A new outbreak of fox rabies at the Russian–Mongolian border

<正>Dear Editor,Lake Baikal and its neighboring territories are an intermediate zone for the"steppe"and"arctic-like"rabies virus lineages in Russia.After the elimination of dog-mediated rabies during the early 1980s,this area remained rabies-free for over 25–30 years.A sudden reappearance of rabies occurred in this zone in the Republic of Buryatia in 2011–2012.A marginal part of the Mongolian steppe penetrates the Siberian taiga forests in this area,and human and animal rabies have been repeatedly recorded in the Republic of Buryatia from the end of the     

Seasonal variation and an “outbreak” of frog predation by tamarins

We report temporal variation and an “outbreak” of frog predation by moustached tamarins, Saguinus mystax, in north-eastern Peruvian Amazonia. Frog predation rates were generally very low, but strongly increased in October 2015. Other high rates, identified by outlier analyses, were also observed in September–November of other years. Over all study years, predation rates in this 3-month period were significantly higher than those in the remainder of the year, suggesting a seasonal pattern of frog predation by tamarins. Reduced fruit availability or increased frog abundance or a combination of both may be responsible for both the seasonal pattern and the specific “outbreak” of frog predation.     

Do warmer growing seasons ameliorate the recovery of mountain birches after winter moth outbreak?

Subarctic mountain birch (Betula pubescens ssp. czerepanovii) forests in northern Fennoscandia have shown a slight recovery from recent severe defoliation by the winter moth (Operophtera brumata). This development in trees is hypothesized to be a result of ameliorated growing conditions through increased summer temperatures. We examined if accumulated thermal sum affects the ability of mountain birches to tolerate foliage losses. We quantified the number of leaf-bearing short shoots, the emergence of inflorescences and the seasonal height growth of long shoots in both intact and defoliated trees. We also determined the concentrations of carbon and nitrogen in leaves and carbohydrates in roots. Our results show that defoliation constrained the growth of long shoots, as well as the emergence of inflorescences regardless of thermal sum accumulation. However, the number of leaf-bearing short shoots did not differ between intact and defoliated trees. In the both tree groups, the amounts of emerging leaves increased as a response to thermal sum accumulation. Also the leaf carbon concentration increased in defoliated trees at higher thermal sums, whereas it decreased in intact controls. Generally, the mean carbohydrate concentrations were greater in roots of defoliated than intact trees. However, with increased thermal sums, root carbohydrates increased in intact trees but remained the same in defoliated trees. We conclude that thermal sum accumulation does not greatly promote the recovery of mountain birches. Although the damaged trees produced more leaves at warmer growing sites, this did not increase their height growth or carbohydrate gain in roots.     

Origin of an insect outbreak: escape in space or time from natural enemies?

Initiation of insect outbreaks is poorly understood, and may involve sporadic events that temporarily release insect populations from predation or parasitism. While studying a declining outbreak of the western tussock moth (Orgyia vetusta) on bush lupine (Lupinus arboreus), we witnessed the onset of a new tussock moth outbreak, separated by 1,000 m in space and 2 months in phenological timing from the original population. This new population underwent explosive growth for 2 years and then collapsed because of a massive die-off of lupines. We tested whether during its growth phase, this new outbreak benefited by escaping in either space or time from the natural enemies attacking the original population. In experimental populations on single bushes, we compared predation and parasitism at the sites of the new and the old outbreak. At the site of the old outbreak, we compared predation and parasitism early and late in the season. Parasitism was significantly lower and population growth significantly higher at the new outbreak site than the old one. Neither seasonal timing, predator exclusion, nor their interaction significantly affected survival at either site. Thus the new outbreak appeared to escape in space from parasitism. These results corroborate our previous experimental findings, which suggest that as predicted by theory, the interaction between the tussock moth and its parasitoids can produce large-scale spatial patterning in population densities.     

Holly leaf‐miners on two continents: what makes an outbreak species?

