The baeSR two-component regulatory system activates transcription of the yegMNOB (mdtABCD) transporter gene cluster in Escherichia coli and increases its resistance to novobiocin and deoxycholate

Development of a logic regression-based approach for the discovery of host- and niche-informative biomarkers in Escherichia coli and their application for microbial source tracking

Microbial source tracking leverages a wide range of approaches designed to trace the origins of fecal contamination in aquatic environments. Although source tracking methods are typically employed within the laboratory setting, computational techniques can be leveraged to advance microbial source tracking methodology. Herein, we present a logic regression-based supervised learning approach for the discovery of source-informative genetic markers within intergenic regions across the Escherichia coli genome that can be used for source tracking. With just single intergenic loci, logic regression was able to identify highly source-specific (i.e., exceeding 97.00%) biomarkers for a wide range of host and niche sources, with sensitivities reaching as high as 30.00%-50.00% for certain source categories, including pig, sheep, mouse, and wastewater, depending on the specific intergenic locus analyzed. Restricting the source range to reflect the most prominent zoonotic sources of E. coli transmission (i.e., bovine, chicken, human, and pig) allowed for the generation of informative biomarkers for all host categories, with specificities of at least 90.00% and sensitivities between 12.50% and 70.00%, using the sequence data from key intergenic regions, including emrKY-evgAS, ibsB-(mdtABCD-baeSR), ompC-rcsDB, and yedS-yedR, that appear to be involved in antibiotic resistance. Remarkably, we were able to use this approach to classify 48 out of 113 river water E. coli isolates collected in Northwestern Sweden as either beaver, human, or reindeer in origin with a high degree of consensus-thus highlighting the potential of logic regression modeling as a novel approach for augmenting current source tracking efforts.IMPORTANCEThe presence of microbial contaminants, particularly from fecal sources, within water poses a serious risk to public health. The health and economic burden of waterborne pathogens can be substantial-as such, the ability to detect and identify the sources of fecal contamination in environmental waters is crucial for the control of waterborne diseases. This can be accomplished through microbial source tracking, which involves the use of various laboratory techniques to trace the origins of microbial pollution in the environment. Building on current source tracking methodology, we describe a novel workflow that uses logic regression, a supervised machine learning method, to discover genetic markers in Escherichia coli, a common fecal indicator bacterium, that can be used for source tracking efforts. Importantly, our research provides an example of how the rise in prominence of machine learning algorithms can be applied to improve upon current microbial source tracking methodology.

Structural analysis of resistance-nodulation cell division transporters

SUMMARYInfectious bacteria have both intrinsic and acquired mechanisms to combat harmful biocides that enter the cell. Through adaptive pressures, many of these pathogens have become resistant to many, if not all, of the current antibiotics used today to treat these often deadly infections. One prominent mechanism is the upregulation of efflux systems, especially the resistance-nodulation-cell division class of exporters. These tripartite systems consist of an inner membrane transporter coupled with a periplasmic adaptor protein and an outer membrane channel to efficiently transport a diverse array of substrates from inside the cell to the extracellular space. Detailed mechanistic insight into how these inner membrane transporters recognize and shuttle their substrates can ultimately inform both new antibiotic and efflux pump inhibitor design. This review examines the structural basis of substrate recognition of these pumps and the molecular mechanisms underlying multidrug extrusion, which in turn mediate antimicrobial resistance in bacterial pathogens.

RND Efflux Pump Induction: A Crucial Network Unveiling Adaptive Antibiotic Resistance Mechanisms of Gram-Negative Bacteria

The rise of multi-drug-resistant (MDR) pathogenic bacteria presents a grave challenge to global public health, with antimicrobial resistance ranking as the third leading cause of mortality worldwide. Understanding the mechanisms underlying antibiotic resistance is crucial for developing effective treatments. Efflux pumps, particularly those of the resistance-nodulation-cell division (RND) superfamily, play a significant role in expelling molecules from bacterial cells, contributing to the emergence of multi-drug resistance. These are transmembrane transporters naturally produced by Gram-negative bacteria. This review provides comprehensive insights into the modulation of RND efflux pump expression in bacterial pathogens by numerous and common molecules (bile, biocides, pharmaceuticals, additives, plant extracts, etc.). The interplay between these molecules and efflux pump regulators underscores the complexity of antibiotic resistance mechanisms. The clinical implications of efflux pump induction by non-antibiotic compounds highlight the challenges posed to public health and the urgent need for further investigation. By addressing antibiotic resistance from multiple angles, we can mitigate its impact and preserve the efficacy of antimicrobial therapies.

Are envelope stress responses essential for persistence to β-lactams in Escherichia coli?

Bacterial persistence to antibiotics defines the ability of small sub-populations of sensitive cells within an isogenic population to survive high doses of bactericidal antibiotics. Here, we investigated the importance of the five main envelope stress responses (ESRs) of Escherichia coli in persistence to five bactericidal β-lactam antibiotics by combining classical time-kill curve experiments and single-cell analysis using time-lapse microscopy. We showed that the survival frequency of mutants for the Bae, Cpx, Psp, and Rcs systems treated with different β-lactams is comparable to that of the wild-type strain, indicating that these ESRs do not play a direct role in persistence to β-lactams. Since the σE-encoding gene is essential, we could not directly test its role. Using fluorescent reporters to monitor the activation of ESRs, we observed that σE is induced by high doses of meropenem. However, the dynamics of σE activation during meropenem treatment did not reveal any difference in persister cells compared to the bulk of the population, indicating that σE activation is not a hallmark of persistence. The Bae, Cpx, Psp, and Rcs responses were neither induced by ampicillin nor by meropenem. However, pre-induction of the Rcs system by polymyxin B increased survival to meropenem in an Rcs-dependent manner, suggesting that this ESR might confer some yet uncharacterized advantages during meropenem treatment or at the post-antibiotic recovery step. Altogether, our data suggest that ESRs are not key actors in E. coli persistence to β-lactams in the conditions we tested.

Mutation in the two-component regulator BaeSR mediates cefiderocol resistance and enhances virulence in Acinetobacter baumannii

