Potential of ancestral sylvatic dengue-2 viruses to re-emerge

Dengue viruses (DENV) are the most important arboviral pathogens in tropical and subtropical regions throughout the world. DENV transmission includes both a sylvatic, enzootic cycle between nonhuman primates and arboreal mosquitoes of the genus Aedes, and an urban, endemic/epidemic cycle between Aedes aegypti, a mosquito with larval development in peridomestic water containers, and human reservoir hosts. All 4 serotypes of endemic DENV evolved independently from ancestral sylvatic viruses and have become both ecologically and evolutionarily distinct; this process may have involved adaptation to (i) peridomestic mosquito vectors and/or (ii) human reservoir hosts. To test the latter hypothesis, we assessed the ability of sylvatic and endemic DENV-2 strains, representing major genotypes from Southeast Asia, West Africa and the Americas, to replicate in two surrogate human model hosts: monocyte-derived, human dendritic cells (moDCs), and mice engrafted with human hepatoma cells. Although the various DENV-2 strains showed significant inter-strain variation in mean replication titers in both models, no overall difference between sylvatic and endemic strains was detected in either model. Our findings suggest that emergence of endemic DENV strains from ancestral sylvatic strains may not have required adaptation to replicate more efficiently in human reservoir hosts, implying that the potential for re-emergence of sylvatic dengue strains into the endemic cycle is high. The shared replication profiles of the American endemic and sylvatic strains suggest that American strains have maintained or regained the ancestral phenotype.     

Genetic and phenotypic characterization of sylvatic dengue virus type 2 strains

The four serotypes of endemic dengue viruses (DENV) circulate between humans and peridomestic Aedes mosquitoes. At present endemic DENV infect 100 million people per year, and a third of the global population is at risk. In contrast, sylvatic DENV strains are maintained in a transmission cycle between nonhuman primates and sylvatic Aedes species, and are evolutionarily and ecologically distinct from endemic DENV strains. Phylogenetic analyses place sylvatic strains basal to each of the endemic serotypes, supporting the hypothesis that each of the endemic DENV serotypes emerged independently from sylvatic ancestors. We utilized complete genome analyses of both sylvatic and endemic DENV serotype 2 (DENV-2) to expand our understanding of their genetic relationships. A high degree of conservation was observed in both the 5'- and 3'-untranslated genome regions, whereas considerable differences at the nucleotide and amino acid levels were observed within the open reading frame. Additionally, replication of the two genotypes was compared in cultured cells, where endemic DENV strains produced a significantly higher output of progeny in human liver cells, but not in monkey kidney or mosquito cells. Understanding the genetic relationships and phenotypic differences between endemic and sylvatic DENV genotypes may provide valuable insight into DENV emergence and guide monitoring of future outbreaks.     

Genetic diversity of rabies virus in different host species and geographic regions of Zambia and Zimbabwe

Virus Genes - Rabies is endemic in Zambia and Zimbabwe. The previously investigated strains of rabies virus in central Zambia belong to the Africa 1b lineage, with similar circulating virus strains...     

Longitudinal study of the molecular epidemiology of methicillin-resistant Staphylococcus aureus at a university hospital

Surveillance for methicillin-resistant Staphylococcus aureus (MRSA) at the University Hospital of Heidelberg revealed an increase in the numbers of newly detected MRSA isolates in recent years. We conducted a study to assess the dynamics of the changes in the MRSA population. Pulsed-field gel electrophoresis (PFGE) typing of MRSA isolates from all patients at the University Hospital of Heidelberg collected between 1993 and 2004 was performed. The microbiology database contained 1,807 entries for newly detected MRSA isolates from 1,301 patients. A total of 1,252 isolates were available for PFGE typing. The isolates could be classified into 109 different PFGE types. Most PFGE types (n=70) were detected less than five times and showed no evidence of transmission (sporadic strains). They accounted for 8.7% of all isolates, with few variations in frequency over the time. Thirty-seven PFGE types were clustered by time of detection, and transmission of the strains was likely (local epidemic strains). A total of 37.3% of the isolates belonged to this group of strains. The remaining 54.0% of the isolates belonged to only two further PFGE types (endemic strains). One endemic strain accounted for 5.0% of all isolates in 1994 and 68.2% in 2004. A second endemic strain was detected in 1.1% of all isolates in 1998 but in 12.4% in 2004. Statistical analysis of the associations between the kind of strain (sporadic, local epidemic, or endemic) and the patients' characteristics revealed a significant association for age and mode of acquisition. The remarkable increase in the rate of MRSA detection at the University Hospital of Heidelberg is mainly due to the dissemination of two different strains. Infection control measures seemed sufficient to prevent further transmission of some but not all of the strains.     

