A Statistically Rigorous Method for Determining Antigenic Switching Networks

Many vector-borne pathogens rely on antigenic variation to prolong infections and increase their likelihood of onward transmission. This immune evasion strategy often involves mutually exclusive switching between members of gene families that encode functionally similar but antigenically different variants during the course of a single infection. Studies of different pathogens have suggested that switching between variant genes is non-random and that genes have intrinsic probabilities of being activated or silenced. These factors could create a hierarchy of gene expression with important implications for both infection dynamics and the acquisition of protective immunity. Inferring complete switching networks from gene transcription data is problematic, however, because of the high dimensionality of the system and uncertainty in the data. Here we present a statistically rigorous method for analysing temporal gene transcription data to reconstruct an underlying switching network. Using artificially generated transcription profiles together with in vitro var gene transcript data from two Plasmodium falciparum laboratory strains, we show that instead of relying on data from long-term parasite cultures, accuracy can be greatly improved by using transcription time courses of several parasite populations from the same isolate, each starting with different variant distributions. The method further provides explicit indications about the reliability of the resulting networks and can thus be used to test competing hypotheses with regards to the underlying switching pathways. Our results demonstrate that antigenic switch pathways can be determined reliably from short gene transcription profiles assessing multiple time points, even when subject to moderate levels of experimental error. This should yield important new information about switching patterns in antigenically variable organisms and might help to shed light on the molecular basis of antigenic variation

A thirteen-year analysis of Plasmodium falciparum populations reveals high conservation of the mutant pfcrt haplotype despite the withdrawal of chloroquine from national treatment guidelines in Gabon

<p>Abstract</p> <p>Background</p> <p>Chloroquine resistance (CR) decreased after the removal of chloroquine from national treatment guidelines in Malawi, Kenia and Tanzania. In this investigation the prevalence of the chloroquine resistance (CQR) conferring mutant <it>pfcrt </it>allele and its associated chromosomal haplotype were determined before and after the change in Gabonese national treatment guidelines from chloroquine (CQ) to artesunate plus amodiaquine (AQ) in 2003.</p> <p>Methods</p> <p>The prevalence of the wild type <it>pfcrt </it>allele was assessed in 144 isolates from the years 2005 - 07 by PCR fragment restriction digest and direct sequencing. For haplotype analysis of the chromosomal regions flanking the <it>pfcrt </it>locus, microsatellite analysis was done on a total of 145 isolates obtained in 1995/96 (43 isolates), 2002 (47 isolates) and 2005 - 07 (55 isolates).</p> <p>Results</p> <p>The prevalence of the mutant <it>pfcrt </it>allele decreased from 100% in the years 1995/96 and 2002 to 97% in 2005 - 07. Haplotype analysis showed that in 1995/96 79% of the isolates carried the same microsatellite alleles in a chromosomal fragment spanning 39 kb surrounding the <it>pfcrt </it>locus. In 2002 and 2005 - 07 the prevalence of this haplotype was 62% and 58%, respectively. <it>Pfcrt </it>haplotype analysis showed that all wild type alleles were CVMNK.</p> <p>Conclusion</p> <p>Four years after the withdrawal of CQ from national treatment guidelines the prevalence of the mutant <it>pfcrt </it>allele remains at 97%. The data suggest that the combination of artesunate plus AQ may result in continued selection for the mutant <it>pfcrt </it>haplotype even after discontinuance of CQ usage.</p

Clinically Relevant Pancreatic Fistula after Pancreaticoduodenectomy: How We Do It

(1) Background: This study’s goals were to investigate possible risk factors for clinically relevant postoperative pancreatic fistula (POPF) grade B/C according to the updated definitions of the International Study Group of Pancreatic Surgery and to analyze possible treatment strategies; (2) Methods: Between 2017 and 2021, 200 patients were analyzed regarding the development of POPF grade B/C with an emphasis on postoperative outcome and treatment strategies; (3) Results: POPF grade B/C was observed in 39 patients (19.5%). These patients were younger, mainly male, had fewer comorbidities and showed a higher body mass index. Also, they had lower CA-19 levels, a smaller tumor size and softer pancreatic parenchyma. They experienced a worse outcome without affecting the overall mortality rate (10% vs. 6%, p = 0.481), however, this lead to a prolonged postoperative stay (28 (32–36) d vs. 20 (15–28) d, p ≤ 0.001). The majority of patients with POPF grade B/C were able to receive conservative treatment, followed by drainage placement, endoscopic vacuum-assisted therapy (EVT) and surgery. Conservative treatment resulted in a shorter length of the postoperative stay (24 (22–28) d vs. 34 (26–43) d, p = 0.012); (4) Conclusions: Patients developing POPF grade B/C had a worse outcome; however, this did not affect the overall mortality rate. The majority of the patients were able to receive conservative treatment, resulting in a shorter length of their hospital stay

Active smokers show ameliorated delayed gastric emptying after pancreatoduodenectomy

