Rapid Leptospira identification by direct sequencing of the diagnostic PCR products in New Caledonia

<p>Abstract</p> <p>Background</p> <p>Most of the current knowledge of leptospirosis epidemiology originates from serological results obtained with the reference Microscopic Agglutination Test (MAT). However, inconsistencies and weaknesses of this diagnostic technique are evident. A growing use of PCR has improved the early diagnosis of leptospirosis but a drawback is that it cannot provide information on the infecting <it>Leptospira </it>strain which provides important epidemiologic data. Our work is aimed at evaluating if the sequence polymorphism of diagnostic PCR products could be used to identify the infecting <it>Leptospira </it>strains in the New Caledonian environment.</p> <p>Results</p> <p>Both the <it>lfb1 </it>and <it>secY </it>diagnostic PCR products displayed a sequence polymorphism that could prove useful in presumptively identifying the infecting leptospire. Using both this polymorphism and MLST results with New Caledonian isolates and clinical samples, we confirmed the epidemiological relevance of the sequence-based identification of <it>Leptospira </it>strains. Additionally, we identified one cluster of <it>L. interrogans </it>that contained no reference strain and one cluster of <it>L. borgpetersenii </it>found only in the introduced Rusa deer <it>Cervus timorensis russa </it>that is its probable reservoir.</p> <p>Conclusions</p> <p>The sequence polymorphism of diagnostic PCR products proved useful in presumptively identifying the infecting <it>Leptospira </it>strains. This could contribute to a better understanding of leptospirosis epidemiology by providing epidemiological information that cannot be directly attained from the use of PCR as an early diagnostic test for leptospirosis.</p

A systematic review of human and animal leptospirosis in the Pacific Islands reveals pathogen and reservoir diversity

Background The Pacific Islands have environmental conditions highly favourable for transmission of leptospirosis, a neglected zoonosis with highest incidence in the tropics, and Oceania in particular. Recent reports confirm the emergence and outbreaks of leptospirosis in the Pacific Islands, but the epidemiology and drivers of transmission of human and animal leptospirosis are poorly documented, especially in the more isolated and less developed islands. Methodology/Principal findings We conducted a systematic review of human and animal leptospirosis within 25 Pacific Islands (Pls) in Polynesia, Melanesia, Micronesia, as well as Easter Island and Hawaii. We performed a literature search using four international databases for articles published between January 1947 and June 2017. We further included grey literature available on the internet. We identified 148 studies describing leptospirosis epidemiology, but the number of studies varied significantly between Pls. No data were available from four Pls. Human leptospirosis has been reported from 13 Pls, with 63% of all studies conducted in Hawaii, French Polynesia and New Caledonia. Animal leptospirosis has been investigated in 19 Pls and from 14 host species, mainly pigs (18% of studies), cattle (16%) and dogs (11%). Only 13 studies provided information on both human and animal leptospirosis from the same location. Serology results were highly diverse in the region, both in humans and animals. Conclusions/Significance Our study suggests that, as in other tropical regions, leptospirosis is widespread in the Pls while showing some epidemiological heterogeneity. Data are scarce or absent from many Pls. Rodents, cattle, pigs and dogs are all likely to be important carriers, but the relative importance of each animal species in human infection needs to be clarified. Epidemiological surveys with appropriate sampling design, pathogen typing and data analysis are needed to improve our understanding of transmission patterns and to develop effective intervention strategies

Arbitrarily primed PCR to type Vibrio spp. pathogenic for shrimp.