Persistent strains of coagulase-negative staphylococci in a neonatal intensive care unit: virulence factors and invasiveness

Coagulase-negative staphylococci (CoNS) are the major cause of nosocomial bacteraemia in neonates. The aim of this study was to investigate whether persistent strains of CoNS possess specific bacterial characteristics as compared with sporadic non-cluster isolates. In total, 180 blood culture isolates (95 contaminants and 85 invasive isolates) obtained from a single neonatal unit over a 12-year period were studied. Pulsed-field gel electrophoresis (PFGE) identified 87 persistent CoNS strains (endemic clones). The two largest PFGE clusters belonged to a single clonal complex according to multilocus sequence typing. Patients colonised or infected with endemic clones were of lower gestational age than those infected with non-cluster strains. One Staphylococcus haemolyticus cluster appeared to selectively colonise and infect the most extreme pre-term infants. Endemic clones were characterised by high levels of antibiotic resistance and biofilm formation. All 51 isolates belonging to the two largest PFGE clusters were ica operon-positive. Genes encoding Staphylococcus epidermidis surface protein B and the production of phenol-soluble modulins (PSMs) were also more prevalent among endemic clones than among non-cluster strains. However, endemic clones were not more prevalent among invasive isolates than among contaminants. These findings indicate that multiple selective factors, including antibiotic resistance, biofilm formation, surface proteins with adhesive properties, and PSMs regulated by agr, increase the ability of CoNS to persist in a hospital environment. It may be more prudent, when searching for new therapeutic targets, to focus on ubiquitous components of CoNS instead of putative virulence factors that do not clearly contribute to increased invasive capacity.     

Monitoring progress toward measles elimination by genetic diversity analysis of measles viruses in China 2009–2010

With the achievement of high coverage for routine immunization and supplementary immunization activities (SIAs), measles incidence in mainland China reached its lowest level in 2010. The proportion of measles cases in the vaccination-targeted population decreased during 2007–2010 after the SIAs. More than 60% of measles cases were in adults or infants, especially in the coastal and eastern provinces during 2009 and 2010. A total 567 isolates of measles virus were obtained from clinical specimens from 27 of 31 provinces in mainland China during 2009 and 2010. Except for two vaccine-associated cases, one genotype D4 strain, two genotype D9 strains, and four genotype D11 strains, the other 558 strains were genotype H1 cluster H1a. Genotype H1 has been the only endemic genotype detected in China since surveillance began in 1993. Only genotype H1 was found in mainland China during 1993–2008, except for one detection of genotype H2. More recently, multiple genotypes of imported measles were detected even with the background of endemic genetotype H1 viruses. Analysis of the 450-nucleotide sequencing window of the measles virus N gene showed that the overall genetic diversity of the recent geneotype H1 strains decreased between 2008 and 2010. The lower genetic diversity of H1 strains suggested that enhanced vaccination may have reduced the co-circulating lineages of endemic genotype H1 strains in mainland China.     