Background!#!Delayed gastric emptying (DGE) is the most common complication following pancreatoduodenectomy (PD). The data about active smoking in relation to gastric motility have been inconsistent and specifically the effect of smoking on gastric emptying after PD has not yet been investigated in detail.!##!Methods!#!295 patients at our department underwent PD between January 2009 and December 2019. Patients were analyzed in relation to demographic factors, diagnosis, pre-existing conditions, intraoperative characteristics, hospital stay, mortality and postoperative complications with special emphasis on DGE. All complications were classified according to the definitions of the International Study Group on Pancreatic Surgery.!##!Results!#!274 patients were included in the study and analyzed regarding their smoking habits (non or former smokers, n = 88, 32.1% vs. active smokers, n = 186, 68.6%). Excluded were patients for whom no information about their smoking habits was available (n = 3), patients who had had gastric resection before (n = 4) and patients with prolonged postoperative resumption to normal diet independently from DGE (long-term ventilation &amp;gt; 7 days, fasting due to pancreatic fistula) (n = 14). Smokers were younger than non-smokers (61 vs. 69 years, p ≤ 0.001) and mainly male (73% male vs. 27% female). Smoking patients showed significantly more pre-existing pulmonary conditions (19% vs. 8%, p = 0.002) and alcohol abuse (48% vs. 23%, p ≤ 0.001). We observe more blood loss in smokers (800 [500-1237.5] vs. 600 [400-1000], p = 0.039), however administration of erythrocyte concentrates did not differ between both groups (0 [0-2] vs. 0 [0-2], p = 0.501). 58 out of 88 smokers (66%) and 147 out of 186 of non-smokers (79%) showed malign tumors (p = 0.019). 35 out of 88 active smokers (40%) and 98 out of 188 non- or former smokers (53%) developed DGE after surgery (p = 0.046) and smokers tolerated solid food intake more quickly than non-smokers (postoperative day (POD7 vs. POD10, p = 0.004). Active smokers were less at risk to develop DGE (p = 0.051) whereas patients with pulmonary preexisting conditions were at higher risk for developing DGE (p = 0.011).!##!Conclusions!#!Our data show that DGE occurs less common in active smokers and they tolerate solid food intake more quickly than non-smokers. Further observation studies and randomized, controlled multicentre studies without the deleterious effect of smoking, for instance by administration of a nicotine patch, are needed to examine if this effect is due to nicotine administration

Obesity Does Not Influence Delayed Gastric Emptying Following Pancreatoduodenectomy

Background: The data about obesity on postoperative outcome after pancreatoduodenectomy (PD) are inconsistent, specifically in relation to gastric motility and delayed gastric emptying (DGE). Methods: Two hundred and eleven patients were included in the study and patients were retrospectively analyzed in respect to pre-existing obesity (obese patients having a body mass index (BMI) &ge; 30 kg/m2 vs. non-obese patients having a BMI &lt; 30 kg/m2, n = 34, 16% vs. n = 177, 84%) in relation to demographic factors, comorbidities, intraoperative characteristics, mortality and postoperative complications with special emphasis on DGE. Results: Obese patients were more likely to develop clinically relevant pancreatic fistula grade B/C (p = 0.008) and intraabdominal abscess formations (p = 0.017). However, clinically relevant DGE grade B/C did not differ (p = 0.231) and, specifically, first day of solid food intake (p = 0.195), duration of intraoperative administered nasogastric tube (NGT) (p = 0.708), rate of re-insertion of NGT (0.123), total length of NGT (p = 0.471) or the need for parenteral nutrition (p = 0.815) were equally distributed. Moreover, mortality (p = 1.000) did not differ between the two groups. Conclusions: Obese patients do not show a higher mortality rate and are not at higher risk to develop DGE. We thus show that in our study, PD is feasible in the obese patient in regard to postoperative outcome with special emphasis on DGE

Chronic Liver Disease Increases Mortality Following Pancreatoduodenectomy

According to the International Study Group of Pancreatic Surgery (ISGPS), data about the impact of pre-existing liver pathologies on delayed gastric emptying (DGE) after pancreatoduodenectomy (PD) according to the definitions of the International Study Group of Pancreatic Surgery (ISGPS) are lacking. We therefore investigated the impact of DGE after PD according to ISGPS in patients with liver cirrhosis (LC) and advanced liver fibrosis (LF). Patients were analyzed with respect to pre-existing liver pathologies (LC and advanced LF, n = 15, 6% vs. no liver pathologies, n = 240, 94%) in relation to demographic factors, comorbidities, intraoperative characteristics, mortality and postoperative complications, with special emphasis on DGE. DGE was equally distributed (DGE grade A, p = 1.000; B, p = 0.396; C, p = 0.607). Particularly, the first day of solid food intake (p = 0.901), the duration of intraoperative administered nasogastric tube (NGT) (p = 0.812), the rate of re-insertion of NGT (p = 0.072), and the need for parenteral nutrition (p = 0.643) did not differ. However, patients with LC and advanced LF showed a higher ASA (American Society of Anesthesiologists) score (p = 0.016), intraoperatively received more erythrocyte transfusions (p = 0.029), stayed longer in the intensive care unit (p = 0.010) and showed more intraabdominal abscess formation (p = 0.006). Moreover, we did observe a higher mortality rate amongst patients with pre-existing liver diseases (p = 0.021), and reoperation was a risk factor for higher mortality (p ≤ 0.001) in the multivariate analysis. In our study, we could not detect a difference with respect to DGE classified by ISGPS; however, we did observe a higher mortality rate amongst these patients and thus, they should be critically evaluated for PD

Mosquito Passage Dramatically Changes var Gene Expression in Controlled Human Plasmodium falciparum Infections

Virulence of the most deadly malaria parasite Plasmodium falciparum is linked to the variant surface antigen PfEMP1, which is encoded by about 60 var genes per parasite genome. Although the expression of particular variants has been associated with different clinical outcomes, little is known about var gene expression at the onset of infection. By analyzing controlled human malaria infections via quantitative real-time PCR, we show that parasite populations from 18 volunteers expressed virtually identical transcript patterns that were dominated by the subtelomeric var gene group B and, to a lesser extent, group A. Furthermore, major changes in composition and frequency of var gene transcripts were detected between the parental parasite culture that was used to infect mosquitoes and Plasmodia recovered from infected volunteers, suggesting that P. falciparum resets its var gene expression during mosquito passage and starts with the broad expression of a specific subset of var genes when entering the human blood phase