Genotype Strains Research Articles

Phylogenetic Characterization of Vibrio vulnificus Strains from Oysters and its Comparison with Clinical vcgE Genotype Strain.

Twenty-one environmental Vibrio vulnificus strains from the Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE) bacteria collection, 20 of them isolated from oyster samples and 1 from a reported clinical case, were sequenced to analyze the genomic divergence between 2 genotypes, E-genotype and C-genotype, proposed by various groups to distinguish clinical (C) from environmental (E) V. vulnificus strains. As indicated in previous analyses of PFGE, MLST, and rtxA, 9 of the CICESE isolates were identified as vcgE, compared with 12 as vcgC. Separation of the genotypes into these 2 groups was confirmed in this study, based on the presence of certain genes in the 21 genomes, the presence of virulence factors, and rtxA sequencing. Most genomes from oyster isolates expressed rtxA-C type, with the exception being rtxA-M type detected in CICESE-594 a vcgE strain isolated from a clinical case. Although several genetic approaches clearly indicate differences between the C- and E-genotypes, none of them, including those in this study, can highlight a single factor that could be used to indicate the potential pathogenicity of V. vulnificus isolated from oysters.

Molecular characterization of human respiratory syncytial virus strains circulating among hospitalized children in Jordan

BackgroundHuman Respiratory Syncytial Virus (HRSV) is a primary cause of severe pediatric respiratory infections, particularly in infants and young children, often resulting in hospitalization. The virus possesses a high degree of mutagenic potential, contributing to significant antigenic diversity, which complicates immune responses and poses challenges for vaccine development and disease management. This study was conducted in Jordan from 2022 to 2023 to epidemiologically determine the prevalence and molecular characteristics of RSV.MethodsA total of 288 nasopharyngeal (NP) swabs were collected from hospitalized children at Prince Hamza Hospital, Amman, Jordan. All samples were screened for common viral and bacterial respiratory pathogens using PCR. A partial segment of the G gene of RSV was amplified for molecular characterization and phylogenetic tree analysis.ResultsViral and/or bacterial infection was identified in 71.9% (207/288) of the tested specimens. Among these, 35 samples (12.2%, 35/288) tested positive for RSV. Specific subgroup PCR analysis identified (25, 71.4%) RSV-A, (4, 11.4%) RSV-B, and (6, 17.1%) could not be identified using our set of primers. Phylogenetic tree analysis revealed that RSV-A ON1 and RSV-B BA9 genotype strains predominate in Jordan. We observed multiple substitutions in our studied sample which would drive variation in the level of antigenicity and pathogenicity of RSV. Glycosylation sites identified were consistent with previously reported studies.ConclusionThis study provides updated epidemiological data on the strains circulating in Amman, Jordan and their molecular characteristics. Continuous RSV surveillance informs vaccine development, guides public health interventions, and enables timely administration of prophylactic treatments, reducing the burden of RSV-related illness.

Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolated from Bloodstream Infections in South Korea

Background/Objectives: Bloodstream infection by carbapenem-resistant Acinetobacter baumannii (CRAB) is a serious clinical problem worldwide. To study its clonal relationship and genetic features, we report the draft genome sequence of CRAB strains isolated from human blood in South Korea. Methods: Among A. baumannii strains isolated from patients at nine general hospitals in 2020, 12 CRAB strains of different genotypes were selected. Genomic DNA was sequenced using a combination of Illumina MiSeq and Oxford Nanopore MinION platforms. Antimicrobial susceptibility testing was performed using the disk diffusion method. Antimicrobial resistance and virulence genes were investigated in silico using the Center for Genomic Epidemiology server and the Virulence Factors Database. Results: The multilocus sequence types of isolates included ST191, ST195, ST357, ST369, ST451, ST469, ST491, ST784, ST862, ST1933, ST2929, and a novel type, ST3326. The predominant sequence type, ST191, demonstrated close genetic relationships with several isolates, including ST469, ST369, ST195, ST784, ST491, and ST3326, with ST3326 classified as a subgroup of ST191. We found 18 antimicrobial resistance genes and one quaternary ammonium compound resistance gene. All examined strains harbored blaOXA-23, which is associated with carbapenem resistance. While variations in antibiotic and disinfectant resistance genes were observed, all isolates exhibited similar virulence factors, with the exception of the biofilm and capsule production genes. Conclusions: This nationwide report of the draft genome sequence of patient-derived strains provides valuable insights into the genomic features associated with clonal relationships and antimicrobial resistance of CRAB in bloodstream infections.

