Mutational Signatures in Wild Type Escherichia coli Strains Reveal Predominance of DNA Polymerase Errors

While mutational processes operating in the Escherichia coli genome have been revealed by multiple laboratory experiments, the contribution of these processes to accumulation of bacterial polymorphism and evolution in natural environments is unknown. To address this question, we reconstruct signatures of distinct mutational processes from experimental data on E. coli hypermutators, and ask how these processes contribute to differences between naturally occurring E. coli strains. We show that both mutations accumulated in the course of evolution of wild-type strains in nature and in the lab-grown nonmutator laboratory strains are explained predominantly by the low fidelity of DNA polymerases II and III. By contrast, contributions specific to disruption of DNA repair systems cannot be detected, suggesting that temporary accelerations of mutagenesis associated with such disruptions are unimportant for within-species evolution. These observations demonstrate that accumulation of diversity in bacterial strains in nature is predominantly associated with errors of DNA polymerases.

Viral Receptor-Binding Protein Evolves New Function through Mutations That Cause Trimer Instability and Functional Heterogeneity

When proteins evolve new activity, a concomitant decrease in stability is often observed because the mutations that confer new activity can destabilize the native fold. In the conventional model of protein evolution, reduced stability is considered a purely deleterious cost of molecular innovation because unstable proteins are prone to aggregation and are sensitive to environmental stressors. However, recent work has revealed that nonnative, often unstable protein conformations play an important role in mediating evolutionary transitions, raising the question of whether instability can itself potentiate the evolution of new activity. We explored this question in a bacteriophage receptor-binding protein during host-range evolution. We studied the properties of the receptor-binding protein of bacteriophage λ before and after host-range evolution and demonstrated that the evolved protein is relatively unstable and may exist in multiple conformations with unique receptor preferences. Through a combination of structural modeling and in vitro oligomeric state analysis, we found that the instability arises from mutations that interfere with trimer formation. This study raises the intriguing possibility that protein instability might play a previously unrecognized role in mediating host-range expansions in viruses.

Revisiting the Role of Genetic Variation in Adaptation

AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.

Shifts in mutation spectra enhance access to beneficial mutations

Biased mutation spectra are pervasive, with wide variation in the magnitude of mutational biases that influence genome evolution and adaptation. How do such diverse biases evolve? Our experiments show that changing the mutation spectrum allows populations to sample previously undersampled mutational space, including beneficial mutations. The resulting shift in the distribution of fitness effects is advantageous: Beneficial mutation supply and beneficial pleiotropy both increase, while deleterious load reduces. More broadly, simulations indicate that reducing or reversing the direction of a long-term bias is always selectively favored. Such changes in mutation bias can occur easily via altered function of DNA repair genes. A phylogenetic analysis shows that these genes are repeatedly gained and lost in bacterial lineages, leading to frequent bias shifts in opposite directions. Thus, shifts in mutation spectra may evolve under selection and can directly alter the outcome of adaptive evolution by facilitating access to beneficial mutations.

Antagonistic pleiotropy for carbon use is rare in new mutations

Pleiotropic effects of mutations underlie diverse biological phenomena such as ageing and specialization. In particular, antagonistic pleiotropy ("AP": when a mutation has opposite fitness effects in different environments) generates tradeoffs, which may constrain adaptation. Models of adaptation typically assume that AP is common - especially among large-effect mutations - and that pleiotropic effect sizes are positively correlated. Empirical tests of these assumptions have focused on de novo beneficial mutations arising under strong selection. However, most mutations are actually deleterious or neutral, and may contribute to standing genetic variation that can subsequently drive adaptation. We quantified the incidence, nature, and effect size of pleiotropy for carbon utilization across 80 single mutations in Escherichia coli that arose under mutation accumulation (i.e., weak selection). Although ∼46% of the mutations were pleiotropic, only 11% showed AP; among beneficial mutations, only ∼4% showed AP. In some environments, AP was more common in large-effect mutations; and AP effect sizes across environments were often negatively correlated. Thus, AP for carbon use is generally rare (especially among beneficial mutations); is not consistently enriched in large-effect mutations; and often involves weakly deleterious antagonistic effects. Our unbiased quantification of mutational effects therefore suggests that antagonistic pleiotropy may be unlikely to cause maladaptive tradeoffs.