Acinetobacter baumannii has become one of the most challenging pathogens in many countries with limited treatment options available. Cefiderocol, a novel siderophore-conjugated cephalosporin, shows potent in vitro activity against A. baumannii, including isolates resistant to carbapenems. To date, few reports on the mechanisms of cefiderocol resistance are available. In order to investigate potential mechanisms of cefiderocol resistance in A. baumannii, we performed in vitro evolution experiments at sub-lethal concentrations of the antibiotic. All four cefiderocol-resistant strains obtained harbored mutations in two-component system BaeS-BaeR. When we engineered the mutations of BaeS (D89V) and BaeR (S104N) into the genome of ATCC 17978, these mutations increased cefiderocol minimum inhibitory concentrations (MICs) by 8-fold to 16-fold. Transcriptome analyses showed that the expression of MacAB-TolC and MFS transporters was up-regulated in BaeSR mutants. Strains over-expressing MFS transporter and MacAB-TolC displayed higher MICs and higher median inhibition concentration (IC50) values, while MICs and IC50 decreased when efflux pump genes were knocked out. In a BaeR mutant with up-regulated csu operon, we observed a higher number of pili, enhanced surface motility, and increased biofilm formation compared to wild-type ATCC 17978. Using the Galleria mellonella infection model, we found that the BaeS mutant in which paa operon was up-regulated exhibited increased virulence. In conclusion, the mutations in BaeSR decreased cefiderocol susceptibility of A. baumannii through up-regulating efflux pumps gene expression. BaeS or BaeR also controls the expression of csu and paa, influencing biofilm formation, surface motility, and virulence in A. baumannii. IMPORTANCE The widespread prevalence of multi-drug-resistant A. baumannii (MDRAB) poses a significant therapeutic challenge. Cefiderocol is considered a promising antibiotic for the treatment of MDRAB infections. Therefore, it is necessary to study the potential resistance mechanisms of cefiderocol to delay the development of bacterial resistance. Here, we demonstrated that mutations in baeS and baeR reduced the susceptibility of A. baumannii to cefiderocol by up-regulating the expression of the MFS family efflux pump and MacAB-TolC efflux pump. We propose that BaeS mutants increase bacterial virulence by up-regulating the expression of the paa operon. This also reports the regulatory effect of BaeSR on csu operon for the first time. This study provides further insights into the role of BaeSR in developing cefiderocol resistance and virulence in A. baumannii.

Temocillin Resistance in the Enterobacter cloacae Complex Is Conferred by a Single Point Mutation in BaeS, Leading to Overexpression of the AcrD Efflux Pump

The Enterobacter cloacae complex (ECC) has become a major opportunistic pathogen with antimicrobial resistance issues. Temocillin, an "old" carboxypenicillin that is remarkably stable toward β-lactamases, has been used as an alternative for the treatment of multidrug-resistant ECC infections. Here, we aimed at deciphering the never-investigated mechanisms of temocillin resistance acquisition in Enterobacterales. By comparative genomic analysis of two clonally related ECC clinical isolates, one susceptible (Temo_S [MIC of 4 mg/L]) and the other resistant (Temo_R [MIC of 32 mg/L]), we found that they differed by only 14 single-nucleotide polymorphisms, including one nonsynonymous mutation (Thr175Pro) in the two-component system (TCS) sensor histidine kinase BaeS. By site-directed mutagenesis in Escherichia coli CFT073, we demonstrated that this unique change in BaeS was responsible for a significant (16-fold) increase in temocillin MIC. Since the BaeSR TCS regulates the expression of two resistance-nodulation-cell division (RND)-type efflux pumps (namely, AcrD and MdtABCD) in E. coli and Salmonella, we demonstrated by quantitative reverse transcription-PCR that mdtB, baeS, and acrD genes were significantly overexpressed (15-, 11-, and 3-fold, respectively) in Temo_R. To confirm the role of each efflux pump in this mechanism, multicopy plasmids harboring mdtABCD or acrD were introduced into either Temo_S or the reference strain E. cloacae subsp. cloacae ATCC 13047. Interestingly, only the overexpression of acrD conferred a significant increase (from 8- to 16-fold) of the temocillin MIC. Altogether, we have shown that temocillin resistance in the ECC can result from a single BaeS alteration, likely resulting in the permanent phosphorylation of BaeR and leading to AcrD overexpression and temocillin resistance through enhanced active efflux.

Antimicrobial Resistance: Two-Component Regulatory Systems and Multidrug Efflux Pumps

The number of multidrug-resistant bacteria is rapidly spreading worldwide. Among the various mechanisms determining resistance to antimicrobial agents, multidrug efflux pumps play a noteworthy role because they export extraneous and noxious substrates from the inside to the outside environment of the bacterial cell contributing to multidrug resistance (MDR) and, consequently, to the failure of anti-infective therapies. The expression of multidrug efflux pumps can be under the control of transcriptional regulators and two-component systems (TCS). TCS are a major mechanism by which microorganisms sense and reply to external and/or intramembrane stimuli by coordinating the expression of genes involved not only in pathogenic pathways but also in antibiotic resistance. In this review, we describe the influence of TCS on multidrug efflux pump expression and activity in some Gram-negative and Gram-positive bacteria. Taking into account the strict correlation between TCS and multidrug efflux pumps, the development of drugs targeting TCS, alone or together with already discovered efflux pump inhibitors, may represent a beneficial strategy to contribute to the fight against growing antibiotic resistance.

The Origins of ST11 KL64 Klebsiella pneumoniae: a Genome-Based Study

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major severe threat for human health, and its spread is largely driven by a few dominant lineages defined by sequence types (ST) and capsular (KL) types. ST11-KL64 is one such dominant lineage that is particularly common in China but also has a worldwide distribution. However, the population structure and origin of ST11-KL64 K. pneumoniae remain to be determined. We retrieved all K. pneumoniae genomes (n = 13,625, as of June 2022) from NCBI, comprising 730 ST11-KL64 strains. Phylogenomic analysis of core-genome single-nucleotide polymorphisms identified two major clades (I and II) plus an additional singleton of ST11-KL64. We performed dated ancestral reconstruction analysis using BactDating and found that clade I likely emerged in 1989 in Brazil, while clade II emerged around 2008 in eastern China. We then investigated the origin of the two clades and the singleton using a phylogenomic approach combined with analysis of potential recombination regions. We found that ST11-KL64 clade I is likely a hybrid with 91.2% (ca. 4.98 Mb) of the chromosome derived from the ST11-KL15 lineage and 8.8% (483 kb) acquired from ST147-KL64. In contrast, ST11-KL64 clade II was derived from ST11-KL47 with swapping of a 157-kb region (3% of the chromosome) containing the capsule gene cluster with clonal complex 1764 (CC1764)-KL64. The singleton also evolved from ST11-KL47 but with swapping of a 126-kb region with ST11-KL64 clade I. In conclusion, ST11-KL64 is a heterogenous lineage comprising two major clades and a singleton with different origins that emerged in different countries at different time points. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as a severe threat globally and is associated with increased lengths of hospital stay and high mortality in affected patients. The spread of CRKP is largely driven by a few dominant lineages, including ST11-KL64, the dominant type in China with a worldwide distribution. Here, we tested the hypothesis that ST11-KL64 K. pneumoniae is a single genomic lineage by performing a genome-based study. However, we found that ST11-KL64 comprises a singleton and two major clades, which emerged in different countries in different years. In particular, the two clades and the singleton have different origins and acquired the KL64 capsule gene cluster from various sources. Our study underscores that the chromosomal region containing the capsule gene cluster is a hot spot of recombination in K. pneumoniae. This represents a major evolutionary mechanism employed by some bacteria for rapid evolution with novel clades that accommodate stress for survival.

Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments

Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.