Deep learning applied to the segmentation of rodent brain MRI data outperforms noisy ground truth on full-fledged brain atlases

Translational magnetic resonance imaging of the rodent brain provides invaluable information for preclinical drug development. However, the automated segmentation of such images for quantitative analyses is limited compared to human brain imaging mainly due to the inferior anatomical contrast and the resulting less advanced registration and atlasing tools. Here, we investigated the potential of deep learning models for the segmentation of magnetic resonance images of rat brains into an entire set of multiple regions of interest (rather than individual loci), focusing on the development of a robust method that accommodates changes in the input based on differences in animal strain (genotype) and size. Manually generated labels are expensive, so we tested the ability of neural networks to learn brain structures from noisy but inexpensive registration-based labels, allowing very large datasets to be leveraged for training. We compared three distinct model architectures (U-Net, Attention-U-Net and DeepLab) by training them on a dataset of >10,000 magnetic resonance images of rat brains and found that each model was able to segment the entire brain into predefined sets of 29 and 58 regions, respectively, with the Attention U-Net achieving the best performance. The models canceled out unstructured label noise in the imperfect training data to provide smoother and more symmetric segmentations than registration-based labeling, and were more robust when presented with input variations, thus outperforming the noisy ground truth. Our pipeline also includes uncertainty estimation and an explainability mechanism, hence providing features essential for anomaly detection and quality assurance. In summary, our study shows that deep learning models do achieve accurate brain segmentation in high-throughput quantitative preclinical imaging without the need for expensive expert-generated labels.

Genome sequences of recombinant African swine fever virus isolated from domestic pigs in Vietnam

ABSTRACT African swine fever is a highly contagious and devastating disease of pigs. Here, we present the draft genome assemblies of three Vietnamese African s wine fever virus (ASFV) isolates: rASF1/2-avac02, rASF1/2-avac03, and rASF1/2-avac07. All isolates were closely related to the Chinese recombinant ASFV strains of genotypes I and II.

Circulation of <i>Mycobacterium tuberculosis</i> strains of the Beijing Central Asian Outbreak genotype in the Kemerovo region — Kuzbass in 2018–2022

Introduction. The Kemerovo region — Kuzbass is characterized by a high prevalence of multidrug-resistant (MDR) tuberculosis (TB), including coinfection with HIV (HIV/TB). A previously unknown in Russia relationship between MDR and the Beijing Central Asian Outbreak (CAO) subtype has been discovered, which updates studies of Mycobacterium tuberculosis taking into account this resistant variant. Objective: to study the molecular genetic structure of the M. tuberculosis population, to assess the prevalence and possible routes of emergence of Beijing CAO strains in the Kemerovo region — Kuzbass. Materials and methods. A total of 325 M. tuberculosis strains were studied in 2018–2022 using spoligotyping, MIRU-VNTR 24 and SNP typing. Whole genome sequencing and bioinformatics analysis were performed for seven Beijing CAO strains. Results. Primary MDR and pre-extensive drug resistance (pre-XDR) were detected in 39.4% and 11.5% of strains, respectively. In the total sample, MDR was 43.4%, pre-XDR — 19.7%. In the structure of the M. tuberculosis population, the Beijing genotype prevailed (78.8%), with its subtypes Central Asian Russian (40.9%) and B0/W148 (32.6%). The Euro-American lineage (27.3%) was represented by the genotypes T (6.5%), LAM (5.8%), Ural (4.9%), H (0.9%); one strain CAS1-Delhi was detected, the genotype of 2.8% of strains was not identified. The proportion of Beijing CAO was 12.6% of the total sample; this subtype was significantly more often detected among HIV/TB (20.6%) than in HIV-negative TB patients (9.1%; p = 0.005). The results of the Beijing CAO genome analysis from the Kemerovo region indicate the absence of a direct chain of transmission between these TB cases. A hypothesis has been put forward about the introduction of Beijing CAO to the Kemerovo region from Central Asia and its endemic circulation in the region. Conclusion. A high level of MDR and pre-XDR was detected in Beijing genotype strains in the M. tuberculosis population of the Kemerovo region — Kuzbass, especially the B0/W148 (97.2%) and CAO (87.5%) subtypes. Beijing CAO strains, detected mainly in newly diagnosed HIV/TB patients, require further monitoring and control of their spreading.