Plasma levels of haemostatic factors in patients with pulmonary embolism on admission and seven months later

INTRODUCTION

With the exception of D-dimer, not much is known about the plasma levels of haemostatic factors during acute venous thromboembolism (VTE) compared to their basic levels in a stable phase. The goal of this study was to examine how plasma levels of factor V, VIII, XIIIa, von Willebrand factor antigen (vWF:Ag), fibrinogen, thrombomodulin evolve from the point of diagnosis of acute VTE to the end of standard treatment period.

METHODS

Sixty-three consecutive patients (mean 57, range 18-86 years, 33 females) with acute pulmonary embolism (PE) were included. Laboratory samples were collected upon arrival (acute phase) and seven months later (stable phase). Fifteen similar aged individuals served as controls.

RESULTS

Plasma levels of factor XIIIa (87.5% vs 117.7%, P < .001) and soluble thrombomodulin (36.6 vs 47.5 ng/L, P < .001) were lower, whereas plasma levels of vWF:Ag (2.66 vs 2.01 IU/mL, P < .001) and fibrinogen (4.3 vs 3.9 g/L, P < .05) were higher on admission compared to the stable phase. In the stable phase, vWF:Ag (2.01 vs 1.43 IU/mL, P < .01) and soluble thrombomodulin (47.5 vs 38.0 ng/mL, P < .05), but not FXIIIa levels, were higher in PE patients compared to healthy controls.

CONCLUSION

This study confirms the concept of FXIIIa consumption during acute phase of VTE by showing its intraindividual normalization during the follow-up. vWF:Ag, known to be associated with the risk of VTE, was constantly elevated in the majority of the patients. Soluble thrombomodulin levels were lower in acute phase compared to stable phase, a finding which significance needs to be evaluated in the future.

Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium

Contrary to previous understanding, recent evidence indicates that synonymous codon changes may sometimes face strong selection. However, it remains difficult to generalize the nature, strength, and mechanism(s) of such selection. Previously, we showed that synonymous variants of a key enzyme-coding gene (fae) of Methylobacterium extorquens AM1 decreased enzyme production and reduced fitness dramatically. We now show that during laboratory evolution, these variants rapidly regained fitness via parallel yet variant-specific, highly beneficial point mutations in the N-terminal region of fae. These mutations (including four synonymous mutations) had weak but consistently positive impacts on transcript levels, enzyme production, or enzyme activity. However, none of the proposed mechanisms (including internal ribosome pause sites or mRNA structure) predicted the fitness impact of evolved or additional, engineered point mutations. This study shows that synonymous mutations can be fixed through strong positive selection, but the mechanism for their benefit varies depending on the local sequence context.

[Epidemiology of the resistance of Mycobacterium tuberculosis to antituberculosis drugs at the main hospital in Dakar, Senegal. A 4-year retrospective study (2000-2003)]

A retrospective study was carried out from January 2000 to December 2003 to assess the resistance of Mycobacterium tuberculosis to antituberculosis drugs and the impact of this on the treatment result. Two hundred and two patients' files were studied (average age: 36 years; sex-ratio: 1.7). Pulmonary localisation (85.7%) or extrapulmonary localisation (14.3%). HIV status is negative (71.3%), positive (10.8%) or unknown (17.9%). The overall recovery rate is 60.7% (61.4% in HIV-; 46.1% in HIV+), the rate of treatment failure is 2.7% (1.1% in HIV-; 15.4% in HIV+), the death rate due to tuberculosis is 6.3% (2.3% in HIV-; 23.1% in HIV+), and the rate of patients who disappeared from the system is 30.3% (35.2% in HIV-; 14.2% in HIV+). Hepatotoxicity that occurred during treatment is observed in 14.3% of cases (recovery: 56.2%; failure: 6.2%; lost from the system: 18.8%). Eighty-four percent of patients never received antituberculosis treatment (group A) versus 15.8% of patients who had already received one or more antituberculosis drugs (group B). The rates of resistance to isoniazid are 6.4% (A) and 12.5% (B), to rifampicin 1.7% (A) and 12.5% (B), to ethambutol 0.5% (A) and 0% (B), to streptomycin 24.1% (A) and 46.8% (B). The percentage of multiresistant strains is 1% in patients not treated previously and 11% in those who had already received antituberculosis treatment. When the patients are carriers of a strain that is responsive to the treatment administered, the recovery rate is 64.2% versus 46.7% in patients whose strain is resistant to at least one of the treatments administered.

