Strains Worldwide Research Articles (Page 3)

Background. Trichophyton indotineae appeared as a new type of dermatophytes causing treatment-resistant skin infections. The first mentions of T. indotineae came from India. Currently, the causative agent has spread in many parts of the world and is rapidly becoming a global healthcare problem. The precise identification of T. indotineae requires complex mycological examinations that transcend routine microbiological testing. Material and methods. Routine laboratory methods, namely KOH microscopy, mycological culture, as well as molecular biological investigation methods were used for the diagnosis of dermatomycoses and species-level identification of fungi. Results and conclusions. The appearance and prevalence of T. indotineae has significantly changed the classical approach to the management of patients with dermatomycosis worldwide. Two clinical observations, namely the first in the Russian Federation description of the skin lesions with genetic confirmation of the causative agent’s belonging to T. indotineae species and its resistant mutation to allylamines — Phe397Leu in the gene encoding squalene epoxidase, have been presented. Patients had a long-term (more than 2 years) pathological process that did not respond to therapy with various options of standard treatment regimens by both topical and systemic drugs. Further development of molecular diagnosis with species-level identification of T. indotineae and detection of mutations in SQLE should be one of the priority directions in domestic medical mycology, considering the increasing prevalence of resistant strains worldwide.

Phytophthora capsici is a major oomycete-based pathogen causing enormous damage to the productivity of peppers and other major crops from different families worldwide by causing fruit rot, root rot and foliar blight diseases. This study utilized molecular signatures present within ITS1-5.8S rRNA-ITS2 and Ras-related GTP binding protein (Ypt1) genes to evaluate haplotype variability and phylogenetic relationships among P. capsici isolates with significant epidemiological implications. Twelve different evolutionary lineages specific to particular hosts and/or geographical regions and differed by SNPs, and 30 haplotypes with maximum diversity in India and Pakistan, were identified by sequence analysis of the ITS regions. It includes country-specific lineages Pc-I and Pc-II in India with multiple host ranges; capsicum-specific lineages Pc-IV, Pc-V and Pc-VIII from Pakistan; papaya-specific lineages Pc-VI from China, and watermelon-specific lineages Pc-VII and Pc-XI from USA. Many lineages showed cross-border infections, such as Pc-III and Pc-X in India and Pakistan, Cocoa-specific lineage Pc-IX in Brazil and Cote d’Ivoire, and Capsicum-specific multi-continental lineage Pc-XII. Similarly, 11 different SNP lineages and 32 haplotypes with maximum diversity in China were identified for the Ypt1 gene. These findings would be very useful for epidemiological surveillance of P. capsici strains worldwide, understanding population and evolutionary dynamics, developing lineage- and haplotype-specific diagnostic assays and disease-resistant varieties.

IntroductionNorovirus (NoV) is one of the most important agents responsible for viral acute gastroenteritis, among which GII.4 NoV is the predominant strain worldwide, and GII.17 NoV surpassed GII.4 in some epidemic seasons. Rapid and accurate gene recognition is essential for a timely response to NoV outbreaks.MethodsIn the present study, the highly conserved regions of GII.4 and GII.17 NoVs were identified in the junction of open reading frame (ORF) 1 and ORF2 and then amplified by isothermal recombinase-aided amplification (RAA), followed by the cleavage of CRISPR-Cas13a with screened CRISPR RNAs (crRNAs) and RAA primers. The entire detection procedure could be completed within 40 min using a thermostat, and the results could be read out by the naked eye under a portable blue light transilluminator.DiscussionThe assay showed a high sensitivity of 97.96% and a high specificity of 100.0%. It offered a low limit of detection (LOD) of 2.5×100 copies/reaction and a coincidence rate of 96.75% in 71 clinical fecal samples. Overall, rapid and inexpensive detection of GII.4/GII.17 NoVs was established, which makes it possible to be used in areas with limited resources, particularly in low-income countries. Furthermore, it will contribute to assessing transmission risks and implementing control measures for GII.4/GII.17 NoVs, making healthcare more accessible worldwide.

