Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations.

How and at what pace bacteria evolve when colonizing healthy hosts remains unclear. Here, by monitoring evolution for more than six thousand generations in the mouse gut, we show that the successful colonization of an invader Escherichia coli depends on the diversity of the existing microbiota and the presence of a closely related strain. Following colonization, two modes of evolution were observed: one in which diversifying selection leads to long-term coexistence of ecotypes and a second in which directional selection propels selective sweeps. These modes can be quantitatively distinguished by the statistics of mutation trajectories. In our experiments, diversifying selection was marked by the emergence of metabolic mutations, and directional selection by acquisition of prophages, which bring their own benefits and costs. In both modes, we observed parallel evolution, with mutation accumulation rates comparable to those typically observed in vitro on similar time scales. Our results show how rapid ecotype formation and phage domestication can be in the mammalian gut.

Criteria for progressive fibrotic hypersensitivity pneumonitis in a Portuguese patient cohort.

Background: Hypersensitivity pneumonitis (HP) is a syndrome caused by sensitisation to inhaled antigens that leads to an abnormal immune response in the airways and lung parenchyma. Some patients previously diagnosed with certain types of fibrotic interstitial lung diseases (f-ILDs), including fibrotic HP (f-HP), are susceptible to develop a progressive fibrosing phenotype (PF-ILD), despite initial state-of-the-art management. Objectives: To characterise a cohort of patients with a multidisciplinary diagnosis (MTD) of chronic f-HP, who were followed up in an ILD outpatient clinic of a hospital in Portugal, and to assess the prevalence of PF-ILD criteria in these patients. Methods: Data were collected from all patients with a definite or provisional diagnosis of f-HP after a multidisciplinary team discussion. Patients were followed up between December 2014 and July 2019. Data included clinical characteristics, high-resolution chest tomography (HRCT) disease patterns, lung function tests, bronchoalveolar lavage and further immunological work-up, biopsy reports (conventional transbronchial lung biopsy, transbronchial lung cryobiopsy or surgical video-assisted thoracoscopic lung biopsy), all ILD multidisciplinary team records and diagnostic confidence levels. Patients were assessed according to PF-ILD criteria as defined in the INBUILD trial. Results: We identified 83 patients with an MTD of HP, who had been followed up for at least 12 months. Of these, 63 (75.9%) were diagnosed with f-HP. Of the 63 f-HP patients, 33.3% (n=21) fulfilled the predefined criteria for PF-HP: 66.7% had a relative decline of ≥10% forced vital capacity (FVC); 5% a relative decline of 5 - 9% FVC, with worsening symptoms or increased fibrosis on HRCT; and 23.8% had worsening respiratory symptoms with radiological progression. Conclusion: This single-centre cohort study demonstrated that a third of f-HP patients presented with PF-ILD, as determined by progression during initial standard-of-care treatment. A usual interstitial pneumonia (UIP)/UIP-like pattern was present in >70% of patients with f-HP, and two-thirds of these patients had an FVC decline of ≥10%. PF-HP patients were also more exacerbation prone. According to recent trial data, this segment of patients can be considered possible candidates for antifibrotic treatment, with a reasonable prospect of effectiveness. Further efforts should focus on refining knowledge of longitudinal behaviour of large multicentric cohorts of f-HP patients, establishing a consensual and uniform definition of progression for use in clinical practice, as well as developing prognostic prediction tools to better (and early) inform the disease course.