[Lung cancer in Senegal]

In Africa the incidence of lung cancer is rising rapidly. The purpose of this prospective study was to analyze clinical, therapeutic, and prognostic features of lung cancer patients treated at the Principal Hospital in Dakar between 2002 and 2007. A total of 72 cases were compiled over the 5-year study period. In 88% of cases the patient was a male smoker with a mean age of 59.2 years. Histological samples were obtained in 79.1% of cases by bronchial fibroscopy (n=33), CT-guided transthoracic needle biopsy (n=17), or from a metastatic site (n=7). The histological diagnosis was squamous cell carcinoma in 23 cases, adenocarcinoma in 14, large-cell carcinoma in 17, small-cell lung cancer in 2, and bronchiolo-alveolar cancer in 1. Tumor staging demonstrated grades I-II in 6 cases, grade II in 17, and grade IV in 49. Symptomatic management was performed in 68% of patients. In the remaining cases management consisted of chemotherapy in 22 cases, radiotherapy for pain relief in 5, and surgery in 1. Ten patients were lost from follow-up. Median survival was 7 or 3 months depending on whether or not chemotherapy was performed. The much higher rate of histological diagnosis than in the sub-region is due mainly to the availability of trained personnel with access to bronchial endoscopy and CT-scan needle biopsy since September 2003. Administration of cytotoxins is feasible but the cost is excessive due to the lack of universal health care coverage: two-thirds of cases were abandoned whereas chemotherapy significantly improved median survival by 4 months (p < 0.0001). Prognosis of the disease is poor because management is undertaken at an advanced stage. Lung cancer is a health issue in Dakar, Senegal. It is urgent to develop therapeutic standards adapted to the African socio-economic setting as well as an anti-tobacco prevention policy.

[Pseudotumoral presentation of American pulmonary histioplasmosis]

In France, American pulmonary histoplasmosis is an imported deep mycosis, caused by inhalation of Histoplasma capsulatum. Clinical and radiological features of this exotic disease are multiple, simulating tuberculosis or cancer. We report two cases of American histoplasmosis with pseudo-tumoral form, in immunocompetent subjects working in Venezuela, with a multinodular pulmonary presentation.

[Clinical and laboratory features of typhoid fever in Senegal. A 70-case study]

Clinical and laboratory features, complications and treatment were retrospectively studied in 70 patients with bacteriologically documented typhoid fever, treated between January 1995 and June 2002 at Principal Hospital in Dakar, Senegal. Data analysis was done on a global basis as well as comparatively between the 37 children (under 15 years) and 33 adults. Mean age was 16.7 years (range, 1 to 52). The sex ratio was 1.4. Clinical manifestations included fever (97%), headache (50%), vomiting (71%), abdominal pain (54%), diarrhoea (49%), nnd splenomegaly (10%) without statistically significant difference between children and adults. Lyinphopenia was found in 51% of patients and anaemia in 78%. Coexisting illnesses Included malaria in 25.5% (mainly children) and hepatitis (transminases > 10N) in 24%. Complications included cholecystitis in 3 patients, gastrointestinal haemorrhage in 2, peritonitis in one, endocnrditis in one and osteomyelitis in one. Only one patient (HIV-positive) died. The incidence of antibiotic resistance was low, i.e., ainoxicilline: 2%, nalidixic acid: 1% and cotrimoxazole: 8.2%. No multidrug resistance was observed. This study shows that typhoid fever remains a major health problem in Dakar with slow resolution and potential complications. Amoxicililne and chloramphenicol can still be used for first-line treatment of typhoid fever. Little difference was found between children and adults.

