Ecological Opportunity, Evolution, and the Emergence of Flea-Borne Plague

The plague bacillusYersinia pestisis unique among the pathogenicEnterobacteriaceaein utilizing an arthropod-borne transmission route. Transmission by fleabite is a recent evolutionary adaptation that followed the divergence ofY. pestisfrom the closely related food- and waterborne enteric pathogenYersinia pseudotuberculosis. A combination of population genetics, comparative genomics, and investigations ofYersinia-flea interactions have disclosed the important steps in the evolution and emergence ofY. pestisas a flea-borne pathogen. Only a few genetic changes, representing both gene gain by lateral transfer and gene loss by loss-of-function mutation (pseudogenization), were fundamental to this process. The emergence ofY. pestisfits evolutionary theories that emphasize ecological opportunity in adaptive diversification and rapid emergence of new species.

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Differential Gene Expression Patterns ofYersinia pestisandYersinia pseudotuberculosisduring Infection and Biofilm Formation in the Flea Digestive Tract

mSystems ◽

10.1128/msystems.00217-18 ◽

2019 ◽

Vol 4 (1) ◽

Cited By ~ 8

Author(s):

Iman Chouikha ◽

Daniel E. Sturdevant ◽

Clayton Jarrett ◽

Yi-Cheng Sun ◽

B. Joseph Hinnebusch

Keyword(s):

Digestive Tract ◽

Biofilm Formation ◽

Yersinia Pseudotuberculosis ◽

Expression Patterns ◽

Type Vi Secretion System ◽

Genetic Changes ◽

Content Type ◽

Biofilm Development

ABSTRACTYersinia pestis, the etiologic agent of plague, emerged as a fleaborne pathogen only within the last 6,000 years. Just five simple genetic changes in theYersinia pseudotuberculosisprogenitor, which served to eliminate toxicity to fleas and to enhance survival and biofilm formation in the flea digestive tract, were key to the transition to the arthropodborne transmission route. To gain a deeper understanding of the genetic basis for the development of a transmissible biofilm infection in the flea foregut, we evaluated additional gene differences and performedin vivotranscriptional profiling ofY. pestis, aY. pseudotuberculosiswild-type strain (unable to form biofilm in the flea foregut), and aY. pseudotuberculosismutant strain (able to produce foregut-blocking biofilm in fleas) recovered from fleas 1 day and 14 days after an infectious blood meal. Surprisingly, theY. pseudotuberculosismutations that increased c-di-GMP levels and enabled biofilm development in the flea did not change the expression levels of thehmsgenes responsible for the synthesis and export of the extracellular polysaccharide matrix required for mature biofilm formation. TheY. pseudotuberculosismutant uniquely expressed much higher levels ofYersiniatype VI secretion system 4 (T6SS-4) in the flea, and this locus was required for flea blockage byY. pseudotuberculosisbut not for blockage byY. pestis. Significant differences between the two species in expression of several metabolism genes, the Psa fimbrial genes, quorum sensing-related genes, transcription regulation genes, and stress response genes were evident during flea infection.IMPORTANCEY. pestisemerged as a highly virulent, arthropod-transmitted pathogen on the basis of relatively few and discrete genetic changes fromY. pseudotuberculosis. Parallel comparisons of thein vitroandin vivotranscriptomes ofY. pestisand twoY. pseudotuberculosisvariants that produce a nontransmissible infection and a transmissible infection of the flea vector, respectively, provided insights into howY. pestishas adapted to life in its flea vector and point to evolutionary changes in the regulation of metabolic and biofilm development pathways in these two closely related species.

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Gene loss during the transition to multicellularity

10.1101/2021.02.16.431445 ◽

2021 ◽

Author(s):

Berenice Jiménez-Marín ◽

Jessica B. Rakijas ◽

Antariksh Tyagi ◽

Aakash Pandey ◽

Erik R. Hanschen ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Gene Loss ◽

Protein Complexes ◽

Gene Gain ◽

Genetic Changes ◽

Gradual Loss ◽

Volvocine Algae ◽

Major Transition ◽

Network States ◽

High Degree

SummaryMulticellular evolution is a major transition associated with momentous diversification of multiple lineages and increased developmental complexity. The volvocine algae comprise a valuable system for the study of this transition, as they span from unicellular to undifferentiated and differentiated multicellular morphologies despite their genomes being highly similar, suggesting multicellular evolution requires few genetic changes to undergo dramatic shifts in developmental complexity. Here, the evolutionary dynamics of five volvocine genomes were examined, where a gradual loss of genes was observed in parallel to the co-option of a few key genes. Protein complexes in the five species exhibited a high degree of novel interactions, suggesting that gene loss promotes evolutionary novelty. This finding was supported by gene network modeling, where gene loss outpaces gene gain in generating novel stable network states. These results suggest developmental complexity may be driven by gene loss rather than gene gain.