Perfil contemporâneo da intervenção coronária percutânea em octogenários / Contemporary profile of percutaneous coronary intervention in octogenarians

INTRODUÇÃO: Com o aumento da longevidade observado nas últimas décadas, as intervenções coronárias percutâneas (ICP) em octogenários são cada vez mais indicadas. OBJETIVO: Traçar o perfil clínico-epidemiológico-angiográfico e os principais detalhes associados à ICP dos pacientes octogenários. MÉTODOS: Cento e cinquenta pacientes octogenários foram submetidos à ICP entre janeiro de 2015 a dezembro de 2016, no Instituto Dante Pazzanese de Cardiologia, correspondendo a 3,7% dos 3987 casos tratados e a 18% dos com idade >70 anos, e incluídos de forma sequencial e prospectiva. Não houve critérios de exclusão. Os resultados clínicos expostos foram restritos à fase hospitalar. RESULTADOS: A maioria (63%) era do sexo masculino, com idade média de 86±3,9 anos (máximo de 102 anos). Do total de pacientes, 91,3% eram hipertensos, 37,4% diabéticos, a ICP prévia foi realizada em para 17,4%, enquanto 34,1% apresentaram infarto prévio. A cinecoronariografia identificou que 70,4% eram multiarteriais, dos quais 4% exibiam lesões não protegidas do tronco da coronária esquerda. A maioria (55%) apresentava disfunção ventricular significativa. Stents farmacológicos (SF) foram utilizados em 97,2% dos casos. O sucesso angiográfico foi obtido em 97,5% e o sucesso clínico em 93,2%. A mortalidade e o infarto ocorreram abaixo de 4,3% dos casos. CONCLUSÃO: Nessa população, observaram-se que os pacientes octogenários constituíram a minoria dos idosos tratados; a doença multiarterial grave foi o achado predominante; os stents farmacológicos foram implantados quase em todos os casos e os sucessos angiográfico e clínico apresentaram-se elevados. (AU)

INTRODUCTION: With the increase in longevity observed in recent decades, percutaneous coronary interventions (PCI) in octogenarians are increasingly indicated. OBJECTIVE: To outline the clinical, epidemiological and angiographic profile and main details associated with PCI in octogenarian patients. METHODS: One hundred and fifty octogenarian patients underwent PCI between January 2015 and December 2016 at the Dante Pazzanese Institute of Cardiology, corresponding to 3.7% of the 3987 cases treated and 18% of those aged> 70 years, and included sequentially and prospectively. There were no exclusion criteria. The clinical results were restricted to the hospital phase. RESULTS: The majority (63%) were males, with a mean age of 86±3.9 years (maximum 102 years). Of the total patients, 91.3% were hypertensive, 37.4% were diabetic, 17.4% had previously undergone PCI, while 34.1% had previous infarction. The coronary angiography indicated that 70.4% were multiarterial, of which 4% had unprotected lesions of the trunk of the left coronary artery. The majority (55%) had significant ventricular dysfunction. Pharmacological stents were used in 97.2% of the cases. Angiographic success was achieved in 97.5% and clinical success in 93.2%. Mortality and infarction occurred in less than 4.3% of the cases. CONCLUSION: In this population, it was observed that octogenarian patients constituted a minority of treated elderly; severe multivessel disease was the predominant finding; pharmacological stents were implanted in almost all cases, and angiographic and clinical success rates were high. (AU)

An experimental model for fatal malaria due to TNF-alpha-dependent hepatic damage.

While BALB/c mice survive infection with blood stages of Plasmodium chabaudi chabaudi (AS), 70% of DBA/2 mice die by day 9-11 of infection, both strains controlling parasitaemia. We describe here that infection of DBA/2 mice results in extensive, multifocal hepatocyte death. Antibody neutralization of TNF-alpha prevents both liver damage and death.

Thymic commitment of regulatory T cells is a pathway of TCR-dependent selection that isolates repertoires undergoing positive or negative selection.

