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Background Worldwide, noroviruses are the leading cause of acute gastroenteritis (AGE) in people of all age groups. In India, norovirus rates between 1.4 to 44.4% have been reported. Only a very few complete norovirus genome sequences from India have been reported. Objective To perform full genome sequencing of noroviruses circulating in India during 2017-2021, identify circulating genotypes, assess evolution including detection of recombination events. Methodology Forty-five archived norovirus-positive samples collected between October 2017 to July 2021 from patients with AGE from two hospitals in Kolkata, India were processed for full genome sequencing. Phylogenetic analysis, recombination breakpoint analysis and comprehensive mutation analysis were also performed. Results Full genome analysis of norovirus sequences revealed that strains belonging to genogroup (G)I were genotyped as GI.3[P13]. Among the different norovirus capsid-polymerase combinations, GII.3[P16], GII.4 Sydney[P16], GII.4 Sydney[P31], GII.13[P16], GII.16[P16] and GII.17 were identified. Phylogenetic analysis confirmed phylogenetic relatedness with previously reported norovirus strains and all viruses were analyzed by Simplot. GII[P16] viruses with multiple residue mutations within the non-structural region were detected among circulating GII.4 and GII.3 strains. Comprehensive mutation analysis and selection pressure analysis of GII[P16] viruses showed positive as well as negative selection sites. A GII.17 strain (NICED-BCH-11889) had an untypeable polymerase type, closely related to GII[P38]. Conclusion This study highlights the circulation of diverse norovirus strains in eastern India. These findings are important for understanding norovirus epidemiology in India and may have implications for future vaccine development., Author(s): Mahadeb Lo[sup.1], Yen Hai Doan[sup.2], Suvrotoa Mitra[sup.1], Ritubrita Saha[sup.1], Shin-ichi Miyoshi[sup.3,4], Kei Kitahara[sup.3], Shanta Dutta[sup.5], Tomoichiro Oka[sup.6] and Mamta Chawla-Sarkar[sup.1] Introduction Noroviruses are a major cause of acute gastroenteritis [...]