Structure-based design of glycoprotein subunit vaccines for mumps

Mumps virus (MuV) is a highly contagious paramyxovirus that is endemic in most regions of the world and continues to cause outbreaks even in highly immunized populations. Outbreaks of mumps in countries with high measles, mumps, and rubella vaccination coverage have been attributed to waning immunity and antigenic differences between the Jeryl Lynn vaccine strain (genotype A) and circulating wild-type viruses. To obtain a subunit vaccine, we used structure-based design to engineer the mumps fusion (F) glycoprotein stabilized in its prefusion conformation (Pre-F) as well as a chimeric immunogen comprising Pre-F linked to mumps hemagglutinin neuraminidase (HN); in mice, both Pre-F antigen and the chimeric antigen elicited potent cross-reactive plaque reducing neutralizing titers to genotypes A, G, and H mumps. A crystal structure of mumps Pre-F at 2.16 Å resolution validated the stabilization strategy, while a post-fusion form of F was engineered as a comparator. Monoclonal antibodies to mumps Pre-F and HN were isolated from immunized mice; 7 of 14 Pre-F-specific antibodies and 9 of 15 HN-specific antibodies were capable of neutralizing genotype G MuV with a range of potencies. Additionally, 7 of 14 Pre-F-specific antibodies neutralized genotype A mumps. Structural and binding analyses of Pre-F-specific antibodies revealed binding to four discrete neutralizing antigenic sites and binding analyses of HN-specific antibodies revealed binding to five discrete neutralizing antigenic sites. Overall, the PreF and the chimeric Pre-F/HN immunogens are promising candidates to boost MMR-elicited immunity to mumps or as a next-generation vaccine.

Comparative analysis of whole-genome sequences of African swine fever virus (Asfarviridae: Asfivirus) isolates сollected on the territory of the left bank of the Dnieper River in 2023.

The lack of data on the whole-genome sequences of African swine fever virus (ASFV) variants circulating on the territory of the left bank of the Dnieper River complicates the understanding of the molecular evolution of the virus and the character of the epidemic process development in Russia and Ukraine. Understanding the genetic divergence and phylogenetic relatedness of isolates can largely adjust the strategy of general and specific prevention of the disease. The aim of the study - search and description of unique mutations (deletions/insertions/substitutions) in isolates collected from domestic pigs in Donetsk, Luhansk and Zaporozhye regions in 2023; determination of relatedness and level of homology with reference strains of ASFV genotype II; sub-genotyping and clustering of isolates based on whole-genome analysis. The samples used were a culture suspension of porcine bone marrow (PBM) cells containing ASFV isolates obtained from pathologic material from domestic pig carcasses. Genomic DNA was prepared by purification and concentration of virus followed by phenol-chloroform extraction of total nucleic acid. The high-throughput sequencing process was performed using MGI technology. Consensus sequences were assembled by mapping reads to the reference genome of strain Georgia 2007/1. All isolates are assigned to genotype II, have a monophyletic origin, are phylogenetically close to the clusters «Europe» (4/5) and «Bryansk 2021» (1/5), and are divergent from the original parental genetic variants that make up the enlarged clades. In addition, numerous substitutions in the loci of the multigene family MGF 110, 505, and 360, encoding virulence proteins, were detected in 4 isolates from Donetsk and Zaporozhye regions. The phylogeny of the genotype II ASFV, which originated from the reference strain Georgia 2007/1, is shown to be sufficient for isolate differentiation. The presented data are of theoretical and practical importance for domestic and international ASFV surveillance.