The seminal work of Le Douarin and colleagues (Ohki et al. 1987; Ohki et al. 1988; Salaun et al. 1990; Coutinho et al. 1993) first demonstrated that peripheral tissue-specific tolerance is centrally established in the thymus, by epithelial stromal cells (TEC). Subsequent experiments have shown that TEC-tolerance is dominant and mediated by CD4 regulatory T cells (Treg) that are generated intrathymically by recognition of antigens expressed on TECs (Modigliani et al. 1995; Modigliani et al. 1996a). From these and other observations, in 1996 Modigliani and colleagues derived a general model for the establishment and maintenance of natural tolerance (MM96) (Modigliani et al. 1996b), with two central propositions: (1) T cell receptor (TCR)-dependent sorting of emergent repertoires generates TEC-specific Treg displaying the highest TCR self-affinities below deletion thresholds, thus isolating repertoires undergoing positive and negative selection; (2) Treg are intrathymically committed (and activated) for a unique differentiative pathway with regulatory effector functions. The model explained the embryonic/perinatal time window of natural tolerance acquisition, by developmental programs determining (1) TCR multireactivity, (2) the cellular composition in the thymic stroma (relative abundance of epithelial vs hemopoietic cells), and (3) the dynamics of peripheral lymphocyte pools, built by accumulation of recent thymic emigrants (RTE) that remain recruitable to regulatory functions. We discuss here the MM96 in the light of recent results demonstrating the promiscuous expression of tissue-specific antigens by medullary TECs (Derbinski et al. 2001; Anderson et al. 2002; Gotter et al. 2004) and indicating that Treg represent a unique differentiative pathway (Fontenot et al. 2003; Hori et al. 2003; Khattri et al. 2003), which is adopted by CD4 T cells with high avidity for TEC-antigens (Bensinger et al. 2001; Jordan et al. 2001; Apostolou et al. 2002). In the likelihood that autoimmune diseases (AID) result from Treg deficits, some of which might have a thymic origin, we also speculate on therapeutic strategies aiming at selectively stimulating their de novo production or peripheral function, within recent findings on Treg responses to inflammation (Caramalho et al. 2003; Lopes-Carvalho et al., submitted, Caramalho et al., submitted). In short, the MM96 argued that natural tolerance is dominant, established and maintained by the activity of Treg, which are selected upon high-affinity recognition of self-ligands on TECs, and committed intrathymically to a unique differentiative pathway geared to anti-inflammatory and antiproliferative effector functions. By postulating the intrathymic deletion of self-reactivities on hemopoietic stromal cells (THC), together with the inability of peripheral resident lymphocytes to engage in the regulatory pathway, the MM96 simultaneously explained the maintenance of responsiveness to non-self in a context of suppression mediating dominant self-tolerance. The major difficulty of the MM96 is related to the apparent tissue specificity of Treg repertoires generated intrathymically. This difficulty has now been principally solved by the work of Hanahan, Kyewski and others (Jolicoeur et al. 1994; Derbinski et al. 2001; Anderson et al. 2002; Gotter et al. 2004), demonstrating the selective expression of a variety of tissue-specific antigens by TECs, in topological patterns that are compatible with the MM96, but difficult to conciliate with recessive tolerance models (Kappler et al. 1987; Kisielow et al. 1988). While the developmentally regulated multireactivity of TCR repertoires (Gavin and Bevan 1995), as well as the peripheral recruitment of Treg among RTE (Modigliani et al. 1996a) might add to this process, it would seem that the establishment of tissue-specific tolerance essentially stems from the "promiscuous expression of tissue antigens" by TEC. The findings of AID resulting from natural mutations (reviewed in Pitkanen and Peterson 2003) or the targeted inactivation (Anderson et al. 2002; Ramsey et al. 2002) of the AIRE transcription factor that regulates promiscuous gene expression on TECs support this conclusion. The observations on the correlation of natural or forced expression of the Foxp3 transcription factor in CD4 T cells with Treg phenotype and function (Fontenot et al. 2003; Hori et al. 2003; Khattri et al. 2003) provided support for the MM96 contention that Treg represent a unique differentiative pathway