scholarly journals Photobacterium damselaesubsp.damselae, a Generalist Pathogen with Unique Virulence Factors and High Genetic Diversity

2018 ◽  
Vol 200 (15) ◽  
Author(s):  
Carlos R. Osorio ◽  
Ana Vences ◽  
Xosé M. Matanza ◽  
Mateus S. Terceti

ABSTRACTPhotobacterium damselaesubsp.damselaecauses vibriosis in a variety of marine animals, including fish species of importance in aquaculture. It also may cause wound infections in humans that can progress to a fatal outcome. Two major virulence factors are encoded within the large conjugative plasmid pPHDD1, the phospholipase D damselysin (Dly) and the pore-forming toxin phobalysin P (PhlyP). The two toxins exert hemolytic and cytolytic activities in a synergistic manner. Even though PhlyP has close homologues in manyVibriospecies, it has unique features that differentiate it from related toxins. Dly phospholipase constitutes a singular trait ofP. damselaesubsp.damselaeamong theVibrionaceae, although related toxins are found in members of theAeromonadaceae. Fish farm outbreaks can also be caused by plasmidless strains. Such observations led to the characterization of two ubiquitous chromosome-encoded toxins with lesser cytolytic activity, the pore forming-toxin phobalysin C (PhlyC) and the phospholipase-hemolysin PlpV. The high genetic diversity of this pathogen deserves special attention, as it has a number of strain-specific features, including the cell envelope polysaccharide synthesis clusters. Fish outbreaks are likely caused by multiclonal populations which contain both plasmidless and pPHDD1-harboring isolates and not by well-adapted clonal complexes. Still, among such genetic heterogeneity, it is feasible to identify conserved weak points in the biology of this bacterium: the two-component regulatory system RstAB (CarSR) was found to be necessary for the maximal production of virulence factors, and its inactivation severely impaired virulence.

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Moein Khojasteh ◽  
S. Mohsen Taghavi ◽  
Pejman Khodaygan ◽  
Habiballah Hamzehzarghani ◽  
Gongyou Chen ◽  
...  

ABSTRACT This study provides a phylogeographic insight into the population diversity of Xanthomonas translucens strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and typing (MLSA and MLST) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD), identified 57 strains as X. translucens pv. undulosa, while eight strains were identified as X. translucens pv. translucens. Although the pathogenicity patterns on oat and ryegrass weed species varied among the strains, all X. translucens pv. undulosa strains were pathogenic on barley, Harding’s grass, rye (except for XtKm35) and wheat, and all X. translucens pv. translucens strains were pathogenic on barley and Harding’s grass, while none of the latter group was pathogenic on rye or wheat (except for XtKm18). MLST using the 65 strains isolated in Iran, as well as the sequences of the four genes from 112 strains of worldwide origin retrieved from the GenBank database, revealed higher genetic diversity (i.e., haplotype frequency, haplotype diversity, and percentage of polymorphic sites) among the Iranian population of X. translucens than among the North American strains of the pathogen. High genetic diversity of the BLS pathogen in Iran was in congruence with the fact that the Iranian Plateau is considered the center of origin of cultivated wheat. However, further studies using larger collections of strains are warranted to precisely elucidate the global population diversity and center of origin of the pathogen. IMPORTANCE Bacterial leaf streak (BLS) of small-grain cereals (i.e., wheat and barley) is one of the economically important diseases of gramineous crops worldwide. The disease occurs in many countries across the globe, with particular importance in regions characterized by high levels of precipitation. Two genetically distinct xanthomonads—namely, Xanthomonas translucens pv. undulosa and X. translucens pv. translucens—have been reported to cause BLS disease on small-grain cereals. As seed-borne pathogens, the causal agents are included in the A2 list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Despite its global distribution and high economic importance, the population structure, genetic diversity, and phylogeography of X. translucens remain undetermined. This study, using MLSA and MLST, provides a global-scale phylogeography of X. translucens strains infecting small-grain cereals. Based on the diversity parameters, neutrality indices, and population structure, we observe higher genetic diversity of the BLS pathogen in Iran, which is geographically close to the center of origin of common wheat, than has so far been observed in other areas of the world, including North America. The results obtained in this study provide a novel insight into the genetic diversity and population structure of the BLS pathogen of small-grain cereals on a global scale.