Cryo-EM Structures of AcrD Illuminate a Mechanism for Capturing Aminoglycosides from Its Central Cavity

The Escherichia coli acriflavine resistance protein D (AcrD) is an efflux pump that belongs to the resistance-nodulation-cell division (RND) superfamily. Its primary function is to provide resistance to aminoglycoside-based drugs by actively extruding these noxious compounds out of E. coli cells. AcrD can also mediate resistance to a limited range of other amphiphilic agents, including bile acids, novobiocin, and fusidic acids. As there is no structural information available for any aminoglycoside-specific RND pump, here we describe cryo-electron microscopy (cryo-EM) structures of AcrD in the absence and presence of bound gentamicin. These structures provide new information about the RND superfamily of efflux pumps, specifically, that three negatively charged residues central to the aminoglycoside-binding site are located within the ceiling of the central cavity of the AcrD trimer. Thus, it is likely that AcrD is capable of picking up aminoglycosides via this central cavity. Through the combination of cryo-EM structural determination, mutagenesis analysis, and molecular simulation, we show that charged residues are critically important for this pump to shuttle drugs directly from the central cavity to the funnel of the AcrD trimer for extrusion. IMPORTANCE Here, we report cryo-EM structures of the AcrD aminoglycoside efflux pump in the absence and presence of bound gentamicin, posing the possibility that this pump is capable of capturing aminoglycosides from the central cavity of the AcrD trimer. The results indicate that AcrD utilizes charged residues to bind and export drugs, mediating resistance to these antibiotics.

Bacterial envelope stress responses: Essential adaptors and attractive targets

Millions of deaths a year across the globe are linked to antimicrobial resistant infections. The need to develop new treatments and repurpose of existing antibiotics grows more pressing as the growing antimicrobial resistance pandemic advances. In this review article, we propose that envelope stress responses, the signaling pathways bacteria use to recognize and adapt to damage to the most vulnerable outer compartments of the microbial cell, are attractive targets. Envelope stress responses (ESRs) support colonization and infection by responding to a plethora of toxic envelope stresses encountered throughout the body; they have been co-opted into virulence networks where they work like global positioning systems to coordinate adhesion, invasion, microbial warfare, and biofilm formation. We highlight progress in the development of therapeutic strategies that target ESR signaling proteins and adaptive networks and posit that further characterization of the molecular mechanisms governing these essential niche adaptation machineries will be important for sparking new therapeutic approaches aimed at short-circuiting bacterial adaptation.

Serratia marcescens antibiotic resistance mechanisms of an opportunistic pathogen: a literature review

Serratia marcescens is a ubiquitous bacterium from order Enterobacterales displaying a high genetic plasticity that allows it to adapt and persist in multiple niches including soil, water, plants, and nosocomial environments. Recently, S. marcescens has gained attention as an emerging pathogen worldwide, provoking infections and outbreaks in debilitated individuals, particularly newborns and patients in intensive care units. S. marcescens isolates recovered from clinical settings are frequently described as multidrug resistant. High levels of antibiotic resistance across Serratia species are a consequence of the combined activity of intrinsic, acquired, and adaptive resistance elements. In this review, we will discuss recent advances in the understanding of mechanisms guiding resistance in this opportunistic pathogen.

Tell me if you prefer bovine or poultry sectors and I'll tell you who you are: Characterization of Salmonella enterica subsp. enterica serovar Mbandaka in France

Introduction

In north-western France, Salmonella enterica susp. enterica serovar Mbandaka (S. Mbandaka) is most frequently isolated from bovine and dairy samples. While this serovar most often results in asymptomatic carriage, for a number of years it has caused episodes of abortions, which have serious economic consequences for the sector. Interestingly, this serovar is also isolated from Gallus gallus in the same geographic zone. Despite its prevalence in bovines in north-western France, S. Mbandaka has not been broadly studied at the genomic level, and its prevalence and host adaptation are still not fully understood.

Methods

In this study, we analyzed the genomic diversity of 304 strains of S. Mbandaka isolated from the bovine and poultry sectors in this area over a period of 5 years. A phylogenetic analysis was carried out and two approaches were followed to identify conserved genes and mutations related to host associations. The first approach targeted the genes compiled in the MEGARESv2, Resfinder, VFDB and SPI databases. Plasmid and phage contents were also investigated. The second approach refers to an in-house algorithm developed for this study that computes sensitivity, specificity, and accuracy of accessory genes and core variants according to predefined genomes groups.

Results and discussion

All the analyzed strains belong to the multi-locus sequence type profile ST413, and the phylogenomic analysis revealed main clustering by host (bovine and poultry), emphasizing the circulation of 12 different major clones, of which seven circulate in poultry and five in the bovine sector in France and a likely food production chain adaptation of these clones. All strains present resistance determinants including heavy metals and biocides that could explain the ability of this serovar to survive and persist in the environment, within herds, and in food processing plants. To explore the wild animal contribution to the spread of this serovar in north-western France, we retrieved S. Mbandaka genomes isolated from wild birds from EnteroBase and included them in the phylogenomic analysis together with our collection. Lastly, screening of accessory genes and major variants allowed us to identify conserved specific mutations characteristic of each major cluster. These mutations could be used to design useful probes for food safety surveillance.

Transcriptomic and metabolomic investigation of molecular inactivation mechanisms in Escherichia coli triggered by graphene quantum dots

Graphene quantum dots (GQDs), a novel broad-spectrum antibacterial agent, are considered potential candidates in the field of biomedical and food safety due to their outstanding antimicrobial properties and excellent biocompatibility. To uncover the molecular regulatory mechanisms underlying the phenotypes, the overall regulation of genes and metabolites in Escherichia coli (E. coli) after GQDs stimulation was investigated by RNA-sequencing and LC-MS. Gene transcription and metabolite expression related to a series of crucial biomolecular processes were influenced by the GQDs stimulation, including biofilm formation, bacterial secretion system, sulfur metabolism and nitrogen metabolism, etc. This study could provide profound insights into the GQDs stress response in E. coli, which would be useful for the development and application of GQDs in food safety.

Structural Basis of Peptide-Based Antimicrobial Inhibition of a Resistance-Nodulation-Cell Division Multidrug Efflux Pump

Bacterial efflux pumps in the resistance-nodulation-cell division (RND) family of Gram-negative bacteria contribute significantly to the development of antimicrobial resistance by many pathogens. In this study, we selected the MtrD transporter protein of Neisseria gonorrhoeae as it is the sole RND pump possessed by this strictly human pathogen and can export multiple antimicrobials, including antibiotics, bile salts, detergents, dyes, and antimicrobial peptides. Using knowledge from our previously published structures of MtrD in the presence or absence of bound antibiotics as a model and the known ability of MtrCDE to export cationic antimicrobial peptides, we hypothesized that cationic peptides could be accommodated within MtrD binding sites. Furthermore, we thought that MtrD-bound peptides lacking antibacterial action could sensitize bacteria to an antibiotic normally exported by the MtrCDE efflux pump or other similar RND-type pumps possessed by different Gram-negative bacteria. We now report the identification of a novel nonantimicrobial cyclic cationic antimicrobial peptide, which we termed CASP (cationic antibiotic-sensitizing peptide). By single-particle cryo-electron microscopy, we found that CASP binds within the periplasmic cleft region of MtrD using overlapping and distinct amino acid contact sites that interact with another cyclic peptide (colistin) or a linear human cationic antimicrobial peptide derived from human LL-37. While CASP could not sensitize Neisseria gonorrhoeae to an antibiotic (novobiocin) that is a substrate for RND pumps, it could do so against multiple Gram-negative, rod-shaped bacteria. We propose that CASP (or future derivatives) could serve as an adjuvant for the antibiotic treatment of certain Gram-negative infections previously thwarted by RND transporters. IMPORTANCE RND efflux pumps can export numerous antimicrobials that enter Gram-negative bacteria, and their action can reduce the efficacy of antibiotics and provide decreased susceptibility to various host antimicrobials. Here, we identified a cationic antibiotic-sensitizing peptide (CASP) that binds within the periplasmic cleft of an RND transporter protein (MtrD) produced by Neisseria gonorrhoeae. Surprisingly, CASP was able to render rod-shaped Gram-negative bacteria, but not gonococci, susceptible to an antibiotic that is a substrate for the gonococcal MtrCDE efflux pump. CASP (or its future derivatives) could be used as an adjuvant to treat infections for which RND efflux contributes to multidrug resistance.

