Characterization and Comparative Analysis of the Staphylococcus aureus Genomic Island vSaβ: an In Silico Approach

ABSTRACT Staphylococcus aureus is a widespread opportunistic pathogen to humans and animals. Of its genome, 20 to 25% varies between strains and consists of phages, pathogenicity islands, transposons, and genomic islands. S. aureus harbors up to three genomic islands, vSaα, vSaβ, and vSaγ. The vSaβ region of S. aureus can encode a number of virulence-associated factors, such as serine proteases, leukocidins, enterotoxins, bacteriocins, or a hyaluronate lyase. In this study, the vSaβ regions of 103 clinically relevant S. aureus strains were characterized in silico and compared to the three predefined vSaβ types. We here suggest a superordinate system of 15 different vSaβ types, of which 12 were newly defined. Each vSaβ type has a distinct structure with a distinct set of genes, which are both highly conserved. Between the different types, gene content and composition vary substantially. Based on our data, a strain’s vSaβ type is strongly coupled with its clonal complex, suggesting that vSaβ was acquired in an ancestral S. aureus strain, arguably by phage mediation, before differentiation into clonal complexes. In addition, we addressed the issue of ambiguous nomenclature in the serine protease gene cluster and propose a novel, phylogeny-based nomenclature of the cluster contained in the vSaβ region. IMPORTANCE With the rapid increase of available sequencing data on clinically relevant bacterial species such as S. aureus, the genomic basis of clinical phenotypes can be investigated in much more detail, allowing a much deeper understanding of the mechanisms involved in disease. We characterized in detail the S. aureus genomic island vSaβ and defined a superordinate system to categorize S. aureus strains based on their vSaβ type, providing information about the strains’ virulence-associated genes and clinical potential.

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No Change, No Life? What We Know about Phase Variation in Staphylococcus aureus

Microorganisms ◽

10.3390/microorganisms9020244 ◽

2021 ◽

Vol 9 (2) ◽

pp. 244

Author(s):

Vishal Gor ◽

Ryosuke L. Ohniwa ◽

Kazuya Morikawa

Keyword(s):

Gene Expression ◽

Staphylococcus Aureus ◽

High Frequency ◽

Direct Evidence ◽

Bacterial Species ◽

Phase Variation ◽

Opportunistic Pathogen ◽

Adaptation Strategy ◽

Innate Immune ◽

Epigenetic Mechanisms

Phase variation (PV) is a well-known phenomenon of high-frequency reversible gene-expression switching. PV arises from genetic and epigenetic mechanisms and confers a range of benefits to bacteria, constituting both an innate immune strategy to infection from bacteriophages as well as an adaptation strategy within an infected host. PV has been well-characterized in numerous bacterial species; however, there is limited direct evidence of PV in the human opportunistic pathogen Staphylococcus aureus. This review provides an overview of the mechanisms that generate PV and focuses on earlier and recent findings of PV in S. aureus, with a brief look at the future of the field.

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Triclosan Promotes Staphylococcus aureus Nasal Colonization

mBio ◽

10.1128/mbio.01015-13 ◽

2014 ◽

Vol 5 (2) ◽

Cited By ~ 29

Author(s):

Adnan K. Syed ◽

Sudeshna Ghosh ◽

Nancy G. Love ◽

Blaise R. Boles

Keyword(s):