Objective To evaluate the clinical accuracy of rapid diagnostic tests for the detection of Ebola virus. Methods We searched MEDLINE[R], Embase[R] and Web of Science for articles published between 1976 and October 2021 reporting on clinical studies assessing the performance of Ebola virus rapid diagnostic tests compared with reverse transcription polymerase chain reaction (RT-PCR). We assessed study quality using the QUADAS-2 criteria. To estimate the pooled sensitivity and specificity of these rapid diagnostic tests, we used a bivariate random-effects meta-analysis. Findings Our search identified 113 unique studies, of which nine met the inclusion criteria. The studies were conducted in the Democratic Republic of the Congo, Guinea, Liberia and Sierra Leone and they evaluated 12 rapid diagnostic tests. We included eight studies in the meta-analysis. The pooled sensitivity and specificity of the rapid tests were 86% (95% confidence interval, CI: 80-91) and 95% (95% CI: 91-97), respectively. However, pooled sensitivity decreased to 83% (95% CI: 77-88) after removing outliers. Pooled sensitivity increased to 90% (95% CI: 82-94) when analysis was restricted to studies using the RT-PCR from altona Diagnostics as gold standard. Pooled sensitivity increased to 99% (95% CI: 67-100) when the analysis was restricted to studies using whole or capillary blood specimens. Conclusion The included rapid diagnostic tests did not detect all the Ebola virus disease cases. While the sensitivity and specificity of these tests are moderate, they are still valuable tools, especially useful for triage and detecting Ebola virus in remote areas. Objectif Evaluer la precision clinique des tests de diagnostic rapide pour depister le virus Ebola. Methodes Nous avons explore les bases de donnees MEDLINE[R], Embase[R] et Web of Science a la recherche d'articles, publies entre 1976 et octobre 2021, qui evoquaient des etudes cliniques mesurant les performances des tests de diagnostic rapide du virus Ebola compares a une reaction en chaine par polymerase apres transcription inverse (RT-PCR). Nous avons determine la qualite de ces etudes a l'aide des criteres QUADAS-2. Enfin, pour estimer la sensibilite et la specificite regroupees de ces tests de diagnostic rapide, nous avons eu recours a une meta-analyse bivariee a effets aleatoires. Resultats Nos recherches nous ont permis d'identifier 113 etudes uniques, dont neuf correspondaient aux criteres d'inclusion. Ces etudes avaient ete menees en Guinee, au Liberia, en Republique democratique du Congo et en Sierra Leone, et portaient sur douze tests de diagnostic rapide. Nous avons inclus huit etudes dans notre meta-analyse. La sensibilite et la specificite combinees des tests rapides s'elevaient respectivement a 86% (intervalle de confiance de 95%, IC: 80-91) et 95% (IC de 95%: 91-97). Neanmoins, la sensibilite combinee baissait a 83% (IC de 95%: 77-88) apres retrait des valeurs aberrantes. Lorsque l'analyse se limitait aux etudes utilisant la RT-PCR d'altona Diagnostics en guise de reference, la sensibilite combinee augmentait jusqu'a 90% (IC de 95%: 82-94). Elle atteignait meme 99% (IC de 95%: 67-100) quand l'analyse se limitait aux etudes basees sur des echantillons de sang total ou capillaire. Conclusion Les tests de diagnostic rapide pris en compte ne detectaient pas tous les cas de maladie a virus Ebola. Neanmoins, en depit d'une sensibilite et d'une specificite moderees, ils demeurent de precieux outils, en particulier pour le triage et le depistage du virus Ebola dans les zones reculees. Objetivo Evaluar la precision clinica de las pruebas diagnosticas rapidas para la deteccion del virus del Ebola. Metodos Se realizaron busquedas en MEDLINE[R], Embase[R] y Web of Science de articulos publicados entre 1976 y octubre de 2021 que informaran sobre estudios clinicos en los que se evaluara el rendimiento de las pruebas diagnosticas rapidas para detectar el virus del Ebola en comparacion con la reaccion en cadena de la polimerasa con retrotranscripcion (RT-PCR). Se evaluo la calidad de los estudios mediante los criterios QUADAS-2. Para estimar la sensibilidad y la especificidad combinadas de estas pruebas diagnosticas rapidas, se utilizo un metanalisis bivariante de efectos aleatorios. Resultados La busqueda identifico 113 estudios singulares, de los que nueve cumplian los criterios de inclusion. Los estudios se realizaron en la Republica Democratica del Congo, Guinea, Liberia y Sierra Leona y evaluaron doce pruebas diagnosticas rapidas. Se incluyeron ocho estudios en el metanalisis. La sensibilidad y la especificidad agrupadas de las pruebas rapidas fueron del 86 % (intervalo de confianza del 95%, IC: 80-91) y del 95% (IC del 95%: 91-97), respectivamente. Sin embargo, la sensibilidad agrupada disminuyo al 83 % (IC del 95%: 77-88) tras eliminar los valores atipicos. La sensibilidad agrupada aumento al 90% (IC del 95%: 82-94) cuando el analisis se restringio a los estudios que utilizaban la RT-PCR de altona Diagnostics como criterio de referencia. La sensibilidad agrupada aumento al 99 % (IC del 95%: 67-100) cuando el analisis se restringio a los estudios que utilizaban muestras de sangre total o capilar. Conclusion Las pruebas diagnosticas rapidas incluidas no detectaron todos los casos de enfermedad por el virus del Ebola. Aunque la sensibilidad y la especificidad de estas pruebas son moderadas, siguen siendo herramientas valiosas, sobre todo utiles para el triaje y la deteccion del virus del Ebola en zonas remotas., Introduction Ebola virus disease was first discovered in 1976 in the Democratic Republic of the Congo and South Sudan. (1) This highly pathogenic disease is often fatal in humans; in [...]

Bacteria in the genus Vibrio are ubiquitous in estuarine and coastal waters. Some species (including Vibrio cholerae and Vibrio vulnificus) are known human pathogens causing ailments like cholera, diarrhea, or septicemia. Notably, V. vulnificus can also cause a severe systemic infection (known as vibriosis) in eels raised in aquaculture facilities. Water samples were periodically collected from the estuary of the Asahi River, located in the southern part of Okayama City, Japan. These samples were directly plated onto CHROMagar Vibrio plates, and colonies displaying turquoise-blue coloration were selected. Thereafter, polymerase chain reaction was used to identify V. cholerae and V. vulnificus. A total of 30 V. cholerae strains and 194 V. vulnificus strains were isolated during the warm season when the water temperature (WT) was higher than 20 °C. Concurrently, an increase in coliforms was observed during this period. Notably, V. vulnificus has two genotypes, designated as genotype 1 and genotype 2. Genotype 1 is pathogenic to humans, while genotype 2 is pathogenic to both humans and eels. The loop-mediated isothermal amplification method was developed to rapidly determine genotypes at a low cost. Of the 194 strains isolated, 80 (41.2%) were identified as genotype 1 strains. Among the 41 strains isolated when the WTs were higher than 28 °C, 25 strains (61.0%) belonged to genotype 1. In contrast, of the 32 strains isolated when the WTs were lower than 24 °C, 27 strains (84.4%) belonged to genotype 2. These results suggest that the distribution of the two genotypes was influenced by WT. [ABSTRACT FROM AUTHOR]

