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Pathogens and Disease Jun 2016ITALIC! Shigella boydiiis one of the four ITALIC! Shigellaspecies that causes disease worldwide; however, there are few published studies that examine the genomic...
ITALIC! Shigella boydiiis one of the four ITALIC! Shigellaspecies that causes disease worldwide; however, there are few published studies that examine the genomic variation of this species. This study compares genomes of 72 total isolates; 28 ITALIC! S. boydiifrom Bangladesh and The Gambia that were recently isolated as part of the Global Enteric Multicenter Study (GEMS), 14 historical ITALIC! S. boydiigenomes in the public domain and 30 ITALIC! Escherichia coliand ITALIC! Shigellareference genomes that represent the genomic diversity of these pathogens. This comparative analysis of these 72 genomes identified that the ITALIC! S. boydiiisolates separate into three phylogenomic clades, each with specific gene content. Each of the clades contains ITALIC! S. boydiiisolates from geographic and temporally distant sources, indicating that the ITALIC! S. boydiiisolates from the GEMS are representative of ITALIC! S. boydii.This study describes the genome sequences of a collection of novel ITALIC! S. boydiiisolates and provides insight into the diversity of this species in comparison to the ITALIC! E. coliand other ITALIC! Shigellaspecies.
Topics: Computational Biology; Dysentery, Bacillary; Genetic Variation; Genome, Bacterial; Genotype; High-Throughput Nucleotide Sequencing; Humans; Phylogeny; Shigella boydii
PubMed: 27056949
DOI: 10.1093/femspd/ftw027 -
Epidemiology and Infection Aug 2018Shigellosis causes significant morbidity and mortality in developing and developed countries, mostly among infants and young children. The World Health Organization...
Shigellosis causes significant morbidity and mortality in developing and developed countries, mostly among infants and young children. The World Health Organization estimates that more than one million people die from Shigellosis every year. In order to evaluate trends in Shigellosis in Israel in the years 2002-2015, we analysed national notifiable disease reporting data. Shigella sonnei was the most commonly identified Shigella species in Israel. Hospitalisation rates due to Shigella flexenri were higher in comparison with other Shigella species. Shigella morbidity was higher among infants and young children (age 0-5 years old). Incidence of Shigella species differed among various ethnic groups, with significantly high rates of S. flexenri among Muslims, in comparison with Jews, Druze and Christians. In order to improve the current Shigellosis clinical diagnosis, we developed machine learning algorithms to predict the Shigella species and whether a patient will be hospitalised or not, based on available demographic and clinical data. The algorithms' performances yielded an accuracy of 93.2% (Shigella species) and 94.9% (hospitalisation) and may consequently improve the diagnosis and treatment of the disease.
Topics: Adolescent; Adult; Aged; Algorithms; Child; Child, Preschool; Christianity; Dysentery, Bacillary; Female; Hospitalization; Humans; Incidence; Infant; Islam; Israel; Jews; Logistic Models; Machine Learning; Male; Middle Aged; Models, Statistical; Neural Networks, Computer; Pattern Recognition, Automated; Shigella boydii; Shigella dysenteriae; Shigella flexneri; Shigella sonnei; Young Adult
PubMed: 29880081
DOI: 10.1017/S0950268818001498 -
Journal of Clinical Microbiology Mar 2015Shigellae cause significant diarrheal disease and mortality in humans, as there are approximately 163 million episodes of shigellosis and 1.1 million deaths annually....
