Strains Worldwide Research Articles

Comparative clinical outcomes evaluation of hospitalized patients infected with Clostridioides difficile ribotype 106 vs. other toxigenic strains

The coronavirus diseases 2019 (COVID-19) caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 has caused more than 140 million infections worldwide by the end of April 2021. As an enveloped single-stranded positive-sense RNA virus, SARS-CoV-2 underwent constant evolution that produced novel variants carrying mutation conferring fitness advantages. The current prevalent D614G variant, with glycine substituted for aspartic acid at position 614 in the spike glycoprotein, is one of such variants that became the main circulating strain worldwide in a short period of time. Over the past year, intensive studies from all over the world had defined the epidemiological characteristics of this highly contagious variant and revealed the underlying mechanisms. This review aims at presenting an overall picture of the impacts of D614G mutation on virus transmission, elucidating the underlying mechanisms of D614G in virus pathogenicity, and providing insights into the development of effective therapeutics.

Pseudomonas syringae-secreted HopA1 effectors are important determinants in host range expansion and increased pathogenicity. Their recent acquisitions via horizontal gene transfer in several non-pathogenic Pseudomonas strains worldwide have caused alarming increase in their virulence capabilities. In Arabidopsis thaliana, RESISTANCE TO PSEUDOMONAS SYRINGAE 6 (RPS6) gene confers effector-triggered immunity (ETI) against HopA1pss derived from P. syringae pv. syringae strain 61. Surprisingly, a closely related HopA1pst from the tomato pathovar evades immune detection. These responsive differences in planta between the two HopA1s represents a unique system to study pathogen adaptation skills and host-jumps. However, molecular understanding of HopA1′s contribution to overall virulence remain undeciphered. Here, we show that immune-suppressive functions of HopA1pst are more potent than HopA1pss. In the resistance-compromised ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) null-mutant, transcriptomic changes associated with HopA1pss-elicited ETI are still induced and carry resemblance to PAMP-triggered immunity (PTI) signatures. Enrichment of HopA1pss interactome identifies proteins with regulatory roles in post-transcriptional and translational processes. With our demonstration here that both HopA1 suppress reporter-gene translations in vitro imply that the above effector-associations with plant target carry inhibitory consequences. Overall, with our results here we unravel possible virulence role(s) of HopA1 in suppressing PTI and provide newer insights into its detection in resistant plants.

Starmerella bacillaris (synonym Candida zemplinina) is a non-Saccharomyces yeast species, frequently found in enological ecosystems. Peculiar aspects of the genetics and metabolism of this yeast species, as well as potential industrial applications of isolated indigenous S. bacillaris strains worldwide, have recently been explored. In this review, we summarize relevant observations from studies conducted on standard laboratory and indigenous isolated S. bacillaris strains.

Marine ecosystems, biodiversity, and fisheries are under strain worldwide due to global changes including climate warming and demographic pressure. To address this issue, many scientists and stakeholders advocate the use of an ecosystem approach for fisheries that integrates the numerous ecological and economic complexities at play rather than focusing on the management of individual target species. However, the operationalization of such an ecosystem approach remains challenging, especially from a bio-economic standpoint. Here, to address this issue, we propose a model of intermediate complexity (MICE) relying on multi-species, multi-fleet, and resource-based dynamics. Climate change effects are incorporated through an envelope model for the biological growth of fish species as a function of sea surface temperature. The model is calibrated for the small-scale fishery in French Guiana using a time series of fish landings and fishing effort from 2006 to 2018. From the calibrated model, a predictive fishing effort projection and RCP climate scenarios derived from IPCC, we explore the ecosystem dynamics and the fishery production at the horizon 2100. Our results demonstrate the long-term detrimental impact of both climate change and ecological competition on fish biodiversity. The prognosis is particularly catastrophic under the most pessimistic climate scenario, with a potential collapse of both biomass targeted species and fishing activity by 2100.

