Bacterial gene loss as a mechanism for gain of antimicrobial resistance

Asp50Glu mutation in MurA results in fosfomycin resistance in Enterococcus faecium

OBJECTIVES

Enterococcus faecium is one of the important pathogens causing nosocomial infection, which can be resistant to fosfomycin by obtaining the plasmid-encoded fosfomycin resistance genes, and the mutation of MurA protein encoded by chromosome is a newly discovered fosfomycin resistance mechanism in recent years.

METHODS

In this study, we found a fosfomycin-resistant clinical isolate of E. faecium Efm_1415 with fosfomycin MIC of 512 mg/L, carrying Asp50Glu mutant of MurA protein, which was never reported before. To study the role and mechanism of this mutant protein in fosfomycin resistance, we used gene cloning, protein expression, and purification, steady-state kinetic, fosfomycin inhibition assay, and next-generation sequencing (NGS) to investigate the functions, characters, and enzymatic kinetic properties of MurA protein.

RESULTS

The results revealed that the Asp50Glu MurA can mediate a 4-fold increase in the fosfomycin MIC of the host bacteria. Compared with the wild-type MurA, the affinity of the Asp50Glu MurA to the substrates was increased, and the enzyme activity cannot be inhibited by the concentration of fosfomycin less than 100 mg/L.

CONCLUSIONS

The research on the mutant MurA had gained a new understanding of the fosfomycin resistance mechanisms and helped to find new antibiotics with MurA enzyme as the target of action.

PARMAP: A Pan-Genome-Based Computational Framework for Predicting Antimicrobial Resistance

Antimicrobial resistance (AMR) has emerged as one of the most urgent global threats to public health. Accurate detection of AMR phenotypes is critical for reducing the spread of AMR strains. Here, we developed PARMAP (Prediction of Antimicrobial Resistance by MAPping genetic alterations in pan-genome) to predict AMR phenotypes and to identify AMR-associated genetic alterations based on the pan-genome of bacteria by utilizing machine learning algorithms. When we applied PARMAP to 1,597 Neisseria gonorrhoeae strains, it successfully predicted their AMR phenotypes based on a pan-genome analysis. Furthermore, it identified 328 genetic alterations in 23 known AMR genes and discovered many new AMR-associated genetic alterations in ciprofloxacin-resistant N. gonorrhoeae, and it clearly indicated the genetic heterogeneity of AMR genes in different subtypes of resistant N. gonorrhoeae. Additionally, PARMAP performed well in predicting the AMR phenotypes of Mycobacterium tuberculosis and Escherichia coli, indicating the robustness of the PARMAP framework. In conclusion, PARMAP not only precisely predicts the AMR of a population of strains of a given species but also uses whole-genome sequencing data to prioritize candidate AMR-associated genetic alterations based on their likelihood of contributing to AMR. Thus, we believe that PARMAP will accelerate investigations into AMR mechanisms in other human pathogens.

Risk factors and pathogenic microorganism characteristics for pneumonia in convalescent patients with stroke: A retrospective study of 380 patients from a rehabilitation hospital

BACKGROUND

Pneumonia is a major complication leading to death after stroke. The risk factors of pneumonia in convalescent patients who have experienced stroke remain poorly defined.

METHODS

To identify the risk factors of pneumonia, we applied logistic regression as a statistical method using SPSS23.0 statistical software, based on a sample of 380 patients. And statistical description method was used to analyze pathogens' characteristics and drug resistance.

RESULTS

Ultimately, the obtained logistic model has statistical significance (χ2(13) = 91.560, P <0.0005). The sensitivity of the model is 41.7%, the specificity is 97.6%, the positive predictive value is 76.9%, and the negative predictive value is 89.8%. The Barthel index (BI) (OR=1.97, 95% CI: 1.01-3.87), basic lung diseases (OR=4.24, 95% CI: 1.02-17.61), trachea ventilation (OR=6.56, 95% CI: 1.18-36.34), feeding tube (OR=6.06, 95% CI: 2.59-14.18), and hypoproteinemia (OR=3.97, 95% CI: 1.56-10.10) were statistically significant (P<0.05). Among patients who have pneumonia, the proportion of gram-positive bacteria, gram-negative bacteria and fungal infection is 10.00%, 54.29%, 5.71% respectively. The study most frequently isolated Pseudomonas aeruginosa (18.57%), followed by Acinetobacter baumannii (10.00%,) and Klebsiella pneumoniae (10.00%). The drug resistance rate of Pseudomonas aeruginosa, Acinetobacter baumannii and Klebsiella pneumoniae to different antibiotics ranged from 0.00-37.77%, 0.00-85.71% and 0.00-57.14%, respectively.