Comparison of TLR4 Genotype and TLR4 Pathway-Related Cytokines in Different Strains of Mice in Response to Pertussis Toxin Challenge.

The genetic background of Toll-like receptor 4 (TLR4) proved to be important in the induction of immune protection against Bordetella pertussis infection in humans. Currently, the evaluation of the acellular pertussis (aP) vaccine depends largely on using different mouse strains, while the TLR4 genotype of different mouse strains in response to pertussis toxin (PT) is not carefully determined. The current study was designed to determine the differences in TLR4 genotype and TLR4 pathway-related cytokines in response to PT stimulation among mouse strains of ICR, NIH, and BALB/c. We first determined the single-nucleotide polymorphisms (SNPs) in the TLR4 gene by using first-generation sequencing. Then, the cellular response, including the TLR4 mRNA expression and TLR4 signaling-related cytokines, of immune cells from different mouse strains after PT stimulation was determined. Three missense mutation sites (rs13489092, rs13489093, rs13489097) of the TLR4 gene were found. ICR mice were homozygous without mutation, NIH mice were partially heterozygous, and BALB/c mice were homozygous with a missense mutation. The expression of TLR4 was repressed while the downstream cytokines were upregulated after PT stimulation differently among mouse strains. The IFN-β cytokine of the TRIF pathway was significantly increased in ICR mice (p < 0.05). The IL-6 cytokine of the MyD88-dependent pathway was significantly increased in BALB/c mice (p < 0.05). The identified SNPs of the TLR4 gene in different mouse strains might account for the differences in cytokines levels determined after PT stimulation. Our studies might provide useful referees to reduce the mouse-derived difference in the determination of vaccine titer and increase the comparability of the vaccine from different origins, as different mouse strains were used for vaccine development in different countries.

Molecular epidemiology and genetic characterization of hepatitis B virus in two major provinces of Pakistan.

Hepatitis B virus (HBV) infection is a major public health issue and is responsible for considerable morbidity and mortality globally. In Pakistan, the prevalence of chronic HBV infection varies from 2% to 4%, with an estimated exposure rate of approximately 34%. The major objective of this study was to determine the prevalence of HBV genotypes and the pattern of escape mutations in the HBV S gene in two major provinces of Pakistan: Punjab and Khyber Pakhtunkhwa. A total of 146 serum/plasma samples collected from hepatitis B patients were sequenced by the Sanger method. Phylogenetic analysis indicated the intermixed circulation of closely related strains of HBV genotype D and subgenotypes HBV/D1, HBV/D2, and HBV/A2 in both provinces, and various escape mutations (Y100C, P120S/T, G119R, C121S/Y, R122K, T126I, A128V, Q129H/R, G130R, T131N/I, M133T/I, Y134N, C137W, S143L, and D144E) were identified. These findings provide important insights into the current prevalence of HBV genotypes in Pakistan and will help in the establishment of more-efficient disease interventions and patient management strategies.

The Impact of Layer Strains Genotype on Egg Quality and Eggshell Ultrastructural

The Impact of Layer Strains Genotype on Egg Quality and Eggshell Ultrastructural

Screening and Immune Efficacy Evaluation of Antigens with Protection Against Feline Calicivirus.

