Complete Genome Sequences of Low-Passage Virulent and High-Passage Avirulent Variants of Pathogenic Leptospira interrogans Serovar Manilae Strain UP-MMC-NIID, Originally Isolated from a Patient with Severe Leptospirosis, Determined Using PacBio Single-Molecule Real-Time Technology

Satou, Kazuhito; Shimoji, Makiko; Tamotsu, Hinako; Juan, Ayaka; Ashimine, Noriko; Shinzato, Misuzu; Toma, Claudia; Nohara, Tomohide; Shiroma, Akino; Nakano, Kazuma; Teruya, Kuniko; Terabayashi, Yasunobu; Ohki, Shun; Koizumi, Nobuo; Okano, Sho; Suzuki, Toshihiko; Hirano, Takashi

doi:10.1128/genomea.00882-15

Cited by 26 publications

(27 citation statements)

References 14 publications

(15 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Analyses can be performed using IPD ratios of cases versus controls or vs an in silico control compared to known epigenetics signatures for 6-mA, 4-mC and (Tet converted) 5-mC (available in SMRT analysis). This has been used to discriminate virulent from avirulent Leptospira interrogans, a cause of leptospirosis in humans ( 90 ). The genome sequences have no major differences between strains, but higher levels of methylation are found in the avirulent strain ( 90 ).…”

Section: Viral and Microbial Medical Sequencingmentioning

confidence: 99%

“…This has been used to discriminate virulent from avirulent Leptospira interrogans, a cause of leptospirosis in humans ( 90 ). The genome sequences have no major differences between strains, but higher levels of methylation are found in the avirulent strain ( 90 ). Methylation analysis has also been used to identify virulence factor genotype-dependent motifs in eight different H. pylori strains, a bacteria that can lead to gastrointestinal diseases ( 91 ).…”

Section: Viral and Microbial Medical Sequencingmentioning

confidence: 99%

See 1 more Smart Citation

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Ardui

Ameur

Vermeesch

et al. 2018

Nucleic Acids Research

569

371

View full text Add to dashboard Cite

Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing.

show abstract

Section: Viral and Microbial Medical Sequencingmentioning

confidence: 99%

Section: Viral and Microbial Medical Sequencingmentioning

confidence: 99%

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Ardui

Ameur

Vermeesch

et al. 2018

Nucleic Acids Research

569

371

View full text Add to dashboard Cite

show abstract

“…Significantly up-and down-regulated ncRNAs upon 1h exposure to 1 mM H 2 O 2 with a Log 2 FC cutoff of 1.5. Gene numeration is according to to Satou et al(52). * ORFs significantly up-regulated by RNASeq analysis (Log 2 FC cutoff of 1).…”

mentioning

confidence: 99%

The adaptive transcriptional response of pathogenicLeptospirato peroxide reveals new defenses against infection-related oxidative stress

Zavala-Alvarado

Sismeiro

Legendre

et al. 2020

Preprint

View full text Add to dashboard Cite

Pathogenic Leptospira spp. are the causative agents of the waterborne zoonotic disease leptospirosis. During infection, Leptospira are confronted with dramatic adverse environmental changes such as deadly reactive oxygen species (ROS). Withstanding ROS produced by the host innate immunity is an important strategy evolved by pathogenic Leptospira for persisting in and colonizing hosts. In L. interrogans, genes encoding defenses against ROS are repressed by the peroxide stress regulator, PerR. In this study, RNA sequencing was performed to characterize both the L. interrogans adaptive response to low and high concentrations of hydrogen peroxide and the PerR regulon. We showed that Leptospira solicit three main peroxidase machineries (catalase, cytochrome C peroxidase and peroxiredoxin) and heme to detoxify oxidants produced during a peroxide stress. In addition, canonical molecular chaperones of the heat shock response and DNA repair proteins from the SOS response were required for Leptospira recovering from oxidative damages. Determining the PerR regulon allowed to identify the PerR-dependent mechanisms of the peroxide adaptive response and has revealed a PerR-independent regulatory network involving other transcriptional regulators, two-component systems and sigma factors as well as non-coding RNAs that putatively orchestrate, in concert with PerR, this adaptive response. In addition, we have identified other PerR-regulated genes encoding a TonB-dependent transport system, a lipoprotein (LipL48) and a two-component system (VicKR) involved in Leptospira tolerance to superoxide and that could represent the first defense mechanism against superoxide in L. interrogans, a bacterium lacking canonical superoxide dismutase. Our findings provide a comprehensive insight into the mechanisms required by pathogenic Leptospira to overcome infection-related oxidants during the arm race with a host. This will participate in framing future hypothesis-driven studies to identify and decipher novel virulence mechanisms in this life-threatening pathogen.Author summaryLeptospirosis is a zoonotic infectious disease responsible for over one million of severe cases and 60 000 fatalities annually worldwide. This neglected and emerging disease has a worldwide distribution, but it mostly affects populations from developing countries in sub-tropical areas. The causative agents of leptospirosis are pathogenic bacterial Leptospira spp. There is a considerable deficit in our knowledge of these atypical bacteria, including their virulence mechanisms. During infection, Leptospira are confronted with the deadly oxidants produced by the host tissues and immune response. Here, we have identified the cellular factors necessary for Leptospira to overcome the oxidative stress response. We found that Leptospira solicit peroxidases to detoxify oxidants as well as chaperones of the heat shock response and DNA repair proteins of the SOS response to recover from oxidative damage. Moreover, our study indicates that adaptation to oxidative stress is orchestrated by a regulatory network involving PerR and other transcriptional regulators, sigma factors, two component systems, and putative non-coding RNAs. These findings provide a comprehensive insight into the mechanisms required by pathogenic Leptospira to tolerate infection-related oxidants, helping identify novel virulence factors, developing new therapeutic targets and vaccines against leptospirosis.