CONCLUSIONS

The lower BI scores, basic lung diseases, trachea ventilation, tube feeding, and hypoproteinemia are independent risk factors of pneumonia among convalescent patients with stroke. The main pathogens that caused pneumonia were gram-negative bacteria, and such organisms have different degrees of resistance to drugs.

The Gene Structure and Expression Level Changes of the GH3 Gene Family in Brassica napus Relative to Its Diploid Ancestors

The GH3 gene family plays a vital role in the phytohormone-related growth and developmental processes. The effects of allopolyploidization on GH3 gene structures and expression levels have not been reported. In this study, a total of 38, 25, and 66 GH3 genes were identified in Brassica rapa (A_rA_r), Brassica oleracea (C_oC_o), and Brassica napus (A_nAC_nC_n), respectively. BnaGH3 genes were unevenly distributed on chromosomes with 39 on A_n and 27 on C_n, in which six BnaGH3 genes may appear as new genes. The whole genome triplication allowed the GH3 gene family to expand in diploid ancestors, and allopolyploidization made the GH3 gene family re-expand in B. napus. For most BnaGH3 genes, the exon-intron compositions were similar to diploid ancestors, while the cis-element distributions were obviously different from its ancestors. After allopolyploidization, the expression patterns of GH3 genes from ancestor species changed greatly in B. napus, and the orthologous gene pairs between A_n/A_r and C_n/C_o had diverged expression patterns across four tissues. Our study provides a comprehensive analysis of the GH3 gene family in B. napus, and these results could contribute to identifying genes with vital roles in phytohormone-related growth and developmental processes.

Diversity and regulation of intrinsic β-lactamases from non-fermenting and other Gram-negative opportunistic pathogens

This review deeply addresses for the first time the diversity, regulation and mechanisms leading to mutational overexpression of intrinsic β-lactamases from non-fermenting and other non-Enterobacteriaceae Gram-negative opportunistic pathogens. After a general overview of the intrinsic β-lactamases described so far in these microorganisms, including circa. 60 species and 100 different enzymes, we review the wide array of regulatory pathways of these β-lactamases. They include diverse LysR-type regulators, which control the expression of β-lactamases from relevant nosocomial pathogens such as Pseudomonas aeruginosa or Stenothrophomonas maltophilia or two-component regulators, with special relevance in Aeromonas spp., along with other pathways. Likewise, the multiple mutational mechanisms leading to β-lactamase overexpression and β-lactam resistance development, including AmpD (N-acetyl-muramyl-L-alanine amidase), DacB (PBP4), MrcA (PPBP1A) and other PBPs, BlrAB (two-component regulator) or several lytic transglycosylases among others, are also described. Moreover, we address the growing evidence of a major interplay between β-lactamase regulation, peptidoglycan metabolism and virulence. Finally, we analyse recent works showing that blocking of peptidoglycan recycling (such as inhibition of NagZ or AmpG) might be useful to prevent and revert β-lactam resistance. Altogether, the provided information and the identified gaps should be valuable for guiding future strategies for combating multidrug-resistant Gram-negative pathogens.