[Exercise-induced dyspnea and hilar enlargement]

We report the case of a 46-year-old man with an uneventful history who was hospitalized for suspected pulmonary embolism. The chest x-ray did not reveal any parenchymatous anomaly but disclosed pseudo-tumoral enlargement of the pulmonary arteries. There was no right ventricular overload at cardiac echography and the pulmonary arterial pressure was normal. Helicoidal angioscan demonstrated aneurismal dilatation of the both pulmonary arteries, complicated by a thrombus on the right. Outcome was favorable with anticoagulation. After ruling out acquired aneurysm, the diagnosis retained was idiopathic aneurysm of the pulmonary arteries.

[Description of the first cases of serotype A, sequence type (ST)-11 meningococcal meningitis in Senegal]

Senegal is located in the African meningitis belt and meningococcal meniningitis outbreaks are yearly events. Occurrence of an epidemic involving serogroup W135 in 2000 and its spread following the Hajj (pilgrimage to Mecca) exposed the strongly Moslem population of Senegal to the risk of early infection. Indeed the first two cases in Dakar occurred simultaneously with the spread of this epidemic strain. The purpose of this article is to describe clinical, laboratory, and therapeutic findings in these two cases and the results of the ensuing epidemiological survey. The relationship with the pilgrimage and consequences on public health in Senegal are discussed.

[The new poor expatriates in the third world]

This report describes four cases involving French expatriates who developed serious health problems while living destitute in Senegal. A 37-year-old man presented with embolism-like symptoms in relation with lung involvement due to spreading of untreated staphylococcal skin infection. A 64-year-old man was admitted for high output cardiac failure secondary to severe anemia caused by malnutrition. A 50-year-old man presented recurrent fever with loss of consciousness after successful treatment of neuromalaria and finally attributed to delirium tremens. A 25-year-old man was hospitalized with presumed meningoencephalitis that had been ongoing for two weeks. All four patients had been in Senegal for several months and had cut all ties to mainland France. Being jobless and homeless, they had been unable to obtain proper nutrition or medications. With minimal entry requirements and low-cost air travel, Senegal has been come a common sight-seeing destination and has developed a small but apparently growing population of destitute travelers. Alienation from the home community and resulting seclusion enhance clinical consequences and delay intervention by foreign service officials.

[Hypothalamo-hypophyseal-adrenal hypofunction caused by the use of bleaching cosmetics in Senegal]

Cosmetic use of bleaching agents to clear skin is widespread among black West African women. In Dakar, most products used for whole body applications contain highly potent corticosteroids. Whereas cutaneous adverse effects are well described, little is known about possible systemic consequences. In order to assess transcutaneous absorption of glucocorticoids, hypothalamo-pituitary-adrenal axis functionality can be tested. We measured plasma cortisol concentration at 8 h and 1 h after intramuscular injection of 250 micrograms of cosyntropin (Synacthen) in 12 women with a more than 10 years use of bleaching agents. Cortisol at 8 H was also measured in 9 non exposed women without disease or treatment able to disturb glucocorticoids metabolism. All controls had 8 H cortisol concentration (mean = 521 +/- 113 nmol/l) above the minimal normal level considered by our laboratory. The 8 H cortisol concentrations were under the minimal normal level in 9 exposed women and the overall mean value was significantly lower than the one observed in controls (264 +/- 81 nmol/l; p < 0.001). After cosyntropin, cortisol concentrations were elevated among all exposed women (469 +/- 196 nmol/l), and less so in 3 of them. Most of the bleaching agents users present a functional inertia of hypothalamo-pituitary adrenal axis. While there is no absolute evidence for risk of stress-induced adrenal insufficiency, our results show conclusively that an excessive corticosteroids charge among users who could be exposed to systemic adverse effects.