Systematic Identification of CpxRA-Regulated Genes and Their Roles in Escherichia coli Stress Response

The two-component system CpxRA can sense environmental stresses and regulate transcription of a wide range of genes for the purpose of adaptation. Despite extensive research on this system, the identification of the CpxR regulon is not systematic or comprehensive. Herein, genome-wide screening was performed using a position-specific scoring matrix, resulting in the discovery of more than 10,000 putative CpxR binding sites, which provides an extensive and selective set of targets based on sequence. More than half of the candidate genes ultimately selected (73/97) were experimentally confirmed to be CpxR-regulated genes through experimental analysis. These genes are involved in various physiological functions, indicating that the CpxRA system regulates complex cellular processes. The study also found for the first time that the CpxR-regulated genes ydeE, xylE, alx, and galP contribute to Escherichia coli resistance to acid stress, whereas prlF, alx, casA, yacH, ydeE, sbmA, and ampH contribute to E. coli resistance to cationic antimicrobial peptide stress. Among these CpxR-regulated genes, ydeE and alx responded to both stressors. In a similar way, a cationic antimicrobial peptide is capable of directly activating the periplasmic domain of CpxA kinase in vitro, which is consistent with the CpxA response to acid stress. These results greatly expand our understanding of the CpxRA-dependent stress response network in E. coli. IMPORTANCE CpxRA system is found in many pathogens and plays an essential role in sensing environmental signals and transducing information inside cells for adaptation. It usually regulates expression of specific genes in response to different environmental stresses and is important for bacterial pathogenesis. However, systematically identifying CpxRA-regulated genes and elucidating the regulative role of CpxRA in bacteria responding to environmental stress remains challenging. This study discovered more than 10,000 putative CpxR binding sites based on sequence. This bioinformatics approach, combined with experimental assays, allowed the identification of many previously unknown CpxR-regulated genes. Among the novel 73 CpxRA-regulated genes identified in this study, the role of nine of them in contributing to E. coli resistance to acid or cationic antimicrobial peptide stress was studied. The potential correlation between these two environmental stress responses provides insight into the CpxRA-dependent stress response network. This also improves our understanding of environment-bacterium interaction and Gram-negative pathogenesis.

Reduced porin expression with EnvZ-OmpR, PhoPQ, BaeSR two-component system down-regulation in carbapenem resistance of Klebsiella Pneumoniae based on proteomic analysis

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has proven to be an urgent threat to human health. Proteomics (TMT/LC-MS/MS) and bioinformatics approaches were employed to explore the potential mechanisms underlying carbapenem resistance. Proteomic profiling of CRKP and susceptible KP (sKP) isolates revealed the involvement of outer membrane, beta-lactam resistance pathway, and two-component systems (TCSs) in carbapenem resistance. 27 CRKP strains and 27 susceptible Klebsiella pneumoniae strains were isolated from inpatients at the Second Xiangya Hospital, China to verify the mechanisms. Modified carbapenem inactivation method (mCIM) and PCR of common carbapenem resistance genes confirmed that 77.8% (21/27) of CRKP isolates were carbapenemase-producing. Porin decrease in CRKP isolates was found by SDS-PAGE and mRNA levels of major porins (OmpK35 and OmpK36). RT-qPCR detection of two-component systems (envZ, ompR, phoP, phoQ, baeS and baeR) revealed down-regulation of EnvZ-OmpR, PhoPQ, BaeSR TCSs. Expression of the TCSs, except ompR, were closely correlated with OMPs with the R-value >0.7. Together, this study reaffirmed the significance of the β-lactam resistance pathway in CRKP based on proteomic analysis. OmpK35/36 porin reduction and the controversial downregulation of EnvZ-OmpR, PhoPQ, and BaeSR TCSs were confirmed in carbapenem resistance of Klebsiella pneumoniae.

CRISPR-Cas systems: role in cellular processes beyond adaptive immunity

Clustered regularly interspaced short palindromic repeats and associated Cas proteins (CRISPR-Cas) are the only known adaptive immune system in prokaryotes. CRISPR-Cas system provides sequence-specific immunity against invasion by foreign genetic elements. It carries out its functions by incorporating a small part of the invading DNA sequence, termed as spacer into the CRISPR array. Although the CRISPR-Cas systems are mainly responsible for adaptive immune functions, their alternative role in the gene regulation, bacterial pathophysiology, virulence, and evolution has started to unravel. In several species, these systems are revealed to regulate the processes beyond adaptive immunity by employing various components of CRISPR-Cas machinery, independently or in combination. The molecular mechanisms entailing the regulatory processes are not clear in most of the instances. In this review, we have discussed some well-known and some recently established noncanonical functions of CRISPR-Cas system and its fast-extending applications in other biological processes.

Evolutionary Instability of Collateral Susceptibility Networks in Ciprofloxacin-Resistant Clinical Escherichia coli Strains

Collateral sensitivity and resistance occur when resistance development toward one antimicrobial either potentiates or deteriorates the effect of others. Previous reports on collateral effects on susceptibility focus on newly acquired resistance determinants and propose that novel treatment guidelines informed by collateral networks may reduce the evolution, selection, and spread of antimicrobial resistance. In this study, we investigate the evolutionary stability of collateral networks in five ciprofloxacin-resistant, clinical Escherichia coli strains. After 300 generations of experimental evolution without antimicrobials, we show complete fitness restoration in four of five genetic backgrounds and demonstrate evolutionary instability in collateral networks of newly acquired resistance determinants. We show that compensatory mutations reducing efflux expression are the main drivers destabilizing initial collateral networks and identify rpoS as a putative target for compensatory evolution. Our results add another layer of complexity to future predictions and clinical application of collateral networks.

Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria

Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.

Elucidation of a complete mechanical signaling and virulence activation pathway in enterohemorrhagic Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important extracellular human pathogen. The initial adherence of EHEC to host cells is a major cue for transcriptional induction of the locus of enterocyte effacement (LEE) genes to promote colonization and pathogenesis, but the mechanism through which this adherence is sensed and the LEE is induced remains largely elusive. Here, we report a complete signal transduction pathway for this virulence activation process. In this pathway, the outer-membrane lipoprotein NlpE senses a mechanical cue generated from initial host adherence and activates the BaeSR two-component regulatory system; the response regulator BaeR then directly activates the expression of airA located on O-island-134 and encoding a LEE transcriptional activator. Disruption of this pathway severely attenuates EHEC O157:H7 virulence both in vitro and in vivo. This study provides further insights into the evolution of EHEC pathogenesis and the host-pathogen interaction.