Antibiotic Resistance Markers in Burkholderia pseudomallei Strain Bp1651 Identified by Genome Sequence Analysis

Burkholderia pseudomallei Bp1651 is resistant to several classes of antibiotics that are usually effective for treatment of melioidosis, including tetracyclines, sulfonamides, and β-lactams such as penicillins (amoxicillin-clavulanic acid), cephalosporins (ceftazidime), and carbapenems (imipenem and meropenem). We sequenced, assembled, and annotated the Bp1651 genome and analyzed the sequence using comparative genomic analyses with susceptible strains, keyword searches of the annotation, publicly available antimicrobial resistance prediction tools, and published reports. More than 100 genes in the Bp1651 sequence were identified as potentially contributing to antimicrobial resistance. Most notably, we identified three previously uncharacterized point mutations in penA, which codes for a class A β-lactamase and was previously implicated in resistance to β-lactam antibiotics. The mutations result in amino acid changes T147A, D240G, and V261I. When individually introduced into select agent-excluded B. pseudomallei strain Bp82, D240G was found to contribute to ceftazidime resistance and T147A contributed to amoxicillin-clavulanic acid and imipenem resistance. This study provides the first evidence that mutations in penA may alter susceptibility to carbapenems in B. pseudomallei Another mutation of interest was a point mutation affecting the dihydrofolate reductase gene folA, which likely explains the trimethoprim resistance of this strain. Bp1651 was susceptible to aminoglycosides likely because of a frameshift in the amrB gene, the transporter subunit of the AmrAB-OprA efflux pump. These findings expand the role of penA to include resistance to carbapenems and may assist in the development of molecular diagnostics that predict antimicrobial resistance and provide guidance for treatment of melioidosis.

A Structure-Based Classification of Class A β-Lactamases, a Broadly Diverse Family of Enzymes

For medical biologists, sequencing has become a commonplace technique to support diagnosis. Rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. This is particularly true for data concerning class A β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. Many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. We analyzed several hundred amino acid sequences of class A β-lactamase enzymes for phylogenic relationships, the presence of specific residues, and cluster patterns. A clear distinction was first made between dd-peptidases and class A enzymes based on a small number of residues (S70, K73, P107, 130SDN132, G144, E166, 234K/R, 235T/S, and 236G [Ambler numbering]). Other residues clearly separated two main branches, which we named subclasses A1 and A2. Various clusters were identified on the major branch (subclass A1) on the basis of signature residues associated with catalytic properties (e.g., limited-spectrum β-lactamases, extended-spectrum β-lactamases, and carbapenemases). For subclass A2 enzymes (e.g., CfxA, CIA-1, CME-1, PER-1, and VEB-1), 43 conserved residues were characterized, and several significant insertions were detected. This diversity in the amino acid sequences of β-lactamases must be taken into account to ensure that new enzymes are accurately identified. However, with the exception of PER types, this diversity is poorly represented in existing X-ray crystallographic data.

Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution

Gene loss is the driving force for changes in genome and morphology; however, this particular evolutionary event has been poorly investigated in leguminous plants. Legumes (Fabaceae) have some lineage-specific and diagnostic characteristics that are distinct from other angiosperms. To understand the potential role of gene loss in the evolution of legumes, we compared six genome-sequenced legume species of Papilionoideae, the largest representative clade of Fabaceae, such as Glycine max, with 34 nonlegume plant species, such as Arabidopsis thaliana. The results showed that the putative orthologs of the 34 Arabidopsis genes belonging to 29 gene families were absent in these legume species but these were conserved in the sequenced nonlegume angiosperm lineages. Further evolutionary analyses indicated that the orthologs of these genes were almost completely lost in the Papillionoideae ancestors, thus designated as the legume lost genes (LLGs), and these underwent purifying selection in nonlegume plants. Most LLGs were functionally unknown. In Arabidopsis, two LLGs were well-known genes that played a role in plant immunity such as HARMLESS TO OZONE LAYER 1 and HOPZ-ACTIVATED RESISTANCE 1, and 16 additional LLGs were predicted to participate in plant-pathogen interactions in in silico expression and protein-protein interaction network analyses. Most of these LLGs' orthologs in various plants were also found to be associated with biotic stress response, indicating the conserved role of these genes in plant defense. The evolutionary implication of LLGs during the development of the ability of symbiotic nitrogen fixation involving plant and bacterial interactions, which is a well-known characteristic of most legumes, is also discussed. Our work sheds light on the evolutionary implication of gene loss events in Papilionoideae evolution, as well as provides new insights into crop design to improve nitrogen fixation capacity.