Plasmid-encoded tetracycline efflux pump protein alters bacterial stress responses and ecological fitness of Acinetobacter oleivorans

Snapshot of resistome, virulome and mobilome in aquaculture

Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of Gram-negative bacteria isolated in seabream and bivalve molluscs, using a WGS approach. Sixty-six Gram-negative strains (Aeromonadaceae, Enterobacteriaceae, Hafniaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Vibrionaceae, and Yersiniaceae families) were selected for genomic characterization. The species and MLST were determined, and antibiotic/disinfectants/heavy metals resistance genes, virulence determinants, MGE, and pathogenicity to humans were investigated. Our study revealed new sequence-types (e.g. Aeromonas spp. ST879, ST880, ST881, ST882, ST883, ST887, ST888; Shewanella spp. ST40, ST57, ST58, ST60, ST61, ST62; Vibrio spp. ST206, ST205). >140 different genes were identified in the resistome of seabream and bivalve molluscs, encompassing genes associated with β-lactams, tetracyclines, aminoglycosides, quinolones, sulfonamides, trimethoprim, phenicols, macrolides and fosfomycin resistance. Disinfectant resistance genes qacE-type, sitABCD-type and formA-type were found. Heavy metals resistance genes mdt, acr and sil stood out as the most frequent. Most resistance genes were associated with antibiotics/disinfectants/heavy metals commonly used in aquaculture settings. We also identified 25 different genes related with increased virulence, namely associated with adherence, colonization, toxins production, red blood cell lysis, iron metabolism, escape from the immune system of the host. Furthermore, 74.2 % of the strains analysed were considered pathogenic to humans. We investigated the genetic environment of several antibiotic resistance genes, including blaTEM-1B, blaFOX-18, aph(3″)-Ib, dfrA-type, aadA1, catA1-type, tet(A)/(E), qnrB19 and sul1/2. Our analysis also focused on identifying MGE in proximity to these genes (e.g. IntI1, plasmids and TnAs), which could potentially facilitate the spread of resistance among bacteria across different environments. This study provides a comprehensive examination of the diversity of resistance genes that can be transferred to both humans and the environment, with the recognition that aquaculture and the broader environment play crucial roles as intermediaries within this complex transmission network.

Dynamics of bacteriophages in gut of giant pandas reveal a potential regulation of dietary intake on bacteriophage composition

Fecal samples of cubs and adults of giant pandas were examined to determine the effects of diets on the diversity and dynamics of gut bacteriophages. Enterobacteria phage, Salmonella phage, Escherichia phage, Shigella phage, Klebsiella phage, and Lactococcus phage were found to be dominant in both cub and adult samples. Citrobacter phage, Cronobacter phage, Pectobacterium phage, Erwinia phage, Dickeya phage, Erwinia phage, Enterococcus phage, and Pseudomonas phage were more abundant in adults, while Lactococcus phage, Streptococcus phage, Lactobacillus phage, and Leuconostoc phage were more abundant in cubs. The abundance and diversity of the majority of phage species were increased in pandas with age. There was an increase in the abundance of Pectobacterium phage and a decrease in the abundance of Lactobacillus phage, Leuconostoc phage, Bacillus phage, and Streptococcus phage in adults. As cubs and adults of giant pandas have different dietary habits, these observations suggest a significant effect of diets on the composition and abundance of gut bacteriophages in giant pandas.

Amentoflavone, a novel cyanobacterial killing agent from Selaginella tamariscina

Harmful cyanobacterial bloom (HCB) by Microcystis aeruginosa is increasingly becoming a serious concern to the environment and human health alike. Currently, many physical, chemical, and biological controls are underway to eliminate HCB, but natural chemicals are rarely used. To find a control agent with low environmental toxicity and high potential for practical use, 60 plant extracts were screened. Only Selaginella tamariscina extract killed all four Microcystis aeruginosa strains, but not the other tested bacteria. Chloroform fraction of S. tamariscina extract (CSE) showed the highest killing activity. The effects of CSE on M. aeruginosa were monitored using differential interference contrast microscopy and flow-cytometry analysis, scanning electron microscopy, and transmission electron microscopy. The images showed that CSE-treated cells were abnormally altered, with damaged cell membranes, peptidoglycan layers, and cytoplasm. Quadrupole time-of-flight liquid chromatography-mass spectrometry was used to identify amentoflavone as a major active compound. Pure amentoflavone, even at low concentrations showed a powerful killing effect on M. aeruginosa, but not on other non-cyanobacteria. Overall, in this study, we have highlighted the potentials of S. tamariscina extracts and amentoflavone as selective HCB control agents.