Two-component system in Rahnella aquatilis is impacted by the hyphosphere of the arbuscular mycorrhizal fungus Rhizophagus irregularis

Two-component systems (TCS) are ubiquitous among bacteria, playing key roles in signalling events. However, to what extent the TCS of Rahnella aquatilis (a Phosphate solubilizing bacteria) is influenced by the hyphosphere of the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis is totally unknown. Here, the expression of 16 genes encoding the TCS of R. aquatilis (i.e. involved in carbon-sensing and nutrient-sensing) and of eight genes regulated by the PhoR TCS (i.e. involved in inorganic and organic phosphorus mobilization) were analysed at regular intervals in presence of hyphae of R. irregularis. The study was conducted under in vitro culture conditions with phytate as the unique source of phosphorus. In presence of the AM fungus, the expression of TCS genes involved in carbon-sensing and nutrient-sensing were stimulated. Only, BaeS at 30 and 120 min, and BaeR at 60 min were inhibited. In addition, the PhoR TCS stimulated the expression of genes encoding phosphatase but inhibited the expression of genes involved in gluconic acid production. As the mechanism of coupling environmental changes with cellular physiological changes, TCS plays a pivotal role in regulating specific gene expression in R. aquatilis, recognizing environmental signals. More importantly, TCS genes may regulate bacteria response to hyphal carbon to mobilize phosphorus efficiently in the hyphosphere.

Adaptation to a Commercial Quaternary Ammonium Compound Sanitizer Leads to Cross-Resistance to Select Antibiotics in Listeria monocytogenes Isolated From Fresh Produce Environments

The effective elimination of Listeria monocytogenes through cleaning and sanitation is of great importance to the food processing industry. Specifically in fresh produce operations, the lack of a kill step requires effective cleaning and sanitation to mitigate the risk of cross-contamination from the environment. As facilities rely on sanitizers to control L. monocytogenes, reports of the development of tolerance to sanitizers and other antimicrobials through cross-resistance is of particular concern. We investigated the potential for six L. monocytogenes isolates from fresh produce handling and processing facilities and packinghouses to develop cross-resistance between a commercial sanitizer and antibiotics. Experimental adaptation of isolates belonging to hypervirulent clonal complexes (CC2, CC4, and CC6) to a commercial quaternary ammonium compound sanitizer (cQAC) resulted in elevated minimum inhibitory concentrations (2–3 ppm) and minimum bactericidal concentrations (3–4 ppm). Susceptibility to cQAC was restored for all adapted (qAD) isolates in the presence of reserpine, a known efflux pump inhibitor. Reduced sensitivity to 7/17 tested antibiotics (chloramphenicol, ciprofloxacin, clindamycin, kanamycin, novobiocin, penicillin, and streptomycin) was observed in all tested isolates. qAD isolates remained susceptible to antibiotics commonly used in the treatment of listeriosis (i.e., ampicillin and gentamicin). The whole genome sequencing of qAD strains, followed by comparative genomic analysis, revealed several mutations in fepR, the regulator for FepA fluoroquinolone efflux pump. The results suggest that mutations in fepR play a role in the reduction in antibiotic susceptibility following low level adaptation to cQAC. Further investigation into the cross-resistance mechanisms and pressures leading to the development of this phenomenon among L. monocytogenes isolates recovered from different sources is needed to better understand the likelihood of cross-resistance development in food chain isolates and the implications for the food industry.

Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistance genes in pigs

Antibiotic-resistant pathogens constitute an escalating public health concern. Hence a better understanding of the underlying processes responsible for this expansion is urgently needed. Co-selection of heavy metal/biocide and antibiotic resistance genes (ARGs) has been suggested as one potential mechanism promoting the proliferation of antimicrobial resistance (AMR). This paper aims to elucidate this interplay and exploit differences in antibiotic usage to infer patterns of co-selection by the non-antibiotic factors metals and biocides in the context of pig farming. We examined 278 gut metagenomes from pigs with continuous antibiotic exposure, only at weaning and at no exposure. Metals as growth promoters and biocides as disinfectants are currently used with little restrictions in stock farming. The pigs under continuous antibiotic exposure displayed the highest co-occurrence of ARGs and other genetic elements while the pigs under limited use of antibiotics still showed abundant co-occurrences. Pathogens belonging to Enterobacteriaceae displayed increased co-occurrence phenomena, suggesting that this maintenance is not a random selection process from a mobilized pool but pertains to specific phylogenetic clades. These results suggest that metals and biocides displayed strong selective pressures on ARGs exerted by intensive farming, regardless of the current use of antibiotics.

Genomic and Phenotypic Analysis of Heat and Sanitizer Resistance in Escherichia coli from Beef in Relation to the Locus of Heat Resistance

The locus of heat resistance (LHR) can confer heat resistance to Escherichia coli to various extents. This study investigated the phylogenetic relationships and the genomic and phenotypic characteristics of E. coli with or without LHR recovered from beef by direct plating or from enrichment broth at 42°C. LHR-positive E. coli isolates (n = 24) were subjected to whole-genome sequencing by short and long reads. LHR-negative isolates (n = 18) from equivalent sources as LHR-positive isolates were short-read sequenced. All isolates were assessed for decimal reduction time at 60°C (D_60°C) and susceptibility to the sanitizers E-SAN and Perox-E. Selected isolates were evaluated for growth at 42°C. The LHR-positive and -negative isolates were well separated on the core genome tree, with 22/24 positive isolates clustering into three clades. Isolates within clade 1 and 2, despite their different D_60°C values, were clonal, as determined by subtyping (multilocus sequence typing [MLST], core genome MLST, and serotyping). Isolates within each clade are of one serotype. The LHR-negative isolates were genetically diverse. The LHR-positive isolates had a larger (P < 0.001) median genome size by 0.3 Mbp (5.0 versus 4.7 Mbp) and overrepresentation of genes related to plasmid maintenance, stress response, and cryptic prophages but underrepresentation of genes involved in epithelial attachment and virulence. All LHR-positive isolates harbored a chromosomal copy of LHR, and all clade 2 isolates had an additional partial copy of LHR on conjugative plasmids. The growth rates at 42°C were 0.71 ± 0.02 and 0.65 ± 0.02 log(OD) h^-1 for LHR-positive and -negative isolates, respectively. No meaningful difference in sanitizer susceptibility was noted between LHR-positive and -negative isolates. IMPORTANCE Resistant bacteria are serious food safety and public health concerns. Heat resistance conferred by the LHR varies largely among different strains of E. coli. The findings in this study show that genomic background and composition of LHR, in addition to the presence of LHR, play an important role in the degree of heat resistance in E. coli and that strains with certain genetic backgrounds are more likely to acquire and maintain the LHR. Also, caution should be exercised when recovering E. coli at elevated temperatures, as the presence of LHR may confer growth advantages to some strains. Interestingly, the LHR-harboring strains seem to have evolved further from their primary animal host to adapt to their secondary habitat, as reflected by fewer genes involved in virulence and epithelial attachment. The phylogenetic relationships among the isolates point toward multiple mechanisms for acquisition of LHR by E. coli, likely prior to its being deposited on meat.