2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Adelaide Milani ◽  
Gianpiero Zamperin ◽  
Alice Fusaro ◽  
Annalisa Salviato ◽  
Luca Bano ◽  
...  

Using a metagenomics approach, we were able to determine for the first time the full-genome sequence of a psittacine adenovirus 1 isolate that was recovered from the liver of a dead Senegal parrot (Poicephalus senegalus) in Italy. The results of the phylogenetic investigations revealed the existence of high genetic diversity among adenoviruses circulating in psittacine birds.


mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Chaofang Zhong ◽  
Maozhen Han ◽  
Pengshuo Yang ◽  
Chaoyun Chen ◽  
Hui Yu ◽  
...  

ABSTRACT The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections. IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.


2016 ◽  
Vol 82 (14) ◽  
pp. 4330-4339 ◽  
Author(s):  
G. Laloi ◽  
J. Montarry ◽  
M. Guibert ◽  
D. Andrivon ◽  
D. Michot ◽  
...  

ABSTRACTAscochyta blight, caused by the necrotrophic ascomyceteDidymella pinodes, is responsible for severe losses in winter and spring pea crops. Despite different climatic conditions, epidemics on winter and spring crops are due to a single population ofD. pinodes, suggesting gene flow either between the two crops or from reservoir sources during the cropping season. This should lead to similar pathogenicity characteristics in isolates sampled from the two crops. However, these hypotheses have never been formally tested. We therefore sampled a total of 520D. pinodesstrains throughout a growing season from winter and spring pea plots (WP and SP, respectively) and from winter and spring trap plants (TWP and TSP). Amplified fragment length polymorphism (AFLP) markers revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. These results support the idea that alloinoculum contributes to the carryover of epidemics between winter and spring crops and that the most aggressive isolates are selected as an epidemic progresses.IMPORTANCEAscochyta blight, caused byDidymella pinodes, is responsible for severe losses in pea crops. While previous studies have shown that ascochyta blight epidemics on winter and spring crops are due to a single population ofD. pinodes, suggesting that isolates from the two crops present similar pathogenicity characteristics, that hypothesis have never been tested. Genetic analysis of subpopulations sampled throughout a growing season from winter and spring pea plots revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic.


2012 ◽  
Vol 56 (8) ◽  
pp. 4354-4359 ◽  
Author(s):  
Jose M. Munita ◽  
Diana Panesso ◽  
Lorena Diaz ◽  
Truc T. Tran ◽  
Jinnethe Reyes ◽  
...  

ABSTRACTMutations inliaFSR, a three-component regulatory system controlling cell-envelope stress response, were recently linked with the emergence of daptomycin (DAP) resistance in enterococci. Our previous work showed that aliaFmutation increased the DAP MIC of a vancomycin-resistantEnterococcus faecalisstrain from 1 to 3 μg/ml (the DAP breakpoint is 4 μg/ml), suggesting that mutations in theliaFSRsystem could be a pivotal initial event in the development of DAP resistance. With the hypothesis that clinical enterococcal isolates with DAP MICs between 3 and 4 μg/ml might harbor mutations inliaFSR, we studied 38Enterococcus faeciumbloodstream isolates, of which 8 had DAP MICs between 3 and 4 μg/ml by Etest in Mueller-Hinton agar. Interestingly, 6 of these 8 isolates had predicted amino acid changes in the LiaFSR system. Moreover, we previously showed that among 6 DAP-resistantE. faeciumisolates (MICs of >4 μg/ml), 5 had mutations inliaFSR. In contrast, none of 16E. faeciumisolates with a DAP MIC of ≤2 μg/ml harbored mutations in this system (P< 0.0001). All but one isolate withliaFSRchanges exhibited DAP MICs of ≥16 μg/ml by Etest using brain heart infusion agar (BHIA), a medium that better supports enterococcal growth. Our findings provide a strong association between DAP MICs within the upper susceptibility range and mutations in theliaFSRsystem. Concomitant susceptibility testing on BHIA may be useful for identifying theseE. faeciumfirst-step mutants. Our results also suggest that the current DAP breakpoint forE. faeciummay need to be reevaluated.


mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Mark T. Anderson ◽  
Lindsay A. Mitchell ◽  
Anna Sintsova ◽  
Katherine A. Rice ◽  
Harry L. T. Mobley

ABSTRACT Sulfur is an essential nutrient that contributes to cellular redox homeostasis, transcriptional regulation, and translation initiation when incorporated into different biomolecules. Transport and reduction of extracellular sulfate followed by cysteine biosynthesis is a major pathway of bacterial sulfur assimilation. For the opportunistic pathogen Serratia marcescens, function of the cysteine biosynthesis pathway is required for extracellular phospholipase activity and flagellum-mediated surface motility, but little else is known about the influence of sulfur assimilation on the physiology of this organism. In this work, it was determined that an S. marcescens cysteine auxotroph fails to differentiate into hyperflagellated and elongated swarmer cells and that cysteine, but not other organic sulfur molecules, restores swarming motility to these bacteria. The S. marcescens cysteine auxotroph further exhibits reduced transcription of phospholipase, hemolysin, and flagellin genes, each of which is subject to transcriptional control by the flagellar regulatory system. Based on these data and the central role of cysteine in sulfur assimilation, it was reasoned that environmental sulfur availability may contribute to the regulation of these functions in S. marcescens. Indeed, bacteria that are starved for sulfate exhibit substantially reduced transcription of the genes for hemolysin, phospholipase, and the FlhD flagellar master regulator. A global transcriptomic analysis further defined a large set of S. marcescens genes that are responsive to extracellular sulfate availability, including genes that encode membrane transport, nutrient utilization, and metabolism functions. Finally, sulfate availability was demonstrated to alter S. marcescens cytolytic activity, suggesting that sulfate assimilation may impact the virulence of this organism. IMPORTANCE Serratia marcescens is a versatile bacterial species that inhabits diverse environmental niches and is capable of pathogenic interactions with host organisms ranging from insects to humans. This report demonstrates for the first time the extensive impacts that environmental sulfate availability and cysteine biosynthesis have on the transcriptome of S. marcescens. The finding that greater than 1,000 S. marcescens genes are differentially expressed depending on sulfate availability suggests that sulfur abundance is a crucial factor that controls the physiology of this organism. Furthermore, the high relative expression levels for the putative virulence factors flagella, phospholipase, and hemolysin in the presence of sulfate suggests that a sulfur-rich host environment could contribute to the transcription of these genes during infection.


2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Ségolène Calvez ◽  
Nora Navarro-Gonzalez ◽  
Charlène Siekoula-Nguedia ◽  
Catherine Fournel ◽  
Eric Duchaud