Mutations in Mycobacterium tuberculosis associated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competitive fitness of M. tuberculosis populations when compared to susceptible populations. This fitness cost, introduced by resistance mutations in the RNA polymerase, can be alleviated by compensatory mutations (CMs) in other regions of the affected protein. CMs are of particular interest clinically since they could lock in resistance mutations, encouraging the spread of resistant strains worldwide. Here, we report the statistical inference of a comprehensive set of CMs in the RNA polymerase of M. tuberculosis, using over 70 000 M. tuberculosis genomes that were collated as part of the CRyPTIC project. The unprecedented size of this data set gave the statistical tests more power to investigate the association of putative CMs with resistance-conferring mutations. Overall, we propose 51 high-confidence CMs by means of statistical association testing and suggest hypotheses for how they exert their compensatory mechanism by mapping them onto the protein structure. In addition, we were able to show an association of CMs with higher in vitro growth densities, and hence presumably with higher fitness, in resistant samples in the more virulent M. tuberculosis lineage 2. Our results suggest the association of CM presence with significantly higher in vitro growth than for wild-type samples, although this association is confounded with lineage and sub-lineage affiliation. Our findings emphasize the integral role of CMs and lineage affiliation in resistance spread and increases the urgency of antibiotic stewardship, which implies accurate, cheap and widely accessible diagnostics for M. tuberculosis infections to not only improve patient outcomes but also prevent the spread of resistant strains.

BackgroundThe Omicron wave of Coronavirus disease 2019 (COVID-19) remains the dominant strain worldwide. The studies of nutritional status in geriatric people with COVID-19 Omicron variant are limited. Thus, the aim of this study was to investigate the incidence of poor nutritional status among Omicron infected older patients, and to explore the correlation between the nutritional status and the severity of Omicron infection in older patients.MethodsThis is a retrospective cross-sectional study. According to the clinical symptoms, patients were divided into two groups: mild and moderate to severe. Mini Nutritional Assessment short-form (MNA-SF) was conducted when patients were admitted and poor nutritional status was defined as MNA-SF score of 0–11. The inflammatory markers including neutrophil lymphocyte ratio (NLR), platelet lymphocyte ratio (PLR) and systemic inflammatory index (SII) were calculated and compared between two groups.ResultsTotal of 324 patients were enrolled, with median [interquartile range (IQR)] age of 73 (17) years. Overall, 241 cases were mild, 83 cases were moderate to severe at the time of diagnosis and that 54.3% of patients had poor nutritional status. Patients with poor nutritional status were found to be older (P < 0.001) and less vaccinated (P < 0.001), with a longer virus shedding duration (P = 0.022), more comorbidities (≥ 2) (P = 0.004) and higher value of NLR (P < 0.001), PLR (P < 0.001) and SII (P = 0.012). Vaccination, cycle threshold value in ORF1ab gene (OR CT value) and female, higher MNA-SF score was negatively connected with probability of moderate to severe infection. For every 1 score increase in MNA-SF, the odds ratio of moderate to severe infection decreased by 14.8% [adjusted odds ratio (aOR), 0.852; 95% confidence interval (CI): 0.734–0.988; P = 0.034].ConclusionsOlder patients with poor nutritional status are more likely to develop moderate to severe Omicron infection.

Extending the shelf life for food is an important aspect for the food industry. Due to the growing demand for semi-finished products and the need to reduce the consumption of residual amounts of antibiotics, as well as harmful synthetic preservatives that prolong the shelf life of products, it becomes necessary to use antimicrobials of natural origin. As is known, the use of antibiotics in large quantities leads to resistance of microorganisms to the latter. Therefore, even a small intake of antibiotics from food leads to a global problem – antibiotic resistance of pathogenic strains worldwide. To date, the most promising preservatives of natural origin are bacteriocins, which do not have a pharmacological effect on the human body, but at the same time are able to suppress the growth and development of undesirable microflora. This paper presents the results of the influence of the most available bacteriocins in the Russian Federation – Nizin and Natamycin on the shelf life and biological safety indicators of chilled meat. It has been established that the antimicrobial substances of bacterial origin considered in this work are able to prolong the shelf life of chilled pork up to 15 days and chicken meat up to 10 days.