Shigellae cause significant diarrheal disease and mortality in humans, as there are approximately 163 million episodes of shigellosis and 1.1 million deaths annually. While significant strides have been made in the understanding of the pathogenesis, few studies on the genomic content of the Shigella species have been completed. The goal of this study was to characterize the genomic diversity of Shigella species through sequencing of 55 isolates representing members of each of the four Shigella species: S. flexneri, S. sonnei, S. boydii, and S. dysenteriae. Phylogeny inferred from 336 available Shigella and Escherichia coli genomes defined exclusive clades of Shigella; conserved genomic markers that can identify each clade were then identified. PCR assays were developed for each clade-specific marker, which was combined with an amplicon for the conserved Shigella invasion antigen, IpaH3, into a multiplex PCR assay. This assay demonstrated high specificity, correctly identifying 218 of 221 presumptive Shigella isolates, and sensitivity, by not identifying any of 151 diverse E. coli isolates incorrectly as Shigella. This new phylogenomics-based PCR assay represents a valuable tool for rapid typing of uncharacterized Shigella isolates and provides a framework that can be utilized for the identification of novel genomic markers from genomic data.
Topics: Cluster Analysis; DNA, Bacterial; Dysentery, Bacillary; Genetic Variation; Genome, Bacterial; Humans; Multiplex Polymerase Chain Reaction; Phylogeny; Sensitivity and Specificity; Sequence Analysis, DNA; Shigella
PubMed: 25588655
DOI: 10.1128/JCM.03527-14 -
MSphere Jun 2022Diarrheal diseases are a leading cause of global morbidity and mortality, disproportionately affecting children in resource-limited settings. Although improvements in...
Diarrheal diseases are a leading cause of global morbidity and mortality, disproportionately affecting children in resource-limited settings. Although improvements in hygiene and access to clean water are helpful, vaccines are considered essential due to the low infectious dose of species and increasing antibiotic resistance. Building on achievements with conjugate vaccines, a safe and immunogenic novel bioconjugate vaccine linking O-antigen to Pseudomonas aeruginosa exoprotein A has been developed to induce immunity against Shigella flexneri 2a, 3a, and 6 and S. sonnei. This study evaluated the breadth of reactivity and functionality of pooled serum from rabbits immunized with monovalent and quadrivalent bioconjugates formulated with or without an adjuvant against serotypes isolated in Kenya. Rabbit sera were assayed by colony blot for reactivity with 67 isolates of serotypes targeted by the vaccine, S. flexneri (2a, 3a, and 6) and S. sonnei, and 42 isolates of serotypes not targeted by the vaccine, S. flexneri (1b, 2b, 4a, and 4b), S. boydii, and S. dysenteriae. isolates testing positive in the colony blot assay were then used to assess functional activity using a bactericidal assay. Of the 41 isolates targeted by the vaccine, 22 were reactive with the adjuvanted quadrivalent and the respective monovalent rabbit sera. The S. flexneri 2a and 3a monovalent rabbit serum cross-reacted with S. flexneri 3a, 2b, and 2a, respectively. Immunization with the adjuvanted quadrivalent vaccine also induced cross-reactivity with isolates of S. flexneri 2b, 4a, and 4b. Collectively, these results suggest that the quadrivalent vaccine may be more broadly protective than designed, offering a promising solution to infections. Diarrheal diseases are the third leading cause of death globally, disproportionally affecting low- to middle-income countries like Kenya, with species being the leading cause of bacterial diarrhea, especially in children. The low infectious dose and high antibiotic resistance levels complicate treatment, leading to long-term sequelae that necessitate control measures such as vaccines to reduce morbidity and mortality rates, especially among children under 5 years of age. A quadrivalent bioconjugate vaccine was recently developed to safely and effectively induce immunity against four important spp. This study demonstrates the breadth of reactivity and functionality of the parenterally administered bioconjugate vaccine by evaluating the ability of rabbit sera to bind and kill isolates recently collected in Kenya. These results suggest that the quadrivalent vaccine may be more broadly protective than designed and may offer a promising solution to the morbidity and mortality associated with infections.