Molecular epidemiology of measles virus in Kenya

Measles causes significant morbidity and mortality globally. Many countries have embarked on immunization programs to control and prevent measles outbreaks and eventually to eliminate endemic measles. Kenya is currently in the outbreak control and prevention stage for measles. Measles virus genotyping is important for molecular epidemiological purposes, including the documentation of the elimination of endemic measles virus strains from a country, and mapping of transmission pathways. In this study, we collected clinical specimens from measles outbreak cases in 2002 in Kenya for measles virus genotyping. We were able to isolate and/or detect measles virus in 10 cases from 5 of the 8 provinces in Kenya. All these Kenyan measles strains were determined to be genotype D4 strains when compared to the standard World Health Organization-designated measles virus reference strains. Interestingly, the Kenyan D4 strains clustered into two distinct D4 subgroups. In addition, the inclusion of other published D4 measles strains in this analysis indicated that there are four distinct D4 clusterings, or subgroups: Montreal-like, India-like, Johannesburg-like, and Ethiopia-like. This is the first measles molecular epidemiology study in Kenya and establishes the current endemic measles strain as genotype D4. Importantly, this study shows that the Kenyan D4 strains are distinct from the B3 measles strain found in West Africa and the D4 strains reported in Ethiopia.     

Genetic diversity of the Junin virus in Argentina: geographic and temporal patterns

RNA was purified from 39 strains of cell-cultured Junin virus (JUN) from central Argentina, which included both human- and rodent-derived isolates (a total of 26 and 13, respectively), as well as from 2 laboratory JUN strains, XJ Cl3 and XJ #44. JUN-specific primers were used to amplify a 511-nucleotide (nt) fragment of the nucleocapsid protein gene and a 495-nt fragment of the glycoprotein 1 (GP1) gene. Genetic diversity among JUN strains studied was up to 13% at the nt level and up to 9% at the amino acid (aa) level for the GP1 gene and up to 9% (nt) and 4% (aa) for the NP gene. Phylogenetic analyses of both genes revealed three distinct clades. The first clade was composed of the JUN strains from the center of the endemic area and included the majority of JUN strains analyzed in the current study. The second clade contained 4 JUN strains isolated between 1963 and 1971 from Cordoba Province, the western-most edge of the known endemic area. The third clade contained 4 JUN strains that originated from Calomys musculinus trapped in Zarate, the northeastern edge of the known endemic area. Certain JUN sequences, which were obtained from GenBank and identified as XJ, XJ #44, and Candid #1 strains, appeared to form a separate clade. Over 400 nt of the GP1 and GP2 genes were additionally sequenced for 7 JUN strains derived from patients with different clinical presentations and outcomes of Argentine hemorrhagic fever. Analysis of the corresponding aa sequences did not allow us to attribute any particular genetic marker to the changing severity or clinical form of the human disease.     

Newly isolated strains of Rickettsia tsutsugamushi in Japan identified by using monoclonal antibodies to Karp, Gilliam, and Kato strains.

Four isolated strains of Rickettsia tsutsugamushi from patients in a new endemic area of Japan were tested for antigenicities by using 12 monoclonal antibodies to Karp, Gilliam, and Kato strains. It was suggested that one isolate was Karp related and that the others were two independent strains.     

Genetic analysis of Asian measles virus strains--new endemic genotype in Nepal

In many parts of Asia measles virus (MV) continues to be endemic. However, little is known about the genetic characteristics of viruses circulating on this continent. This study reports the molecular epidemiological analysis based on the entire nucleocapsid (N) and hemagglutinin (H) genes of the first isolates from Nepal and Taiwan, as well as of recent MV strains from India, Indonesia, and China. Four isolates collected in various regions in Nepal during 1999 belonged to a new genotype, tentatively called D8. Another Nepalese isolate and one from India belonged to genotype D4. The diversity of the Nepalese strains indicated that measles continues to be endemic in this country. The isolate from Taiwan grouped with D3 viruses and one Chinese strain isolated in The Netherlands was assigned to the previously described clade H, known to be endemic in Mainland China. Molecular characterization emerges as an important tool for monitoring virus endemicity and vaccination efforts.     

