Emerging bacterial pathogens: the past and beyond.

Since the 1950s, medical communities have been facing with emerging and reemerging infectious diseases, and emerging pathogens are now considered to be a major microbiologic public health threat. In this review, we focus on bacterial emerging diseases and explore factors involved in their emergence as well as future challenges. We identified 26 major emerging and reemerging infectious diseases of bacterial origin; most of them originated either from an animal and are considered to be zoonoses or from water sources. Major contributing factors in the emergence of these bacterial infections are: (1) development of new diagnostic tools, such as improvements in culture methods, development of molecular techniques and implementation of mass spectrometry in microbiology; (2) increase in human exposure to bacterial pathogens as a result of sociodemographic and environmental changes; and (3) emergence of more virulent bacterial strains and opportunistic infections, especially affecting immunocompromised populations. A precise definition of their implications in human disease is challenging and requires the comprehensive integration of microbiological, clinical and epidemiologic aspects as well as the use of experimental models. It is now urgent to allocate financial resources to gather international data to provide a better understanding of the clinical relevance of these waterborne and zoonotic emerging diseases

Simkania negevensis, an insight into the biology and clinical importance of a novel member of the Chlamydiales order.

Simkania negevensis is a Chlamydia-related bacterium discovered in 1993 and represents the founding member of the Simkaniaceae family within the Chlamydiales order. As other Chlamydiales, it is an obligate intracellular bacterium characterized by a biphasic developmental cycle. Its similarities with the pathogenic Chlamydia trachomatis and Chlamydia pneumoniae make it an interesting bacterium. So far, little is known about its biology, but S. negevensis harbors various microbiological characteristics of interest, including a strong association of the Simkania-containing vacuole with the ER and the presence of an intron in the 23S rRNA encoding gene. Evidence of human exposition has been reported worldwide. However, there is a lack of robust clinical studies evaluating its implication in human diseases; current data suggest an association with pneumonia and bronchiolitis making S. negevensis a potential emerging pathogen. Owing to its fastidious growth requirements, the clinical relevance of S. negevensis is probably underestimated. In this review, we summarize the current knowledge on S. negevensis and explore future research challenges

Simkania negevensis may produce long-lasting infections in human pneumocytes and endometrial cells.

Simkania negevensis is a novel Chlamydia-related bacterium and the founding member of the Simkaniaceae family within the Chlamydiales order. Little is known about the biology and pathogenesis of this bacterium. So far, S. negevensis has been considered as an amoebal symbiont, but its natural host remains unknown. Moreover, evidence of human exposition has been reported worldwide and an association with pneumonia and bronchiolitis is suspected. Here, we evaluated the ability of S. negevensis to replicate in potential environmental reservoirs, namely amoebae and arthropods, as well as in mammalian cells (Vero cells, pneumocytes and endometrial cells) and further evaluated the characteristics of its replicative vacuole. We demonstrated that S. negevensis efficiently replicates in all cell lines tested, with the shortest doubling time and an increased adhesion observed in pneumocytes. Our work highlights the specificities of the Simkania-containing vacuole compared to other Chlamydiales; contrarily to Chlamydia trachomatis, S. negevensis does not disrupt the Golgi apparatus. Importantly, our work suggests that S. negevensis infection is associated with few cytopathic effects and might persist for a prolonged time in infected cells. Further evaluation of its implication in human diseases is required; an implication in chronic or subacute respiratory infections might be suspected

Simkania negevensis, an Example of the Diversity of the Antimicrobial Susceptibility Pattern among Chlamydiales.

In past years, several <i>Chlamydia</i> -related bacteria have been discovered, including <i>Simkania negevensis</i> , the founding member of the <i>Simkaniaceae</i> family. We evaluated the antimicrobial susceptibility patterns of this emerging intracellular bacterium and highlighted significant differences, compared with related <i>Chlamydiales</i> members. <i>S. negevensis</i> was susceptible to macrolides, clindamycin, cyclines, rifampin, and quinolones. Importantly, unlike other <i>Chlamydiales</i> members, treatment with β-lactams and vancomycin did not induce the formation of aberrant bodies, leading to a completely resistant phenotype

Impact of Waddlia chondrophila infection on pregnancy in the mouse.

The intracellular bacterium Waddlia chondrophila, which belongs to the Chlamydiales order, was found to be associated with miscarriage in humans. There is little to no knowledge regarding the mode of infection, impact on the neonate and pathophysiology of this emerging bacterium. We have previously shown that W. chondrophila induces a systemic infection, organ pathology and elicits T helper type 1-associated humoral immunity in a murine model of genital infection. In the present study, we took advantage of this model of infection to evaluate the impact of this bacterium on the mouse pregnancy. We used two routes of inoculation, vaginal and intrauterine, to introduce infection before and after mating. Our results show that genital infection by W. chondrophila did not have any significant impact on gestation length and maternal weight gain, nor on the number of offspring and their weight. This observation indicates that the mouse model of infection is not suitable to study the effect of W. chondrophila on pregnancy and alternative models of infection, including in vitro ones, should be used. Moreover, an indirect immunopathological mechanism activated by this bacterium should be further explored

Antibiotic susceptibility of Neochlamydia hartmanellae and Parachlamydia acanthamoebae in amoebae.