A novel anti-infective molecule nesfactin identified from sponge associated bacteria Nesterenkonia sp. MSA31 against multidrug resistant Pseudomonas aeruginosa

Glaesserella parasuis strains were characterized by serotyping PCR, vtaA virulence marker Leader Sequence (LS)-PCR, clinical significance, and geographic region. Overall, the serovars 4, 5/12, 7, 1, and 13 were the most commonly detected. Serovars of greatest clinical relevance were systemic isolates that had a higher probability of being serovar 5/12, 13, or 7. In comparison, pulmonary isolates had a higher likelihood of being serovars 2, 4, 7, or 14. Serovars 5/12 and 13 have previously been considered disease-associated, but this study agrees with other recent studies showing that serovar 7 is indeed associated with systemic G. parasuis disease. Serovar 4 strains illustrated how isolates can have varying degrees of virulence and be obtained from pulmonary, systemic, or nasal sites. Serovars 8, 9, 15, and 10 were predominantly obtained from nasal samples, which indicates a limited clinical significance of these serovars. Additionally, most internal G. parasuis isolates were classified as virulent by LS-PCR and were disease-associated isolates, including serovars 1, 2, 4, 5/12, 7, 13, and 14. Isolates from the nasal cavity, including serovars 6, 9, 10, 11, and 15, were classified as non-virulent by LS-PCR. In conclusion, the distribution of G. parasuis serovars remains constant, with few serovars representing most of the strains isolated from affected pigs. Moreover, it was confirmed that the LS-PCR can be used for G. parasuis virulence prediction of field strains worldwide.

IntroductionWhile Campylobacter jejuni is a leading foodborne bacterial pathogen worldwide, it poses a particular risk to susceptible populations in low- and middle-income countries (LMICs). A capsule-conjugate vaccine approach has been proposed as a potential solution, but little information exists on circulating C. jejuni capsule types in LMICs. The capsule is the major serodeterminant of the Penner typing scheme, which is based on serum recognition of Campylobacter heat-stable antigens. We conducted a systematic review and meta-analysis to estimate the distribution of Penner serotypes associated with C. jejuni enteritis in LMICs. Vaccine coverage assessments for hypothetical regional and global C. jejuni vaccines were also estimated.MethodsA systematic review of the literature published from 1980 to 2019 was performed using PubMed, Scopus, and Web of Science databases. Articles were assessed for eligibility and data were abstracted. Pooled C. jejuni serotype prevalence in LMICs was estimated by region and globally using random-effects models.ResultsA total of 36 studies were included, capturing 4,434 isolates from LMICs. Fifteen serotypes were present in a sufficient number of studies to be included in analyses. Among these, HS4c was the most common serotype globally (12.6%), though leading capsule types varied among regions. HS2, HS3c, HS4c, HS5/31, HS8/17, and HS10 were all among the 10 most common region-specific serotypes.ConclusionsThe results of this review suggest that an octavalent vaccine could provide up to 66.9% coverage of typable strains worldwide, and 56.8–69.0% regionally. This review also highlights the paucity of available data on capsules in LMICs; more testing is needed to inform vaccine development efforts.

The coronavirus disease 2019 (COVID-19) pandemic has caused unprecedented system and clinician strain worldwide, disproportionately impacting resource poor settings. This project describes the use of a virtual nurse coaching session to improve the well-being of a nurse-led community-based palliative care team in Liberia, West Africa. Staff response was overwhelmingly positive. Discussion is underway to expand this educational coaching intervention to support additional teams confronting COVID-19 in both East and West Africa. Virtual nurse coaching is an innovative way to enhance staff well-being, improve global health partnerships and knowledge exchange, and foster communication across all levels of education and clinical practice.

The COVID-19 pandemic continues to cause an immense psychosocial strain worldwide. Excessive use of the internet during these psychologically trying times, fueled by physical isolation as a result of lockdowns, has translated into dysfunctional behaviors. A growing body of evidence suggests an unprecedented increase in internet use and consumption of online pornography during the pandemic, and possibly even directly caused by it. In this review, the authors report data from relevant sources to show the rise in pornography use during lockdowns in different countries worldwide. In addition to a brief overview of the neurobiology of internet addiction broadly and problematic online pornography use specifically, similarities with substance use disorders are explained. Further, the current status of the debate about defining diagnostic criteria is discussed. Finally, the review sheds light on the potential detrimental outcomes during the future post-pandemic “re-adaptation,” while simultaneously offering preventative and management strategies for harm reduction. The authors conclude that foresightedness with utilizing existing tools and therapies and exercising appropriate amounts of caution could go a long way in addressing the challenges that lie ahead in the post-pandemic era.