1. Some herbivore species periodically undergo damaging, high‐density outbreak phases followed by less damaging low‐density phases. Others maintain steady, low to moderate density levels that do little damage to their hosts. 2. Two closely related holly leaf‐miner species were compared that share many ecological traits and have very similar life cycles, but only one of which exhibits outbreaks. Phytomyza ilicicola in the eastern U.S.A. varied widely in mortality and infestation levels, reaching local densities of over 10 mines per leaf. In contrast, Phytomyza ilicis in the U.K. showed low infestation and high mortality at all sites. Using data from the literature and from field studies, the factors responsible for these contrasting dynamics were sought. 3. Phytomyza ilicicola oviposits into the leaf lamina, and experiences weak larval competition only at high densities. Phytomyza ilicis oviposits into the leaf midrib, which leads to high mortality of young larvae before mine formation. Multiply mined leaves were therefore very common in P. ilicicola but rare in P. ilicis. 4. Differences in the parasitoid complexes of the two systems accounted for further differences in survival to adulthood. The main (larval) parasitoid, which was found to impose high, density‐dependent mortality on P. ilicis, is missing on P. ilicicola. It is replaced by an egg–pupal parasitoid, which varies in its impact at differe～t sites. Multiple emergence of adults from multiply mined leaves is therefore widespread in P. ilicicola but does not occur in P. ilicis. 5. The differences in oviposition behaviour and in the parasitoid complexes are likely to allow P. ilicicola to outbreak when habitat conditions are favourable, while P. ilicis is always tightly regulated.     

Clonality and α-a recombination in the Australian Cryptococcus gattii VGII population--an emerging outbreak in Australia

Background

Cryptococcus gattii is a basidiomycetous yeast that causes life-threatening disease in humans and animals. Within C. gattii, four molecular types are recognized (VGI to VGIV). The Australian VGII population has been in the spotlight since 2005, when it was suggested as the possible origin for the ongoing outbreak at Vancouver Island (British Columbia, Canada), with same-sex mating being suggested as the driving force behind the emergence of this outbreak, and is nowadays hypothesized as a widespread phenomenon in C. gattii. However, an in-depth characterization of the Australian VGII population is still lacking. The present work aimed to define the genetic variability within the Australian VGII population and determine processes shaping its population structure.

Methodology/Principal Findings

A total of 54 clinical, veterinary and environmental VGII isolates from different parts of the Australian continent were studied. To place the Australian population in a global context, 17 isolates from North America, Europe, Asia and South America were included. Genetic variability was assessed using the newly adopted international consensus multi-locus sequence typing (MLST) scheme, including seven genetic loci: CAP59, GPD1, LAC1, PLB1, SOD1, URA5 and IGS1. Despite the overall clonality observed, the presence of MAT a VGII isolates in Australia was demonstrated for the first time in association with recombination in MATα-MAT a populations. Our results also support the hypothesis of a “smouldering” outbreak throughout the Australian continent, involving a limited number of VGII genotypes, which is possibly caused by a founder effect followed by a clonal expansion.

Conclusions/Significance

The detection of sexual recombination in MATα-MAT a population in Australia is in accordance with the natural life cycle of C. gattii involving opposite mating types and presents an alternative to the same-sex mating strategy suggested elsewhere. The potential for an Australian wide outbreak highlights the crucial issue to develop active surveillance procedures.     

Type Ⅰ interferon receptor knockout mice as models for infection of highly pathogenic viruses with outbreak potential

Due to their inability to generate a complete immune response, mice knockout for type Ⅰ interferon(IFN) receptors(Ifnar~(–/–)) are more susceptible to viral infections, and are thus commonly used for pathogenesis studies. This mouse model has been used to study many diseases caused by highly pathogenic viruses from many families, including the Flaviviridae, Filoviridae, Arenaviridae, Bunyaviridae, Henipaviridae, and Togaviridae. In this review, we summarize the findings from these animal studies, and discuss the pros and cons of using this model versus other known methods for studying pathogenesis in animals.     

Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires’ disease outbreak

Background

Legionnaires’ disease is a severe form of pneumonia caused by the environmental bacterium Legionella pneumophila. Outbreaks commonly affect people with known risk factors, but the genetic and pathogenic complexity of L. pneumophila within an outbreak is not well understood. Here, we investigate the etiology of the major Legionnaires’ disease outbreak that occurred in Edinburgh, UK, in 2012, by examining the evolutionary history, genome content, and virulence of L. pneumophila clinical isolates.

Results

Our high resolution genomic approach reveals that the outbreak was caused by multiple genetic subtypes of L. pneumophila, the majority of which had diversified from a single progenitor through mutation, recombination, and horizontal gene transfer within an environmental reservoir prior to release. In addition, we discover that some patients were infected with multiple L. pneumophila subtypes, a finding which can affect the certainty of source attribution. Importantly, variation in the complement of type IV secretion systems encoded by different genetic subtypes correlates with virulence in a Galleria mellonella model of infection, revealing variation in pathogenic potential among the outbreak source population of L. pneumophila.