show abstract

“…These findings could lead to the development of antimicrobials for leptospirosis targeting the pathogens’ adhesion and crawling motility and provides a significant step forward to confront other host-dependent bacterial infections. Meanwhile, microarray analyses have revealed that regulation of gene expression in Leptospira is affected by its interaction with host cells 27,28 . Although host immune responses against Leptospira infection remain mostly unknown, pathogenic leptospires interfere with the complement system through the degradation of complement proteins 29 and inhibition of coagulation via binding to thrombin 30 .…”

Section: Figmentioning

confidence: 99%

Insight into motility-dependent pathogenicity of the zoonotic spirocheteLeptospira

Koizumi

Nakamura

2020

Preprint

Self Cite

View full text Add to dashboard Cite

Bacterial pathogens can infect particular hosts or have a broad range of host species. 20 Mechanisms of host preferences involve complicated host-pathogen associations 21 such as bacterial adherence, gene regulation, and the host's immune responses 1 . 22 Here, we show the role of adhesivity and motility of the zoonotic spirochete 23 Leptospira in host-dependent pathogenicity. Leptospira spp. are classified into more 24 than 300 serovars and whereas infection of susceptible mammals can cause clinical 25 symptoms, it can also result in an asymptomatic colonization in some cases, thereby 26 generating maintenance hosts 2-5 . Although the severity of leptospirosis is generally 27 dependent on a combination of Leptospira serovars and host species, the scenarios 28 leading to such diverse consequences of infection remain unclear. To investigate the 29 underlying mechanisms of the different outcomes of Leptospira infection, we infected 30 kidney cells with various prepared pairs of Leptospira serovars and analyzed the 31 Leptospira dynamics on the host cells. Quantitatively monitoring the behavior of 32 individual Leptospira cells showed that adherence and movement on the host cell 33 surface, called "crawling" correlated with the severity of infection in the host. In the 34 2 most severe cases, a large fraction of leptospires attached to the host cells and 35 persistently traveled long distances using the crawling mechanism. The biophysical 36 implications of the kinetics and kinematic features of these bacterial pathogens were 37 found to be critical factors for disease severity in their hosts. 38 Some bacterial pathogens are specialized to invade a very limited array of hosts, 39 whereas others can infect multiple host species. The host range differs for each pathogen 40 and the clinical symptoms depend on each host-pathogen combination. For example, 41 Bacillus anthracis primarily infects livestock and wild herbivores, transmitting to humans via 42 direct or indirect contact with infected animals or animal products. However, its occurrence in 43 carnivores is rare. Salmonellosis is caused by over 2000 serovars of Salmonella enterica 44 and its transmission occurs from reptile reservoirs to a wide range of susceptible hosts 45 including humans and other mammals. Virulence in the case of plant bacterial pathogens 46 like Actinobacteria spp. and Pantoea spp. is host specific, and is believed to be related to the 47 structure of the root microbiome and other factors that optimize their symbiosis (e.g., plant 48 hormones, drought stress, temperature and salinity) 6,7 . In some cases, the mechanisms 49 correlating host dependency to bacterial pathogenicity have been investigated. A correlation 50 was found between the host range of the opportunistic food-poisoning bacterium Listeria 51 monocytogenes and its host binding affinity through the listerial protein internalin A, which 52 interacted with E-cadherin in intestinal epithelial cells thereby facilitating its invasion 8 . Here, 53 we show that the adhesivity and motil...

show abstract

Complete Genome Sequences of Low-Passage Virulent and High-Passage Avirulent Variants of Pathogenic Leptospira interrogans Serovar Manilae Strain UP-MMC-NIID, Originally Isolated from a Patient with Severe Leptospirosis, Determined Using PacBio Single-Molecule Real-Time Technology

Cited by 26 publications

References 14 publications

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

The adaptive transcriptional response of pathogenicLeptospirato peroxide reveals new defenses against infection-related oxidative stress

Insight into motility-dependent pathogenicity of the zoonotic spirocheteLeptospira

Contact Info

Product

Resources

About