International audienceA molecular typing study on Vibrio strains implicated in shrimp disease outbreaks in New Caledonia and Japan was conducted by using AP-PCR (arbitrarily primed PCR). It allowed rapid identification of isolates at the genospecies level and studies of infraspecific population structures of epidemiological interest. Clusters identified within the species Vibrio penaeicida were related to their area of origin, allowing discrimination between Japanese and New Caledonian isolates, as well as between those from two different bays in New Caledonia separated by only 50 km. Other subclusters of New Caledonian V. penaeicida isolates could be identified, but it was not possible to link those differences to accurate epidemiological features. This contribution of AP-PCR to the study of vibriosis in penaeid shrimps demonstrates its high discriminating power and the relevance of the epidemiological information provided. This approach would contribute to better knowledge of the ecology of Vibrio spp. and their implication in shrimp disease in aquaculture

Health challenges of the Pacific Region: insights from history, geography, social determinants, genetics, and the microbiome

The Pacific region, also referred to as Oceania, is a geographically widespread region populated by people of diverse cultures and ethnicities. Indigenous people in the region (Melanesians, Polynesians, Micronesians, Papuans, and Indigenous Australians) are over-represented on national, regional, and global scales for the burden of infectious and non-communicable diseases. Although social and environmental factors such as poverty, education, and access to health-care are assumed to be major drivers of this disease burden, there is also developing evidence that genetic and microbiotic factors should also be considered. To date, studies investigating genetic and/or microbiotic links with vulnerabilities to infectious and non-communicable diseases have mostly focused on populations in Europe, Asia, and USA, with uncertain associations for other populations such as indigenous communities in Oceania. Recent developments in personalized medicine have shown that identifying ethnicity-linked genetic vulnerabilities can be important for medical management. Although our understanding of the impacts of the gut microbiome on health is still in the early stages, it is likely that equivalent vulnerabilities will also be identified through the interaction between gut microbiome composition and function with pathogens and the host immune system. As rapid economic, dietary, and cultural changes occur throughout Oceania it becomes increasingly important that further research is conducted within indigenous populations to address the double burden of high rates of infectious diseases and rapidly rising non-communicable diseases so that comprehensive development goals can be planned. In this article, we review the current knowledge on the impact of nutrition, genetics, and the gut microbiome on infectious diseases in indigenous people of the Pacific region

Counting Oceanians of Non-European, Non-Asian Descent (ONENA) in the South Pacific to make them count in global health

Several diseases and vulnerabilities associated with genetic or microbial factors are more frequent among populations of Oceanian, Non-European, Non-Asian descent (ONENA). ONENA are specific and have long been isolated geographically. To our knowledge, there are no published official, quantitative, aggregated data on the populations impacted by these excess vulnerabilities in Oceania. We searched official census reports for updated estimates of the total population for each of the Pacific Island Countries and Territories (including Australia) and the US State of Hawaii, privileging local official statistical or censual sources. We multiplied the most recent total population estimate by the cumulative percentage of the ONENA population as determined in official reports. Including Australia and the US State of Hawaii, Oceania counts 27 countries and territories, populated in 2016 by approximately 41 M inhabitants (17 M not counting Australia) among which approximately 12.5 M (11.6 M not counting Australia) consider themselves of entire or partial ONENA ancestry. Specific genetic and microbiome traits of ONENA may be unique and need further investigation to adjust risk estimates, risk prevention, diagnostic and therapeutic strategies, to the benefit of populations in the Pacific and beyond

Correlation between antibiotic susceptibilities and genotypes in Neisseria gonorrhoeae from different geographical origins: determinants monitoring by real- time PCR as a complementary tool for surveillance

ABSTRACT Objective To determine in Neisseria gonorrhoeae (NG) isolates from different geographical areas whether monitoring of major determinants involved in chromosomal antimicrobial resistance correlated with phenotypes and could constitute complementary tools for surveillance. Methods Real-time multiplex PCR assays targeting penA, mtrR, penB, ponA, gyrA and parC determinants were applied to 169 NG extracts. Minimum inhibitory concentrations for penicillin and ciprofloxacin were determined by E tests, and b-lactamase production was analysed using nitrocefin discs

Differential Cytokine Gene Expression According to Outcome in a Hamster Model of Leptospirosis

