Genome-facilitated discovery of RND efflux pump-mediated resistance to cephalosporins in Vibrio spp. isolated from the mummichog fish gut

Dynamics of efflux pumps in antimicrobial resistance, persistence, and community living of Vibrionaceae

The marine bacteria of the Vibrionaceae family are significant from the point of view of their role in the marine geochemical cycle, as well as symbionts and opportunistic pathogens of aquatic animals and humans. The well-known pathogens of this group, Vibrio cholerae, V. parahaemolyticus, and V. vulnificus, are responsible for significant morbidity and mortality associated with a range of infections from gastroenteritis to bacteremia acquired through the consumption of raw or undercooked seafood and exposure to seawater containing these pathogens. Although generally regarded as susceptible to commonly employed antibiotics, the antimicrobial resistance of Vibrio spp. has been on the rise in the last two decades, which has raised concern about future infections by these bacteria becoming increasingly challenging to treat. Diverse mechanisms of antimicrobial resistance have been discovered in pathogenic vibrios, the most important being the membrane efflux pumps, which contribute to antimicrobial resistance and their virulence, environmental fitness, and persistence through biofilm formation and quorum sensing. In this review, we discuss the evolution of antimicrobial resistance in pathogenic vibrios and some of the well-characterized efflux pumps' contributions to the physiology of antimicrobial resistance, host and environment survival, and their pathogenicity.

Antibiotics resistance evolution of isolated Vibrio parahaemolyticus from mariculture under the continuous culture of sub-inhibitory concentrations of Ulva fasciata hydroponic solution

The outbreak of vibriosis from Vibrio (V.) parahaemolyticus is widespread in the mariculture, and live macroalgae has been considered to be effective and eco-friendly approach for the control of vibriosis. Three V. parahaemolyticus strains with β-lactam antibiotics resistance (resistant to ampicillin (AM), amoxicillin (AMX)) were isolated from mariculture in study, and the antibiotics resistance evolution mechanism was examined at the sub-inhibitory concentration (SIC) of hydroponic solution of Ulva (U.) fasciata (HSUF). The HSUF with the highest density (20 g fresh weight U. fasciata L^-1) demonstrated the strongest inhibitory rates (47.0 %-65.8 %) on the three strains during the stable phase (8-24 h) of growth curve, which indicated that the HSUF (≤20 g L^-1) could be considered to be at SIC for V. parahaemolyticus strains. After continuous subculture of V. parahaemolyticus with three dilutes (1/2 (HT), 1/20 (MT) and 1/50 (LT)) of HSUF (20 g L^-1), all the strains of 20th generation were still resistant to AM and AMX. However, the LT condition reduced MIC of AM (2-16 times) and AMX (0-2 times) to strains, while MT and HT showed significantly various effect of β-lactam antibiotics resistance on different strains. The biofilm formation and ROS content of V. parahaemolyticus were almost positively correlated to the concentrations of HSUF. Transcriptome sequencing analysis of a representative strain showed that the lower concentrations of HSUF caused more down-regulated DEGs of the strains, and more down-regulated (vmeA, vmeB, sapA, mrdA) DEGs of strains were related to the pathway of β-lactam antibiotics resistance at LT condition. Thus, low concentration of HSUF was seemed to have better improvement for V. parahaemolyticus strains resistant to β-lactam antibiotics, which were mainly related to the impairment of biofilm formation, ROS and efflux pump.

Drug Efflux Pump Inhibitors: A Promising Approach to Counter Multidrug Resistance in Gram-Negative Pathogens by Targeting AcrB Protein from AcrAB-TolC Multidrug Efflux Pump from Escherichia coli

Simple Summary

Multidrug-resistant bacterial infections, especially that caused by Gram-negative bacteria, have posed serious health issues worldwide. Bacteria have different mechanisms that can confer multidrug resistance to bacteria, among these mechanisms are drug efflux pumps that play the main role in conferring multidrug resistance by recognizing then expelling a wide range of compounds, especially antibiotics, and reducing their concentration to sub-toxic levels. Small molecule inhibitors that target drug efflux pumps especially the AcrAB-TolC multidrug efflux pump, from E. coli, appear as a new promising and attractive approach that could increase the required accumulation of antimicrobials to eliminate bacteria as well as leading to reverse antibiotic resistance and prevent the development of resistance in clinically relevant bacterial pathogens and enhances the activity of antibiotics or prolong their effectiveness.

Abstract

Infections caused by multidrug resistance (MDR) of Gram-negative bacteria have become one of the most severe public health problems worldwide. The main mechanism that confers MDR to bacteria is drug efflux pumps, as they expel a wide range of compounds, especially antibiotics. Among the different types of drug efflux pumps, the resistance nodulation division (RND) superfamily confers MDR to various Gram-negative bacteria species. The AcrAB-TolC multidrug efflux pump, from E. coli, a member of RND, is the best-characterized example and an excellent model for understanding MDR because of an abundance of functional and structural data. Small molecule inhibitors that target the AcrAB-TolC drug efflux pump represent a new solution to reversing MDR in Gram-negative bacteria and restoring the efficacy of various used drugs that are clinically relevant to these pathogens, especially in the high shortage of drugs for multidrug-resistant Gram-negative bacteria. This review will investigate solutions of MDR in Gram-negative bacteria by studying the inhibition of the AcrAB-TolC multidrug efflux pump.