Conclusions

Taken together, our study indicates previously cryptic levels of pathogen heterogeneity within a Legionnaires’ disease outbreak, a discovery that impacts on source attribution for future outbreak investigations. Furthermore, our data suggest that in addition to host immune status, pathogen diversity may be an important influence on the clinical outcome of individual outbreak infections.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0504-1) contains supplementary material, which is available to authorized users.     

Detection,isolation, and characterization of chikungunya viruses associated with the Pakistan outbreak of 2016–2017

The chikungunya virus(CHIKV) is a mosquito-transmitted alphavirus, which has infected millions of people in Africa, Asia, Americas, and Europe since it reemerged in India and Indian Ocean regions in 2005–2006. Starting in the middle of November 2016, CHIKV has been widely spread, and more than 4,000 cases of infections in humans were confirmed in Pakistan. Here, we report the first isolation and characterization of CHIKV from the Pakistan outbreak. Eight CHIKV strains were newly isolated from human serum samples using a cell culture procedure. A full-length genome sequence and eight complete envelope(E1) sequences of CHIKV from Pakistan were obtained in this study. Alignment of the CHIKV E1 sequences revealed that the eight new CHIKV isolates were highly homogeneous, with only two nonsynonymous substitutions found at generally conserved sites(E99 and Q235). Based on the comparison of 342 E1 sequences, the two nonsynonymous mutations were located in well-recognized domains associated with viral functions such as the cell fusion and vector specificity, suggesting their potential functional importance. Phylogenetic analysis indicated that the CHIKV strains from Pakistan originated from CHIKV circulating in the Indian region. This study helps elucidate the epidemics of CHIKV in Pakistan and also provides a foundation for studies of evolution and expansion of CHIKV in South Asia.     

National outbreak of Salmonella serotype saintpaul infections: importance of Texas restaurant investigations in implicating jalapeño peppers

Background

In May 2008, PulseNet detected a multistate outbreak of Salmonella enterica serotype Saintpaul infections. Initial investigations identified an epidemiologic association between illness and consumption of raw tomatoes, yet cases continued. In mid-June, we investigated two clusters of outbreak strain infections in Texas among patrons of Restaurant A and two establishments of Restaurant Chain B to determine the outbreak''s source.

Methodology/Principal Findings

We conducted independent case-control studies of Restaurant A and B patrons. Patients were matched to well controls by meal date. We conducted restaurant environmental investigations and traced the origin of implicated products. Forty-seven case-patients and 40 controls were enrolled in the Restaurant A study. Thirty case-patients and 31 controls were enrolled in the Restaurant Chain B study. In both studies, illness was independently associated with only one menu item, fresh salsa (Restaurant A: matched odds ratio [mOR], 37; 95% confidence interval [CI], 7.2–386; Restaurant B: mOR, 13; 95% CI 1.3–infinity). The only ingredient in common between the two salsas was raw jalapeño peppers. Cultures of jalapeño peppers collected from an importer that supplied Restaurant Chain B and serrano peppers and irrigation water from a Mexican farm that supplied that importer with jalapeño and serrano peppers grew the outbreak strain.

Conclusions/Significance

Jalapeño peppers, contaminated before arrival at the restaurants and served in uncooked fresh salsas, were the source of these infections. Our investigations, critical in understanding the broader multistate outbreak, exemplify an effective approach to investigating large foodborne outbreaks. Additional measures are needed to reduce produce contamination.     

Dynamics of an outbreak population of Acanthaster planci at Lizard Island, northern Great Barrier Reef (1995–1999)

Despite their significant influence on coral reef ecosystems, causes of population outbreaks of crown-of-thorns starfish (Acanthaster planci L.) are still poorly understood. Essentially, outbreaks of A. planci could arise from either (1) a single mass recruitment event or (2) the progressive accumulation of starfish from multiple cohorts. This study explored fine-scale variation in the size, distribution, and abundance of A. planci, during an outbreak at Lizard Island in the northern Great Barrier Reef, to assess the mechanism by which the outbreak occurred. Densities of A. planci around Lizard Island increased very gradually from October 1994 until December 1996, then remained at around 1.0 starfish per 200 m² until June 1998. The population of A. planci comprised individuals ranging in size from 11-cm to 62-cm diameter, representing individuals from multiple (at least four) different cohorts. These data suggest that the outbreak of A. planci at Lizard Island resulted from a prolonged build-up in starfish numbers through multiple successive recruitment events. This study shows that outbreaks of A. planci may arise independently of any sudden or substantial increase in rates of recruitment, such that any factor(s) responsible for the initial onset of outbreaks are likely to be very subtle and difficult to detect.     