Cholera affects about three million people annually and kills several thousands. Since 1817 seven cholera pandemics have been described. While the nature of the strains responsible for the first four pandemics are not known, the fifth and sixth pandemics are associated with Vibrio cholerae O1 classical biotype. In the 1960s, V. cholerae El Tor replaced classical strains worldwide, ushering in the seventh pandemic. El Tor cholera is typified with less severe diarrhea, a lower case fatality rate and a higher percentage of asymptomatic cases. Historically, the Indian subcontinent was thought to be the homeland where cholera originated and has been implicated in spreading of the disease. Cholera broke out in Africa and now seems to be continuous and recurrent, leading to high morbidity and mortality in some countries. Current conflicts in the Middle East have been associated with the breakdown of healthcare systems and the emergence of cholera there in a big way. Several discoveries in the past two centuries helped us to understand and manage the disease. Some of the greatest inventions such as rehydration therapy have saved the lives of countless people afflicted with cholera. Whole genome sequencing of V. cholerae and the modern molecular epidemiology of cholera have led to advancements in understanding of the disease and also how the organism has persisted and re-emerged in new areas during the seventh pandemic. Currently, water, sanitation, and hygiene along with the new generation oral cholera vaccines are considered as important interventions and beneficial public health tools in cholera endemic countries and in areas at risk for outbreaks. This review highlights the pandemics that lead to important discoveries and also the new molecular approach in understanding the epidemiology of cholera.

BackgroundCampylobacter jejuni (C. jejuni) is a leading cause of acute gastroenteritis in human worldwide. The aim of study was to assess the distribution of sialylated lipooligosaccharide (LOS) classes and capsular genotypes in C. jejuni isolated from Iranian children with gastroenteritis. Furthermore, the level of dnaK gene expression in C. jejuni strains with selected capsular genotypes and LOS classes was intended. Moreover, a comprehensive study of C. jejuni MLST-genotypes and inclusive comparison with peer sequences worldwide was intended.MethodsTwenty clinical C. jejuni strains were isolated from fecal specimens of 280 children aged 0–5 years, suspected of bacterial gastroenteritis, which admitted to 3 children hospitals from May to October, 2018. Distribution of sialylated LOS classes and specific capsular genotypes were investigated in C. jejuni of clinical origin. The expression of dnaK in C. jejuni strains was measured by Real-Time-PCR. MLST-genotyping was performed to investigate the clonal relationship of clinical C. jejuni strains and comparison with inclusive sequences worldwide.ResultsC. jejuni HS23/36c was the predominant genotype (45%), followed by HS2 (20%), and HS19 and HS4 (each 10%). A total of 80% of isolates were assigned to LOS class B and C. Higher expression level of dnaK gene was detected in strains with HS23/36c, HS2 and HS4 capsular genotypes and sialylated LOS classes B or C. MLST analysis showed that isolates were highly diverse and represented 6 different sequence types (STs) and 3 clonal complexes (CCs). CC21 and CC257 were the most dominant CCs (75%) among our C. jejuni strains. No new ST and no common ST with our neighbor countries was detected.ConclusionsThe C. jejuni isolates with LOS class B or C, and capsular genotypes of HS23/36, HS2, HS4 and HS19 were dominant in population under study. The CC21 and CC257 were the largest CCs among our isolates. In overall picture, CC21 and CC353 complexes were the most frequently and widely distributed clonal complexes worldwide, although members of CC353 were not detected in our isolates. This provides a universal picture of movement of dominant Campylobacter strains worldwide.

The emergence of new viruses is a matter of significant concern in the current decade. It has dazed the indigenous healthcare systems in various parts of the world. Consequently, the resources for fighting the rapid spread of the DENV are ineffectual, insufficient, and incompetent. Several environmental factors have been allied with dengue fever transmission. High documentation of neuropathogenesis in dengue-infected individuals in recent years reflects the significance of our study, and the information discussed in this review can be used to enhance clinical awareness along with advances in diagnostic approaches. The replication of the DENV genome is usually engaged in a membrane-linked replication complex; the virion budding and morphogenesis have been found to take place in the modified endoplasmic reticulum membranes. Most of these non-structural proteins are believed to be responsible for RNA replication and polyprotein processing. The nucleic acid-based strategies have provided high sensitivity and progressively replacing conventional techniques. Advanced technologies like PCR have offered timely serotyping of dengue viruses, which illustrates the early warning of dengue epidemics. The molecular methods help to characterize the key factors responsible for the rapid spread of viruses and thereby update the vector control programmes targeted at extenuating their adverse impacts on public health. The vast diversity of dengue virus strains worldwide with special inference on their clinical manifestations and genetic characteristics was also analyzed in this study. As dengue threatens one third of the world's population, practical applications of advanced molecular strategies from an environmental and phylogenetic perspective are critical for disease control.