Feline calicivirus (FCV), a pathogen that causes upper respiratory tract diseases in felids, primarily leads to oral ulcers and various respiratory symptoms, which can be fatal in severe cases. Currently, FCV prevention and control rely primarily on vaccination; however, the existing vaccine types in China are mainly inactivated vaccines, leading to a single prevention and control method with suboptimal outcomes. This study commences with a genetic evolution analysis of Chinese FCV isolates, confirming the presence of two major genotypes, GI and GII with GI emerging as the dominant form. We subsequently selected the broadly neutralizing vaccine candidate strain DL39 as the template for the truncation and expression of multiple recombinant proteins. Through serological assays, we successfully confirmed the optimal protective antigen region, which is designated CE39 (CDE). Further investigation revealed the location of the optimal protective antigen region within the CE region for both the GI and GII genotype strains. Capitalizing on this discovery, a bivalent recombinant protein, designated CE39-CEFB, was generated. Cat antisera generated against CE39 and CE39-CEFB proteins were used in cross-neutralization against various strains of different genotypes, yielding high neutralization titers ranging from 1:45 to 1:15 and from 1:48 to 1:29, respectively, which surpassed those induced by antisera from cats vaccinated with Mi-aosanduo (commercial vaccine, strain 255). Ultimately, in vivo challenge experiments were per-formed after immunizing cats with the CE39 and CE39-CEFB proteins, utilizing Miaosanduo as a control for comparison. The results demonstrated that immunization with both proteins effectively made cats less susceptible to FCV GI, GII, and VSD strains infection, resulting in superior immune efficacy compared with that in the Miaosanduo group. These results indicate that this study successfully identified the antigen CE39, which has broad-spectrum antigenicity, through in vivo and in vitro experiments. These findings pre-liminarily demonstrate that the optimal protective antigen region of FCV strains is the CE region, laying a theoretical foundation for the development of novel broad-spectrum vaccines against FCV disease.

Strain- and Subtype-Specific Replication of Genotype 3 Hepatitis E Viruses in Mongolian Gerbils

Since Mongolian gerbils are broadly susceptible to hepatitis E virus (HEV), including genotypes 1, 4, 5, and 8 (HEV-1, HEV-5, HEV-5, and HEV-8) and rat HEV, they are a useful small animal model for HEV. However, we have observed that the subtypes HEV-3k and HEV-3ra in genotype 3 HEV (HEV-3) were not infected efficiently in the gerbils. A small-animal model for HEV-3 is also needed since HEV-3 is responsible for major zoonotic HEV infections. To investigate whether gerbils can be used as animal models for other subtypes of HEV-3, we injected gerbils with five HEV-3 subtypes (HEV-3b, -3e, -3f, -3k, and -3ra) and compared the infectivity of the subtypes. We detected viral RNA in the gerbils’ feces. High titers of anti-HEV IgG antibodies in serum were induced in all HEV-3b/ch-, HEV-3f-, and HEV-3e-injected gerbils. Especially, the HEV-3e-injected animals released high levels of viruses into their feces for an extended period. The virus replication was limited in the HEV-3b/wb-injected and HEV-3k-injected groups. Although viral RNA was detected in HEV-3ra-injected gerbils, the copy numbers in fecal specimens were low; no antibodies were detected in the sera. These results indicate that although HEV-3′s infectivity in gerbils depends on the subtype and strain, Mongolian gerbils have potential as a small-animal model for HEV-3. A further comparison of HEV-3e with different genotype strains (HEV-4i and HEV-5) and different genera (rat HEV) revealed different ALT elevations among the strains, and liver damage occurred in HEV-4i- and HEV-5-infected but not HEV-3e- or rat HEV-infected gerbils, demonstrating variable pathogenicity across HEVs from different genera and genotypes in Mongolian gerbils. HEV-4i- and HEV-5-infected Mongolian gerbils might be candidate animal models to examine HEV’s pathogenicity.

Antifungal susceptibility, molecular epidemiology, and clinical risk factors of Candida glabrata in intensive care unit in a Chinese Tertiary Hospital.

The increasing incidence and high mortality rate of Candida glabrata infection in ICU patients is an important issue. Therefore, it is imperative to investigate the antifungal susceptibility profiles and epidemiological characteristics in local regions. Herein, antifungal susceptibility testing was conducted to determine the minimum inhibitory concentrations (MICs) of eight antifungal drugs. Multilocus sequence typing (MLST) was used to study the strain genotype, geographical distribution, and susceptibility to antifungal agents among C. glabrata isolates. The mechanism of echinocandin resistance was explored by sequencing the FKS1 and FKS2 genes (encoding 1,3-β-D-glucan synthases) of echinocandin-resistant C. glabrata strains. Moreover, we further investigated the clinical manifestations and the various risk factors of patients infected with C. glabrata in the ICU. We selected 234 C. glabrata isolates from 234 patients in the ICU randomly for the follow-up study. Cross-resistance was found among the ICU C. glabrata isolates. Analysis using MLST showed that the genetic diversity among the C. glabrata isolates was low. Furthermore, sequence type showed no correlation with the antifungal resistance profiles, but was associated with geographical distribution. We also revealed novel mutations in FKS1 (S629P) and FKS2 (W1497stop) that mediated high-level echinocandin resistance (MIC >8 µg/mL). More than 14 days' stay in ICU (P=0.007), Acute Physiology and Chronic Health Evaluation II (APACHE-II) score (P=0.024), prior antifungal exposure (P=0.039) and lung disease (P=0.036) were significantly associated with antifungal resistant/non-wild-type C. glabrata infection. Our study shed light on the antifungal susceptibility, molecular epidemiology, and clinical risk factors of C. glabrata in the ICU of a Chinese Tertiary Hospital. Importantly, we revealed the molecular mechanism of echinocandin resistance. These results highlight the significance of continued surveillance in ICUs and provide data support for the treatment of C. glabrata in clinics.