Antimicrobial resistance (AMR) is a global health threat requiring urgent attention and effective strategies for containment. AMR is fueled by wastewater mismanagement and global mobility, disseminating multidrug-resistant (MDR) strains worldwide. While global estimates of AMR burden have been informative, community-level understanding has received little attention despite reports of high AMR prevalence in healthy communities. We assessed the "invasion" of antibiotic resistance genes (ARGs) into the normal human flora by characterizing AMR Escherichia coli in local wastewaters contributed by a healthy youth population. This study estimated 26% (out of 300 isolates) resistant and 59% plasmid-bearing E. coli in local wastewater. Of the 78 AMR isolates, the frequency of mono-resistance was higher against tetracycline (32%), followed by kanamycin (17%) and chloramphenicol (9%). Five isolates were potentially MDR. We further sequenced four MDRs and four sensitive strains to comprehend the genome and resistome diversity in comparison to the global wastewater E. coli (genomes from the PATRIC database). The whole-genome analysis revealed extensive genome similarity among global isolates, suggesting global dissemination and colonization of E. coli. Global wastewater resistome majorly comprised ARGs against aminoglycosides (26%), beta-lactam (17%), sulfonamide (11%), and trimethoprim (8%). Resistance to colistin, a last-resort antibiotic, was prevalent in MDRs of European and South Asian isolates. A systems approach is required to address the AMR crisis on a global scale, reduce antibiotic usage, and increase the efficiency of wastewater management and disinfection.

IntroductionMycobacterium orygis, a member of MTBC has been identified in higher numbers in the recent years from animals of South Asia. Comparative genomics of this important zoonotic pathogen is not available which can provide data on the molecular difference between other MTBC members. Hence, the present study was carried out to isolate, whole genome sequence M. orygis from different animal species (cattle, buffalo and deer) and to identify molecular marker for the differentiation of M. orygis from other MTBC members.MethodsIsolation and whole genome sequencing of M. orygis was carried out for 9 samples (4 cattle, 4 deer and 1 buffalo) died due to tuberculosis. Comparative genomics employing 53 genomes (44 from database and 9 newly sequenced) was performed to identify SNPs, spoligotype, pangenome structure, and region of difference.ResultsM. orygis was isolated from water buffalo and sambar deer which is the first of its kind report worldwide. Comparative pangenomics of all M. orygis strains worldwide (n= 53) showed a closed pangenome structure which is also reported for the first time. Pairwise SNP between TANUVAS_2, TANUVAS_4, TANUVAS_5, TANUVAS_7 and NIRTAH144 was less than 15 indicating that the same M. orygis strain may be the cause for infection. Region of difference prediction showed absence of RD7, RD8, RD9, RD10, RD12, RD301, RD315 in all the M. orygis analyzed. SNPs in virulence gene, PE35 was found to be unique to M. orygis which can be used as marker for identification.ConclusionThe present study is yet another supportive evidence that M. orygis is more prevalent among animals in South Asia and the zoonotic potential of this organism needs to be evaluated.