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Gene Loss and Lineage-Specific Restriction-Modification Systems Associated with Niche Differentiation in the Campylobacter jejuni Sequence Type 403 Clonal Complex

Applied and Environmental Microbiology ◽

10.1128/aem.00546-15 ◽

2015 ◽

Vol 81 (11) ◽

pp. 3641-3647 ◽

Cited By ~ 13

Author(s):

Laura Morley ◽

Alan McNally ◽

Konrad Paszkiewicz ◽

Jukka Corander ◽

Guillaume Méric ◽

...

Keyword(s):

Campylobacter Jejuni ◽

Gene Loss ◽

Clonal Complex ◽

Niche Differentiation ◽

Gene Gain ◽

Nonsense Mutations ◽

Content Type ◽

Specific Restriction ◽

Restriction Modification ◽

Restriction Modification Systems

ABSTRACTCampylobacter jejuniis a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex ofC. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts ofC. jejuniST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation.

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Identification of Pathogenicity Island Genes Associated with Loss of Type IV Secretion Function during Murine Infection with Helicobacter pylori

Infection and Immunity ◽

10.1128/iai.00801-19 ◽

2020 ◽

Vol 88 (6) ◽

Cited By ~ 2

Author(s):

Lori M. Hansen ◽

Dylan J. Dekalb ◽

Lucy P. Cai ◽

Jay V. Solnick

Keyword(s):

Helicobacter Pylori ◽

Single Molecule ◽

Pathogenicity Island ◽

Type Iv Secretion ◽

Common Mechanism ◽

Loss Of Function ◽

Genetic Changes ◽

Content Type ◽

Type Iv ◽

H Pylori

ABSTRACT Chronic Helicobacter pylori colonization in animal models often leads to downregulation of the type IV secretion system (T4SS), typically by recombination in cagY, which is an essential T4SS gene. However, 17 other cag pathogenicity island (cagPAI) genes, as well as some non-cagPAI genes, are also essential for T4SS function. To get a more complete picture of how H. pylori regulates the T4SS during animal colonization, we examined cagY in 534 mouse-passaged isolates that lost T4SS function, defined as a normalized interleukin-8 (IL-8) value of <0.3 relative to the input H. pylori strain PMSS1. In order to analyze the genetic changes in the strains with unchanged cagY, we sequenced the entire pathogenicity island of 60 such isolates using single-molecule, real-time (SMRT) sequencing technology (PacBio, Menlo Park, CA), and we compared the results to the PMSS1 wild type (WT). Of the 534 strains, 271 (51%) showed evidence of recombination in cagY, but we also found indels or nonsynonymous changes in 13 other essential cagPAI genes implicated in H. pylori T4SS function, most commonly cag5, cag10, and cagA. While cagY recombination is the most common mechanism by which H. pylori downregulates T4SS function during murine infection, loss of function is also associated with changes in other essential cagPAI genes.

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Stepwise Decrease in Daptomycin Susceptibility in Clinical Staphylococcus aureus Isolates Associated with an Initial Mutation inrpoBand a Compensatory Inactivation of theclpXGene

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01303-15 ◽

2015 ◽

Vol 59 (11) ◽

pp. 6983-6991 ◽

Cited By ~ 29

Author(s):