Background: The primary aim of this study was to investigate the occurrence, characteristics, and antimicrobial resistance patterns of various Shigella serotypes isolated from patients with acute diarrhea of the Infectious Diseases Hospital in Kolkata from 2011–2019. Principal findings: During the study period, Shigella isolates were tested for their serotypes, antibiotic resistance pattern and virulence gene profiles. A total of 5.8% of Shigella spp. were isolated, among which S. flexneri (76.1%) was the highest, followed by S. sonnei (18.7%), S. boydii (3.4%), and S. dysenteriae (1.8%). Antimicrobial resistance against nalidixic acid was higher in almost all the Shigella isolates, while the resistance to β-lactamases, fluoroquinolones, tetracycline, and chloramphenicol diverged. The occurrence of multidrug resistance was found to be linked with various genes encoding drug-resistance, multiple mutations in the topoisomerase genes, and mobile genetic elements. All the isolates were positive for the invasion plasmid antigen H gene (ipaH). Dendrogram analysis of the plasmid and pulsed-field electrophoresis (PFGE) profiles revealed 70–80% clonal similarity among each Shigella serotype. Conclusion: This comprehensive long-term surveillance report highlights the clonal diversity of clinical Shigella strains circulating in Kolkata, India, and shows alarming resistance trends towards recommended antibiotics. The elucidation of this study's outcome is helpful not only in identifying emerging antimicrobial resistance patterns of Shigella spp. but also in developing treatment guidelines appropriate for this region. Author summary: Shigella spp. is one of the WHO-designated "antibiotic-resistant priority pathogens" that is the leading cause of bacterial diarrhea among children worldwide. The distribution of Shigella species varies depending on the geographic location, particularly in regions where environmental risk factors like substandard water quality, limited healthcare accessibility, and insufficient sanitation are widespread. The presence of serotype diversity and drug resistance combinations often leads to treatment failures. Therefore, it is crucial to comprehend the prevailing serogroups and antimicrobial resistance patterns of Shigella species in different geographical areas to implement effective treatment strategies. We have identified 535 Shigella positive cases from 9276 diarrheal cases. Multidrug-resistant (MDR) Shigella globally requires a profound understanding of its genetic diversity, as there is significant regional variation in MDR strains. In our study, we observed a broad spectrum of resistance among the Shigella strains, with over 53.6% of the isolates demonstrating multidrug resistance. Representative isolates were evaluated for antimicrobial resistance encoding and virulence-associated genes as they enact significantly in disease development and interaction with the host immune system. This report marks the initial presentation of the outcomes from long-term surveillance and molecular characterization of antimicrobial resistances in clinical Shigella strains in Kolkata since 2011. The outcome of this investigations will guide in identifying emerging antimicrobial resistance trend, formulating suitable treatment guidelines tailored to the community's needs, and establishing baseline data for comparison with potential outbreak strains in the future. [ABSTRACT FROM AUTHOR]

