Comparative genomic analysis of Mycoplasma anatis strains

Zhou, Qi; Mai, Kaijie; Yang, Dehong; Liu, Junfa; Zhang, Yan; Luo, Cuifen; Tan, Yi; Cao, Sheng; Zhou, Qingfeng; Chen, Li; Chen, Feng

doi:10.1007/s13258-021-01129-5

Cited by 3 publications

(1 citation statement)

References 35 publications

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“…Prokka was used to annotate the 778 E. coli isolates, and Roary software was adopted to obtain multiple sequence alignment files of 1,222 core genes ( Zhou et al, 2021 ), which were further used to acquire the single nucleotide polymorphism information through SNP sites. Finally, RaxML was used to construct the maximum likelihood tree, and the evolution tree results were visualized by itol ( Liu et al, 2022 ).…”

Section: Methodsmentioning

confidence: 99%

Epidemiological and genomic characteristics of global mcr-positive Escherichia coli isolates

et al. 2023

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ObjectiveThe worldwide dissemination of colistin-resistant Escherichia coli (E. coli) endangers public health. This study aimed to better understand the global genomic epidemiology of E. coli isolates carrying mobilized colistin resistance (mcr) genes, providing information to assist in infection and prevention.MethodsEscherichia coli genomes were downloaded from NCBI, and mcr was detected using BLASTP. Per software was used to extract information on hosts, resources, collection data, and countries of origin from GenBank. Sequence types (STs), prevalence of plasmids, antimicrobial resistance genes (ARG), and virulence factors (VF) in these genomes were analyzed. Statistical analyses were performed to assess the relationships between mcr, ARGs, plasmids, and STs.ResultsIn total, 778 mcr-positive isolates were identified. Four mcr variants were detected, with mcr-1 (86.1%) being the most widespread, followed by mcr-9 (5.7%), mcr-5 (4.4%), and mcr-3 (3.0%). Multiple ARGs were identified, with blaCTX–M (53.3%), fosA (28.8%), qnr (26.1%), blaNDM (19.8%), and aac (6’)-Ib-cr (14.5%) being the most common. Overall, 239 distinct STs were identified, of which ST10 (13.8%) was the most prevalent. A total of 113 different VFs were found, terC (99.9%) and gad (83.0%) were most frequently detected. Twenty types of plasmids were identified; IncFIB (64.1%), IncX (42.3%), and IncX (42.3%) were the most common replicons. IncI2 and IncX4 were frequently detected in mcr-1-positive isolates, whereas IncFII, IncI1-I, and IncHI2 were dominant plasmids in mcr-3, mcr-5, and mcr-9-positive isolates, respectively. A higher frequency of ARGs and VFs was observed among ST156 and ST131 isolates.ConclusionOur data indicated that more than half of the mcr-positive E. coli strains carried endemic ARGs and VFs. ST10 and ST156 isolates deserved further attention, given the rapid transmission of ST10 and the convergence of ARGs and VFs in ST156.

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Section: Methodsmentioning

confidence: 99%

Epidemiological and genomic characteristics of global mcr-positive Escherichia coli isolates

et al. 2023

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Genomic diversity, antibiotic resistance, and virulence in South African Enterococcus faecalis and Enterococcus lactis isolates

Olanrewaju,

Molale-Tom,

Bezuidenhout

2024

World J Microbiol Biotechnol

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This study presents the empirical findings of an in-depth genomic analysis of Enterococcus faecalis and Enterococcus lactis isolates from South Africa. It offers valuable insights into their genetic characteristics and their significant implications for public health. The study uncovers nuanced variations in the gene content of these isolates, despite their similar GC contents, providing a comprehensive view of the evolutionary diversity within the species. Genomic islands are identified, particularly in E. faecalis, emphasizing its propensity for horizontal gene transfer and genetic diversity, especially in terms of antibiotic resistance genes. Pangenome analysis reveals the existence of a core genome, accounting for a modest proportion of the total genes, with 2157 core genes, 1164 shell genes, and 4638 cloud genes out of 7959 genes in 52 South African E. faecalis genomes (2 from this study, 49 south Africa genomes downloaded from NCBI, and E. faecalis reference genome). Detecting large-scale genomic rearrangements, including chromosomal inversions, underscores the dynamic nature of bacterial genomes and their role in generating genetic diversity. The study uncovers an array of antibiotic resistance genes, with trimethoprim, tetracycline, glycopeptide, and multidrug resistance genes prevalent, raising concerns about the effectiveness of antibiotic treatment. Virulence gene profiling unveils a diverse repertoire of factors contributing to pathogenicity, encompassing adhesion, biofilm formation, stress resistance, and tissue damage. These empirical findings provide indispensable insights into these bacteria’s genomic dynamics, antibiotic resistance mechanisms, and virulence potential, underlining the pressing need to address antibiotic resistance and implement robust control measures.

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