Kristoffer T. Bæk ◽

Louise Thøgersen ◽

René G. Mogenssen ◽

Maiken Mellergaard ◽

Line E. Thomsen ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Cell Wall ◽

Wall Stress ◽

Growth Defect ◽

Loss Of Function ◽

Genetic Changes ◽

Content Type ◽

Virulence Traits ◽

Lipopeptide Antibiotic

ABSTRACTDaptomycin is a lipopeptide antibiotic used clinically for the treatment of methicillin-resistantStaphylococcus aureus(MRSA) infections. The emergence of daptomycin-nonsusceptibleS. aureusisolates during therapy is often associated with multiple genetic changes; however, the relative contributions of these changes to resistance and other phenotypic changes usually remain unclear. The present study was undertaken to investigate this issue using a genetically characterized series of four isogenic clinical MRSA strains derived from a patient with bacteremia before and during daptomycin treatment. The first strain obtained after daptomycin therapy carried a single-nucleotide polymorphism (SNP) inrpoB(RpoB A477D) that decreased susceptibility not only to daptomycin but also to vancomycin, β-lactams, and rifampin. Furthermore, therpoBmutant exhibited pleiotropic phenotypes, including increased cell wall thickness, reduced expression of virulence traits, induced expression of the stress-associated transcriptional regulator Spx, and slow growth. A subsequently acquired loss-of-function mutation inclpXpartly alleviated the growth defect conferred by therpoBmutation without changing antibiotic susceptibility. The final isolate acquired three additional mutations, including an SNP inmprF(MprF S295L) known to confer daptomycin nonsusceptibility, and accordingly, this isolate was the only daptomycin-nonsusceptible strain of this series. Interestingly, in this isolate, the cell wall had regained the same thickness as that of the parental strain, while the level of transcription of thevraSR(cell wall stress regulator) was increased. In conclusion, this study illustrates how serial genetic changes selectedin vivocontribute to daptomycin nonsusceptibility, growth fitness, and virulence traits.

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Mutations in fbiD (Rv2983) as a Novel Determinant of Resistance to Pretomanid and Delamanid in Mycobacterium tuberculosis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01948-20 ◽

2020 ◽

Vol 65 (1) ◽

pp. e01948-20

Author(s):

Dalin Rifat ◽

Si-Yang Li ◽

Thomas Ioerger ◽

Keshav Shah ◽

Jean-Philippe Lanoix ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Clinical Evidence ◽

Clinical Samples ◽

Loss Of Function ◽

Wild Type ◽

Content Type ◽

Solid Media ◽

High Level ◽

Level Resistance

ABSTRACTThe nitroimidazole prodrugs delamanid and pretomanid comprise one of only two new antimicrobial classes approved to treat tuberculosis (TB) in 50 years. Prior in vitro studies suggest a relatively low barrier to nitroimidazole resistance in Mycobacterium tuberculosis, but clinical evidence is limited to date. We selected pretomanid-resistant M. tuberculosis mutants in two mouse models of TB using a range of pretomanid doses. The frequency of spontaneous resistance was approximately 10−5 CFU. Whole-genome sequencing of 161 resistant isolates from 47 mice revealed 99 unique mutations, of which 91% occurred in 1 of 5 genes previously associated with nitroimidazole activation and resistance, namely, fbiC (56%), fbiA (15%), ddn (12%), fgd (4%), and fbiB (4%). Nearly all mutations were unique to a single mouse and not previously identified. The remaining 9% of resistant mutants harbored mutations in Rv2983 (fbiD), a gene not previously associated with nitroimidazole resistance but recently shown to be a guanylyltransferase necessary for cofactor F420 synthesis. Most mutants exhibited high-level resistance to pretomanid and delamanid, although Rv2983 and fbiB mutants exhibited high-level pretomanid resistance but relatively small changes in delamanid susceptibility. Complementing an Rv2983 mutant with wild-type Rv2983 restored susceptibility to pretomanid and delamanid. By quantifying intracellular F420 and its precursor Fo in overexpressing and loss-of-function mutants, we provide further evidence that Rv2983 is necessary for F420 biosynthesis. Finally, Rv2983 mutants and other F420H2-deficient mutants displayed hypersusceptibility to some antibiotics and to concentrations of malachite green found in solid media used to isolate and propagate mycobacteria from clinical samples.

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Loss of the Conserved Alveolate Kinase MAPK2 Decouples Toxoplasma Cell Growth from Cell Division

mBio ◽

10.1128/mbio.02517-20 ◽

2020 ◽

Vol 11 (6) ◽

Author(s):

Xiaoyu Hu ◽

William J. O’Shaughnessy ◽

Tsebaot G. Beraki ◽

Michael L. Reese

Keyword(s):