Cross-feeding modulates antibiotic tolerance in bacterial communities

Microbes frequently rely on metabolites excreted by other bacterial species, but little is known about how this cross-feeding influences the effect of antibiotics. We hypothesized that when species rely on each other for essential metabolites, the minimum inhibitory concentration (MIC) for all species will drop to that of the “weakest link”—the species least resistant in monoculture. We tested this hypothesis in an obligate cross-feeding system that was engineered between Escherichia coli, Salmonella enterica, and Methylobacterium extorquens. The effect of tetracycline and ampicillin were tested on both liquid and solid media. In all cases, resistant species were inhibited at significantly lower antibiotic concentrations in the cross-feeding community than in monoculture or a competitive community. However, deviation from the “weakest link” hypothesis was also observed in cross-feeding communities apparently as result of changes in the timing of growth and cross-protection. Comparable results were also observed in a clinically relevant system involving facultative cross-feeding between Pseudomonas aeruginosa and an anaerobic consortium found in the lungs of cystic fibrosis patients. P. aeruginosa was inhibited by lower concentrations of ampicillin when cross-feeding than when grown in isolation. These results suggest that cross-feeding significantly alters tolerance to antibiotics in a variety of systems.

Expression and deletion analyses of cspE encoding cold-shock protein E in Acinetobacter oleivorans DR1

Six genes encoding cold-shock-like proteins, including cspE, are contained within the genome of Acinetobacter oleivorans DR1. All six genes are similar in size as well as amino acid identity, but appear to be differentially regulated under stressful conditions. Four of these genes (cspA, cspB, cspC and cspE) were functionally important during cold shock because of their gradual upregulation during a temperature decrease under our assay conditions. cspE also showed higher expression during alkane degradation and antibiotic exposure. The transcriptional start site of the cspE gene was determined using 5' rapid amplification of complementary DNA ends. Next, promoter analysis using numerous constructed gfp reporter strains containing deleted fragments of cspE upstream regions identified possible 5' untranslated region (UTR) cis-DNA elements that could be involved in modulating cspE expression. Deletion of cspE led to a growth defect and enhanced biofilm formation, but only at a low temperature. Collectively, our findings show the importance of CspE during cold shock, dynamic regulation of cspE expression under various stressful conditions and a possible 5'-UTR cis-DNA element for regulation of cspE expression. These data provide molecular insight into cspE gene expression during cold-shock adaptation in soil bacteria.

Expression of the TetA gene encoding TetA efflux protein in E. coli contributes to its increased bacterial resistance toward berberine

Berberine (BBR) is a traditional Chinese medicine in various applications due to its antibacterial effect. Here we investigated the increased bacterial resistance of E. coli toward BBR. The median effective concentration (EC₅₀) of BBR against E. coli was increased when TetA efflux protein (TEP) was introduced. Sixty-five percent of the intracellular BBR was expelled and molecular docking demonstrated the intensive interaction of TEP to BBR. Finally, the combined antibacterial experiment identified that BBR acted as an inhibitor of TEP in detoxification of tetracycline. TEP is the first discovered protein that was related to the bacterial susceptibility to BBR.

Tetracycline alters gene expression in Salmonella strains that harbor the Tn10 transposon

In this report, we show that bacterial plasmids that harbor the Tn10 transposon (i.e., the IncHI1 plasmid R27) modify expression of different Salmonella regulons responding to the presence of tetracycline (Tc) in the medium. By using as a model the Tc-dependent upregulation of the ibpAB operon (which belongs to the heat shock regulon), we have identified Tn10-tetA (coding for a Tc efflux pump) and adjacent tetC sequences as required for ibpAB upregulation. Characterization of transcripts in the tetAC region showed that tetA transcription can continue into tetC sequences, generating a long 3'UTR sequence, which can protect transcripts from RNA processing, thus increasing the expression of TetA protein. In the presence of Tc, the DnaK and IbpA chaperones are overexpressed and translocated to the periplasm and to the membrane fraction respectively. DnaK targeting unfolded proteins is known to induce heat shock by avoiding RpoH proteolysis. We correlate expression levels of Tn10-encoded TetA protein with heat shock induction in Salmonella, likely because TetA activity compromises protein secretion.