Staphylococcus Aureus ◽

Risk Factor ◽

Human Microbiome ◽

Opportunistic Pathogen ◽

Unintended Consequences ◽

Nasal Colonization ◽

Content Type ◽

Test Population ◽

Human Proteins ◽

Nasal Secretions

ABSTRACT The biocide triclosan is used in many personal care products, including toothpastes, soaps, clothing, and medical equipment. Consequently, it is present as a contaminant in the environment and has been detected in some human fluids, including serum, urine, and milk. Staphylococcus aureus is an opportunistic pathogen that colonizes the noses and throats of approximately 30% of the population. Colonization with S. aureus is known to be a risk factor for several types of infection. Here we demonstrate that triclosan is commonly found in the nasal secretions of healthy adults and the presence of triclosan trends positively with nasal colonization by S. aureus. We demonstrate that triclosan can promote the binding of S. aureus to host proteins such as collagen, fibronectin, and keratin, as well as inanimate surfaces such as plastic and glass. Lastly, triclosan-exposed rats are more susceptible to nasal colonization with S. aureus. These data reveal a novel factor that influences the ability of S. aureus to bind surfaces and alters S. aureus nasal colonization. IMPORTANCE Triclosan has been used as a biocide for over 40 years, but the broader effects that it has on the human microbiome have not been investigated. We demonstrate that triclosan is present in nasal secretions of a large portion of a test population and its presence correlates with Staphylococcus aureus nasal colonization. Triclosan also promotes the binding of S. aureus to human proteins and increases the susceptibility of rats to nasal colonization by S. aureus. These findings are significant because S. aureus colonization is a known risk factor for the development of several types of infections. Our data demonstrate the unintended consequences of unregulated triclosan use and contribute to the growing body of research demonstrating inadvertent effects of triclosan on the environment and human health.

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Spatiotemporal Distribution of Pseudomonas aeruginosa Alkyl Quinolones under Metabolic and Competitive Stress

mSphere ◽

10.1128/msphere.00426-20 ◽

2020 ◽

Vol 5 (4) ◽

Author(s):

Tianyuan Cao ◽

Jonathan V. Sweedler ◽

Paul W. Bohn ◽

Joshua D. Shrout

Keyword(s):

Pseudomonas Aeruginosa ◽

Bacterial Species ◽

Metabolic Stress ◽

Opportunistic Pathogen ◽

Cell Interaction ◽

Chemical Imaging ◽

Carbon Limitation ◽

Bacterial Strains ◽

Content Type ◽

High Level

ABSTRACT Pseudomonas aeruginosa is an opportunistic human pathogen important to diseases such as cystic fibrosis. P. aeruginosa has multiple quorum-sensing (QS) systems, one of which utilizes the signaling molecule 2-heptyl-3-hydroxy-4-quinolone (Pseudomonas quinolone signal [PQS]). Here, we use hyperspectral Raman imaging to elucidate the spatiotemporal PQS distributions that determine how P. aeruginosa regulates surface colonization and its response to both metabolic stress and competition from other bacterial strains. These chemical imaging experiments illustrate the strong link between environmental challenges, such as metabolic stress caused by nutritional limitations or the presence of another bacterial species, and PQS signaling. Metabolic stress elicits a complex response in which limited nutrients induce the bacteria to produce PQS earlier, but the bacteria may also pause PQS production entirely if the nutrient concentration is too low. Separately, coculturing P. aeruginosa in the proximity of another bacterial species, or its culture supernatant, results in earlier production of PQS. However, these differences in PQS appearance are not observed for all alkyl quinolones (AQs) measured; the spatiotemporal response of 2-heptyl-4-hydroxyquinoline N-oxide (HQNO) is highly uniform for most conditions. These insights on the spatiotemporal distributions of quinolones provide additional perspective on the behavior of P. aeruginosa in response to different environmental cues. IMPORTANCE Alkyl quinolones (AQs), including Pseudomonas quinolone signal (PQS), made by the opportunistic pathogen Pseudomonas aeruginosa have been associated with both population density and stress. The regulation of AQ production is known to be complex, and the stimuli that modulate AQ responses are not fully clear. Here, we have used hyperspectral Raman chemical imaging to examine the temporal and spatial profiles of AQs exhibited by P. aeruginosa under several potentially stressful conditions. We found that metabolic stress, effected by carbon limitation, or competition stress, effected by proximity to other species, resulted in accelerated PQS production. This competition effect did not require cell-to-cell interaction, as evidenced by the fact that the addition of supernatants from either Escherichia coli or Staphylococcus aureus led to early appearance of PQS. Lastly, the fact that these modulations were observed for PQS but not for all AQs suggests a high level of complexity in AQ regulation that remains to be discerned.