ABSTRACT Flavobacterium psychrophilum affects salmonid health worldwide and causes economic losses. The genetic diversity of the pathogen must be considered to develop control methods. However, previous studies have reported both high and low levels of genetic diversity. The present longitudinal study aimed at assessing the genetic diversity of F. psychrophilum at a small temporal and geographic scale. Four farms located on the same watershed in France were studied. Rainbow trout (Oncorhynchus mykiss) batches were monitored, and apparently healthy individuals were sampled over 1 year. A total of 288 isolates were recovered from fish organs (gills and spleen) and eggs. Pulsed field gel electrophoresis revealed high genetic diversity. Multilocus sequence typing performed on a selection of 31 isolates provided congruent results, as follows: 18 sequence types (STs) were found, of which 13 were novel. The mean gene diversity (H = 0.8413) was much higher than that previously reported for this host species, although the sampling was restricted to a single watershed and 1 year. Seven isolates out of 31 were assigned to clonal complex ST10 (CC-ST10), which is the predominant clonal complex in the main salmonid production areas. A split decomposition tree reflected a panmictic population. This finding is important for aquaculture veterinarians in their diagnostic procedure, as the choice of adequate antibiotic treatment is conditioned by the correct identification of the causative agent. Furthermore, this study expands our knowledge on genetic diversity required for the development of an effective vaccine against F. psychrophilum. IMPORTANCE The bacterium Flavobacterium psychrophilum is a serious pathogen in many fish species, especially salmonids, that is responsible for considerable economic losses worldwide. In order to treat infections and to develop vaccines, the genetic diversity of this bacterium needs to be known. We assessed the genetic diversity of F. psychrophilum isolates from apparently healthy rainbow trout raised in several fish farms in the same watershed in France. Two different genotyping methods revealed high diversity. The majority of isolates were unrelated to clonal complex sequence type 10 (CC-ST10), the clonal complex that is predominant worldwide and associated with disease in rainbow trout. In addition, we found 13 novel sequence types. These results suggest that a diverse subpopulation of F. psychrophilum may be harbored by rainbow trout.


2014 ◽  
Vol 58 (8) ◽  
pp. 4527-4534 ◽  
Author(s):  
Lorena Diaz ◽  
Truc T. Tran ◽  
Jose M. Munita ◽  
William R. Miller ◽  
Sandra Rincon ◽  
...  

ABSTRACTDaptomycin (DAP) is a lipopeptide antibiotic frequently used as a “last-resort” antibiotic against vancomycin-resistantEnterococcus faecium(VRE). However, an important limitation for DAP therapy against VRE is the emergence of resistance during therapy. Mutations in regulatory systems involved in cell envelope homeostasis are postulated to be important mediators of DAP resistance inE. faecium. Thus, in order to gain insights into the genetic bases of DAP resistance inE. faecium, we investigated the presence of changes in 43 predicted proteins previously associated with DAP resistance in enterococci and staphylococci using the genomes of 19E. faeciumwith different DAP MICs (range, 3 to 48 μg/ml). Bodipy-DAP (BDP-DAP) binding to the cell membrane assays and time-kill curves (DAP alone and with ampicillin) were performed. Genetic changes involving two major pathways were identified: (i) LiaFSR, a regulatory system associated with the cell envelope stress response, and (ii) YycFGHIJ, a system involved in the regulation of cell wall homeostasis. Thr120→Ala and Trp73→Cys substitutions in LiaS and LiaR, respectively, were the most common changes identified. DAP bactericidal activity was abolished in the presence ofliaFSRoryycFGHIJmutations regardless of the DAP MIC and was restored in the presence of ampicillin, but only in representatives of the LiaFSR pathway. Reduced binding of BDP-DAP to the cell surface was the predominant finding correlating with resistance in isolates with DAP MICs above the susceptibility breakpoint. Our findings suggest that genotypic information may be crucial to predict response to DAP plus β-lactam combinations and continue to question the DAP breakpoint of 4 μg/ml.


2016 ◽  
Vol 198 (6) ◽  
pp. 951-963 ◽  
Author(s):  
Manita Guragain ◽  
Michelle M. King ◽  
Kerry S. Williamson ◽  
Ailyn C. Pérez-Osorio ◽  
Tatsuya Akiyama ◽  
...  