Topics: Animals; Antibodies, Bacterial; Antigens, Bacterial; Diarrhea; Dysentery, Bacillary; Kenya; Rabbits; Shigella; Shigella Vaccines; Shigella sonnei; Vaccination; Vaccines, Combined
PubMed: 35611657
DOI: 10.1128/msphere.01020-21 -
Gastroenterology and Hepatology From... 2017In the present study, we investigated the prevalence of pathotypes and sero-groups and their antimicrobial profiles among diarrheic children in Nairobi city, Kenya.
AIM
In the present study, we investigated the prevalence of pathotypes and sero-groups and their antimicrobial profiles among diarrheic children in Nairobi city, Kenya.
BACKGROUND
Although diarrheagenic pathotypes and sero-groups are leading causes of diarrhea in children under five years in developing countries, their distribution and antimicrobial resistance vary from place to place and over time in a given region.
METHODS
In a cross-sectional study, we enrolled diarrheic children (n=354) under five years seeking treatment at Mbagathi Hospital, Nairobi city, Kenya,. Stool samples were collected from all children for bacterial culture. Bacterial isolation and identification was performed by conventional microbiological methods. Polymerase chain amplification was used to detect aspU, aggR, andpcvd432 for EAEC, est and elt for ETEC, eae for EPEC, stx for EHEC, and ipaH for EIEC and Shigella species. Antimicrobial profile was determined by disk diffusion method.
RESULTS
The prevalence of EAEC, ETEC, EPEC (eae), EIEC (ipaH) was 21.2%, 10.5%, 4.5%, and 0.6%, respectively, while that of mixed infection was 0.6%for ETEC/EAEC and 0.3%for EAEC/EPEC/ETEC. No EHEC strain was isolated. Pathogenetic analysis for EAEC showed that5.9% carried aspU,8.2% possessed both aspU and aggR and 7.1% had a combination of aspU, aggR andpcvd432 while that of ETEC was 2.3% for elt, 6.5% for both elt and est and 1.7% for est. The combination of aspU with aggR, elt and est, and pcvd432 with aggR, aspU and est was 0.3% for each case of ETEC/EAEC mixed infection. The aspU gene co-existed with aggR, pcvd432, eae and elt in the EAEC/EPEC/ETEC mixed infection. The prevalence of , , was 0.8%, 0.6%, 1.7%, and 0.8%, respectively. No pathotype and co-infection was detected. In addition, both pathotypes and species were resistant to ampicillin, trimethoprim/sulfamethoxazole, streptomycin, chloramphenicol and tetracycline while gentamycin and kanamycin resistance occurred in diarrheagenic
CONCLUSION
pathotypes and sero-groups harboring virulent genes are important causes of diarrhea in children in Kenya. The increasing spectrum of antibiotic resistance in diarrheagenic and species necessitates the development of antimicrobial stewardship education-programs to influence prescribing behavior as well as optimizing the use of effective antimicrobials in Kenya.
PubMed: 29118939
DOI: No ID Found -
Virulence Dec 2022Although four species (. , , and ) have been reported, . sp. PAMC 28760, an Antarctica isolate, is the only one with a complete genome deposited in NCBI database as an...
Although four species (. , , and ) have been reported, . sp. PAMC 28760, an Antarctica isolate, is the only one with a complete genome deposited in NCBI database as an uncharacterized isolate. Because it is the world's driest, windiest, and coldest continent, Antarctica provides an unfavourable environment for microorganisms. Computational analysis of genomic sequences of four species and our uncategorized Antarctica isolates sp. PAMC28760 was performed using MP3 (offline version) program to predict trehalase encoding genes as a pathogenic or non-pathogenic form. Additionally, we employed RAST and Prokka (offline version) annotation programs to determine locations of periplasmic () and cytoplasmic () trehalase genes in studied genomes. Our results showed that only 56 out of 134 strains had two different trehalase genes ( and ). It was revealed that the gene tends to be prevalent in species. In addition, both and genes were present in our strain . sp. PAMC28760. The main objective of this study was to predict the prevalence of two different trehalase genes ( and ) in the complete genome of sp. PAMC28760 and other complete genomes of species. Till date, it is the first study to show that two types of trehalase genes are involved in species, which could offer insight on how the bacteria use accessible carbohydrate like glucose produced from the trehalose degradation pathway, and importance of periplasmic trehalase involvement in bacterial virulence.