[Hepatitis C virus and chronic hepatopathies in Dakar: case-control study]

In Black Africa, the role of hepatitis C virus (HCV) in the onset of chronic hepatic disease is unclear. This is particularly true in Senegal where the prevalence of HCV is moderate. To gain insight into this question, a case-control study including 73 patients and 73 controls was carried out at Principal Hospital in Dakar in 1995. The patients included in this study presented chronic hepatitis in 2 cases cirrhosis in 25 and hepatocellular carcinoma in 46. Patients and controls underwent serologic testing for HCV (ELISA screening test followed by 3rd generation ELISA test in case of positive results and confirmation by immunoblot) with determination of HCV serotype using the immunoenzymatic method. Testing also included research for infection by hepatitis B virus and for anti-delta antibodies. Anti-HCV antibodies were detected in two patients (3 p. 100) and serology was suspicious in two others. Serotype 2 was detected in one of these patients. No positive results were recorded in controls. Fifty-four patients (74 p. 100) and 15 controls (21 p. 100) presented the HBs antigen including 13 patients (24 p. 100) and I control (7 p. 100) with anti-delta antibodies. This study shows that HCV currently plays a minor role in the onset of hepatic disease in hospitalized patients in Senegal. It also confirms the predominant role of hepatitis B and complicating effect of the delta hepatitis virus. These findings are compared with reported data for Black African countries. The impact of HCV appears to be lower in Senegal than in central Africa.

[Adult T-cell leukemia-lymphoma due to HTLV 1. Two cases of the acute form at the Principal Hospital of Dakar]

HTLV1 virus is a retrovirus that has been endemic in Africa. It is the responsible for tropical spastic paraparesis and adult's T Cell leukemia-lymphoma. Few cases of adult T-Cell leukemia-lymphoma have been described in Africa, contrary to Japan and Caribbean. Were are reporting two cases of acute adult T-Cell leukemia-lymphoma which characterised by blood lymphoma signs, tumoral nodes and extranods lesions, hypercalcemia and positive retroviral serology of HTLV1 virus. The prognosis of these acute forms was bad after a six month survey approximately. The treatment is disappointing. Investigations of this affection must be carried out in every patient who presents lymphoma manifestations all the more because they are associated with hypercalcemia.

[Adults with sickle cell anemia in Senegal. Clinical study of 40 homozygote subjects]

While the well-documented life expectancy of patients with homozygous sickle cell anemia (SS) is 40 years in industrialized countries, this question remains unanswered in black Africa. The purpose of this prospective study was to establish the clinical phenotype for Senegal. A severity score based on 12 clinical, laboratory, radiological, and prognostic findings was calculated and correlated with age and hemoglobin F level. A total of 40 SS homozygotes over 15 years of age (mean age: 25 years) were hospitalized between January 1996 and January 1998 at the Principal Hospital in Dakar. The most common events requiring hospitalization were vasoocclusive phenomena (n = 26) but the incidence of these complications declined significantly with age (p < 0.05). The mean hemoglobin level was 4.4 mmol/l and the mean hemoglobin F level was 6.2 p. 100. The incidence of visceral involvement was low (lithiasic vesicules in 17 cases, necrosis of the head of the femur in 7, and abnormal cardiac ultrasound findings in 10). Only one patient died during the study. No correlation was found between severity score and either age or hemoglobin F level. These findings confirm that the phenotype is less severe in Senegal. However they also show that organ damage is common by the time that patients reach adulthood and thus underline the need for prevention and education to improve survival of SS homozygotes in Senegal.

[Pulmonary manifestations associated with malaria]

Pulmonary manifestations are frequently observed in children, pregnant women and travellers with malaria. The pathophysiology of these pulmonary manifestations is poorly understood but would appear to be secondary to an interaction between the parasitized red cells and the pulmonary capillary endothelium. Bronchitis and pneumonia do not directly compromise outcome but, left unrecognized, the delay in diagnosis and treatment may be fatal. Acute respiratory distress in children is the first cause of overmortality, coming before neurological involvement. The acute respiratory distress caused by severe malaria has no specific characteristics. Iatrogenic complications and pulmonary superinfections must be differentiated. The prevention of pulmonary manifestations associated with malaria can easily be accomplished by limiting water intake and carefully monitoring urinary output and weight. Treatment is the same as for acute flare-ups in combination with symptomatic respiratory treatment when required.