that is naturally established inside the thymus. Furthermore, Caton and colleagues (Jordan et al. 2001), as well as several other groups (Bensinger et al. 2001; Apostolou et al. 2002), have provided direct evidence for our postulate that Treg are selected among differentiating CD4 T cells with high affinity for ligands expressed on TECs (Modigliani et al. 1996b). Finally, the demonstration by Caramalho et al. that Treg express innate immunity receptors (Caramalho et al. 2003) and respond to pro-inflammatory signals and products of inflammation (Caramalho et al., submitted) brought about a new understanding on the peripheral regulation of Treg function. Together with the observation that Treg also respond to ongoing activities of "naïve/effector" T cells--possibly through the IL-2 produced in these conditions--these findings explain the participation of Treg in all immune responses (Onizuka et al. 1999; Shimizu et al. 1999; Annacker et al. 2001; Curotto de Lafaille et al. 2001; Almeida et al. 2002; Shevach 2002; Bach and Francois Bach 2003; Wood and Sakaguchi 2003; Mittrucker and Kaufmann 2004; Sakaguchi 2004), beyond their fundamental role in ensuring self-tolerance (e.g., Modigliani et al. 1996a; Shevach 2000; Hori et al. 2003; Sakaguchi 2004; Thompson and Powrie 2004). Thus, anti-inflammatory and anti-proliferative Treg are amplified by signals that promote or mediate inflammation and proliferation, accounting for the quality control of responses (Coutinho et al. 2001). In turn, such natural regulation of Treg by immune responses to non-self may well explain the alarming epidemiology of allergic and AID in wealthy societies (Wills-Karp et al. 2001; Bach 2002; Yazdanbakhsh et al. 2002), where a variety of childhood infections have become rare or absent. Thus, it is plausible that Treg were evolutionarily set by a given density of infectious agents in the environment. With hindsight, it is not too surprising that natural Treg performance falls once hygiene, vaccination, and antibiotics suddenly (i.e., 100 years) plunged infectious density to below some critical physiological threshold. As the immune system is not adapted to modern clean conditions of postnatal development, clinical immunologists must now deal with frequent Treg deficiencies (allergies and AID) for which they have no curative or rational treatments. It is essential, therefore, that basic immunologists concentrate on strategies to selectively stimulate the production, survival, and activity of this set of lymphocytes that is instrumental in preventing immune pathology. We have argued that the culprit of this inability of basic research to solve major clinical problems has been the self-righteousness of recessive tolerance champions, from Ehrlich to some of our contemporaries. It is ironical, however, that none of us--including the heretic opponents of horror autotoxicus--had understood that self-tolerance, or its robustness at least, is in part determined by the frequency and intensity of the responses to non-self. In the evolution of ideas on immunological tolerance, the time might be ripe for some kinds of synthesis. First, conventional theory reduced self-tolerance to negative selection and microbial defense to positive selection, while the MM96 solution was the precise opposite: positive selection of autoreactivities for self-tolerance (Treg) and negative selection (of Treg) for ridding responses. In contrast, it would now appear that positive and negative selection of autoreactive T cells are both necessary to establish either self-tolerance or competence to eliminate microbes, two processes that actually reinforce each other in the maintenance of self-integrity. Second, V-region recognition has generally been held responsible for specific discrimination between what should be either tolerated or eliminated from the organism. In contrast again, it would now seem that both processes of self-tolerance and microbial defense (self/non-self discrimination) also operate on the basis of evolutionarily ancient, germ-line-encoded innate, nonspecific receptors (Medzhitov and Janeway 2000) capable of a coarse level of self/non-self discrimination (Coutinho 1975). It could thus be interesting to revisit notions of cooperativity between V-regions and such mitogen receptors, both in single cell functions (Coutinho et al. 1974) and in the system's evolution (Coutinho 1975, 1980) as well. After all, major transitions in evolution were cooperative (Maynard-Smith and Szathmary 1995).