High rates of hepatic involvement associated with new epidemic measles strains in Romania.

Similar to other European countries, a measles epidemic dominated by D8 genotype strains is ongoing since 2022 in our country. Recent reports of liver involvement associated with new measles virus (MeV) strains are scarce. The aim of the study was to compare the clinical characteristics between hospitalized patients with measles from the current epidemic and those from the previous outbreak and to analyze the risk factors associated with hepatic involvement. Data were collected retrospectively for all consecutive adult ( ≥18 years old) patients admitted between October 2022-April 2024 and January 2018-December 2019. A number of 228 patients from the current and 130 from the previous MeV epidemic were included. The main statistically significant differences were those regarding hepatic involvement (77.2% vs. 45.4%, p < 0.001) and significant hepatocellular injury (23.6% vs. 10.7%, p = 0.003). Compared to cases without liver involvement (123), patients with hepatocytolysis (235) had a higher prevalence of keratoconjunctivitis (42.5% vs. 28.4%, p = 0.01), thrombocytopenia (47.6% vs. 34.9%, p = 0.02), severe lymphopenia (51% vs. 35.7%, p = 0.007) and high fibrinogen levels (58.7% vs. 47.1%, p = 0.04). MeV strains from the 2022-2024 epidemic were the strongest predictors of hepatic involvement in the multivariable analysis (odds ratio = 4.3, 95% confidence interval: 2.5-7.4, p < 0.001). The mortality rate of patients with hepatocellular injury was 1.2%. The current measles epidemic is dominated by high rates of hepatic involvement compared to the previous outbreak. Although not associated with a significant mortality, the potential change in MeV hepatotropism could have important clinical implications and warrants further monitoring.

Beijing Central Asian Outbreak strain cluster of Mycobacterium tuberculosis detected in Irkutsk region, Russia

Background. Irkutsk region maintains a high incidence rate of multidrug-resistant (MDR) tuberculosis (TB). Detection of MDR-associated Mycobacterium tuberculosis strains in Irkutsk region requires dynamic assessment of the TB pathogen population, taking into account the emergence of a new resistant variant of Beijing Central Asian Outbreak (CAO).The aim of the study. To assess changes in the genotypic structure of M. tuberculosis strains circulating in the Irkutsk region over a ten-year period.Materials and methods. A total of 732 M. tuberculosis strains (196 strains for 2021– 2022, 536 strains for 2011–2015) were studied using MIRU-VNTR and SNP typing.Results. The MDR level increased to 67.4 % with an increase of pre-extensive drug resistance (pre-XDR) (33.2 %) (p &lt; 0.001). In the modern sample, the dominance of the Beijing genotype increased (83.7 %) due to an increase in the proportions of the B0/W148 (38.8 %) and CAO (12.8 %) subtypes with a stable overall level of Central Asian Russian (36.8 %) and other Beijing strains (8.2 %). Strains other than the Beijing genotype belonged mainly to the Euro-American lineage (Lineage 4): LAM (8.9 %), Ural (2.7 %), Haarlem (2.0 %), S (0.5 %) and L4-unclassified (5.3 %); 25 isolates were not classified. In the 2011–2015 sample, LAM was more common than in the modern sample (10.8 % vs. 3.6 %; p &lt; 0.01). The increase in MDR and preXDR was statistically significant among Beijing B0/W148 strains (93.4 % vs. 66.1 %; p &lt; 0.001).Conclusion. Unfavorable trends of significant spread of MDR and pre-XDR of the Beijing genotype strains were revealed. Among the Beijing strains, not only B0/W148 but also the Beijing CAO subtype, which was previously rare in Siberia, are the most successful; they have the highest levels of MDR and pre-XDR and a tendency to widespread distribution in all groups of TB patients.