Plasmid persistence: costs, benefits, and the plasmid paradox

Plasmids are extrachromosomal DNA elements that can be found throughout bacteria, as well as in other domains of life. Nonetheless, the evolutionary processes underlying the persistence of plasmids are incompletely understood. Bacterial plasmids may encode genes for traits that are sometimes beneficial to their hosts, such as antimicrobial resistance, virulence, heavy metal tolerance, and the catabolism of unique nutrient sources. In the absence of selection for these traits, however, plasmids generally impose a fitness cost on their hosts. As such, plasmid persistence presents a conundrum: models predict that costly plasmids will be lost over time or that beneficial plasmid genes will be integrated into the host genome. However, laboratory and comparative studies have shown that plasmids can persist for long periods, even in the absence of positive selection. Several hypotheses have been proposed to explain plasmid persistence, including host-plasmid co-adaptation, plasmid hitchhiking, cross-ecotype transfer, and high plasmid transfer rates, but there is no clear evidence that any one model adequately resolves the plasmid paradox.

Trueperella pyogenes isolated from dairy cows with endometritis in Inner Mongolia, China: Tetracycline susceptibility and tetracycline-resistance gene distribution

Trueperella pyogenes plays a crucial role in endometritis pathogenesis and is also associated with many infections, including metritis, mastitis, arthritis and liver abscessation, in many domestic animals. In this study, we investigated the prevalence of tetracycline resistance in T. pyogenes isolated from dairy cows with endometritis in Inner Mongolia, China, and we assessed tetracycline-resistance gene distribution among the isolates. Our results indicated that 68.7% and 62.5% of the isolates were resistant to tetracycline and doxycycline, respectively, and the rate of resistance to metacycline was 18.8%. The tetracycline resistance gene tetK was present in all isolates (n = 32), whereas the tetM gene was identified in 12.5% and 9.4% of the isolates, in the chromosome and plasmid, respectively. Strains carrying tetW were also common in the chromosome and plasmid, with abundances of 53.1% and 46.9%, respectively. However, tetO and otrA were absent in all isolates. The resistance phenotype analysis indicated that 6.3% of strains were susceptible to all tetracyclines, while 3.1% showed resistance to all tetracyclines.

Stenotrophomonas maltophilia PhoP, a Two-Component Response Regulator, Involved in Antimicrobial Susceptibilities

Stenotrophomonas maltophilia, a gram-negative bacterium, has increasingly emerged as an important nosocomial pathogen. It is well-known for resistance to a variety of antimicrobial agents including cationic antimicrobial polypeptides (CAPs). Resistance to polymyxin B, a kind of CAPs, is known to be controlled by the two-component system PhoPQ. To unravel the role of PhoPQ in polymyxin B resistance of S. maltophilia, a phoP mutant was constructed. We found MICs of polymyxin B, chloramphenicol, ampicillin, gentamicin, kanamycin, streptomycin and spectinomycin decreased 2-64 fold in the phoP mutant. Complementation of the phoP mutant by the wild-type phoP gene restored all of the MICs to the wild type levels. Expression of PhoP was shown to be autoregulated and responsive to Mg2+ levels. The polymyxin B and gentamicin killing tests indicated that pretreatment of low Mg2+ can protect the wild-type S. maltophilia from killing but not phoP mutant. Interestingly, we found phoP mutant had a decrease in expression of SmeZ, an efflux transporter protein for aminoglycosides in S. maltophilia. Moreover, phoP mutant showed increased permeability in the cell membrane relative to the wild-type. In summary, we demonstrated the two-component regulator PhoP of S. maltophilia is involved in antimicrobial susceptibilities and low Mg2+ serves as a signal for triggering the pathway. Both the alteration in membrane permeability and downregulation of SmeZ efflux transporter in the phoP mutant contributed to the increased drug susceptibilities of S. maltophilia, in particular for aminoglycosides. This is the first report to describe the role of the Mg2+-sensing PhoP signaling pathway of S. maltophilia in regulation of the SmeZ efflux transporter and in antimicrobial susceptibilities. This study suggests PhoPQ TCS may serve as a target for development of antimicrobial agents against multidrug-resistant S. maltophilia.

