Infection Genetics and Evolution最新文献

Large numbers of infections and effective treatment or control depend on the ability to identify the causative agents of animal infections. Here we describe a study of an isolate DG22/1209/12 obtained from vaginal pus exudate collected from a Siamese cat. The isolate was believed to be a member of Trueperella abortisuis, which is related to problems with reproduction. The most important was to identify this isolate by applying different techniques of diagnosis. It included phenotypic testing, Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS), and molecular techniques such as amplification and sequencing of the 16S rRNA gene, intergenic spacer region (ISR), and the gap and tuf genes. Phenotypic tests confirmed the identification of DG22/1209/12 as T. abortisuis. Finally, the identification was confirmed with MALDI-TOF MS analysis which demonstrated log (score) value of 2.09 indicating a secure genus identification, probable species identification on T. abortisuis. Molecular analysis revealed a high sequence identity of 99.9 %, 99.5 %, 99.4 %, and 99.5 % for the 16S rRNA gene, ISR, gap, and tuf genes, respectively, for both the isolate DG22/1209/12 and the reference isolate T. abortisuis DSM 19515^T. The study highlights the effectiveness of combining phenotypic and genomic methods to accurately identify bacterial pathogens in veterinary medicine, leading towards focused intervention strategies.

Pseudomonas aeruginosa exhibits significant antibiotic resistance facilitated by both intrinsic and acquired mechanisms, prominently through Pseudomonas-derived cephalosporinase (PDC), serine Ambler class C β-lactamases encoded by the AmpC. AmpC, involved in the peptidoglycan recycling pathway, is regulated by genes such as ampD, ampR, and ampG, leading to increased expression and resistance to various beta-lactams. PDCs are classified into three main types: classical class C β-lactamases, extended-spectrum class C β-lactamases (ESAC β-lactamases), and inhibitor-resistant class C β-lactamases. This study aimed to identify prevalent PDC variants and its genetic characteristics in Indian and global P. aeruginosa isolates, focusing on their role in β-lactam resistance. Analyzing PDC sequences from 111 P. aeruginosa isolates collected at Christian Medical College (CMC), Vellore, we found the ESAC allele PDC-447 to be the most widespread among Indian isolates, present in 18 % of carbapenem-resistant and 11 % of carbapenem-susceptible strains. Global and Indian isolates PDC variants were validated using the NCBI PathogenWatch database, and the sequenced PDC region compared to PDC-1. PDC-398 and PDC-397 followed in prevalence among carbapenem-resistant isolates, while PDC-5 (ESAC) and PDC-1 (classical class C) were common in carbapenem-susceptible strains. A global analysis of 19,478 genomes revealed significant prevalence of ESAC variants such as PDC-3 (17.28 %) and PDC-5 (12.91 %), alongside classical class C beta-lactamases like PDC-8 (10.65 %). Indian isolates exhibited distinct patterns with PDC-3 and PDC-5 prevailing at 19.84 % and 10 %, respectively. Mutations in the omega loop, H-helix, and R2 region of PDCs were linked to enhanced antibiotic resistance, particularly the T105A mutation in the H-helix region. These findings underscore the complexity of antimicrobial resistance mechanisms in P. aeruginosa and highlight the need for novel therapeutic strategies and continuous surveillance to manage infections by this versatile pathogen. Understanding the prevalence and genetic characteristics of PDC variants is crucial for effective treatment strategies against P. aeruginosa and combating antibiotic resistance.

The recent discovery that the trimeric SARS-CoV-2 spike S glycoprotein carries heme within an NTD domain pocket of the S1 subunits, suggested that this virus may be cleverly utilizing heme, in addition to the S1 RBD domains, for invading target cells carrying a specific entry receptor like ACE2, TMEM106B and others. Studies during the COVID-19 pandemic revealed that the infectivity of this virus depends on cell surface heparan sulfate and that the infection induces non-canonical activation of the Complement Alternative pathway (AP) on the surface of infected cells. In our recent COVID-19 genomic studies, among the coding SNPs of interest we also detected the presence of the CFH rs1061170, rs800292 and rs1065489 within all the infected patient subgroups examined. The minor C allele of rs1061170 encodes CFH 402H that over the years has been associated with diseases characterized by complement dysregulation namely the age-related macular degeneration (AMD) and the atypical haemolytic uremic syndrome (aHUS). Also, more recently with the diminishment of CD4⁺ T cell responses with ageing. The rs800292 minor allele A encodes CFH 62I that supports enhanced cofactor activity for Complement factor I (CFI). Also, the rs1065489 minor allele T encodes CFH 936D and is located within the CCP16 domain that influences the affinity of CFH with extracellular laminins. A subsequent computational analysis revealed that the CFH residue 402 is located centrally within a heme-binding motif (HBM) in domain CCP7 (³⁹⁸YNQNYGRKF⁴⁰⁶). Heme on the viral spike glycoprotein S1 subunit could recruit CFH 402H for masking free viral particles from opsonisation, and when in proximity to cell surface, act as a bait disrupting CFH 402H from the heparan sulphate coat of the target cells. Publicly available genetic data for European populations indicate that the minor C allele of rs1061170 is present only in haplotypes that carry the major alleles of rs800292 and rs1065489. This combination encodes for CFH 402H that exhibits increased biochemical affinity for heme in proximity, without enhanced cofactor activity for CFI and weaker association with the extracellular matrix. In the theatre of infection, this combination can promote heme-mediated viral infection with weaker complement opsonisation and potential AP deregulation. This strategy may be evolutionary conserved among various classes of infectious agents.