[Pulmonic plague]

One hundred years after Yersin discovered Yersinia pestis during the plague epidemic in Hong Kong in 1894, human plague still has not been eliminated. The epidemic in 1994 in India, a country where no cases had been observed since 1996, raised great concern. Plague is an epizootic bacterial infection caused by a Gram negative coccobacillus, Y. pestis, transmitted by the bite of infected fleas. Bubonic plague is the most common form. Other clinical presentations include asymptomatic plague, abortive plague, pharyngeal plague, septicemic plague, meningeal plague, and primary or secondary pneumonic plague which is observed in 5 to 20% of cases. Plague is a highly communicable disease between humans despite antibiotic therapy which has reduced mortality by 80%. The prognosis depends on early diagnosis. Streptomycin and cyclines are the gold standard treatment.

[Fulminant hepatitis in the course of antitubercular treatment (apropos of 2 cases)]

We report two cases of fulminant hepatitis induced by antitubercular drugs. The mechanism is both immunoallergic and toxic. The fatal case appears in patient with acquired immunodeficiency syndrome. Liver tests must be realized during antitubercular treatment, that is difficult in sub-Saharan Africa.

[Cardiac manifestations of polymyositis. Apropos of 2 Senegalese cases]

INTRODUCTION

Polymyositis cardiac involvement varies between 37% and 70%. EXEGENESIS: The authors report two cases of polymyositis with myocardial involvement observed in Senegal; the first case is a cardiac failure revealing an acute polymyositis occurring in a 44-year-old woman; the second case is a 34-year-old woman who had polymyositis with tachycardia and dyspnea: in the two cases echocardiography showed a left ventricular concentric hypertrophy with preserved systolic function and altered diastolic function; clinical and echocardiographic resolution were obtained by corticosteroid medication.

CONCLUSION

Myocardial localization is the most common polymyositis cardiac involvement; clinical symptomatology is rare (3.3% to 6%). sometimes revealing polymyositis; electrocardiographic abnormalities are found in 18% to 81% cases and echographic abnormality in 42% cases; cardiac involvement is of bad prognosis.

[Clinical exercise: recalcitrant diarrhea in the main hospital of Dakar ]

It's the case of a Senegalese man who presents a chronic rebel diarrhea with alteration of the general condition and a malabsorption. The aetiologic management has been very difficult to achieve after we have eliminated the infectious and parasitological causes. The clinical and epidemiological context with the histopathological arguments allowed us to establish the diagnosis of intestinal tuberculosis.

[Etiopathogenic, ultrasonographic and prognostic features of postpartum cardiomyopathy]

Peripartum cardiomyopathy is a classic but uncommon entity in African women about which there is little etiologic understanding. From January 1990 to March 1996 a series of 30 cases of peripartum cardiomyopathy was collected at the Principal Hospital in Dakar, Senegal. Peripartum cardiomyopathy was defined as the occurrence of cardiac insufficiency in a woman with no previous history of heart disease, during the period between the second and twentieth weeks after delivery confirmed by ultrasound evidence of dilated cardiomyopathy. The overall incidence of peripartum cardiomyopathy during the study period was 30 out of 1200 deliveries. The mean age of the women in the study was 34 years and mean parity was 5.2. In 13.3% of cases births involved twins. There were no predisposing socio-economic or climatic factors. The clinical picture was severe cardiac failure in 80.3% of cases and left ventricular insufficiency in 16.6%. In all cases ultrasound findings were typical of dilated cardiomyopathy. Serum selenium and vitamin B1 levels were normal. Measurements of T CD4 and CD8 in eight patients were normal. Conversion enzyme inhibitors were administered to twenty patients. Complete remission was achieved in 14 patients, three patients died, and thirteen patients presented ultrasonic evidence of persistent dilated cardiomyopathy. One patient relapsed after a subsequent delivery. These findings are in agreement with previous reports concerning the clinical and prognostic features of peripartum cardiomyopathy in Africa.