Leptospirosis is a widespread bacterial infection that is transmitted by soil or water contaminated by the urine of infected animals, or directly from these animals. It has highly diverse clinical presentations, making its differential diagnosis difficult. Though most cases are minor and self-resolving, there are also severe forms that include a sepsis pattern and multiple organ failure, and have possible fatal outcomes. Predictors of disease evolution and outcome are scarce, yet they would be very valuable to clinicians as well as to better decipher disease pathogenesis. In this study, we used a hamster model of leptospirosis to evaluate if immune genes were differentially expressed between individuals and if their expression levels could help forecast the outcome of the disease. We found that hamsters that later died from leptospirosis had significantly higher expression levels of both pro- and anti-inflammatory mediators compared to survivors. These results suggest that expression levels of these immune effectors might be helpful predictors of outcome in leptospirosis and that septic shock contributes to fatal leptospirosis

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Epidémiologie et facteurs de virulence des bactéries du genre Vibrio responsables de mortalité de crevettes d'élevage en Nouvelle-Calédonie. Perspectives de lutte.

New Caledonia has a number of assets for marine shrimp culture. However, its rapid growth encountered a slowdown in 1993, due to the emergence of a seasonal pathology that was named Syndrome 93. Involving bacteria from the Vibrio genus, this disease affects juvenile shrimp during grow out. Strains of significant importance belong to the species Vibrio penaeicida and V. nigripulchritudo and are highly pathogenic to juvenile shrimp. A molecular typing study was conducted in order to clarify their epidemiology and to draw zoosanitary advice. A wide epidemiological survey of V. penaeicida (currently in progress) demonstrates the important impact of ecological events in the outbreak of the disease. Virulence of V. penaeicida was studied as a function of host developmental stage. Toxic factors were shown in bacterial culture supernatants. An hypothesis was drawn regarding the route of entry of these bacterial pathogens into their host. Plasmids harboured by these pathogenic strains are currently being studied with regards to virulence. Means of minimising the impact of Syndrome 93 in grow out ponds have been studied, and zoosanitary practices are discussed. Genetic selection for a disease-resistant shrimp strain seem to be a promising issue. Research outlooks include the study of bacterial ecology in shrimp environment, pathogeny of Syndrome 93 disease with regards to Vibrio virulence factors and the study of the host – pathogen relationship. These future studies could eventually beneficiate from the background knowledge on other Vibrio species.La Nouvelle-Calédonie présente de nombreux atouts pour la pénéiculture. Le ralentissement brutal de son développement en 1993 s'explique par l'émergence d'une pathologie saisonnière qui affecte les crevettes juvéniles en grossissement, mettant en cause des bactéries du genre Vibrio et qui a reçu le nom de Syndrome 93. Vibrio penaeicida et V. nigripulchritudo sont deux espèces au pouvoir pathogène particulièrement élevé qui affectent les élevages. Une étude de typage moléculaire a permis de préciser leur épidémiologie et de proposer quelques conseils d'ordre zoosanitaire. Un suivi épidémiologique par amplification génique est en cours pour V. penaeicida, qui montre l'importance des facteurs écologiques dans l'apparition des épisodes pathologiques. La pathogénicité de V. penaeicida a été étudiée en fonction du stade de développement de l'hôte, et des facteurs toxiques ont été mis en évidence dans les surnageants de culture. Une hypothèse a été émise sur la voie d'entrée du pathogène dans l'hôte. L'hypothèse d'un support plasmidique de la virulence a été émise et est actuellement étudiée. Des moyens de lutte ont été étudiés, des aspects de gestion zoosanitaires discutés. La sélection de lignées de crevettes à moindre sensibilité à l'infection apparaît comme une piste prometteuse. Des perspectives de recherches sont proposées, notamment l'étude de l'écologie de ces Vibrio pathogènes dans l'environnement d'élevage, de la pathogénie des vibrioses engendrées en terme de facteurs de virulence, des relations hôte – pathogène. Ces travaux pourront s'appuyer sur les nombreuses connaissances acquises depuis plusieurs années pour d'autres espèces du genre Vibrio