Molecular surveillance of candidemia due to Candida albicans among cancer patients during 2009 to 2013 by microsatellite typing

BackgroundSince the high morbidity and mortality of candidemia among cancer patients, the epidemiology has been underlined. In recent years, Candida species genotyping has been established, which could provide detail characteristics of epidemiology and has been underscored for candidemia preventing strategies.MethodsData of cancer patients with candidemia and hospitalized in Tianjin Medical University Cancer Institute and Hospital (TMUCIH) during 2009–2013 were reviewed. Species identification was carried out by using VITEK-2 Compact. Microsatellite typing was performed for molecular analysis. SPSS 20.0 and MVSP 3.22 software were used for statistical and clustering analysis, respectively.ResultsTotal of 36 isolates of Candida albicans were recovered from 36 cancer patients with nosocomial candidemia in TMUCIH during the period of 2009–2013 included in the study. Total of 17 genotypes were identified and 2 of them were endemic genotypes, which caused 21 (58.3%) of 36 episodes of candidemia. Hepatobiliary oncology, ICU and gastrointestinal oncology were the main wards of infections due to endemic strains. Gastrointestinal cancer and insertion of a nasogastric tube were the predictors of infections caused by endemic strains (p = 0.014 and p = 0.041, respectively). For the 36 cases, crude mortality was up to 30.6%, and there was no significant difference between infections due to endemic and non-endemic strains (p = 0.077).ConclusionsThis study proved that endemic stains of C. albicans could exist for a long period and mainly in a few wards. Patients with gastrointestinal cancer or nasogastric tube insertion were more sensitive to endemic C. albicans.     

Enterotoxigenic Escherichia coli and temperate areas childhood diarrheas (author's transl)

We test for CFA and LT toxin 159 E. coli strains issued from endemic diarrheas in hospitalized children. Three strains belong to the CFA1 group but only one is LT toxin producing. This last one is isolated in feces of a child coming from topical areas.     

Use of variations in staphylococcal interspersed repeat units for molecular typing of methicillin-resistant Staphylococcus aureus strains

Staphylococcal interspersed repeat unit typing has previously been shown to have the ability to discriminate between epidemic methicillin-resistant Staphylococcus aureus strains in the United Kingdom. The current study illustrates its ability to distinguish between strains within an endemic setting thereby providing a rapid transportable typing method for the identification of transmission events.     

Dissemination of multisusceptible methicillin-resistant Staphylococcus aureus in Singapore

Analysis of hospital-acquired methicillin-resistant Staphylococcus aureus strains isolated from a tertiary public hospital in Singapore revealed that multisusceptible strains had gradually started to replace the endemic multiresistant strain (ST239-MRSA-III) since 2002. Molecular typing showed that this was a predominantly clonal outbreak of a UK-EMRSA-15 strain (ST22-MRSA-IV).     

Large-scale DNA fingerprinting of Mycobacterium tuberculosis strains as a tool for epidemiological studies of tuberculosis.

We conducted a large-scale DNA fingerprinting analysis of Mycobacterium tuberculosis strains in a country in which tuberculosis is endemic (Tunisia) in order to evaluate the importance of microepidemics in the maintenance of the disease within the population. The genetic polymorphisms of 201 strains of M. tuberculosis isolated from 196 unrelated patients living in four districts of northern Tunisia during a 3-year period were studied by restriction fragment length polymorphism (RFLP) analysis by using the insertion sequence IS6110 as a probe. Seventy-three strains isolated from 68 patients living in the districts of Tunis, Nabeul, and Jendouba generated 67 different RFLPs, indicating a high degree of polymorphism of the M. tuberculosis strains within these areas. In contrast, the 128 strains isolated from individuals in the district of Menzel Bourguiba appeared much less heterogeneous since they often generated identical or very similar fingerprints. Seventeen of 29 cases (58%) of active tuberculosis in the city of Menzel Bourguiba could be traced to as few as four M. tuberculosis strains. These results indicate the persistence of underestimated microepidemics in this region. The RFLP typing of a large number of randomly collected strains provides a general picture of the strains involved in tuberculosis. The systematic study of limited areas where tuberculosis is endemic can provide evidence for the existence of persisting epidemics. This stresses the different problems which remain to be solved in order to improve the control of tuberculosis.     

Auxotypes, plasmid content and serovars of 3 strains of Neisseria gonorrhoeae isolated in Bordeaux in 1955

Penicillinase-producing gonococci are isolated with increasing frequency. Epidemiologic markers, auxotypes, serovars, plasmids have been studied for three strains isolated in Bordeaux, responsible for therapeutic failure. For two of them, the source of contamination could be identified as endemic countries.     