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Lipoprotein N-Acylation in Staphylococcus aureus Is Catalyzed by a Two-Component Acyl Transferase System

mBio ◽

10.1128/mbio.01619-20 ◽

2020 ◽

Vol 11 (4) ◽

Cited By ~ 2

Author(s):

John H. Gardiner ◽

Gloria Komazin ◽

Miki Matsuo ◽

Kaitlin Cole ◽

Friedrich Götz ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Cell Envelope ◽

Opportunistic Pathogen ◽

Structural Heterogeneity ◽

Cysteine Residue ◽

Acyl Transfer ◽

Acyl Transferase ◽

Content Type ◽

Tailoring Enzymes ◽

And Shifts

ABSTRACT Bacterial lipoproteins (Lpps) are a class of membrane-associated proteins universally distributed among all bacteria. A characteristic N-terminal cysteine residue that is variably acylated anchors C-terminal globular domains to the extracellular surface, where they serve numerous roles, including in the capture and transport of essential nutrients. Lpps are also ligands for the Toll-like receptor 2 (TLR2) family, a key component of the innate immune system tasked with bacterial recognition. While Lpp function is conserved in all prokaryotes, structural heterogeneity in the N-terminal acylation state is widespread among Firmicutes and can differ between otherwise closely related species. In this study, we identify a novel two-gene system that directs the synthesis of N-acylated Lpps in the commensal and opportunistic pathogen subset of staphylococci. The two genes, which we have named the lipoprotein N-acylation transferase system (Lns), bear no resemblance to previously characterized N-terminal Lpp tailoring enzymes. LnsA (SAOUHSC_00822) is an NlpC/P60 superfamily enzyme, whereas LnsB (SAOHSC_02761) has remote homology to the CAAX protease and bacteriocin-processing enzyme (CPBP) family. Both LnsA and LnsB are together necessary and alone sufficient for N-acylation in Staphylococcus aureus and convert the Lpp chemotype from diacyl to triacyl when heterologously expressed in Listeria monocytogenes. Acquisition of lnsAB decreases TLR2-mediated detection of S. aureus by nearly 10-fold and shifts the activated TLR2 complex from TLR2/6 to TLR2/1. LnsAB thus has a dual role in attenuating TLR2 signaling in addition to a broader role in bacterial cell envelope physiology. IMPORTANCE Although it has long been known that S. aureus forms triacylated Lpps, a lack of homologs to known N-acylation genes found in Gram-negative bacteria has until now precluded identification of the genes responsible for this Lpp modification. Here, we demonstrate N-terminal Lpp acylation and chemotype conversion to the tri-acylated state is directed by a unique acyl transferase system encoded by two noncontiguous staphylococci genes (lnsAB). Since triacylated Lpps stimulate TLR2 more weakly than their diacylated counterparts, Lpp N-acylation is an important TLR2 immunoevasion factor for determining tolerance or nontolerance in niches such as in the skin microbiota. The discovery of the LnsAB system expands the known diversity of Lpp biosynthesis pathways and acyl transfer biochemistry in bacteria, advances our understanding of Lpp structural heterogeneity, and helps differentiate commensal and noncommensal microbiota.

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Disruption of Glycolysis by Nutritional Immunity Activates a Two-Component System That Coordinates a Metabolic and Antihost Response by Staphylococcus aureus

mBio ◽

10.1128/mbio.01321-19 ◽

2019 ◽

Vol 10 (4) ◽

Cited By ~ 4

Author(s):

Paola K. Párraga Solórzano ◽

Jiangwei Yao ◽

Charles O. Rock ◽

Thomas E. Kehl-Fie

Keyword(s):