Genotyping of oral Candida albicans and Candida tropicalis strains in patients with orofacial clefts undergoing surgical rehabilitation by MALDI-TOF MS: Case-series study

Patients with orofacial clefts are more likely to develop oral fungal diseases due to anatomo-physiological changes and surgical rehabilitation treatment. This case-series study evaluated the genetic diversity and dynamics of oral colonization and spread of C. albicans and C. tropicalis in four patients with orofacial clefts, from the time of hospital admission, perioperative and outpatient follow-up, with specialized physician. Candida biotypes previously identified by CHROMagar Candida and PCR methods were studied by MALDI-TOF MS assays and clustering analyses. Possible correlations with pathogenicity characteristics were observed, including production of hydrolytic exoenzymes and the antifungal sensitivity profiles. Amphotericin B-sensitive and fluconazole-resistant (low frequency) C. tropicalis and C. albicans, including clinically compatible MIC of nystatin, were found in the oral cavity of these patients. Clusters of isolates revealed phenomena of (i) elimination in the operative phase, (ii) maintenance or (iii) acquisition of oral C. tropicalis in the perioperative period and specialized outpatient and medical follow-up. For C. albicans, these phenomena included (i) elimination in the operative phase, (ii) acquisition in the operative phase and propagation from the hospital environment, and (iii) maintenance during hospitalization and operative phase. Amphotericin B and nystatin were shown to be effective in cases of clinical treatment and/or prophylaxis, especially considering the pre-existence of fluconazole-resistant strains. This study confirmed the phenomena of septic maintenance, septic neocolonization and septic elimination involving the opportunistic pathogens. MALDI-TOF MS associated with clustering analysis may assist the monitoring of clinical isolates or groups of epidemiologically important microbial strains in the hospital setting.

Multidrug-resistant tuberculosis clusters and transmission in Taiwan: a population-based cohort study.

Multidrug-resistant tuberculosis (MDR-TB) remains a challenge in the TB program of Taiwan, where 0.5% of new cases and 2.1% of previously treated cases were resistant to at least rifampin (RIF) and isoniazid (INH). Since >80% of our MDR-TB are new cases, genotyping of MDR Mycobacterium tuberculosis is implemented to facilitate contact investigation, cluster identification, and outbreak delineation. This is a population-based retrospective cohort study analyzing MDR-TB cases from 2019 to 2022. Whole genome sequencing (WGS) was performed using the Illumina MiSeq and analyzed using the TB Profiler. A single nucleotide polymorphism (SNP) threshold of ≤ 12 and phylogenetic methods were used to identify putative transmission clusters. An outbreak was confirmed using genomic data and epidemiologic links. Of the 297 MDR-TB cases, 246 (82.8%), 45 (15.2%), and 6 (2.0%) were simple MDR, extensively drug-resistant tuberculosis (pre-XDR-TB) and extensively drug-resistant tuberculosis (XDR-TB), respectively. The sublineage 2.2 modern Beijing was the predominant (48.8%) MDR-TB strain in Taiwan. Phylogenetic analysis identified 25.3% isolates in 20 clusters, with cluster sizes ranging from 2 to 13 isolates. Nevertheless, only 2 clusters, one household and one community, were confirmed as outbreaks. In this study, we found that males had a higher risk of MDR-TB transmission compared to females, and those infected with the sublineage 2.1-proto-Beijing genotype isolates were at a higher risk of transmission. Furthermore, 161 (54.2%) isolates harbored compensatory mutations in the rpoC and non-rifampicin resistant determinant region (non-RRDR) of the rpoB gene. MDR-TB strains containing rpoB S450L and other compensatory mutations concurrently were significantly associated with clusters, especially the proto-Beijing genotype strains with the compensatory mutation rpoC E750D or the modern Beijing genotype strains with rpoC D485Y/rpoC E1140D. Routine and continuous surveillance using WGS-based analysis is recommended to warn of risks and delineate transmission clusters of MDR-TB. We proposed the use of compensatory mutations as epidemiological markers of M. tuberculosis to interrupt putative MDR-TB transmission.