Are elite track and field athletes on track? The impact of COVID-19 outbreak on sleep behavior and training characteristics

The Covid-19 outbreak forced many governments to enter a nationwide lockdown. The aim of this study was to evaluate, by means of a survey, changes in sleep parameters and physical activity characteristics of elite track and field athletes in three periods: before the lockdown (T0), during the lockdown (09th March – 03rd May 2020, T1) and the first month after the lockdown (T2). This study was conducted from May 2020 to June 2020 and data were collected using an offline survey with 89 elite track and field athletes (mean age: 24.7 ± 5.4; n = 43 males; n = 46 females). The survey consisted of demographic data and questions on physical activity and sleep behavior at T0, T1 and T2. Athletes reported lower sleep quality scores at T1 compared to T0 and T2 (p < 0.0001) and registered delayed bedtime, wake-up time and longer sleep latency during the lockdown compared to pre-lockdown and post-lockdown whereas no changes in total sleep time were reported. No inter-group differences were detected in sleep characteristics between short- and long-term disciplines and between genders. The weekly training volume decreased from 16.1 ± 5.7 hours at T0 to 10.7 ± 5.7 hours at T1 (p < 0.0001) whereas no significant differences were detected in training volume during the lockdown in relation to the square footage of the house (p = 0.309). Alcohol (p = 0.136) and caffeine intake (p = 0.990) and use of electronic devices (p = 0.317) were similar pre-, during, and post-lockdown. The unprecedented circumstances of the Covid-19 pandemic had negative impacts on the Italian track and field athletes’ sleep and training volumes.     

Changes in coral assemblages during an outbreak of Acanthaster planci at Lizard Island, northern Great Barrier Reef (1995–1999)

Population outbreaks of crown-of-thorns starfish (Acanthaster planci L.) represent one of the most significant biological disturbances on tropical coral reefs and have the potential to devastate coral communities, thereby altering the biological and physical structure of reef habitats. This study reports on changes in area cover, species diversity and taxonomic composition of corals during an outbreak of A. planci at Lizard Island, in the northern Great Barrier Reef, Australia. Mean coral cover declined by 28.8% across ten locations studied. However, densities of A. planci, and their effects on local coral assemblages, were very patchy. Declines in coral cover were mostly due to the selective removal of certain coral taxa (mainly Acropora and Pocilloporidae corals); such that the greatest coral loss occurred at locations with highest initial cover of preferred coral prey. Most notably, coral assemblages in back-reef locations were transformed from topographically complex staghorn Acropora-dominated habitats, to relatively depauperate assemblages dominated by alcyonacean soft corals. Although coral loss was greatest among formerly dominant taxa (especially Acropora), effects were sufficiently widespread across different coral taxa, such that overall coral diversity tended to decline. Clearly, moderate outbreaks of A. planci have the potential to greatly alter community structure of coral communities even if they do not devastate live corals. Recovery in this instance is expected to be very rapid given that all coral taxa persisted, and effects were greatest among fast growing corals.     

Growth rates in outbreak populations of the corallivorous gastropod Drupella cornus (Röding 1798) at Ningaloo Reef,Western Australia

Mark and recapture experiments were used to estimate the size-at-age relationship of the coral-eating gastropod Drupella cornus at Ningaloo Reef, Western Australia. Animals 15 mm long increased in length by 5.2 mm in six months at a site in an early stage of an outbreak, but by only 3.8 mm at a site within an established outbreak. Snails larger than 35 mm grew very little. Based on observed growth rates fitted to a Richards function growth equation, snails 28 mm long judged to be reproductively mature would be 2.5 to 3.5 years old, suggesting that local outbreaks represent no more than one or two generations of recruits. Indirect evidence indicates that growth is more rapid in the earlier than in later stages of outbreaking populations. The growth and timing of life-history transitions of D. cornus are not unusual among other muricid species.     

