 non-survivors (13° (6.3-35) versus 0.83° (-2.8-13), p = 0.0167). CA estimation using the NIRS-only methodology seems feasible in an ICU population using segment selection for more robust and consistent CA estimations. The 'NIRS-only' methodology needs further validation, but has the advantage of being non-invasive without the need for arterial blood pressure monitoring

A Draft Genome of \u3ci\u3eYersinia Pestis\u3c/i\u3e From Victims of the Black Death

Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard1. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348–1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347–1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections

Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue

Dear Editor, The bacterium Treponema pallidum (TP) causes human syphilis (subsp. pallidum; TPA), bejel (subsp. endemicum; TEN), and yaws (subsp. pertenue; TPE) (1). Although syphilis has reached a worldwide distribution (2), bejel and yaws have remained endemic diseases. Bejel affects individuals in dry areas of Sahelian Africa and Saudi Arabia, whereas yaws affects those living in the humid tropics (1). Yaws is currently reported as endemic in 14 countries, and an additional 84 countries have a known history of yaws but lack recent epidemiological data (3,4). Although this disease was subject to global eradication efforts in the mid-20th century, it later reemerged in West Africa, Southern Asia, and the Pacific region (5). New large-scale treatment options triggered the ongoing second eradication campaign, the goal of which is to eradicate yaws globally by 2020 (5). References: (1) Giacani, L. & Lukehart, S.A. The endemic treponematoses. Clin. Microbiol. Rev. 27, 89–115 (2014). (2) Arora, N. et al. Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster. Nat. Microbiol. 2, 16245 (2016). (3) Marks, M. Yaws: towards the WHO eradication target. Trans. R Soc. Trop. Med. Hyg. 110, 319–320 (2016). (4) World Health Organization. Eradication of yaws: procedures for verification and certification of interruption of transmission (World Health Organization, Geneva, 2018). (5) Asiedu, K., Fitzpatrick, C. & Jannin, J. Eradication of yaws: historical efforts and achieving WHO’s 2020 target. PLoS Negl. Trop. Dis. 8, e3016 (2014)

Quantitative Assessment of the Sensitivity of Various Commercial Reverse Transcriptases Based on Armored HIV RNA

The in-vitro reverse transcription of RNA to its complementary DNA, catalyzed by the enzyme reverse transcriptase, is the most fundamental step in the quantitative RNA detection in genomic studies. As such, this step should be as analytically sensitive, efficient and reproducible as possible, especially when dealing with degraded or low copy RNA samples. While there are many reverse transcriptases in the market, all claiming to be highly sensitive, there is need for a systematic independent comparison of their applicability in quantification of rare RNA transcripts or low copy RNA, such as those obtained from archival tissues.We performed RT-qPCR to assess the sensitivity and reproducibility of 11 commercially available reverse transcriptases in cDNA synthesis from low copy number RNA levels. As target RNA, we used a serially known number of Armored HIV RNA molecules, and observed that 9 enzymes we tested were consistently sensitive to ∼1,000 copies, seven of which were sensitive to ∼100 copies, while only 5 were sensitive to ∼10 RNA template copies across all replicates tested. Despite their demonstrated sensitivity, these five best performing enzymes (Accuscript, HIV-RT, M-MLV, Superscript III and Thermoscript) showed considerable variation in their reproducibility as well as their overall amplification efficiency. Accuscript and Superscript III were the most sensitive and consistent within runs, with Accuscript and Superscript II ranking as the most reproducible enzymes between assays.We therefore recommend the use of Accuscript or Superscript III when dealing with low copy number RNA levels, and suggest purification of the RT reactions prior to downstream applications (eg qPCR) to augment detection. Although the results presented in this study were based on a viral RNA surrogate, and applied to nucleic acid lysates derived from archival formalin-fixed paraffin embedded tissue, their relative performance on RNA obtained from other tissue types may vary, and needs future evaluation

Heterokaryon Incompatibility Is Suppressed Following Conidial Anastomosis Tube Fusion in a Fungal Plant Pathogen