The Omicron variant of SARS-CoV-2 has rapidly become the dominant strain worldwide due to its high transmissibility, although it appears to be less pathogenic than previous strains. However, individuals with hematological malignancy (HM) and COVID-19 remain susceptible to severe infection and mortality, especially those with chronic lymphocytic leukemia (CLL) and those undergoing chimeric antigen receptor T-cell (CAR-T) treatment. Hematologists should thoroughly assess the severity of the patient’s hematological disease and the potential risk of SARS-CoV-2 infection before initiating chemotherapy or immunosuppressive treatment. Vaccination and booster doses are strongly recommended and patients with a poor vaccine response may benefit from long-acting COVID-19 neutralizing monoclonal antibodies (such as Evusheld). Early use of small molecule antiviral drugs is recommended for managing mild COVID-19 in HM patients and those with severe immunodeficiency may benefit from SARS-CoV-2 neutralizing monoclonal antibody therapy and high-titer COVID-19 convalescent plasma (CCP). For moderate to severe cases, low-dose glucocorticoids in combination with early antiviral treatment can be administered, with cytokine receptor antagonists or JAK inhibitors added if the condition persists or worsens. In the treatment of hematological malignancies, delaying chemotherapy is preferable for CLL, acute leukemia (AL), and low-risk myelodysplastic syndrome (MDS), but if the disease progresses, appropriate adjustments in dosage and frequency of treatment are required, with the avoidance of anti-CD20 monoclonal antibody, CAR-T and hematopoietic stem cell transplantation (HSCT). Patients with chronic myelocytic leukemia (CML) and myeloproliferative neoplasms (MPNs) can continue current treatment. What’s more, non-drug protective measures, the development of new vaccines and antiviral drugs, and monitoring of mutations in immunocompromised populations are particularly important.

Asthma is a widespread disease affecting approximately 300-million people globally. This condition leads to significant morbidity, mortality, and economic strain worldwide. Recent clinical and laboratory research advancements have illuminated the immunological factors contributing to asthma. As of now, asthma is understood to be a heterogeneous disease. Personalized medicine involves categorizing asthma by its endotypes, linking observable characteristics to specific immunological mechanisms. Identifying these endotypic mechanisms is paramount in accurately profiling patients and tailoring therapeutic approaches using innovative biological agents targeting distinct immune pathways. This article presents a synopsis of the key immunological mechanisms implicated in the pathogenesis and manifestation of the disease's phenotypic traits and individualized treatments for severe asthma subtypes.

Atypical Escherichia coli forms exhibit unusual characteristics compared to typical strains. The H2S-producing variants of some atypical E. coli strains cause a wide range of illnesses in humans and animals. However, there are sparse reports on such strains worldwide. We performed whole-genome sequencing (WGS) and detailed characterization of four H2S-producing E. coli variants from poultry and human clinical sources in Dhaka, Bangladesh. All four isolates were confirmed as E. coli using biochemical tests and genomic analysis, and were multidrug-resistant (MDR). WGS analysis including an additional Chinese strain, revealed diverse STs among the five H2S-producing E. coli genomes, with clonal complex ST10 being detected in 2 out of 5 genomes. The predominant phylogroup detected was group A (n = 4/5). The blaTEM1B (n = 5/5) was the most predominant extended-spectrum beta-lactamase (ESBL) gene, followed by different alleles of blaCTX-M (blaCTX-M -55,-65,-123; n = 3/5). Multiple plasmid replicons were detected, with IncX being the most common. One E. coli strain was classified as enteropathogenic E. coli. The genomes of all five isolates harbored five primary and four secondary function genes related to H2S production. These findings suggest the potential of these isolates to cause disease and spread antibiotic resistance. Therefore, such atypical E. coli forms should be included in differential diagnosis to understand the pathogenicity, antimicrobial resistance and evolution of H2S-producing E. coli.

Genomic insights into linezolid-resistant Enterococci revealed its evolutionary diversity and poxtA copy number heterogeneity

Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly increasing in some countries. Exploring their receptor binding and interspecies transmission risk is urgently needed. Herein, we examine the binding capacities of human and other 28 animal ACE2 orthologs covering nine orders towards S proteins of these sub-variants. The binding affinities between hACE2 and these sub-variants remain in the range as that of previous variants of concerns (VOCs) or interests (VOIs). Notably, R493Q reverse mutation enhances the bindings towards ACE2s from humans and many animals closely related to human life, suggesting an increased risk of cross-species transmission. Structures of S/hACE2 or RBD/hACE2 complexes for these sub-variants and BA.2 S binding to ACE2 of mouse, rat or golden hamster are determined to reveal the molecular basis for receptor binding and broader interspecies recognition.