Methicillin-resistant Staphylococcus aureus (MRSA) colonization can lead to subsequent severe infections. Unlike community and hospital-associated types, Livestock-associated MRSA (LA-MRSA) transmits to humans through direct contact with livestock and contaminated livestock products. This study aimed to investigate MRSA prevalence and molecular epidemiology in livestock farmers, livestock, and livestock products, including LA-MRSA presence and MRSA abundance in human and animal nasal microbiome, in southern Sri Lanka using a One Health approach. Nasal swabs from farmers and livestock on 50 farms (Nov 2020 - Dec 2021) and livestock products were collected. MRSA was isolated and confirmed using standard microbiological techniques. Staphylococcal chromosomal cassette mec typing, spa typing, and multilocus sequence typing were performed. Identified clones were compared with hospital isolates. Metagenomics analysis was performed on selected samples. MRSA prevalence was 24.0 % (12/50) in farms, 7.9 % (12/152) in farmers, 2.1 % (5/240) in livestock, and 1.9 % (3/157) in products. Of 372 S. aureus collected from clinical cultures, 59.4 % were MRSA. MRSA clones were identified in farm personnel (CC5/ST5/t002, CC1/ST1/t127, and ST45/CC45/t026), livestock (CC5/ST5/t002), and clinical cultures (CC5/ST5/t002 and CC5/ST6/t304), with ST45/CC45/t026 and CC5/ST6/t304 reported for the first time in Sri Lanka. LA-MRSA clones (ST389/ST9) were not detected. Animals had more diverse nasal microbiomes and lower MRSA abundance (<1.4 %) compared to humans (>82.3 %). MRSA colonization prevalence in southern Sri Lanka was relatively low. Two new clones and no LA-MRSA clones were identified. This study highlights the importance of continuing MRSA surveillance under the One Health framework to identify MRSA transmission between humans, animals, and the environment.

The prevalence and evolution of foamy viruses (FVs) have become the focus of research because of the risk of new zoonotic diseases. FVs have been isolated from various mammals and exhibit long-term co-speciation with their hosts. They also appear to be mild and nonpathogenic to their hosts. However, they may increase the risk of infection by other pathogens or exacerbate the symptoms of other diseases. Based on the data obtained using next-generation sequencing (NGS), we amplified and obtained the complete genomes of the two new FVs discovered in the bottlenose dolphin (Tursiops truncatus) and the South American sea lion (Otaria byronia) at the Qingdao Polar Haichang Ocean Park. Analysis and prediction of the novel FV's genomic structure revealed that it was consistent with that of the known mammalian FVs. The polmerase (pol) genes of the novel OFVoby_1 and DFVttr_1 showed less than 61.87 % and 61.83 % amino acid identity, respectively, with other known FVs belonging to the Retroviridae family. The host was likely to carry the FV for a considerable amount of time, as evidenced by the different times DFVttr_1 was discovered. The phylogenetic analysis revealed that the pol of OFVoby_1 and DFVttr_1 closely clustered with the FVs of Simiispumavirus and Felispumavirus, respectively. However, they both displayed distinct branches. According to the international committee on taxonomy of viruses (ICTV) FV classification criteria, FVs carried by dolphins and sea lions belong to two new genera within the Spumaretrovirinae subfamily. Using Bayesian analysis to simultaneously determine divergence dates and phylogenetic relationships revealed unique FVs with a divergence date of approximately 60 million years. This study helps us understand the FVs evolution and provides a scientific basis for future investigations into animal-borne infectious diseases.