Coronavirus (CoV), which causes animal diseases, has become a human health concern. Prior to 2003, CoV caused respiratory diseases and enteric disorders, but after 2003, CoV caused three acute respiratory syndromes, resulting in significant human deaths. Since then, research on CoV has multiplied, leading to a deeper knowledge of the species. It is in this context that this article reviews the history, the biological aspect, the evolution and the crossing of the CoV species barrier. This review shows that CoVs are formed by a large genome (27 to 33 kb) and by structural proteins (spike S, hemagglutinin esterase HE and membran protein M). Various coronaviruses have been described in a wide range of species including chickens (<i>IBV-CoV</i>), pigs (<i>PHE-CoV, PED-CoV, TGE-CoV PR-CoV, PD-CoV, SADS-CoV</i>), cattle (<i>BCoV</i>), cats (<i>FCoV</i>), dogs (<i>CCoV</i>), and humans (<i>HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, SARS-CoV, MERS-CoV</i>, and <i>SARS-CoV2</i>). Birds and bats are the main reservoirs of CoVs, but due to the low fidelity of the replication complex, CoVs have the ability to adapt to various species. Due to the crossing of the species barrier, CoVs have a wide host range resulting in the emergence of various strains worldwide. This information can help researchers develop intervention strategies to prevent the re-emergence of CoVs in the future.

Objective Establishing a highly sensitive real-time fluorescence quantitative PCR (qPCR) method for universal testing of epidemic African swine fever virus (ASFV) strains. Methods The ASFV p72 gene was targeted to design primer probes covering 24 p72 genotypes. The optimal amount of dimethylsulphoxide (DMSO) for qPCR amplification was determined, Various sensitivity and limit of detection (LOD) tests were performed, and clinical samples from China and imported goods were tested. Results The optimal primer-probe combination could specifically detect ASFV, 1.5% DMSO was optimal for qPCR, and LOD reached 3.2 copies/μL with good reproducibility (n = 20, p = 0.369). The method was employed to test 142 clinically suspected samples, of which 30 pig blood and 37 pig tissue samples were ASFV-positive. Moreover, the positive testing rate for ASFV was higher than for the standard qPCR method recommended by the Office International Des Epizooties (OIE), and for the commercially available kit. Thus, our method is superior for testing weakly positive samples with low virus titre, and epidemic strains present in imported goods. Conclusion Our method could be employed for universal testing of epidemic ASFV strains worldwide, ensuring wider coverage of hosts and ASFV strains/endemic strains, reducing false negatives, and benefitting early diagnosis.

Despite highly variable efficacy, BCG (Bacillus Calmette-Guérin) is the only vaccine available to prevent the tuberculosis (TB). Genomic heterogeneity between attenuated BCG strains and virulent Mycobacterium tuberculosis might help to explain this vaccine’s impaired capacity to induce long-term protection. Here, we investigate the lipid-related genes absent in attenuated BCG strains in order to correlate changes in both lipid metabolism and cell-wall lipid content to vaccine impairment. Whole genome sequences of M. tuberculosis H37Rv and the six most used BCG strains worldwide were aligned and the absent regions functionally categorized. Genomes of the BCG strains showed a total of 14 non-homologous lipid-related genes, including those belonging to mce3 operon, as well as the gene echaA1, which encodes an enoyl-CoA hydratase, and the genes encoding phospholipases PlcA, PlcB and PlcC. Taken together, the depletion of these M. tuberculosis H37Rv genomic regions were associated with marked alterations in lipid-related genes of BCG strains. Such alterations may indicate a dormant-like state and can be determining factors to the vaccine’s inability to induce long-term protection. These lipids can be further evaluated as an adjuvant to boost the current BCG-based vaccine.

Efficient protection against Asia1 type foot-and-mouth disease using a chimeric vaccine strain suitable for East Asia

Genetic diversity of major surface protein 1a of Anaplasma marginale in dairy cattle.

