The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Tick-borne rickettsioses are caused by obligate intracellular bacteria belonging to the spotted fever group of the genus Rickettsia. These zoonoses are among the oldest known vector-borne diseases. However, in the past 25 years, the scope and importance of the recognized tick-associated rickettsial pathogens have increased dramatically, making this complex of diseases an ideal paradigm for the understanding of emerging and reemerging infections. Several species of tick-borne rickettsiae that were considered nonpathogenic for decades are now associated with human infections, and novel Rickettsia species of undetermined pathogenicity continue to be detected in or isolated from ticks around the world. This remarkable expansion of information has been driven largely by the use of molecular techniques that have facilitated the identification of novel and previously recognized rickettsiae in ticks. New approaches, such as swabbing of eschars to obtain material to be tested by PCR, have emerged in recent years and have played a role in describing emerging tick-borne rickettsioses. Here, we present the current knowledge on tick-borne rickettsiae and rickettsioses using a geographic approach toward the epidemiology of these diseases.

Update on Tick-Borne Rickettsioses around the World: a Geographic Approach

Summary
Most intracellular parasites employ sophisticated mechanisms to direct biogenesis of a vacuolar replicative niche that circumvents default maturation through the endolysosomal cascade. However, this is not the case of the Q fever bacterium, Coxiella burnetii. This hardy, obligate intracellular pathogen has evolved to not only survive, but to thrive, in the harshest of intracellular compartments: the phagolysosome. Following internalization, the nascent Coxiella phagosome ultimately develops into a large and spacious parasitophorous vacuole (PV) that acquires lysosomal characteristics such as acidic pH, acid hydrolases and cationic peptides, defences designed to rid the host of intruders. However, transit of Coxiella to this environment is initially stalled, a process that is apparently modulated by interactions with the autophagic pathway. Coxiella actively participates in biogenesis of its PV by synthesizing proteins that mediate phagosome stalling, autophagic interactions, and development and maintenance of the mature vacuole. Among the potential mechanisms mediating these processes is deployment of a type IV secretion system to deliver effector proteins to the host cytosol. Here we summarize our current understanding of the cellular events that occur during parasitism of host cells by Coxiella.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1462-5822.2007.00901.x

Lounging in a lysosome: the intracellular lifestyle of Coxiella burnetii.

Summary: To date, most Leishmania and human immunodeficiency virus (HIV) coinfection cases reported to WHO come from Southern Europe. Up to the year 2001, nearly 2,000 cases of coinfection were identified, of which 90% were from Spain, Italy, France, and Portugal. However, these figures are misleading because they do not account for the large proportion of cases in many African and Asian countries that are missed due to a lack of diagnostic facilities and poor reporting systems. Most cases of coinfection in the Americas are reported in Brazil, where the incidence of leishmaniasis has spread in recent years due to overlap with major areas of HIV transmission. In some areas of Africa, the number of coinfection cases has increased dramatically due to social phenomena such as mass migration and wars. In northwest Ethiopia, up to 30% of all visceral leishmaniasis patients are also infected with HIV. In Asia, coinfections are increasingly being reported in India, which also has the highest global burden of leishmaniasis and a high rate of resistance to antimonial drugs. Based on the previous experience of 20 years of coinfection in Europe, this review focuses on the management of Leishmania-HIV-coinfected patients in low-income countries where leishmaniasis is endemic.

https://www.who.int/leishmaniasis/burden/hiv_coinfection/Clinical_Microbiology_Reviews_2008.pdf

The Relationship between Leishmaniasis and AIDS: the Second 10 Years

Asevere type of jaundice that appeared in epidemic form was described by Adolf W eil of " eisbaden in 1880, and from this time for some years there was a tendency to refer to all cases ? severe jaundice that appeared in epidemic !?nn as Weil's disease. In 1915 some Japanese Investigators associated a slender coiled oiganwith a severe febrile attack, usually accompanied by jaundice, that occurred in both cPiclemic and sporadic form in Japan, this 0rganism they recovered from the blood and **** ^ Patients during life, and from the livci 'n(> kidneys post mortem.

專題討論－細螺旋體病（Leptospirosis）

Between 1984 and 2004, nine more species or subspecies of spotted fever rickettsiae were identified as emerging agents of tick-borne rickettsioses throughout the world. Six of these species had first been isolated from ticks and later found to be pathogenic to humans. The most recent example is Rickettsia parkeri, recognized as a human pathogen more than 60 years after its initial isolation from ticks. A new spotted fever rickettsia, R. felis was also found to be associated with fleas and to be a human pathogen. Similarly, bacteria within the family Anaplasmataceae have been considered to be of veterinary importance only, yet three species have been implicated in human diseases in recent years, including Ehrlichia chaffeensis, the agent of human monocytic ehrlichiosis, Anaplasma phagocytophilum, the agent of human anaplasmosis (formerly known as "human granulocytic ehrlichiosis agent", E. equi and E. phagocytophila), and finally Ehrlichia ewingii, which causes granulocytic ehrlichiosis in humans. We present here an overview of the various tick- and flea-borne rickettsial zoonoses described in the last 20 years, focusing on the ecological, epidemiological and clinical aspects.