Toxoplasma Gondii ◽

Protein Kinases ◽

Daughter Cell ◽

Protozoan Parasite ◽

Productive Infection ◽

Centrosome Duplication ◽

Loss Of Function ◽

Content Type ◽

Mitogen Activated Protein ◽

Parasite Replication

ABSTRACT Mitogen-activated protein kinases (MAPKs) are a conserved family of protein kinases that regulate signal transduction, proliferation, and development throughout eukaryotes. The apicomplexan parasite Toxoplasma gondii expresses three MAPKs. Two of these, extracellular signal-regulated kinase 7 (ERK7) and MAPKL1, have been implicated in the regulation of conoid biogenesis and centrosome duplication, respectively. The third kinase, MAPK2, is specific to and conserved throughout the Alveolata, although its function is unknown. We used the auxin-inducible degron system to determine phenotypes associated with MAPK2 loss of function in Toxoplasma. We observed that parasites lacking MAPK2 failed to duplicate their centrosomes and therefore did not initiate daughter cell budding, which ultimately led to parasite death. MAPK2-deficient parasites initiated but did not complete DNA replication and arrested prior to mitosis. Surprisingly, the parasites continued to grow and replicate their Golgi apparatus, mitochondria, and apicoplasts. We found that the failure in centrosome duplication is distinct from the phenotype caused by the depletion of MAPKL1. As we did not observe MAPK2 localization at the centrosome at any point in the cell cycle, our data suggest that MAPK2 regulates a process at a distal site that is required for the completion of centrosome duplication and the initiation of parasite mitosis. IMPORTANCE Toxoplasma gondii is a ubiquitous intracellular protozoan parasite that can cause severe and fatal disease in immunocompromised patients and the developing fetus. Rapid parasite replication is critical for establishing a productive infection. Here, we demonstrate that a Toxoplasma protein kinase called MAPK2 is conserved throughout the Alveolata and essential for parasite replication. We found that parasites lacking MAPK2 protein were defective in the initiation of daughter cell budding and were rendered inviable. Specifically, T. gondii MAPK2 (TgMAPK2) appears to be required for centrosome replication at the basal end of the nucleus, and its loss causes arrest early in parasite division. MAPK2 is unique to the Alveolata and not found in metazoa and likely is a critical component of an essential parasite-specific signaling network.

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Mutation ofRv2887, amarR-Like Gene, Confers Mycobacterium tuberculosis Resistance to an Imidazopyridine-Based Agent

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01341-15 ◽

2015 ◽

Vol 59 (11) ◽

pp. 6873-6881 ◽

Cited By ~ 13

Author(s):

Kathryn Winglee ◽

Shichun Lun ◽

Marco Pieroni ◽

Alan Kozikowski ◽

William Bishai

Keyword(s):

Mycobacterium Tuberculosis ◽

Drug Targets ◽

Efflux Pump ◽

Transcriptional Regulator ◽

Cross Resistance ◽

Loss Of Function ◽

Strong Activity ◽

Content Type ◽

Novel Drug

ABSTRACTDrug resistance is a major problem inMycobacterium tuberculosiscontrol, and it is critical to identify novel drug targets and new antimycobacterial compounds. We have previously identified an imidazo[1,2-a]pyridine-4-carbonitrile-based agent, MP-III-71, with strong activity againstM. tuberculosis. In this study, we evaluated mechanisms of resistance to MP-III-71. We derived three independentM. tuberculosismutants resistant to MP-III-71 and conducted whole-genome sequencing of these mutants. Loss-of-function mutations inRv2887were common to all three MP-III-71-resistant mutants, and we confirmed the role ofRv2887as a gene required for MP-III-71 susceptibility using complementation. The Rv2887 protein was previously unannotated, but domain and homology analyses suggested it to be a transcriptional regulator in the MarR (multiple antibiotic resistance repressor) family, a group of proteins first identified inEscherichia colito negatively regulate efflux pumps and other mechanisms of multidrug resistance. We found that two efflux pump inhibitors, verapamil and chlorpromazine, potentiate the action of MP-III-71 and that mutation ofRv2887abrogates their activity. We also used transcriptome sequencing (RNA-seq) to identify genes which are differentially expressed in the presence and absence of a functional Rv2887 protein. We found that genes involved in benzoquinone and menaquinone biosynthesis were repressed by functional Rv2887. Thus, inactivating mutations ofRv2887, encoding a putative MarR-like transcriptional regulator, confer resistance to MP-III-71, an effective antimycobacterial compound that shows no cross-resistance to existing antituberculosis drugs. The mechanism of resistance ofM. tuberculosisRv2887mutants may involve efflux pump upregulation and also drug methylation.