Topics: Antarctic Regions; Genomics; Shigella; Trehalase
PubMed: 36040103
DOI: 10.1080/21505594.2022.2117679 -
Molecules (Basel, Switzerland) May 2017In this paper, a Whole-Bacteria SELEX (WB-SELEX) strategy was adopted to isolate specific aptamers against . Real-time PCR amplification and post-SELEX experiment...
In this paper, a Whole-Bacteria SELEX (WB-SELEX) strategy was adopted to isolate specific aptamers against . Real-time PCR amplification and post-SELEX experiment revealed that the selected aptmers possessed a high binding affinity and specificity for . Of the 21 aptamers tested, the C(t) values of the SS-3 and SS-4 aptamers (Ct = 13.89 and Ct = 12.23, respectively) had the lowest value compared to other aptamer candidates. The SS-3 and SS-4 aptamers also displayed a binding affinity () of 39.32 ± 5.02 nM and 15.89 ± 1.77 nM, respectively. An aptamer-based fluorescent biosensor assay was designed to detect and discriminate cells using a sandwich complex pair of SS-3 and SS-4. The detection of by the aptamer based fluorescent biosensor platform consisted of three elements: (1) 5'amine-SS-4 modification in a 96-well type microtiter plate surface (-oxysuccinimide, NOS) as capture probes; (2) the incubation with and test microbes in functionalized 96 assay wells in parallel; (3) the readout of fluorescent activity using a Cy5-labeled SS-3 aptamer as the detector. Our platform showed a significant ability to detect and discriminate from other enteric species such as , and other species (, ). In this study, we demonstrated the feasibility of an aptamer sensor platform to detect in a variety of foods and pave the way for its use in diagnosing shigellosis through multiple, portable designs.
Topics: Aptamers, Nucleotide; Biosensing Techniques; Escherichia coli; Fluorescence; Real-Time Polymerase Chain Reaction; SELEX Aptamer Technique; Salmonella typhimurium; Sensitivity and Specificity; Shigella sonnei
PubMed: 28513559
DOI: 10.3390/molecules22050825 -
Infection, Genetics and Evolution :... Nov 2018Shigella infections account for a considerable burden of acute diarrheal diseases worldwide and remain a major cause of childhood mortality in developing countries....
Shigella infections account for a considerable burden of acute diarrheal diseases worldwide and remain a major cause of childhood mortality in developing countries. Although, all four species of Shigella (S. dysenteriae, S. flexneri, S. boydii, and S. sonnei) cause bacillary dysentery, historically only S. dysenteriae type 1 has been recognized as carrying the genes for Shiga toxin (stx). Recent epidemiological data, however, have suggested that the emergence of stx carrying S. flexneri strains may have originated from bacteriophage-mediated inter-species horizontal gene transfer in one specific geographical area, Hispaniola. To test this hypothesis, we analyzed whole genome sequences of stx-encoding phages carried by S. flexneri strains isolated in Haiti and S. flexneri S. boydii and S. dysenteriae strains isolated from international travelers who likely acquired the infection in Haiti or the Dominican Republic. Phylogenetic analysis showed that phage sequences encoded in the Shigella strains from Hispaniola were bacteriophage φPOC-J13 and they were all closely related to a phage isolated from a USA isolate, E. coli 2009C-3133 serotype O119:H4. In addition, despite the low genetic heterogeneity of phages from different Shigella spp. circulating in the Caribbean island between 2001 and 2014, two distinct clusters emerged in Haiti and the Dominican Republic. Each cluster possibly originated from phages isolated from S. flexneri 2a, and within each cluster several instances of horizontal phage transfer from S. flexneri 2a to other species were detected. The implications of the emergence of stx-producing non-S. dysenteriae type 1 Shigella species, such as S. flexneri, spans not only the basic science behind horizontal phage spread, but also extends to medical treatment of patients infected with this pathogen.