It has been hypothesized that horizontal gene/chromosome transfer and parasexual recombination following hyphal fusion between different strains may contribute to the emergence of wide genetic variability in plant pathogenic and other fungi. However, the significance of vegetative (heterokaryon) incompatibility responses, which commonly result in cell death, in preventing these processes is not known. In this study, we have assessed this issue following different types of hyphal fusion during colony initiation and in the mature colony. We used vegetatively compatible and incompatible strains of the common bean pathogen Colletotrichum lindemuthianum in which nuclei were labelled with either a green or red fluorescent protein in order to microscopically monitor the fates of nuclei and heterokaryotic cells following hyphal fusion. As opposed to fusion of hyphae in mature colonies that resulted in cell death within 3 h, fusions by conidial anastomosis tubes (CAT) between two incompatible strains during colony initiation did not induce the vegetative incompatibility response. Instead, fused conidia and germlings survived and formed heterokaryotic colonies that in turn produced uninucleate conidia that germinated to form colonies with phenotypic features different to those of either parental strain. Our results demonstrate that the vegetative incompatibility response is suppressed during colony initiation in C. lindemuthianum. Thus, CAT fusion may allow asexual fungi to increase their genetic diversity, and to acquire new pathogenic traits

Ten millennia of hepatitis B virus evolution

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic

Epidemiology and outcomes of source control procedures in critically ill patients with intra-abdominal infection

PURPOSE: To describe the characteristics and procedural outcomes of source control interventions among Intensive Care Unit (ICU) patients with severe intra-abdominal-infection (IAI). MATERIAL AND METHODS: We identified consecutive patients with suspected IAI in whom a source control intervention had been performed in two tertiary ICUs in the Netherlands, and performed retrospective in-depth case reviews to evaluate procedure type, diagnostic yield, and adequacy of source control after 14 days. RESULTS: A total of 785 procedures were observed among 353 patients, with initial interventions involving 266 (75%) surgical versus 87 (25%) percutaneous approaches. Surgical index procedures typically involved IAI of (presumed) gastrointestinal origin (72%), whereas percutaneous index procedures were mostly performed for infections of the biliary tract/pancreas (50%) or peritoneal cavity (33%). Overall, 178 (50%) patients required multiple interventions (median 3 (IQR 2-4)). In a subgroup of 236 patients having their first procedure upon ICU admission, effective source control was ultimately achieved for 159 (67%) subjects. Persistence of organ failure was associated with inadequacy of source control at day 14, whereas trends in inflammatory markers were non-predictive. CONCLUSIONS: Approximately half of ICU patients with IAI require more than one intervention, yet successful source control is eventually achieved in a majority of cases

Epidemiology and outcomes of source control procedures in critically ill patients with intra-abdominal infection

PURPOSE: To describe the characteristics and procedural outcomes of source control interventions among Intensive Care Unit (ICU) patients with severe intra-abdominal-infection (IAI). MATERIAL AND METHODS: We identified consecutive patients with suspected IAI in whom a source control intervention had been performed in two tertiary ICUs in the Netherlands, and performed retrospective in-depth case reviews to evaluate procedure type, diagnostic yield, and adequacy of source control after 14 days. RESULTS: A total of 785 procedures were observed among 353 patients, with initial interventions involving 266 (75%) surgical versus 87 (25%) percutaneous approaches. Surgical index procedures typically involved IAI of (presumed) gastrointestinal origin (72%), whereas percutaneous index procedures were mostly performed for infections of the biliary tract/pancreas (50%) or peritoneal cavity (33%). Overall, 178 (50%) patients required multiple interventions (median 3 (IQR 2-4)). In a subgroup of 236 patients having their first procedure upon ICU admission, effective source control was ultimately achieved for 159 (67%) subjects. Persistence of organ failure was associated with inadequacy of source control at day 14, whereas trends in inflammatory markers were non-predictive. CONCLUSIONS: Approximately half of ICU patients with IAI require more than one intervention, yet successful source control is eventually achieved in a majority of cases