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Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes

Journal of Clinical Microbiology ◽

10.1128/jcm.01798-16 ◽

2016 ◽

Vol 55 (3) ◽

pp. 844-858 ◽

Cited By ~ 16

Author(s):

Per Sikora ◽

Sofia Andersson ◽

Jadwiga Winiecka-Krusnell ◽

Björn Hallström ◽

Cecilia Alsmark ◽

...

Keyword(s):

Parasite Burden ◽

Genomic Variation ◽

Loss Of Function ◽

Oocyst Wall ◽

Gene Encoding ◽

Cryptosporidium Hominis ◽

Content Type ◽

Successful Isolation ◽

Target Dna ◽

Stool Samples

ABSTRACTIn order to improve genotyping and epidemiological analysis ofCryptosporidiumspp., genomic data need to be generated directly from a broad range of clinical specimens. Utilizing a robust method that we developed for the purification and generation of amplified target DNA, we present its application for the successful isolation and whole-genome sequencing of 14 differentCryptosporidium hominispatient specimens. Six isolates of subtype IbA10G2 were analyzed together with a single representative each of 8 other subtypes: IaA20R3, IaA23R3, IbA9G3, IbA13G3, IdA14, IeA11G3T3, IfA12G1, and IkA18G1. Parasite burden was measured over a range of more than 2 orders of magnitude for all samples, while the genomes were sequenced to mean depths of between 17× and 490× coverage. Sequence homology-based functional annotation identified several genes of interest, including the gene encodingCryptosporidiumoocyst wall protein 9 (COWP9), which presented a predicted loss-of-function mutation in all the sequence subtypes, except for that seen with IbA10G2, which has a sequence identical to theCryptosporidium parvumreference Iowa II sequence. Furthermore, phylogenetic analysis showed that all the IbA10G2 genomes form a monophyletic clade in theC. hoministree as expected and yet display some heterogeneity within the IbA10G2 subtype. The current report validates the aforementioned method for isolating and sequencingCryptosporidiumdirectly from clinical stool samples. In addition, the analysis demonstrates the potential in mining data generated from sequencing multiple whole genomes ofCryptosporidiumfrom human fecal samples, while alluding to the potential for a higher degree of genotyping withinCryptosporidiumepidemiology.

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High-Level Carbapenem Resistance in OXA-232-Producing Raoultella ornithinolytica Triggered by Ertapenem Therapy

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01335-19 ◽

2019 ◽

Vol 64 (1) ◽

Cited By ~ 2

Author(s):

Alina Iovleva ◽

Roberta T. Mettus ◽

Christi L. McElheny ◽

Marissa P. Griffith ◽

Mustapha M. Mustapha ◽

...

Keyword(s):

Rapid Development ◽

Carbapenem Resistance ◽

Resistant Isolate ◽

Clinical Microbiology Laboratory ◽

Loss Of Function ◽

Content Type ◽

Carbapenem Resistant ◽

Class D ◽

Fold Reduction ◽

High Level

ABSTRACT OXA-232 is an OXA-48-group class D β-lactamase that hydrolyzes expanded-spectrum cephalosporins and carbapenems at low levels. Clinical strains producing OXA-232 are sometimes susceptible to carbapenems, making it difficult to identify them in the clinical microbiology laboratory. We describe the development of carbapenem resistance in sequential clinical isolates of Raoultella ornithinolytica carrying blaOXA-232 in a hospitalized patient, where the ertapenem MIC increased from 0.5 μg/ml to 512 μg/ml and the meropenem MIC increased from 0.125 μg/ml to 32 μg/ml during the course of ertapenem therapy. Whole-genome sequencing (WGS) analysis identified loss-of-function mutations in ompC and ompF in carbapenem-resistant isolates that were not present in the initial carbapenem-susceptible isolate. Complementation of a carbapenem-resistant isolate with an intact ompF gene resulted in 16- to 32-fold reductions in carbapenem MICs, whereas complementation with intact ompC resulted in a 2-fold reduction in carbapenem MICs. Additionally, blaOXA-232 expression increased 2.9-fold in a carbapenem-resistant isolate. Rapid development of high-level carbapenem resistance in initially carbapenem-susceptible OXA-232-producing R. ornithinolytica under selective pressure from carbapenem therapy highlights the diagnostic challenges in detecting Enterobacteriaceae strains producing this inefficient carbapenemase.

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