Molecular analysis of rpoB gene mutation in MTB detected isolates in a tertiary care centre (AGMC) of North-East, India

Synthesis, antibacterial screening and computational studies of quinazoline-4 (3H)-one-triazole conjugates

The Omicron variants of SARS-CoV-2 have emerged as the dominant strains worldwide, causing the COVID-19 pandemic. Each Omicron subvariant contains at least 30 mutations on the spike protein (S protein) compared to the original wild-type (WT) strain. Here we report the cryo-EM structures of the trimeric S proteins from the BA.1, BA.2, BA.3, and BA.4/BA.5 subvariants, with BA.4 and BA.5 sharing the same S protein mutations, each in complex with the surface receptor ACE2. All three receptor-binding domains of the S protein from BA.2 and BA.4/BA.5 are "up", while the BA.1 S protein has two "up" and one "down". The BA.3 S protein displays increased heterogeneity, with the majority in the all "up" RBD state. The different conformations preferences of the S protein are consistent with their varied transmissibility. By analyzing the position of the glycan modification on Asn343, which is located at the S309 epitopes, we have uncovered the underlying immune evasion mechanism of the Omicron subvariants. Our findings provide a molecular basis of high infectivity and immune evasion of Omicron subvariants, thereby offering insights into potential therapeutic interventions against SARS-CoV-2 variants.

Cold-blooded hosts, particularly exotic frogs, have become a newly recognized reservoir for atypical Brucella species and strains worldwide, but their pathogenicity to humans remains largely unknown. Here we report the isolation and molecular characterization of a B. inopinata strain (FO700662) cultured from clinical samples taken from a captive diseased White's Tree Frog (Litoria caerulea) in Switzerland. The isolation of B. inopinata from a frog along with other reports of human infection by atypical Brucella raises the question of whether atypical Brucella could pose a risk to human health and deserves further attention. The investigations included histopathological analysis of the frog, bacterial culture and in-depth molecular characterization of strain FO700662 based on genome sequencing data. Originally identified as Ochrobactrum based on its rapid growth and biochemical profile, strain FO700622 was positive for the Brucella- specific markers bcsp31 and IS711. It showed the specific banding pattern of B. inopinata in conventional Bruce-ladder multiplex PCR and also had identical 16S rRNA and recA gene sequences as B. inopinata. Subsequent genome sequencing followed by core genome-based MLST (cgMLST) analysis using 2704 targets (74% of the total chromosome) revealed only 173 allelic differences compared to the type strain of B. inopinata BO1T, while previously considered the closest related strain BO2 differed in 2046 alleles. The overall average nucleotide identity (ANI) between the type strain BO1T and FO700622 was 99,89%, confirming that both strains were almost identical. In silico MLST-21 and MLVA-16 also identified strain FO700662 as B. inopinata. The nucleotide and amino acid-based phylogenetic reconstruction and comparative genome analysis again placed the isolate together with B. inopinata with 100% support. In conclusion, our data unequivocally classified strain FO700622, isolated from an exotic frog, as belonging to B. inopinata.