H5N2 avian influenza outbreak in Texas in 2004: the first highly pathogenic strain in the United States in 20 years?

In early 2004, an H5N2 avian influenza virus (AIV) that met the molecular criteria for classification as a highly pathogenic AIV was isolated from chickens in the state of Texas in the United States. However, clinical manifestations in the affected flock were consistent with avian influenza caused by a low-pathogenicity AIV and the representative virus (A/chicken/Texas/298313/04 [TX/04]) was not virulent for experimentally inoculated chickens. The hemagglutinin (HA) gene of the TX/04 isolate was similar in sequence to A/chicken/Texas/167280-4/02 (TX/02), a low-pathogenicity AIV isolate recovered from chickens in Texas in 2002. However, the TX/04 isolate had one additional basic amino acid at the HA cleavage site, which could be attributed to a single point mutation. The TX/04 isolate was similar in sequence to TX/02 isolate in several internal genes (NP, M, and NS), but some genes (PA, PB1, and PB2) had sequence of a clearly different origin. The TX/04 isolate also had a stalk deletion in the NA gene, characteristic of a chicken-adapted AIV. By analyzing viruses constructed by in vitro mutagenesis followed by reverse genetics, we found that the pathogenicity of the TX/04 virus could be increased in vitro and in vivo by the insertion of an additional basic amino acid at the HA cleavage site and not by the loss of a glycosylation site near the cleavage site. Our study provides the genetic and biologic characteristics of the TX/04 isolate, which highlight the complexity of the polygenic nature of the virulence of influenza viruses.     

Shifting altitudinal distribution of outbreak zones of winter moth Operophtera brumata in sub‐arctic birch forest: a response to recent climate warming?

Climatic change is expected to affect the extent and severity of geometrid moth outbreaks, a major disturbance factor in sub-arctic birch forests. Previous studies have reported that the two geometrid species involved, autumnal moth and winter moth, differ in their temperature requirements and, consequently, in their altitudinal and latitudinal distribution patterns. In this study, we document the altitudinal distribution of winter moth outbreaks in a large coastal area in northern Norway. We show that, in the present winter moth outbreak, defoliated birch stands were seen as distinct zones with a rather constant width in the uppermost part of the forest and where the upper limit coincided with the forest line. The outbreak zone closely followed the spatially variable forest line as an undulating belt, although some of the variation in outbreak zone width was also related to variation in topographical variables, such as distance from the coast, forest line altitude, and slope of the terrain. A distinct outbreak zone at the altitudinal forest line is the typical picture that has been depicted in more qualitative historical records on previous outbreaks of autumnal moth rather than winter moth. We suggest that the recent documented climate warming in this region may have induced a shift in distribution of the winter moth both relative to topography and geography. Further investigation is, however, required to substantiate these suspicions.     

Detection of natural infection with Mycobacterium intracellulare in healthy wild-caught Chacma baboons (Papio ursinus) by ESAT-6 and CFP-10 IFN-γ ELISPOT tests following a tuberculosis outbreak

Background

The current tuberculosis vaccine is a live vaccine derived from Mycobacterium bovis and attenuated by serial in vitro passaging. All vaccine substrains in use stem from one source, strain Bacille Calmette-Guérin. However, they differ in regions of genomic deletions, antigen expression levels, immunogenicity, and protective efficacy.

Results

As a RecA phenotype increases genetic stability and may contribute restricting the ongoing evolution of the various BCG substrains while maintaining their protective efficacy, we aimed to inactivate recA by allelic replacement in BCG vaccine strains representing different phylogenetic lineages (Pasteur, Frappier, Denmark, Russia). Homologous gene replacement was achieved successfully in three out of four strains. However, only illegitimate recombination was observed in BCG substrain Russia. Sequence analyses of recA revealed that a single nucleotide insertion in the 5' part of recA led to a translational frameshift with an early stop codon making BCG Russia a natural recA mutant. At the protein level BCG Russia failed to express RecA.

Conclusion

According to phylogenetic analyses BCG Russia is an ancient vaccine strain most closely related to the parental M. bovis. We hypothesize that recA inactivation in BCG Russia occurred early and is in part responsible for its high degree of genomic stability, resulting in a substrain that has less genetic alterations than other vaccine substrains with respect to M. bovis AF2122/97 wild-type.