Staphylococcus Aureus ◽

Metabolic Flux ◽

Bacterial Species ◽

Critical Role ◽

Dependent Manner ◽

Two Component System ◽

Component System ◽

Content Type ◽

Nutritional Immunity ◽

Two Component

ABSTRACT During infection, bacteria use two-component signal transduction systems to sense and adapt to the dynamic host environment. Despite critically contributing to infection, the activating signals of most of these regulators remain unknown. This also applies to the Staphylococcus aureus ArlRS two-component system, which contributes to virulence by coordinating the production of toxins, adhesins, and a metabolic response that enables the bacterium to overcome host-imposed manganese starvation. Restricting the availability of essential transition metals, a strategy known as nutritional immunity, constitutes a critical defense against infection. In this work, expression analysis revealed that manganese starvation imposed by the immune effector calprotectin or by the absence of glycolytic substrates activates ArlRS. Manganese starvation imposed by calprotectin also activated the ArlRS system even when glycolytic substrates were present. A combination of metabolomics, mutational analysis, and metabolic feeding experiments revealed that ArlRS is activated by alterations in metabolic flux occurring in the latter half of the glycolytic pathway. Moreover, calprotectin was found to induce expression of staphylococcal leukocidins in an ArlRS-dependent manner. These studies indicated that ArlRS is a metabolic sensor that allows S. aureus to integrate multiple environmental stresses that alter glycolytic flux to coordinate an antihost response and to adapt to manganese starvation. They also established that the latter half of glycolysis represents a checkpoint to monitor metabolic state in S. aureus. Altogether, these findings contribute to understanding how invading pathogens, such as S. aureus, adapt to the host during infection and suggest the existence of similar mechanisms in other bacterial species. IMPORTANCE Two-component regulatory systems enable bacteria to adapt to changes in their environment during infection by altering gene expression and coordinating antihost responses. Despite the critical role of two-component systems in bacterial survival and pathogenesis, the activating signals for most of these regulators remain unidentified. This is exemplified by ArlRS, a Staphylococcus aureus global regulator that contributes to virulence and to resisting host-mediated restriction of essential nutrients, such as manganese. In this report, we demonstrate that manganese starvation and the absence of glycolytic substrates activate ArlRS. Further investigations revealed that ArlRS is activated when the latter half of glycolysis is disrupted, suggesting that S. aureus monitors flux through the second half of this pathway. Host-imposed manganese starvation also induced the expression of pore-forming toxins in an ArlRS-dependent manner. Cumulatively, this work reveals that ArlRS acts as a sensor that links nutritional status, cellular metabolism, and virulence regulation.

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Regulation of OmpA Translation and Shigella dysenteriae Virulence by an RNA Thermometer

Infection and Immunity ◽

10.1128/iai.00871-19 ◽

2019 ◽

Vol 88 (3) ◽

Cited By ~ 1

Author(s):

Erin R. Murphy ◽

Johanna Roßmanith ◽

Jacob Sieg ◽

Megan E. Fris ◽

Hebaallaha Hussein ◽

...

Keyword(s):

In Silico ◽

Bacterial Species ◽

Regulation Of Gene Expression ◽

Structure And Function ◽

Shigella Dysenteriae ◽

Content Type ◽

Bacterial Physiology ◽

Wide Range ◽

Rna Thermometer ◽

And Function

ABSTRACT RNA thermometers are cis-acting riboregulators that mediate the posttranscriptional regulation of gene expression in response to environmental temperature. Such regulation is conferred by temperature-responsive structural changes within the RNA thermometer that directly result in differential ribosomal binding to the regulated transcript. The significance of RNA thermometers in controlling bacterial physiology and pathogenesis is becoming increasingly clear. This study combines in silico, molecular genetics, and biochemical analyses to characterize both the structure and function of a newly identified RNA thermometer within the ompA transcript of Shigella dysenteriae. First identified by in silico structural predictions, genetic analyses have demonstrated that the ompA RNA thermometer is a functional riboregulator sufficient to confer posttranscriptional temperature-dependent regulation, with optimal expression observed at the host-associated temperature of 37°C. Structural studies and ribosomal binding analyses have revealed both increased exposure of the ribosomal binding site and increased ribosomal binding to the ompA transcript at permissive temperatures. The introduction of site-specific mutations predicted to alter the temperature responsiveness of the ompA RNA thermometer has predictable consequences for both the structure and function of the regulatory element. Finally, in vitro tissue culture-based analyses implicate the ompA RNA thermometer as a bona fide S. dysenteriae virulence factor in this bacterial pathogen. Given that ompA is highly conserved among Gram-negative pathogens, these studies not only provide insight into the significance of riboregulation in controlling Shigella virulence, but they also have the potential to facilitate further understanding of the physiology and/or pathogenesis of a wide range of bacterial species.