Novel murine closed-loop auditory stimulation paradigm elicits macrostructural sleep benefits in neurodegeneration.

Boosting slow-wave activity (SWA) by modulating slow waves through closed-loop auditory stimulation (CLAS) might provide a powerful non-pharmacological tool to investigate the link between sleep and neurodegeneration. Here, we established mouse CLAS (mCLAS)-mediated SWA enhancement and explored its effects on sleep deficits in neurodegeneration, by targeting the up-phase of slow waves in mouse models of Alzheimer's disease (AD, Tg2576) and Parkinson's disease (PD, M83). We found that tracking a 2 Hz component of slow waves leads to highest precision of non-rapid eye movement (NREM) sleep detection in mice, and that its combination with a 30° up-phase target produces a significant 15-30% SWA increase from baseline in wild-type (WTAD)and transgenic (TGAD) mice versus a mock stimulation group. Conversely, combining 2 Hz with a 40° phase target yields a significant increase ranging 30-35% in WTPD and TGPD mice. Interestingly, these phase-target-triggered SWA increases are not genotype dependent but strain specific. Sleep alterations that may contribute to disease progression and burden were described in AD and PD lines. Notably, pathological sleep traits were rescued by mCLAS, which elicited a 14% decrease of pathologically heightened NREM sleep fragmentation in TGAD mice, accompanied by a steep decrease in microarousal events during both light and dark periods. Overall, our results indicate that model-tailored phase targeting is key to modulate SWA through mCLAS, prompting the acute alleviation of key neurodegeneration-associated sleep phenotypes and potentiating sleep regulation and consolidation. Further experiments assessing the long-term effect of mCLAS in neurodegeneration may majorly impact the establishment of sleep-based therapies.

Isolation of a more aggressive GVI-1 genotype strain HX of the avian infectious bronchitis virus

The avian infectious bronchitis virus (IBV) poses a significant economic threat to the global poultry industry. Although in recent years, the GVI-1 lineage of IBV has proliferated throughout China, there is still a lack of comprehensive studies regarding the pathogenicity of this lineage, particularly with respect to infections of the digestive tract and the antigenic characteristics of the S1 gene. In this study, we investigated the effects of infecting 14-day-old chicks with the HX strain of the GVI-1 lineage over a 14-d period postinfection. Assessment of the pathogenicity of the HX strain included clinical observations; monitoring of body weight, organ viral load, viral shedding, and gross anatomy; histopathological analysis, and bioinformatics-based antigenic characterization of the S1 protein. The findings revealed that compared with previously reported GVI-1 lineage strains, the HX strain is characterized by greater virulence, with infection leading to approximately 26% mortality and extensive severe organ damage, including that of the proventriculus and kidneys. Moreover, at 14 d postinfection, 80% of oral swabs and 100% of cloacal swabs from chickens infected with the HX strain tested positive, indicating a prolonged period of viral shedding relative to that previously reported for GVI-1 lineage strains. Bioinformatic analysis of B-cell epitopes on the S1 protein revealed 7 potential antigenic epitopes. Collectively, our findings in this study provide clear evidence to indicate that compared previously reported GVI-1 lineage strains, chicks infected with the IBV GVI-1 lineage strain HX are characterized by heightened rates of mortality, more pronounced organ damage, and an extended period of viral shedding. This comprehensive characterization highlights the pathogenic potential of the GVI-1 lineage and its capacity to induce severe kidney and proventriculus damage, thereby emphasizing the imperative of early initiated preventive measures. Furthermore, on the basis of our analysis of the antigenic properties of the S1 protein, we have identified 7 potential linear B-cell epitopes, which will provide valuable insights for the development of epitope-based vaccines.