Purpose: The multidrug resistance Enterobacteriaceae cause many serious infections resulting in prolonged hospitalization, increased treatment charges and mortality rate. In this study, we characterized blaNDM-5-positive multidrug resistance commensal Escherichia coli (CE) isolated from diarrheal patients in Kolkata, India. Methods: Three CE strains were isolated from diarrheal stools, which were negative for different pathogroups of diarrheagenic E. coli (DEC). The presence of carbapenemases encoding genes and other antimicrobial resistance genes (ARGs) was detected using PCR. The genetic arrangement adjoining blaNDM-5 was investigated by plasmid genome sequencing. The genetic relatedness of the strains was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) methods. Results: In addition to colistin, the blaNDM-5-positive CE strains showed resistance to most of the antibiotics. Higher MICs were detected for ciprofloxacin (> 32 mg/L) and imipenem (8 mg/L). Molecular typing revealed that three CE strains belonged to two different STs (ST 101 and ST 648) but they were 95% similar in the PFGE analysis. Screening for ARGs revealed that CE strains harbored Int-1, blaTEM, blaCTX-M3, blaOXA-1, blaOXA-7, blaOXA-9, tetA, strA, aadA1, aadB, sul2, floR, mph(A), and aac(6´)-Ib-cr. In conjugation experiment, transfer frequencies ranged from 2.5× 10− 3 to 8.4x10− 5. The blaNDM-5 gene was located on a 94-kb pNDM-TC-CE-89 type plasmid, which is highly similar to the IncFII plasmid harboring an IS26-IS30-blaNDM-5-bleMBL-trpF-dsbd-IS 91-dhps structure. Conclusion: To the best of our knowledge, this is the first report on carbapenem resistance involving the blaNDM-5 gene in CE from diarrheal patients. The circulation of blaNDM-5 gene in CE is worrisome, since it has the potential to transfer blaNDM-5 gene to other enteric pathogens. [ABSTRACT FROM AUTHOR]

In response to low iron availability, Vibrio parahaemolyticus synthesizes and secretes a polyhydroxycarboxylate-type siderophore vibrioferrin which is composed of 1 mol each of 2-ketoglutaric acid, L-alanine, ethanolamine, and citric acid. We have previously reported the cloning and characterization of the pvuA gene, which encodes the 78-kDa outer membrane receptor protein for ferric vibrioferrin. In this study, nine genes involved in the biosynthesis and transport of vibrioferrin have been identified in the genomic regions surrounding the pvuA gene. The genes were sequenced, and gene disruptants were constructed by insertion mutation for phenotype analysis. Five of the genes, named pvsABCDE, constitute an operon that is expressed under iron-limiting conditions. Homology searches of their predicted protein products suggested that the four genes pvsABDE are implicated in the biosynthesis of the siderophore. Another gene in the same operon, pvsC, encodes a putative exporter that is homologous to members of the major facilitator superfamily of multidrug efflux pumps. The remaining four genes, named pvuBCDE, encode proteins strongly homologous to Escherichia coli FecBCDE, respectively, which are components of the ATP-binding cassette transporter system for ferric dicitrate. Reverse transcriptase PCR analysis revealed that these transport genes are transcribed as a single mRNA with the upstream genes, psuA and pvuA. Phenotypic comparison between the wild-type strain and its targeted gene disruptants supported the biological functions for the respective operons that were expected on the basis of the homology search.

The Fur target genes from Vibrio parahaemolyticus reveal a siderophore utilization gene containing operon that encodes a TonB-dependent receptor and the ferric vibrioferrin receptor. Insertion mutation and genetic complementation analyses indicate that the ferric vibrioferrin receptor mediates iron transport in V. parahaemolyticus.

Research was conducted to examine the functional domains of a zinc metalloprotease from Vibrio vulnificus, a human pathogen that causes infection and septicemia. A plasmid was transformed into Escherichia coli DH5-alpha for the overproduction of the protease. Results showed that the recombinant protease was similar to that produced by V. vulnificus. They also indicated that the 35-kDa recombinant protease had enough proteolytic activity toward oligopeptides and soluble proteins.

Classical swine fever (CSF, hog cholera) has reemerged in Japan after 26 years and affected domestic pigs and wild boars. CSF was reported in Gifu prefecture on September 2018. Approximately 90,000 breeding domestic pigs were sacrificed by farmers of Gifu and Aichi prefectures to prevent expansion of CSF outbreak. In mid September 2019, CSF outbreaks have occurred in 8 prefectures in central Japan. African swine fever (ASF) is another viral infectious disease that affects domestic pigs and wild boars, although the etiologic agent is different from that of CSF. Both CSF and ASF affect pig farmers because of their intense infectivity to domesticated pigs. Fortunately, the causative agents are not pathogenic to human. However, an enteric bacterium Salmonella enterica serovar Choleraesuis is pathogenic to pigs and humans. As Salmonella Choleraesuis causes food poisoning in humans, the infection is monitored by "Food Sanitation Law" in Japan. CSF, ASF, and Salmonella enterica serovar Choleraesuis salmonellosis are translated in Japanese as "ton-korera," "afurika ton-korera," and "buta-korera," respectively, wherein "ton" and "buta" both mean pig or hog. Therefore the above Japanese words mean hog cholera. [ABSTRACT FROM AUTHOR]