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The 5′ NAD Cap of RNAIII Modulates Toxin Production in Staphylococcus aureus Isolates

Journal of Bacteriology ◽

10.1128/jb.00591-19 ◽

2019 ◽

Vol 202 (6) ◽

Cited By ~ 3

Author(s):

Hector Gabriel Morales-Filloy ◽

Yaqing Zhang ◽

Gabriele Nübel ◽

Shilpa Elizabeth George ◽

Natalya Korn ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Secondary Structure ◽

Quorum Sensing ◽

Opportunistic Pathogen ◽

Toxin Production ◽

Dual Function ◽

Content Type ◽

The Stability

ABSTRACT Nicotinamide adenosine dinucleotide (NAD) has been found to be covalently attached to the 5′ ends of specific RNAs in many different organisms, but the physiological consequences of this modification are largely unknown. Here, we report the occurrence of several NAD-RNAs in the opportunistic pathogen Staphylococcus aureus. Most prominently, RNAIII, a central quorum-sensing regulator of this bacterium’s physiology, was found to be 5′ NAD capped in a range from 10 to 35%. NAD incorporation efficiency into RNAIII was found to depend in vivo on the −1 position of the P3 promoter. An increase in RNAIII’s NAD content led to a decreased expression of alpha- and delta-toxins, resulting in reduced cytotoxicity of the modified strains. These effects seem to be caused neither by changes in RNAIII’s secondary structure nor by a different translatability upon NAD attachment, as indicated by unaltered patterns in in vitro chemical probing and toeprinting experiments. Even though we did not observe any effect of this modification on RNAIII’s secondary structure or translatability in vitro, additional unidentified factors might account for the modulation of exotoxins in vivo. Ultimately, the study constitutes a step forward in the discovery of new roles of the NAD molecule in bacteria. IMPORTANCE Numerous organisms, including bacteria, are endowed with a 5′ NAD cap in specific RNAs. While the presence of the 5′ NAD cap modulates the stability of the modified RNA species, a significant biological function and phenotype have not been assigned so far. Here, we show the presence of a 5′ NAD cap in RNAIII from S. aureus, a dual-function regulatory RNA involved in quorum-sensing processes and regulation of virulence factor expression. We also demonstrate that altering the natural NAD modification ratio of RNAIII leads to a decrease in exotoxin production, thereby modulating the bacterium’s virulence. Our work unveils a new layer of regulation of RNAIII and the agr system that might be linked to the redox state of the NAD molecule in the cell.

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MroQ Is a Novel Abi-Domain Protein That Influences Virulence Gene Expression in Staphylococcus aureus via Modulation of Agr Activity

Infection and Immunity ◽

10.1128/iai.00002-19 ◽

2019 ◽

Vol 87 (5) ◽

Cited By ~ 3

Author(s):

Stephanie Marroquin ◽

Brittney Gimza ◽

Brooke Tomlinson ◽

Michelle Stein ◽

Andrew Frey ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Virulence Gene ◽

Transcriptional Analysis ◽

Data Sets ◽

Virulence Determinants ◽

Sequencing Data ◽

Content Type ◽

Virulence Gene Expression ◽

Function Mechanism ◽

Family Protein

ABSTRACT Numerous factors have, to date, been identified as playing a role in the regulation of Agr activity in Staphylococcus aureus, including transcription factors, antisense RNAs, and host elements. Herein we investigated the product of SAUSA300_1984 (termed MroQ), a transmembrane Abi-domain/M79 protease-family protein, as a novel effector of this system. Using a USA300 mroQ mutant, we observed a drastic reduction in proteolysis, hemolysis, and pigmentation that was fully complementable. This appears to result from diminished agr activity, as transcriptional analysis revealed significant decreases in expression of both RNAII and RNAIII in the mroQ mutant. Such effects appear to be direct, rather than indirect, as known agr effectors demonstrated limited alterations in their activity upon mroQ disruption. A comparison of RNA sequencing data sets for both mroQ and agr mutants revealed a profound overlap in their regulomes, with the majority of factors affected being known virulence determinants. Importantly, the preponderance of alterations in expression were more striking in the agr mutant, indicating that MroQ is necessary, but not sufficient, for Agr function. Mechanism profiling revealed that putative residues for metalloprotease activity within MroQ are required for its Agr-controlling effect; however, this was not wielded at the level of AgrD processing. Virulence assessment demonstrated that both mroQ and agr mutants exhibited increased formation of renal abscesses but decreased skin abscess formation alongside diminished dermonecrosis. Collectively, we present the characterization of a novel agr effector in S. aureus which would appear to be a direct regulator, potentially functioning via interaction with the AgrC histidine kinase.