Ins and Outs: Recent Advancements in Membrane Protein-Mediated Prokaryotic Ferrous Iron Transport

Iron is an essential nutrient for virtually every living organism, especially pathogenic prokaryotes. Despite its importance, however, both the acquisition and the export of this element require dedicated pathways that are dependent on oxidation state. Due to its solubility and kinetic lability, reduced ferrous iron (Fe²⁺) is useful to bacteria for import, chaperoning, and efflux. Once imported, ferrous iron may be loaded into apo and nascent enzymes and even sequestered into storage proteins under certain conditions. However, excess labile ferrous iron can impart toxicity as it may spuriously catalyze Fenton chemistry, thereby generating reactive oxygen species and leading to cellular damage. In response, it is becoming increasingly evident that bacteria have evolved Fe²⁺ efflux pumps to deal with conditions of ferrous iron excess and to prevent intracellular oxidative stress. In this work, we highlight recent structural and mechanistic advancements in our understanding of prokaryotic ferrous iron import and export systems, with a focus on the connection of these essential transport systems to pathogenesis. Given the connection of these pathways to the virulence of many increasingly antibiotic resistant bacterial strains, a greater understanding of the mechanistic details of ferrous iron cycling in pathogens could illuminate new pathways for future therapeutic developments.

Identification and Antibiotic Profiling of Wohlfahrtiimonas chitiniclastica, an Underestimated Human Pathogen

In the past 12 years, several case reports have clearly demonstrated that Wohlfahrtiimonas chitiniclastica is capable of causing sepsis and bacteremia in humans. However, since most clinicians are not familiar with this species, little is known about its pathogenicity and treatment options while it is as rare but underestimated human pathogen. Therefore, a larger strain collection is required so that methods can be identified that are most suitable to obtain rapid and reliable identification. Moreover, the antimicrobial resistance profile needs to be elucidated in order to explore possible treatment options. Over a period of 6 years, we therefore have collected a total of 14 W. chitiniclastica isolates in routine diagnostics, which now served as the basis for a comprehensive characterization with respect to identification and antibiotic profiling. We compared the accuracy and convenience of several identification techniques in which MALDI-TOF MS and sequencing of the 16S rRNA gene have proven to be suitable for identification of W. chitiniclastica. In addition, whole genome sequencing (WGS)-based digital DNA-DNA hybridization (dDDH) was used as a reference method for strain identification, and surprised with the detection of a novel W. chitiniclastica subspecies. A combination of in silico and in vitro analyses revealed a first insight into the antimicrobial resistance profile and the molecular basis of antimicrobial resistance. Based on our findings, trimethoprim/sulfamethoxazole, levofloxacin, and cephalosporins (e.g., ceftazidime) may be the best antibiotics to use in order to treat infections caused by W. chitiniclastica, while resistance to fosfomycin, amikacin and tobramycin is observed.

Bacterial surface properties influence the activity of the TAT-RasGAP317-326 antimicrobial peptide

Antibiotic resistance is an increasing threat for public health, underscoring the need for new antibacterial agents. Antimicrobial peptides (AMPs) represent an alternative to classical antibiotics. TAT-RasGAP_317-326 is a recently described AMP effective against a broad range of bacteria, but little is known about the conditions that may influence its activity. Using RNA-sequencing and screening of mutant libraries, we show that Escherichia coli and Pseudomonas aeruginosa respond to TAT-RasGAP_317-326 by regulating metabolic and stress response pathways, possibly implicating two-component systems. Our results also indicate that bacterial surface properties, in particular integrity of the lipopolysaccharide layer, influence peptide binding and entry. Finally, we found differences between bacterial species with respect to their rate of resistance emergence against this peptide. Our findings provide the basis for future investigation on the mode of action of TAT-RasGAP_317-326, which may help developing antimicrobial treatments based on this peptide.

Genomic Insights into Drug Resistance Determinants in Cedecea neteri, A Rare Opportunistic Pathogen

Cedecea, a genus in the Enterobacteriaceae family, includes several opportunistic pathogens reported to cause an array of sporadic acute infections, most notably of the lung and bloodstream. One species, Cedecea neteri, is associated with cases of bacteremia in immunocompromised hosts and has documented resistance to different antibiotics, including β-lactams and colistin. Despite the potential to inflict serious infections, knowledge about drug resistance determinants in Cedecea is limited. In this study, we utilized whole-genome sequence data available for three environmental strains (SSMD04, M006, ND14a) of C. neteri and various bioinformatics tools to analyze drug resistance genes in this bacterium. All three genomes harbor multiple chromosome-encoded β-lactamase genes. A deeper analysis of β-lactamase genes in SSMD04 revealed four metallo-β-lactamases, a novel variant, and a CMY/ACT-type AmpC putatively regulated by a divergently transcribed AmpR. Homologs of known resistance-nodulation-cell division (RND)-type multidrug efflux pumps such as OqxB, AcrB, AcrD, and MdtBC were also identified. Genomic island prediction for SSMD04 indicated that tolC, involved in drug and toxin export across the outer membrane of Gram-negative bacteria, was acquired by a transposase-mediated genetic transfer mechanism. Our study provides new insights into drug resistance mechanisms of an environmental microorganism capable of behaving as a clinically relevant opportunistic pathogen.

Loss of RND-type multidrug efflux pumps triggers iron starvation and lipid A modifications in Pseudomonas aeruginosa

Transporters belonging to the Resistance-Nodulation-Division (RND) superfamily of proteins are invariably present in the genomes of Gram-negative bacteria and are largely responsible for the intrinsic antibiotic resistance of these organisms. The number of genes encoding RND transporters per genome vary from one to sixteen and correlates with environmental versatilities of bacterial species. Pseudomonas aeruginosa PAO1 strain, a ubiquitous nosocomial pathogen, possesses twelve RND pumps, which are implicated in development of clinical multidrug resistance and known to contribute to virulence, quorum sensing and many other physiological functions. In this study, we analyzed how P. aeruginosa physiology adapts to the lack of RND-mediated efflux activities. A combination of transcriptomics, metabolomics, genetic and analytical approaches showed that the P. aeruginosa PΔ6 strain lacking six best characterized RND pumps activates a specific adaptation response that involves significant changes in abundance and activities of several transport systems, quorum sensing, iron acquisition and lipid A modifications. Our results demonstrate that these cells accumulate large quantities of pseudomonas quorum signal (PQS), which triggers iron starvation and activation of siderophore biosynthesis and acquisition pathways. The accumulation of iron in turn activates lipid A modification and membrane protection pathways. A transcriptionally regulated RND pump MuxABC-OpmB contributes to these transformations by controlling concentrations of coumarins. Our results suggest that these changes reduce the permeability barrier of the outer membrane and are needed to protect the cell envelope of efflux-deficient P. aeruginosa.