<i>Introduction: </i>Tuberculosis (TB) is a pathology considered one of the main causes of death by single infectious agent, ranking just after HIV / AIDS. Indeed, its emergence and the difficulty of its treatment, especially in the resistant form, in patients with co-infection with other diseases immundéprimante as HIV.<i> Observation 1:</i> 31 years old presented with febrile headaches complicated by epileptic seizures. The MRI scan showed 3 cockeyed and multilocular lesions suggesting neuromeningeal tuberculosis. HIV serology came back positive and during the first line treatment he relapsed and the resistance test was positive.<i> Observation 2:</i> 45 progressive alteration of the state associated with signs of tuberculosis impregnation and a meningeal syndrome. BK in the CSF and in the sputum was positive and brain imaging allowed us to retain the diagnosis of a neuromeningeal tuberculosis. The patient was put on anti-bacillary ERIP k4 and a corticotherapy. The workup for co-infection was able to establish an HIV infection. After 3 weeks of anti-bacillary treatment, the patient had a bad evolution and the search for resistance came back positive. <i>Observation 3: </i>25 years old, pulmonary tuberculosis manifested by a hemoptysis of small abundance associated with a deep alteration of the general state, 3 BK positive sputum, as well as the image of a tuberculous cavern on the thoracic CT. Bad evolution after 2 months of treatment of first worsening of symptoms neuro and systemic involvement the search for resistance came back positive. <i>Discussion:</i> Drug-resistant tuberculosis is a major global public health challenge. In this article, we present three cases of drug-resistant TB in HIV-coinfected patients, highlighting the emergence and increasing prevalence of multidrug-resistant TB (MDR-TB) strains worldwide. In order to control the spread of this dreaded disease, it is essential to improve treatment regimens, promote vaccination, educate affected patients, and promote adherence to treatment. <i>conclusion: </i>Diagnosis of drug-resistant tuberculosis should be prompt and considered if there is a delay or lack of improvement with conventional tuberculosis treatment.

G3 rotaviruses rank among the most common rotavirus strains worldwide in humans and animals. However, despite a robust long-term rotavirus surveillance system from 1997 at Queen Elizabeth Central Hospital in Blantyre, Malawi, these strains were only detected from 1997 to 1999 and then disappeared and re-emerged in 2017, 5 years after the introduction of the Rotarix rotavirus vaccine. Here, we analysed representative twenty-seven whole genome sequences (G3P[4], n = 20; G3P[6], n = 1; and G3P[8], n = 6) randomly selected each month between November 2017 and August 2019 to understand how G3 strains re-emerged in Malawi. We found four genotype constellations that were associated with the emergent G3 strains and co-circulated in Malawi post-Rotarix vaccine introduction: G3P[4] and G3P[6] strains with the DS-1-like genetic backbone genes (G3-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2), G3P[8] strains with the Wa-like genetic backbone genes (G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1), and reassortant G3P[4] strains consisting of the DS-1-like genetic backbone genes and a Wa-like NSP2 (N1) gene (G3-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2). Time-resolved phylogenetic trees demonstrated that the most recent common ancestor for each ribonucleic acid (RNA) segment of the emergent G3 strains was between 1996 and 2012, possibly through introductions from outside the country due to the limited genetic similarity with G3 strains which circulated before their disappearance in the late 1990s. Further genomic analysis revealed that the reassortant DS-1-like G3P[4] strains acquired a Wa-like NSP2 genome segment (N1 genotype) through intergenogroup reassortment; an artiodactyl-like VP3 through intergenogroup interspecies reassortment; and VP6, NSP1, and NSP4 segments through intragenogroup reassortment likely before importation into Malawi. Additionally, the emergent G3 strains contain amino acid substitutions within the antigenic regions of the VP4 proteins which could potentially impact the binding of rotavirus vaccine-induced antibodies. Altogether, our findings show that multiple strains with either Wa-like or DS-1-like genotype constellations have driven the re-emergence of G3 strains. The findings also highlight the role of human mobility and genome reassortment events in the cross-border dissemination and evolution of rotavirus strains in Malawi necessitating the need for long-term genomic surveillance of rotavirus in high disease-burden settings to inform disease prevention and control.

Asymmetric expression of CA2 and CA13 linked to calcification in the bilateral mandibular condyles cause crossed beaks in chickens