Effect of the IncP-1β plasmid pHB44 on the population dynamics of Burkholderia terrae BS001 in the Lyophyllum sp. strain Karsten mycosphere under different iron conditions

Burkholderia terrae strain BS001 is a well-described inhabitant of the mycosphere of diverse fungi. In the interaction between this bacterium and its fungal host in soil, competition for iron might be a key process. Here, we address the capacity of the broad-host-range IncP-1β plasmid pHB44, originally isolated in Variovorax paradoxus HB44, to enhance or modulate the competitiveness of B. terrae BS001 under different soil iron levels when confronted with (young versus ageing) mycelia of Lyophyllum sp. strain Karsten in microcosms. The data revealed that, in most cases, plasmid pHB44 reduced the fitness of its host in the mycosphere, possibly due to a metabolic burden effect. However, an opposite effect was found under low-iron conditions at the extreme tips of the soil-exploring Lyophyllum sp. strain Karsten mycelium. The negative effect of plasmid pHB44 on strain BS001 population sizes was clearly offset by fitness enhancement under these conditions. Moreover, as evidenced by using plasmid pSUP104 as a tracer, plasmid pHB44 was transferred from the B. terrae BS001 host into V. paradoxus BS64 in the ageing mycosphere, but not in bulk soil. Strikingly, successful plasmid establishment in the new host was more prominent in the iron-limited than in the 'high-iron' mycosphere habitat, indicating plasmid pHB44 was required in the V. paradoxus host as a fitness stimulator in the iron-limited condition. Taken together, the data suggest that efficiency of iron acquisition only served as the selective mechanism under certain conditions of iron availability in the soil, specifically promoting the fitness of V. paradoxus transconjugants. Not only is the mycosphere to be regarded as a selective arena in which horizontal gene transfer across the bacterial inhabitants is spurred, but the outcome of the adaptive processes is strongly shaped by competitive events among the local organisms.

Synergistic Effect of Oleanolic Acid on Aminoglycoside Antibiotics against Acinetobacter baumannii

Difficulties involved in treating drug-resistant pathogens have created a need for new therapies. In this study, we investigated the possibility of using oleanolic acid (OA), a natural pentacyclic triterpenoid, as a natural adjuvant for antibiotics against Acinetobacter baumannii. High concentrations of OA can kill cells, partly because it generates reactive oxygen species. Measurement of the fractional inhibitory concentration (FIC) for OA and time-kill experiments demonstrated that it only synergizes with aminoglycoside antibiotics (e.g., gentamicin, kanamycin). Other classes of antibiotics (e.g., ampicillin, rifampicin, norfloxacin, chloramphenicol, and tetracycline) have no interactions with OA. Microarray and quantitative reverse transcription-PCR analysis indicated that genes involved in ATP synthesis and cell membrane permeability, the gene encoding glycosyltransferase, peptidoglycan-related genes, phage-related genes, and DNA repair genes were upregulated under OA. OA highly induces the expression of adk, which encodes an adenylate kinase, and des6, which encodes a linoleoyl-CoA desaturase, and deletion of these genes increased FICs; these observations indicate that adk and des6 are involved in the synergism of OA with aminoglycosides. Data obtained using 8-anilino-1-naphthalenesulfonic acid, fluorescence-conjugated gentamicin, and membrane fatty acid analysis indicates that adk and des6 are involved in changes in membrane permeability. Proton-motive force and ATP synthesis tests show that those genes are also involved in energy metabolism. Taken together, our data show that OA boosts aminoglycoside uptake by changing membrane permeability and energy metabolism in A. baumannii.

Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives

Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.