Surveillance of Plasmodium falciparum drug sensitivity in Yaounde and its surroundings (Cameroon). In vivo and in vitro study

Among 172 strains collected in Yaoundé 60% are chloroquine-resistant, 37% are amodiaquine-resistant, instead of quinine and mefloquine which are completely efficient. Among 30 strains collected at a rural health center (where self treatment decreases), 27% are chloroquine-resistant. New therapeutic schemes for first and second line treatment in endemic areas must be evaluated.     

Detection of hepatitis A virus genotype IB variants in clams from Maputo Bay, Mozambique

Clams provide an important source of food and income for the population of Maputo, Mozambique, where conditions of poor water supply and inadequate sanitation favor endemic infection with hepatitis A virus (HAV). To determine the role of bivalves in an endemic area, clams gathered from Maputo Bay were bought from market and examined for HAV. Four batches, total 150 clams, were sampled over the year. RNA extracted from individual digestive glands was assayed by nested RT-PCR and sequencing of HAV 5' noncoding region (5' NCR). Specific HAV signals were detected in one batch, 23 of 34 clams (67%) testing positive. Phylogenetic analyses of VP3/VP1, VP1/P2A, and 5' NCR determined clustering of clam strains as genotype I, subtype B. In addition to identifying HAV IB strains with predicted conserved amino acid sequence, IB variants exhibiting novel amino acid substitutions at the VP1/P2A junction were detected. HAV strains from clams showed 93%-99% homology with wild-type IB strains from South African outbreaks and from a panel of HAV IgM positive Swedish patients. DNA from enteric human adenovirus 40/41 was found in a limited number of clams from two batches, 6/34 (17%) and 4/35 (11%). Detection of HAV subgenotype IB in bivalves provided indirect evidence of the strains circulating in a densely populated coastal region where HAV is presumed to be hyperendemic. The results suggest that clams may be an important source of HAV in Maputo region, and indicate the need for further molecular study of strains circulating in the indigenous population.     

Analysis of Salmonella typhi isolates from Southeast Asia by pulsed-field gel electrophoresis.

Pulsed-field gel electrophoresis (PFGE) revealed that multiple genetic variants of Salmonella typhi are simultaneously present in Southeast Asia and are associated with sporadic cases of typhoid fever and occasional outbreaks. Comparative analysis of PFGE patterns also suggested that considerable genetic diversity exists among S. typhi strains and that some PFGE patterns are shared between isolates obtained from Malaysia, Indonesia, and Thailand, implying movement of these strains within these regions of Southeast Asia, where they are endemic.     

Methicillin-resistant Staphylococcal aureus evolution in Australia over 35 years

Australia has a long association methicillin-resistant Staphylococcus aureus (MRSA). Its unique geographic and demographic features have led to the emergence and spread of three types of MRSA over 35 years. Classical multiresistant hospital-acquired MRSA were first noted in Australia in 1965. By the end of the 1970s, strains of this type of MRSA were well established in the complex tertiary care hospitals in the capital cities on the eastern seaboard of mainland Australia. Characterized by resistance to beta-lactams, erythromycin, tetracycline, gentamicin, and trimethoprim-sulfamethoxazole, these strains have persisted and diversified genetically and have acquired a variety of new resistances. They have proven pathogenicity and are a prominent cause of hospital infection in the endemic institutions. More recently they have become endemic in some central state tertiary care hospitals. Community-acquired strains of MRSA first appeared in the north of Western Australia in the mid-1980s. Strains have subsequently appeared in the south of the state and in the two adjacent central states, and are more frequently isolated from Aboriginal patients. Although harboring few or no additional resistances apart from resistance to beta-lactams initially, these strains are also accumulating additional resistances. A different variety of community-acquired MRSA has recently been noted in eastern Australia. It has a similar antibiogram to the western strains, but an entirely different epidemiology, resembling that currently being experienced in parts of New Zealand, and associated with patients of south Pacific island origin.