Direct activation of dendritic cells by the malaria parasite, Plasmodium chabaudi chabaudi.

A primary infection of mice with Plasmodium chabaudi chabaudi (AS) is characterized by a rapid and marked inflammatory response. Typically, IL-12, TNF-alpha and IFN-gamma are produced in the spleen, and are transiently present in plasma. The cells involved in this early response are unknown. Here we show that dendritic cells derived from GM-CSF-stimulated mouse bone marrow cultures produce TNF-alpha within 30 min of exposure to P.c.chabaudi schizonts. IL-6, IL-12p40 and p70 follow this. The production of these cytokines was not dependent on the presence of T cells or NK cells and did not require CD40. Incubation of dendritic cells with P.c.chabaudi schizonts also resulted in up-regulation of MHC class II, CD40 and CD86 but not CD80. In contrast to some strains of the human parasite, P. falciparum, P.c. chabaudi (AS) did not inhibit the up-regulation of MHC class II, CD86 or CD40 induced by LPS. Therefore, the erythrocytic stages of P.c.chabaudi are able to activate dendritic cells directly. The consequences of such an interaction could be rapid activation of TH1 cells and induction of immunity, and in the event of a large response also induction of TNF-alpha associated pathology.

Complement contributes to protective immunity against reinfection by Plasmodium chabaudi chabaudi parasites.

We have studied the impact of deficiency of the complement system on the progression and control of the erythrocyte stages of the malarial parasite Plasmodium chabaudi chabaudi. C1q-deficient mice and factor B- and C2-deficient mice, deficient in the classical complement pathway and in both the alternative and classical complement activation pathways, respectively, exhibited only a slight delay in the resolution of the acute phase of parasitemia. Complement-deficient mice showed a transiently elevated level of gamma interferon (IFN-gamma) in the plasma at the time of the acute parasitemia compared with that of wild-type mice. Although there was a trend for increased precursor frequencies in CD4(+) T cells from C1q-deficient mice producing IFN-gamma in response to malarial antigens in vitro, intracellular cytokine staining of spleen cells ex vivo showed no difference in the numbers of IFN-gamma(+) splenic CD4(+) and CD8(+) cells. In contrast, C1q-deficient animals were significantly more susceptible to a second challenge with the same parasite. C1q-deficient animals showed a reduced level of anti-malarial immunoglobulin G2a (IgG2a) antibody 100 days after primary infection. However, following a significantly higher parasitemia, C1q-deficient mice had increased levels of IgM and IgG2a anti-malarial antibodies. In summary, this study indicates that while complement plays only a minor role in the control of the acute phase of parasitemia of a primary infection, it does contribute to parasite control in reinfection.

Low CD4(+) T cell responses to the C-terminal region of the malaria merozoite surface protein-1 may be attributed to processing within distinct MHC class II pathways.

The C-terminal fragment of merozoite surface protein-1 (MSP-1) of the mouse malaria parasite Plasmodium chabaudi chabaudi (AS) stimulates a weak CD4 T cell response when compared to the response to a more structurally simple region of the molecule. The tertiary structure of the C-terminal region of MSP-1 is maintained by five disulfide bonds. A peptide from this region could only be processed and loaded onto newly synthesized MHC class II molecules, whereas a peptide from the structurally simple region was available for loading onto recycling MHC class II. CD4(+) T cell hybridomas took longer to recognize an epitope derived from the disulfide-bonded region whether native parasite or recombinant MSP-1 antigen was used. Reduction of disulfide bonds in the C-terminal region subsequently allowed peptides to be loaded onto recycling MHC class II and greatly enhanced the rapidity of the T cell response. These data demonstrate that differential processing occurs intramolecularly in MSP-1, which may be responsible for the observed weak CD4 T cell responses against this region. The consequences of this in vivo may be that limited T cell help is available for protective antibody production which has important implications for designing vaccines based on MSP-1.

The effect of chloroquine on the production of interferon-gamma, interleukin (IL)-4, IL-6, and IL-10 in Plasmodium chabaudi chabaudi in infected C57BL6 mice.