Parachlamydia acanthamoebae and Neochlamydia hartmanellae are Chlamydia-related bacteria naturally infecting free-living amoebae. These strict intracellular bacteria might represent emerging pathogens. Recent studies report an association with lower respiratory tract infections, especially with pneumonia where they have been identified as a potential causative agent in 1-2% of cases. In this study, we defined the antibiotic susceptibility of N. hartmanellae, two strains of P. acanthamoebae and two yet unclassified Parachlamydiaceae strains using a quantitative approach. We confirmed the results obtained earlier for P. acanthamoebae strain Bn9 in an observational study. Macrolides (MICs < 0.06-0.5 μg/ml), rifampicin (MICs 0.25-2) and doxycycline (2-4 μg/ml) were active against P. acanthamoebae strains and Neochlamydia. All strains were resistant to amoxicillin, ceftriaxone and imipenem (MIC ≥32 μg/ml). Similarly to other Chlamydia-related bacteria, all investigated Parachlamydiaceae were resistant to quinolones (MICs ≥ 16 μg/ml). Therefore, we recommend a treatment with macrolides for Parachlamydia-associated pneumonia

Correction: Absence of Zika virus among pregnant women in Vietnam in 2008.

International audienc

Simit: A Language for Physical Simulation

Using existing programming tools, writing high-performance simulation code is labor intensive and requires sacrificing readability and portability. The alternative is to prototype simulations in a high-level language like Matlab, thereby sacrificing performance. The Matlab programming model naturally describes the behavior of an entire physical system using the language of linear algebra. However, simulations also manipulate individual geometric elements, which are best represented using linked data structures like meshes. Translating between the linked data structures and linear algebra comes at significant cost, both to the programmer and the machine. High-performance implementations avoid the cost by rephrasing the computation in terms of linked or index data structures, leaving the code complicated and monolithic, often increasing its size by an order of magnitude. In this paper, we present Simit, a new language for physical simulations that lets the programmer view the system both as a linked data structure in the form of a hypergraph, and as a set of global vectors, matrices and tensors depending on what is convenient at any given time. Simit provides a novel assembly construct that makes it conceptually easy and computationally efficient to move between the two abstractions. Using the information provided by the assembly construct, the compiler generates efficient in-place computation on the graph. We demonstrate that Simit is easy to use: a Simit program is typically shorter than a Matlab program; that it is high-performance: a Simit program running sequentially on a CPU performs comparably to hand-optimized simulations; and that it is portable: Simit programs can be compiled for GPUs with no change to the program, delivering 5-25x speedups over our optimized CPU code

What is the true clinical relevance of Simkania negevensis and other emerging Chlamydiales members?

<i>Waddlia</i>   <i>chondrophila</i> and <i>Simkania negevensis</i> are emerging <i>Chlamydia-</i> related bacteria. Similar to the pathogenic organisms <i>Chlamydia pneumoniae</i> and <i>Chlamydia trachomatis,</i> these emerging bacteria are implicated in human genital infections and respiratory diseases. We used a screening strategy based on a newly developed <i>S. negevensis</i> -specific quantitative real-time PCR (qPCR) and a pan- <i>Chlamydiales</i> qPCR. We could not detect <i>S. negevensis</i> in 458 respiratory, genitourinary, cardiac and hepatic samples tested. One urethral swab was positive for <i>W. chondrophila.</i> We observed a low prevalence of <i>Chlamydiales</i> in respiratory samples (1/200, 0.5%), which suggests that <i>C. pneumoniae</i> is an uncommon respiratory pathogen. Furthermore, we screened 414 human serum samples from Switzerland, England and Israel and observed a low prevalence (<1%) of exposure to <i>S. negevensis.</i> Conversely, humans were commonly exposed to <i>W. chondrophila,</i> with seroprevalences ranging from 8.6% to 32.5%. <i>S. negevensis</i> is not a clinically relevant pathogen, but further research investigating the role of <i>W. chondrophila</i> is needed

Congenital Zika virus syndrome…what else? Two case reports of severe combined fetal pathologies.

Zika virus (ZIKV) has recently emerged as a teratogenic infectious agent associated with severe fetal cerebral anomalies. Other microorganisms (TORCH agents) as well as genetic disorders and toxic agents may lead to similar anomalies. In case of fetal anomalies, the exact etiology might be difficult to establish, especially in ZIKV endemic countries. As the risks associated with maternal infection remain unclear adequate parental counseling is difficult. We present two cases of severe fetal pathologies managed in our multidisciplinary center during the ZIKV outbreak in Martinique, a French Caribbean Island. Both fetuses had congenital ZIKV infection confirmed by RT-PCR. While one case presented with significant cerebral anomalies, the other one presented with hydrops fetalis. A complete analysis revealed that the fetal lesions observed resulted from a combination of ZIKV congenital infection and a genetic disorder (trisomy 18) in case 1 or congenital Parvovirus B19 infection in case 2. We highlight the difficulties related to adequate diagnosis in case of suspected ZIKV congenital syndrome. Additional factors may contribute to or cause fetal pathology, even in the presence of a confirmed ZIKV fetal infection. An exact diagnosis is mandatory to draw definitive conclusions. We further emphasize that, similarly to other congenital infections, it is very likely that not all infected fetuses will become symptomatic