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Formation of Staphylococcus aureus Biofilm in the Presence of Sublethal Concentrations of Disinfectants Studied via a Transcriptomic Analysis Using Transcriptome Sequencing (RNA-seq)

Applied and Environmental Microbiology ◽

10.1128/aem.01643-17 ◽

2017 ◽

Vol 83 (24) ◽

Cited By ~ 12

Author(s):

M. Slany ◽

J. Oppelt ◽

L. Cincarova

Keyword(s):

Gene Expression ◽

Staphylococcus Aureus ◽

Biofilm Formation ◽

Transcriptome Sequencing ◽

Expression Profiles ◽

Bacterial Species ◽

Rna Seq ◽

Altered Expression ◽

Content Type ◽

Sublethal Concentrations

ABSTRACT Staphylococcus aureus is a common biofilm-forming pathogen. Low doses of disinfectants have previously been reported to promote biofilm formation and to increase virulence. The aim of this study was to use transcriptome sequencing (RNA-seq) analysis to investigate global transcriptional changes in S. aureus in response to sublethal concentrations of the commonly used food industry disinfectants ethanol (EtOH) and chloramine T (ChT) and their combination (EtOH_ChT) in order to better understand the effects of these agents on biofilm formation. Treatment with EtOH and EtOH_ChT resulted in more significantly altered expression profiles than treatment with ChT. Our results revealed that EtOH and EtOH_ChT treatments enhanced the expression of genes responsible for regulation of gene expression (sigB), cell surface factors (clfAB), adhesins (sdrDE), and capsular polysaccharides (cap8EFGL), resulting in more intact biofilm. In addition, in this study we were able to identify the pathways involved in the adaptation of S. aureus to the stress of ChT treatment. Further, EtOH suppressed the effect of ChT on gene expression when these agents were used together at sublethal concentrations. These data show that in the presence of sublethal concentrations of tested disinfectants, S. aureus cells trigger protective mechanisms and try to cope with them. IMPORTANCE So far, the effect of disinfectants is not satisfactorily explained. The presented data will allow a better understanding of the mode of disinfectant action with regard to biofilm formation and the ability of bacteria to survive the treatment. Such an understanding could contribute to the effort to eliminate possible sources of bacteria, making disinfectant application as efficient as possible. Biofilm formation plays significant role in the spread and pathogenesis of bacterial species.

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Emergence of Extensively Drug-Resistant Proteus mirabilis Harboring a Conjugative NDM-1 Plasmid and a Novel Salmonella Genomic Island 1 Variant, SGI1-Z

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00292-15 ◽

2015 ◽

Vol 59 (10) ◽

pp. 6601-6604 ◽

Cited By ~ 22

Author(s):

Shangshang Qin ◽

Hui Qi ◽

Qijing Zhang ◽

Di Zhao ◽

Zhen-Zhen Liu ◽

...

Keyword(s):

Clinical Isolate ◽

Molecular Analysis ◽

Proteus Mirabilis ◽

Genomic Island ◽

Bacterial Species ◽

Clinical Treatment ◽

Drug Resistant ◽

Content Type ◽

Extensively Drug Resistant

ABSTRACTAcquisition ofblaNDM-1in bacterial species, such asProteus mirabilisthat is intrinsically resistant to tetracycline, tigecycline and colistin, will make clinical treatment extremely difficult. Here, we characterized an NDM-1-producing clinical isolate ofP. mirabilis(PM58) that displayed an extensively drug-resistant (XDR) phenotype, susceptible only to aztreonam. Molecular analysis revealed that PM58 harbored both a conjugative NDM-1 plasmid and a novelSalmonellagenomic island 1 variant on chromosome.

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