/pdf/tick-and-flea-borne-rickettsial-emerging-zoonoses-91096royn7.pdf

Tick- and flea-borne rickettsial emerging zoonoses.

The prevalences of Bartonella, Rickettsia, and Wolbachia were investigated in 309 cat fleas from France by polymerase chain reaction (PCR) assay and sequencing with primers derived from the gltA gene for Rickettsia, the its and pap31 genes for Bartonella, and the 16S rRNA gene for Anaplasmataceae Positive PCR results were confirmed by using the Lightcycler and specific primers for the rOmpB of Rickettsia and gltA of Bartonella R felis was detected in 25 fleas (81%), W pipientis, an insect symbiont, in 55 (178%), and Bartonella in 81 (262%), including B henselae (9/81; 111%), B clarridgeiae (55/81; 679%), B quintana (14/81; 173%), and B koehlerae (3/81; 37%) This is the first report of the amplification of B quintana from fleas and the first description of B koehlerae in fleas from an area outside the United States Cat fleas may be more important vectors of human diseases than previously reported

/pdf/molecular-detection-of-bartonella-quintana-b-koehlerae-b-2r28o2agdt.pdf

Molecular Detection of Bartonella quintana, B. koehlerae, B. henselae, B. clarridgeiae, Rickettsia felis, and Wolbachia pipientis in Cat Fleas, France

Tick-borne lymphadenopathy (TIBOLA), also called Dermacentor-borne necrosis erythema and lymphadenopathy (DEBONEL), is defined as the association of a tick bite, an inoculation eschar on the scalp, and cervical adenopathies. We identified the etiologic agent for 65% of 86 patients with TIBOLA/DEBONEL as either Rickettsia slovaca (49/86, 57%) or R. raoultii (7/86, 8%).

/pdf/rickettsia-slovaca-and-r-raoultii-in-tick-borne-4iw1hlmba3.pdf

Rickettsia slovaca and R. raoultii in tick-borne Rickettsioses.

Background. The reservoir of the agent of Whipple disease is unknown. Asymptomatic carriage of Tropheryma whipplei in human stool and saliva is controversial. Methods. Stools and saliva specimens from 231 workers at a sewage treatment facility and from 10 patients with Whipple disease, stool specimens from 102 healthy people, and stool specimens from 127 monkeys or apes were tested for T. whipplei DNA by a quantitative real-time polymerase chain reaction with probe detection. Genotyping and culture of T. whipplei-positive samples were performed. Results. Asymptomatic carriage in stool was found in humans (ranging from a prevalence of 4% in the control group to 12% among a subgroup of sewer workers) but not in monkeys and apes. The T. whipplei load in stool was significantly lower in carriers than in patients with Whipple disease (P <.001). There was a significant prevalence gradient associated with employment responsibilities at the sewage treatment facility: workers who cleaned the underground portion of the sewers were more likely than other workers to carry T. whipplei in stool. Seven of 9 sewer workers tested positive 8 months later. Patients with Whipple disease were significantly more likely to have T. whipplei-positive saliva specimens (P =.005) and had a significantly greater T. whipplei load in saliva (P =.015), compared with asymptomatic stool carriers from the sewage facility. All non-stool carriers had T. whipplei-negative saliva specimens. T. whipplei strains were heterogeneic among sewer workers but identical within individual workers. Conclusion. Chronic asymptomatic carriage of T. whipplei occurs in humans. Bacterial loads are lower in asymptomatic carriers, and the prevalence of carriage increases with exposure to sewage.

Prevalence of Asymptomatic Tropheryma whipplei Carriage among Humans and Nonhuman Primates

We describe the characterization of a novel Rickettsia species cultivated from Dermacentor ticks collected in Russia and France, for which we propose the name Rickettsia raoultii sp. nov. Using multigene sequencing, we demonstrated that five rickettsial isolates from Dermacentor silvarum, Dermacentor reticulatus, Dermacentor marginatus and Dermacentor nuttalli ticks were classified within this novel spotted fever rickettsia species. This rickettsia also exhibited a serotype distinct from previously described Rickettsia species. The type strain of Rickettsia raoultii sp. nov. is strain KhabarovskT (=CSUR R3T =ATCC VR-1596T).

/pdf/rickettsia-raoultii-sp-nov-a-spotted-fever-group-rickettsia-23bvwbyo00.pdf

Bernard Davoust

Papers

Tick- and flea-borne rickettsial emerging zoonoses.

Molecular Detection of Bartonella quintana, B. koehlerae, B. henselae, B. clarridgeiae, Rickettsia felis, and Wolbachia pipientis in Cat Fleas, France

Rickettsia slovaca and R. raoultii in tick-borne Rickettsioses.

Prevalence of Asymptomatic Tropheryma whipplei Carriage among Humans and Nonhuman Primates

Rickettsia raoultii sp. nov., a spotted fever group rickettsia associated with Dermacentor ticks in Europe and Russia