Mutational Activation of Antibiotic-Resistant Mechanisms in the Absence of Major Drug Efflux Systems of Escherichia coli

Mutations are one of the common means by which bacteria acquire resistance to antibiotics. In an Escherichia coli mutant lacking major antibiotic efflux pumps AcrAB and AcrEF, mutations can activate alternative pathways that lead to increased antibiotic resistance. In this work, we isolated and characterized compensatory mutations of this nature mapping in four different regulatory genes, baeS, crp, hns, and rpoB. The gain-of-function mutations in baeS constitutively activated the BaeSR two-component regulatory system to increase the expression of the MdtABC efflux pump. Missense or insertion mutations in crp and hns caused derepression of an operon coding for the MdtEF efflux pump. Interestingly, despite the dependence of rpoB missense mutations on MdtABC for their antibiotic resistance phenotype, neither the expression of the mdtABCD-baeSR operon nor that of other known antibiotic efflux pumps went up. Instead, the transcriptome sequencing (RNA-seq) data revealed a gene expression profile resembling that of a "stringent" RNA polymerase where protein and DNA biosynthesis pathways were downregulated but pathways to combat various stresses were upregulated. Some of these activated stress pathways are also controlled by the general stress sigma factor RpoS. The data presented here also show that compensatory mutations can act synergistically to further increase antibiotic resistance to a level similar to the efflux pump-proficient parental strain. Together, the findings highlight a remarkable genetic ability of bacteria to circumvent antibiotic assault, even in the absence of a major intrinsic antibiotic resistance mechanism. IMPORTANCE Antibiotic resistance among bacterial pathogens is a chronic health concern. Bacteria possess or acquire various mechanisms of antibiotic resistance, and chief among them is the ability to accumulate beneficial mutations that often alter antibiotic targets. Here, we explored E. coli's ability to amass mutations in a background devoid of a major constitutively expressed efflux pump and identified mutations in several regulatory genes that confer resistance by activating specific or pleiotropic mechanisms.

BaeR participates in cephalosporins susceptibility by regulating the expression level of outer membrane proteins in Escherichia coli

The two-component system BaeSR participates in antibiotics resistance of Escherichia coli. To know whether the outer membrane proteins involve in the antibiotics resistance mediated by BaeSR, deletion of acrB was constructed and the recombined plasmid p-baeR was introduced into E. coli K12 and K12△acrB. Minimum inhibitory concentrations (MICs) of antibacterial agents were determined by 2-fold broth micro-dilution method. Gene expressions related with major outer membrane proteins and multidrug efflux pump-related genes were determined by real-time quantitative reverse transcription polymerase chain reaction. The results revealed that the MICs of K12ΔacrB to the tested drugs except for gentamycin and amikacin decreased 2- to 16.75-folds compared with those of K12. When BaeR was overexpressed, the MICs of K12ΔacrB/p-baeR to ceftiofur and cefotaxime increased 2.5- and 2-fold, respectively, compared with their corresponding that of K12△acrB. At the same time, the expression levels of ompC, ompF, ompW, ompA and ompX showed significant reduction in K12ΔacrB/p-baeR as compared with K12△acrB. Moreover, the expression levels of ompR, marA, rob and tolC also significantly 'decreased' in K12ΔacrB/p-baeR. These findings indicated that BaeR overproduction can decrease cephalosporins susceptibility in acrB-free E. coli by decreasing the expression level of outer membrane proteins.

Subtractive proteomics approach to Unravel the druggable proteins of the emerging pathogen Waddlia chondrophila and drug repositioning on its MurB protein

Waddlia chondrophila is an emerging pathogen that has been implicated in numerous unpropitious pregnancy events in humans and ruminants. Taking into account its association with abortigenic events, possible modes of transmission, and future risk, immediate clinical measures are required to prevent widespread damage caused by this organism and hence this study. Here, a subtractive proteomics approach was employed to identify druggable proteins of W. chondrophila. Considering the essential genes, antibiotic resistance proteins, and virulence factors, 676 unique important proteins were initially identified for this bacterium. Afterward, NCBI BLASTp performed against human proteome identified 223 proteins that were further pushed into KEGG Automatic Annotation Server (KAAS) for automatic annotation. Using the information from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database 14 Waddlia specific metabolic pathways were identified with respect to humans. Analyzing the data from KAAS and KEGG databases, forty-eight metabolic pathway-dependent, and seventy metabolic pathway independent proteins were identified. Standalone BLAST search against DrugBank FDA approved drug targets revealed eight proteins that are finally considered druggable proteins. Prediction of three-dimensional structures was done for the eight proteins through homology modeling and the Ramachandran plot model showed six models as a valid prediction. Finally, virtual screening against MurB protein was performed using FDA approved drugs to employ the drug repositioning strategy. Three drugs showed promising docking results that can be used for therapeutic purposes against W. chondrophila following the clinical validation of the study.

Insights into Emergence of Antibiotic Resistance in Acid-Adapted Enterohaemorrhagic Escherichia coli

The emergence of multidrug-resistant pathogens presents a global challenge for treating and preventing disease spread through zoonotic transmission. The water and foodborne Enterohaemorrhagic Escherichia coli (EHEC) are capable of causing intestinal and systemic diseases. The root cause of the emergence of these strains is their metabolic adaptation to environmental stressors, especially acidic pH. Acid treatment is desired to kill pathogens, but the protective mechanisms employed by EHECs cross-protect against antimicrobial peptides and thus facilitate opportunities for survival and pathogenesis. In this review, we have discussed the correlation between acid tolerance and antibiotic resistance, highlighting the identification of novel targets for potential production of antimicrobial therapeutics. We have also summarized the molecular mechanisms used by acid-adapted EHECs, such as the two-component response systems mediating structural modifications, competitive inhibition, and efflux activation that facilitate cross-protection against antimicrobial compounds. Moving beyond the descriptive studies, this review highlights low pH stress as an emerging player in the development of cross-protection against antimicrobial agents. We have also described potential gene targets for innovative therapeutic approaches to overcome the risk of multidrug-resistant diseases in healthcare and industry.

The two-component system TarR-TarS is regulated by c-di-GMP/FleQ and FliA and modulates antibiotic susceptibility in Pseudomonas putida

Two-component systems (TCSs) are predominant means by which bacteria sense and respond to environment signals. Genome of Pseudomonas putida contains dozens of putative TCS-encoding genes, but phenotypical-genotypical correlation and transcriptional regulation of these genes are largely unknown. Herein, we characterized function and transcriptional regulation of a conserved P. putida TCS, named TarR-TarS. TarS (PP_0769) encodes a potential histidine kinase, and tarR (PP_0768) encodes a potential response regulator. Protein-protein interaction assay and phosphorylation assay confirmed that TarR-TarS was a functional TCS. Growth assay under antibiotics revealed that TarR-TarS positively regulated bacterial resistance to multiple antibiotics. Pull-down assay revealed that TarR directly interacted with PP_0800 (a hypothetical protein) and GroEL (the chaperonin). GroEL played a positive role in antibiotic resistance, while PP_0800 seemed to have no effect on antibiotic resistance. The regulator FleQ indirectly activated tarR-tarS transcription. However, the second messenger c-di-GMP antagonized FleQ activation to inhibit tarR-tarS transcription. The sigma factor FliA directly activated tarR-tarS transcription via a consensus motif. These findings reveal function and transcriptional regulation of TarR-TarS, and enrich knowledge regarding the relationship between c-di-GMP and antibiotic susceptibility in P. putida.