Topics: Bacteriophages; Dominican Republic; Dysentery, Bacillary; Gene Transfer, Horizontal; Genetic Variation; Haiti; Humans; Phylogeography; Polymorphism, Single Nucleotide; Shiga Toxin; Shigella flexneri
PubMed: 30075254
DOI: 10.1016/j.meegid.2018.07.038 -
Gastroenterology and Hepatology From... 2017In This study focused on the detection of dominant clones and genetic relationship of spp. isolated from children with diarrhea in the main pediatric hospital in Ahvaz...
AIM
In This study focused on the detection of dominant clones and genetic relationship of spp. isolated from children with diarrhea in the main pediatric hospital in Ahvaz by multi-locus sequence typing (MLST) technique.
BACKGROUND
Shigellosis is considered as one of the problematic bacterial infections for public health in the world. Khuzestan province in the Southwestern part of Iran is a known endemic area for infections due to . There are limited molecular epidemiological data for spp. in this area.
METHODS
A total of 50 spp. were isolated from January-June 2015 based on conventional microbiology and serology tests. The Sequence types (ST) of isolates which are characterized by repetitive intergenic consensus (ERIC-PCR) were detected by MLST technique.
RESULTS
Among 50 isolates, a total of 31(62%), 16(32%) and 3 (6%) of isolates were identified as , , and , respectively. Two different sequence types (ST152 and ST245) were identified in isolates. ST152 was detected in S and ST245 in and isolates.
CONCLUSION
Based on MLST data, the stable and genetically linked clones are the cause of infections in children in Southwestern Iran.
PubMed: 29379598
DOI: No ID Found -
Clinical and Vaccine Immunology : CVI Apr 2015In developing countries, Shigella is a primary cause of diarrhea in infants and young children. Although antibiotic therapy is an effective treatment for shigellosis,...
In developing countries, Shigella is a primary cause of diarrhea in infants and young children. Although antibiotic therapy is an effective treatment for shigellosis, therapeutic options are narrowing due to the emergence of antibiotic resistance. Thus, preventive vaccination could become the most efficacious approach for controlling shigellosis. We have identified several conserved protein antigens that are shared by multiple Shigella serotypes and species. Among these, one antigen induced cross-protection against experimental shigellosis, and we have named it pan-Shigella surface protein 1 (PSSP-1). PSSP-1-induced protection requires a mucosal administration route and coadministration of an adjuvant. When PSSP-1 was administered intranasally, it induced cross-protection against Shigella flexneri serotypes 2a, 5a, and 6, Shigella boydii, Shigella sonnei, and Shigella dysenteriae serotype 1. Intradermally administered PSSP-1 induced strong serum antibody responses but failed to induce protection in the mouse lung pneumonia model. In contrast, intranasal administration elicited efficient local and systemic antibody responses and production of interleukin 17A and gamma interferon. Interestingly, blood samples from patients with recent-onset shigellosis showed variable but significant mucosal antibody responses to other conserved Shigella protein antigens but not to PSSP-1. We suggest that PSSP-1 is a promising antigen for a broadly protective vaccine against Shigella.
Topics: Administration, Intranasal; Animals; Antibodies, Bacterial; Bacterial Outer Membrane Proteins; Child, Preschool; Cross Protection; Dysentery, Bacillary; Female; Humans; Immunity, Heterologous; Infant; Injections, Intradermal; Interferon-gamma; Interleukin-17; Mice; Mice, Inbred BALB C; Pneumonia, Bacterial; Shigella; Shigella Vaccines
PubMed: 25651919
DOI: 10.1128/CVI.00661-14