Mycoviruses are widespread and purportedly common throughout the fungal kingdom, although most are known from hosts in the two most recently diverged phyla, Ascomycota and Basidiomycota, together called Dikarya. To augment our knowledge of mycovirus prevalence and diversity in underexplored fungi, we conducted a large-scale survey of fungi in the earlier-diverging lineages, using both culture-based and transcriptome-mining approaches to search for RNA viruses. In total, 21.6% of 333 isolates were positive for RNA mycoviruses. This is a greater proportion than expected based on previous taxonomically broad mycovirus surveys and is suggestive of a strong phylogenetic component to mycoviral infection. Our newly found viral sequences are diverse, composed of double-stranded RNA, positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA genomes and include novel lineages lacking representation in the public databases. These identified viruses could be classified into 2 orders, 5 families, and 5 genera; however, half of the viruses remain taxonomically unassigned. Further, we identified a lineage of virus-like sequences in the genomes of members of Phycomycetaceae and Mortierellales that appear to be novel genes derived from integration of a viral RNA-dependent RNA polymerase gene. The two screening methods largely agreed in their detection of viruses; thus, we suggest that the culture-based assay is a cost-effective means to quickly assess whether a laboratory culture is virally infected. This study used culture collections and publicly available transcriptomes to demonstrate that mycoviruses are abundant in laboratory cultures of early-diverging fungal lineages. The function and diversity of mycoviruses found here will help guide future studies into mycovirus origins and ecological functions.IMPORTANCE Viruses are key drivers of evolution and ecosystem function and are increasingly recognized as symbionts of fungi. Fungi in early-diverging lineages are widespread, ecologically important, and comprise the majority of the phylogenetic diversity of the kingdom. Viruses infecting early-diverging lineages of fungi have been almost entirely unstudied. In this study, we screened fungi for viruses by two alternative approaches: a classic culture-based method and by transcriptome-mining. The results of our large-scale survey demonstrate that early-diverging lineages have higher infection rates than have been previously reported in other fungal taxa and that laboratory strains worldwide are host to infections, the implications of which are unknown. The function and diversity of mycoviruses found in these basal fungal lineages will help guide future studies into mycovirus origins and their evolutionary ramifications and ecological impacts.

Scrub typhus is a zoonotic disease caused by Orientia tsutsugamushi (O. tsutsugamushi). Orientia tsutsugamushi has various genotypes and more new strains with difference in sequences increasingly appeared. Whether the accurateness of one special nested PCR method which amplifies segment instead of entire open reading frame (ORF) sequence meets the current work of identifying new strains and classifying genotypes remains to be confirmed. And the origins and evolution of this organism have not been thoroughly elucidated. Accordingly, in this study, segments and the entire ORF of the 56-kDa type-specific antigen (TSA56) gene of O. tsutsugamushi were collected, including 209 clinically isolated strains in Guangzhou, China from 2012 to 2016 and 139 reference strains worldwide. By performing phylogenetic analysis, we proved that the accurateness of the particular PCR method which almost met detection need. This re-grouping result showed that segments perfectly represented and identified strains of Karp, Boryong, Gilliam, TA763, Kawasaki and part of Kato genotype, and this accuracy is not restricted by region and time. Sequence diversification of Shimokoshi and some Kato strains made their genotyping need to consider entire ORF sequences, but their weak recognition might not be due to recombination. The frequent genetic recombination and high point mutations contributed to genetic diversification of the TSA56 gene. Major overlapping regions of most recombination events occurred between strains of the same genotype, especially Karp and Kato genotype. And cross-genotype overlapping events occurred between Karp and Boryong/Gilliam/TA763/Kato, Kato and Kawasaki/Gilliam/TA686, Boryong and TA686, and Gilliam and Kawasaki. But Segment has quite low recombination frequency and stable mutation trend from 1943 to 2016. So segment is a relatively conserved part of the TSA56 ORF as for its stable trend of genetic diversity, and it may anchor and represent the entire TSA56 ORF gene. And genetic diversity is rejected as one potential reason for the increased incidence of scrub typhus. But an occasional recombination event created an unrecognized genotype which might be due to the breakage of VD II and AD II. Additionally, strains in Guangzhou were homologous and Karp genotype was detected as a dominant.