ABSTRACTPseudomonas aeruginosais an opportunistic human pathogen that causes severe, life-threatening infections in patients with cystic fibrosis (CF), endocarditis, wounds, or artificial implants. During CF pulmonary infections,P. aeruginosaoften encounters environments where the levels of calcium (Ca2+) are elevated. Previously, we showed thatP. aeruginosaresponds to externally added Ca2+through enhanced biofilm formation, increased production of several secreted virulence factors, and by developing a transient increase in the intracellular Ca2+level, followed by its removal to the basal submicromolar level. However, the molecular mechanisms responsible for regulating Ca2+-induced virulence factor production and Ca2+homeostasis are not known. Here, we characterized the genome-wide transcriptional response ofP. aeruginosato elevated [Ca2+] in both planktonic cultures and biofilms. Among the genes induced by CaCl2in strain PAO1 was an operon containing the two-component regulator PA2656-PA2657 (here calledcarSandcarR), while the closely related two-component regulatorsphoPQandpmrABwere repressed by CaCl2addition. To identify the regulatory targets of CarSR, we constructed a deletion mutant ofcarRand performed transcriptome analysis of the mutant strain at low and high [Ca2+]. Among the genes regulated by CarSR in response to CaCl2are the predicted periplasmic OB-fold protein, PA0320 (here calledcarO), and the inner membrane-anchored five-bladed β-propeller protein, PA0327 (here calledcarP). Mutations in bothcarOandcarPaffected Ca2+homeostasis, reducing the ability ofP. aeruginosato export excess Ca2+. In addition, a mutation incarPhad a pleotropic effect in a Ca2+-dependent manner, altering swarming motility, pyocyanin production, and tobramycin sensitivity. Overall, the results indicate that the two-component system CarSR is responsible for sensing high levels of external Ca2+and responding through its regulatory targets that modulate Ca2+homeostasis, surface-associated motility, and the production of the virulence factor pyocyanin.IMPORTANCEDuring infectious disease,Pseudomonas aeruginosaencounters environments with high calcium (Ca2+) concentrations, yet the cells maintain intracellular Ca2+at levels that are orders of magnitude less than that of the external environment. In addition, Ca2+signalsP. aeruginosato induce the production of several virulence factors. Compared to eukaryotes, little is known about how bacteria maintain Ca2+homeostasis or how Ca2+acts as a signal. In this study, we identified a two-component regulatory system inP. aeruginosaPAO1, termed CarRS, that is induced at elevated Ca2+levels. CarRS modulates Ca2+signaling and Ca2+homeostasis through its regulatory targets, CarO and CarP. The results demonstrate thatP. aeruginosauses a two-component regulatory system to sense external Ca2+and relays that information for Ca2+-dependent cellular processes.


2013 ◽  
Vol 81 (11) ◽  
pp. 4160-4170 ◽  
Author(s):  
Maria Labandeira-Rey ◽  
Dana A. Dodd ◽  
Chad A. Brautigam ◽  
Kate R. Fortney ◽  
Stanley M. Spinola ◽  
...  

ABSTRACTExpression of thelspB-lspA2operon encoding a virulence-related two-partner secretion system inHaemophilus ducreyi35000HP is directly regulated by the CpxRA regulatory system (M. Labandeira-Rey, J. R. Mock, and E. J. Hansen, Infect. Immun. 77:3402–3411, 2009). In the present study, we show that this secretion system is also regulated by the small nucleoid-associated protein Fis. Inactivation of theH. ducreyi fisgene resulted in a reduction in expression of both theH. ducreyiLspB and LspA2 proteins. DNA microarray experiments showed that aH. ducreyi fisdeletion mutant exhibited altered expression levels of genes encoding other importantH. ducreyivirulence factors, including DsrA and Flp1, suggesting a possible global role for Fis in the control of virulence in this obligate human pathogen. While theH. ducreyiFis protein has a high degree of sequence and structural similarity to the Fis proteins of other bacteria, its temporal pattern of expression was very different from that of enterobacterial Fis proteins. The use of alacZ-based transcriptional reporter provided evidence which indicated that theH. ducreyiFis homolog is a positive regulator ofgyrB, a gene that is negatively regulated by Fis in enteric bacteria. Taken together, the Fis protein expression data and the observed regulatory effects of Fis inH. ducreyisuggest that this small DNA binding protein has a regulatory role inH. ducreyiwhich may differ in substantial ways from that of other Fis proteins.


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