The effect of chloroquine (CQ) on the production pattern of interferon (IFN)-gamma, interleukin (IL)-4, IL-6, and IL-10 in female C57BL6 mice infected with Plasmodium chabaudi chabaudi AS was evaluated during a period of 35 days. Our data confirm that there is a switch from a T helper cell (Th)1 to a Th2 response during malaria infection in this model. Proliferation assays showed a decreased stimulation index in infected mice that was further reduced in infected mice treated with CQ. Noninfected control mice treated with CQ showed an increase production of IFN-gamma. However, no detectable changes in IL-4, IL-6, and IL-10 production were observed in this group. CQ treatment of infected mice resulted in parasite clearance that was associated with an earlier production of IL-4, IL-6, and IL-10 when compared with nontreated infected mice. We suggest that this earlier switch to a Th2 response is a consequence of parasite killing rather than CQ interference with cytokine production.

gammadelta T cells contribute to control of chronic parasitemia in Plasmodium chabaudi infections in mice.

During a primary infection of mice with Plasmodium chabaudi, gammadelta T cells are stimulated and their expansion coincides with recovery from the acute phase of infection in normal mice or with chronic infections in B cell-deficient mice (mu-MT). To determine whether the large gammadelta T cell pool observed in female B cell-deficient mice is responsible for controlling the chronic infection, studies were done using double-knockout mice deficient in both B and gammadelta cells (mu-MT x delta-/-TCR) and in gammadelta T cell-depleted mu-MT mice. In both types of gammadelta T cell-deficient mice, the early parasitemia following the peak of infection was exacerbated, and the chronic parasitemia was maintained at significantly higher levels in the absence of gammadelta T cells. The majority of gammadelta T cells in C57BL/6 and mu-MT mice responding to infection belonged predominantly to a single family of gammadelta T cells with TCR composed of Vgamma2Vdelta4 chains and which produced IFN-gamma rather than IL-4.

A role for B cells in the development of T cell helper function in a malaria infection in mice.

B cell knockout mice are unable to clear a primary erythrocytic infection of Plasmodium chabaudi chabaudi. However, the early acute infection is controlled to some extent, giving rise to a chronic relapsing parasitemia that can be reduced either by drug treatment or by adoptive transfer of B cells. Similar to mice rendered B-cell deficient by lifelong treatment with anti-mu antibodies, B cell knockout mice (muMT) retain a predominant CD4+ Th1-like response to malarial antigens throughout a primary infection. This contrasts with the response seen in control C57BL/6 mice in which the CD4+ T-cell response has switched to that characteristic of Th2 cells at the later stages of infection, manifesting efficient help for specific antibodies in vitro and interleukin 4 production. Both chloroquine and adoptive transfer of immune B cells reduced parasite load. However, the adoptive transfer of B cells resulted in a Th2 response in recipient muMT mice, as indicated by a relative increase in the precursor frequency of helper cells for antibody production. These data support the idea that B cells play a role in the regulation of CD4+ T subset responses.

Plasmodium berghei: selection of mefloquine-resistant parasites through drug pressure in mosquitoes.

Mefloquine is an antimalarial drug with schizonticidal activity on blood-stage parasites. Studies of the role of mefloquine on the development of Plasmodium berghei ANKA in anopheles stephensi have been carried out that showed a dose-dependent effect on the sporogonic cycle of these parasites, with changes in the numbers of oocysts and the extent of sporozoite invasion of salivary glands. In this study, we show that mefloquine-resistant P. berghei ANKA blood stage parasites could be selected through drug pressure during continuous cyclical transmission of Anopheles gambiae s.l.

Investigation of chloroquine intake in Biombo region, Guinea Bissau.

The use of chloroquine (CQ), during the dry season was determined for 236 patients from 5 villages in Biombo, Republic of Guinea Bissau, West Africa. The antimalarial drug was measured in whole blood (dried samples) using High Performance Liquid Chromatography (HPLC) and in urine samples by Enzyme Linked Immunosorbent Assay (ELISA). The results showed that CQ consumption is low.