Comparative Analysis of Proteomes of a Number of Nosocomial Pathogens by KEGG Modules and KEGG Pathways

Published on Oct 22, 2020in International Journal of Molecular Sciences4.556
· DOI :10.3390/IJMS21217839
Mikhail V. Slizen2
Estimated H-index: 2
(RAS: Russian Academy of Sciences),
Oxana V. Galzitskaya22
Estimated H-index: 22
(RAS: Russian Academy of Sciences)
Sources
Abstract
Nosocomial (hospital-acquired) infections remain a serious challenge for health systems. The reason for this lies not only in the local imperfection of medical practices and protocols. The frequency of infection with antibiotic-resistant strains of bacteria is growing every year, both in developed and developing countries. In this work, a pangenome and comparative analysis of 201 genomes of Staphylococcus aureus, Enterobacter spp., Pseudomonas aeruginosa, and Mycoplasma spp. was performed on the basis of high-level functional annotations-KEGG pathways and KEGG modules. The first three organisms are serious nosocomial pathogens, often exhibiting multidrug resistance. Analysis of KEGG modules revealed methicillin resistance in 25% of S. aureus strains and resistance to carbapenems in 21% of Enterobacter spp. strains. P. aeruginosa has a wide range of unique efflux systems. One hundred percent of the analyzed strains have at least two drug resistance systems, and 75% of the strains have seven. Each of the organisms has a characteristic set of metabolic features, whose impact on drug resistance can be considered in future studies. Comparing the genomes of nosocomial pathogens with each other and with Mycoplasma genomes can expand our understanding of the versatility of certain metabolic features and mechanisms of drug resistance.
References28
Newest
#1Adel M. Malek (URMC: University of Rochester Medical Center)H-Index: 58
#2Kelly McGlynn (URMC: University of Rochester Medical Center)H-Index: 2
Last. Nicole D. Pecora (URMC: University of Rochester Medical Center)H-Index: 11
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: Klebsiella aerogenes is a nosocomial pathogen associated with drug resistance and outbreaks in intensive care units. In a 5-month period in 2017, we experienced an increased incidence of cultures for carbapenem-resistant K. aerogenes (CR-KA) from an adult cardiothoracic intensive care unit (CICU) involving 15 patients. Phylogenomic analysis following whole-genome sequencing (WGS) identified the outbreak CR-KA isolates to group together as a tight monoclonal cluster (with no more than six singl...
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: Recent reports have established the escalating threat of carbapenem-resistant Enterobacter cloacae complex (CREC). Here, we demonstrate that CREC has evolved as a highly antibiotic-resistant rather than highly virulent nosocomial pathogen. Applying genomics and Bayesian phylogenetic analyses to a 7-year collection of CREC isolates from a northern Manhattan hospital system and to a large set of publicly available, geographically diverse genomes, we demonstrate clonal spread of a single clone, S...
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: Pseudomonas aeruginosa can cause complicated urinary tract infections, particularly in people with catheters, which can lead to pyelonephritis. Whilst some subgroups appear more susceptible to infection, such as the elderly and women, the contribution of other host factors and bacterial virulence factors to successful infection remains relatively understudied. In this review, we explore the potential role of P. aeruginosa virulence factors including phenazines, quorum sensing, biofilm formatio...
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#2V.N. Kos (AstraZeneca)H-Index: 1
Last. Didier Hocquet (University of Burgundy)H-Index: 29
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Abstract Objectives Despite the non-clonal epidemic population structure of Pseudomonas aeruginosa , several multi-locus sequence types are distributed worldwide and are frequently associated with epidemics where multidrug resistance confounds treatment. ST235 is the most prevalent of these widespread clones. In this study we aimed to understand the origin of ST235 and the molecular basis for its success. Methods The genomes of 79 P. aeruginosa ST235 isolates collected worldwide over a 27-year p...
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#2Elizabeth Kiss (St. John Fisher College)H-Index: 2
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Whole genome sequencing (WGS) was used for the characterization of the, frequently extensively-drug resistant (XDR), P. aeruginosa high-risk clone ST175. A total of eighteen ST175 isolates recovered from 8 different Spanish hospitals were analyzed; four isolates from four different French hospitals were included for comparison. The typical resistance profile of ST175 included penicillins, cephalosporins, monobactams, carbapenems, aminoglycosides, and fluoroquinolones. In the phylogenetic analysi...
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#1Afreenish Hassan (National University of Sciences and Technology)H-Index: 6
#2Anam Naz (National University of Sciences and Technology)H-Index: 12
Last. Amjad Ali (National University of Sciences and Technology)H-Index: 24
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Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets. The pan-genome of a...
52 CitationsSource
#1Victor I. Band (Emory University)H-Index: 7
#2Emily K. Crispell (Emory University)H-Index: 11
Last. David J. WeissH-Index: 66
view all 12 authors...
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