The High Risk of Bivalve Farming in Coastal Areas With Heavy Metal Pollution and Antibiotic-Resistant Bacteria: A Chilean Perspective

Anthropogenic pollution has a huge impact on the water quality of marine ecosystems. Heavy metals and antibiotics are anthropogenic stressors that have a major effect on the health of the marine organisms. Although heavy metals are also associate with volcanic eruptions, wind erosion or evaporation, most of them come from industrial and urban waste. Such contamination, coupled to the use and subsequent misuse of antimicrobials in aquatic environments, is an important stress factor capable of affecting the marine communities in the ecosystem. Bivalves are important ecological components of the oceanic environments and can bioaccumulate pollutants during their feeding through water filtration, acting as environmental sentinels. However, heavy metals and antibiotics pollution can affect several of their physiologic and immunological processes, including their microbiome. In fact, heavy metals and antibiotics have the potential to select resistance genes in bacteria, including those that are part of the microbiota of bivalves, such as Vibrio spp. Worryingly, antibiotic-resistant phenotypes have been shown to be more tolerant to heavy metals, and vice versa, which probably occurs through co- and cross-resistance pathways. In this regard, a crucial role of heavy metal resistance genes in the spread of mobile element-mediated antibiotic resistance has been suggested. Thus, it might be expected that antibiotic resistance of Vibrio spp. associated with bivalves would be higher in contaminated environments. In this review, we focused on co-occurrence of heavy metal and antibiotic resistance in Vibrio spp. In addition, we explore the Chilean situation with respect to the contaminants described above, focusing on the main bivalves-producing region for human consumption, considering bivalves as potential vehicles of antibiotic resistance genes to humans through the ingestion of contaminated seafood.

Characteristics of Antimicrobial-Resistant Vibrio parahaemolyticus Strains and Identification of Related Antimicrobial Resistance Gene Mutations

Multidrug-resistant (MDR) Vibrio parahaemolyticus strains have become a great threat to public health. The purpose of this study was to investigate differences in biological characteristics and antimicrobial resistance gene (ARG) mutations of V. parahaemolyticus that displayed different levels of antimicrobial resistance. The susceptibility of 74 V. parahaemolyticus strains to 9 common antimicrobials was investigated, of which 88% were resistant to 3-4 antimicrobials and 3% to 5-7 antimicrobials. Interestingly, only 9% were resistant to 1-2 antimicrobials. The MDR strains possessed longer growth lag time than the non-MDR strains and displayed weaker swimming abilities. Whole genome sequencing was performed on strains VP41, VP44, 460, and 469 that were resistant to two to three classes of antimicrobials. ARGs were identified and compared with that of reference strain ATCC17802, and some important mutations were deduced. The Val189Ile mutation emerged in qnr gene of a single strain. Besides, the nonsynonymous mutations existed in four ARGs in different strains, including CatB (Pro165Ser, Gly208Asp), VmeA (Ile313Thr), VmeC (Glu329Ala), and VmeD (Asn205Ser). These results linked resistance gene mutations to enhance resistance in V. parahaemolyticus strains and provide a reference for more effective monitoring and prevention of V. parahaemolyticus infections.

Alpha-Carbonic Anhydrases from Hydrothermal Vent Sources as Potential Carbon Dioxide Sequestration Agents: In Silico Sequence, Structure and Dynamics Analyses

With the increase in CO2 emissions worldwide and its dire effects, there is a need to reduce CO2 concentrations in the atmosphere. Alpha-carbonic anhydrases (α-CAs) have been identified as suitable sequestration agents. This study reports the sequence and structural analysis of 15 α-CAs from bacteria, originating from hydrothermal vent systems. Structural analysis of the multimers enabled the identification of hotspot and interface residues. Molecular dynamics simulations of the homo-multimers were performed at 300 K, 363 K, 393 K and 423 K to unearth potentially thermostable α-CAs. Average betweenness centrality (BC) calculations confirmed the relevance of some hotspot and interface residues. The key residues responsible for dimer thermostability were identified by comparing fluctuating interfaces with stable ones, and were part of conserved motifs. Crucial long-lived hydrogen bond networks were observed around residues with high BC values. Dynamic cross correlation fortified the relevance of oligomerization of these proteins, thus the importance of simulating them in their multimeric forms. A consensus of the simulation analyses used in this study suggested high thermostability for the α-CA from Nitratiruptor tergarcus. Overall, our novel findings enhance the potential of biotechnology applications through the discovery of alternative thermostable CO2 sequestration agents and their potential protein design.

Insights on genomic diversity of Vibrio spp. through Pan-genome analysis

Purpose

The aquaculture sector is a major contributor to the economic and nutritional security for a number of countries. India’s total seafood exports for the year 2017–2018 accounted for US$ Million 7082. One of the major setbacks in this sector is the frequent outbreaks of diseases often due to bacterial pathogens. Vibriosis is one of the major diseases caused by bacteria of Vibrio spp., causing significant economic loss to the aquaculture sector. The objective of this study was to understand the genetic composition of Vibrio spp.

Methods

Thirty-five complete genomes were downloaded from GenBank comprising seven vibrio species, namely, Vibrio alginolyticus, V. anguillarum, V. campbellii, V. harveyi, V. furnissii, V. parahaemolyticus, and V. vulnificus. Pan-genome analysis was carried out with coding sequences (CDS) generated from all the Vibrio genomes. In addition, genomes were mined for genes coding for toxin-antitoxin systems, antibiotic resistance, genomic islands, and virulence factors.

Results

Results revealed an open pan-genome comprising of 2004 core, 8249 accessory, and 6780 unique genes. Downstream analysis of genomes and the identified unique genes resulted in 312 antibiotic resistance genes, 430 genes coding for toxin and antitoxin systems along with 4802, and 4825 putative virulent genes from genomic island regions and unique gene sets, respectively.

Conclusion

Pan-genome and other downstream analytical procedures followed in this study have the potential to predict strain-specific genes and their association with habitat and pathogenicity.