Disbalancing Envelope Stress Responses as a Strategy for Sensitization of Escherichia coli to Antimicrobial Agents

Disbalancing envelope stress responses was investigated as a strategy for sensitization of Escherichia coli to antimicrobial agents. Seventeen isogenic strains were selected from the KEIO collection with deletions in genes corresponding to the σ^E, Cpx, Rcs, Bae, and Psp responses. Antimicrobial activity against 20 drugs with different targets was evaluated by disk diffusion and gradient strip tests. Growth curves and time-kill curves were also determined for selected mutant-antimicrobial combinations. An increase in susceptibility to ampicillin, ceftazidime, cefepime, aztreonam, ertapenem, and fosfomycin was detected. Growth curves for Psp response mutants showed a decrease in optical density (OD) using sub-MIC concentrations of ceftazidime and aztreonam (ΔpspA and ΔpspB mutants), cefepime (ΔpspB and ΔpspC mutants) and ertapenem (ΔpspB mutant). Time-kill curves were also performed using 1xMIC concentrations of these antimicrobials. For ceftazidime, 2.9 log₁₀ (ΔpspA mutant) and 0.9 log₁₀ (ΔpspB mutant) decreases were observed at 24 and 8 h, respectively. For aztreonam, a decrease of 3.1 log₁₀ (ΔpspA mutant) and 4 log10₁₀ (ΔpspB mutant) was shown after 4–6 h. For cefepime, 4.2 log₁₀ (ΔpspB mutant) and 2.6 log₁₀ (ΔpspC mutant) decreases were observed at 8 and 4 h, respectively. For ertapenem, a decrease of up to 6 log₁₀ (ΔpspB mutant) was observed at 24 h. A deficient Psp envelope stress response increased E. coli susceptibility to beta-lactam agents such as cefepime, ceftazidime, aztreonam and ertapenem. Its role in repairing extensive inner membrane disruptions makes this pathway essential to bacterial survival, so that disbalancing the Psp response could be an appropriate target for sensitization strategies.

An overview of Salmonella enterica metal homeostasis pathways during infection

Nutritional immunity is a powerful strategy at the core of the battlefield between host survival and pathogen proliferation. A host can prevent pathogens from accessing biological metals such as Mg, Fe, Zn, Mn, Cu, Co or Ni, or actively intoxicate them with metal overload. While the importance of metal homeostasis for the enteric pathogen Salmonella enterica Typhimurium was demonstrated many decades ago, inconsistent results across various mouse models, diverse Salmonella genotypes, and differing infection routes challenge aspects of our understanding of this phenomenon. With expanding access to CRISPR-Cas9 for host genome manipulation, it is now pertinent to re-visit past results in the context of specific mouse models, identify gaps and incongruities in current knowledge landscape of Salmonella homeostasis, and recommend a straight path forward towards a more universal understanding of this historic host-microbe relationship.

Overexpression of Efflux Pumps Mediate Pan Resistance of Klebsiella pneumoniae Sequence Type 11

A clinically isolated pan-resistant Klebsiella pneumoniae strain (ST11), KPN142 was subjected to whole-genome sequencing. Genomic sequence of KPN142 showed that limited antibiotic resistances (β-lactams [bla_shv-11], sulfonamides [sul1 and dfrA22], bacitracin [bacA], tetracycline [tet34], aminoglycosides [ksgA, kdpE, aph(3)Ia, aac(3)III, and ant(3)Ia], and chloramphenicol [catA1]) were mediated by enzymes, and efflux pumps contributed most to pan resistance. Five types of multidrug resistance efflux pump families were identified, including the resistance nodulation division superfamily (AcrAB-TolC, AcrD, MdtABC, and KexD), the ATP-binding cascade superfamily (MacAB), the small multidrug resistance family (KpnEF), the multidrug and toxic compound extrusion family (KdeA), and the major facilitator superfamily (EmrAB). There was an AcrAB-TolC efflux pump system, and inhibitory regulatory gene acrR and ramR of system carried deletion mutation, which lead to overexpression of AcrAB-TolC efflux pump, and in turn plays key role in the pan resistance of KPN142. Moreover, we did not find mgrb, a suppressor in the expression of phoPQ, overexpression of which may confer the resistance of KPN142 to colistin B. In addition, K. pneumoniae KPN142 carries IS1, IS3, and IntI1, which means that KPN142 is able to transfer drug-resistance genes. Of note, we detected the overexpression of acrB, ramA, phoP, and phoQ by real-time quantitative reverse transcription-polymerase chain reaction, and carbonyl cyanide chlorophenylhydrazone was able to reverse the resistance patterns of K. pneumoniae KPN142. In conclusion, we consider that the overexpression of AcrAB-TolC efflux pump mediates the resistance to most common clinical antimicrobial agents, and the overexpression of phoPQ mediates the resistance to colistin B in K. pneumoniae KPN142.

Complete genome analysis of a virulent Vibrio scophthalmi strain VSc190401 isolated from diseased marine fish half-smooth tongue sole, Cynoglossus semilaevis

Background

Vibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in the marine environment. Earlier studies have suggested that it is a normal microorganism in the turbot gut. However, recent studies have confirmed that this bacterial strain can cause diseases in many different marine animals. Therefore, it is necessary to investigate its whole genome for better understanding its physiological and pathogenic mechanisms.

Results

In the present study, we obtained a pathogenic strain of V. scophthalmi from diseased half-smooth tongue sole (Cynoglossus semilaevis) and sequenced its whole genome. Its genome contained two circular chromosomes and two plasmids with a total size of 3,541,838 bp, which harbored 3185 coding genes. Among these genes, 2648, 2298, and 1915 genes could be found through annotation information in COG, Blast2GO, and KEGG databases, respectively. Moreover, 10 genomic islands were predicted to exist in the chromosome I through IslandViewer online system. Comparison analysis in VFDB and PHI databases showed that this strain had 334 potential virulence-related genes and 518 pathogen-host interaction-related genes. Although it contained genes related to four secretion systems of T1SS, T2SS, T4SS, and T6SS, there was only one complete T2SS secretion system. Based on CARD database blast results, 180 drug resistance genes belonging to 27 antibiotic resistance categories were found in the whole genome of such strain. However, there were many differences between the phenotype and genotype of drug resistance.

Conclusions

Based on the whole genome analysis, the pathogenic V. scophthalmi strain contained many types of genes related to pathogenicity and drug resistance. Moreover, it showed inconsistency between phenotype and genotype on drug resistance. These results suggested that the physiological mechanism seemed to be complex.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-020-02028-7.

Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships

Escherichia coli uses two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of E. coli's global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs in E. coli MG1655: BaeSR and CpxAR, which were stimulated by ethanol stress; KdpDE and PhoRB, induced by limiting potassium and phosphate, respectively; and ZraSR, stimulated by zinc. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data were used to validate condition-specific target gene binding sites. Based on these data, we do the following: (i) identify the target genes for each TCS; (ii) show how the target genes are transcribed in response to stimulus; and (iii) reveal novel relationships between TCSs, which indicate noncognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress. Our understanding of the TRN in E. coli is thus notably expanded.IMPORTANCE E. coli is a common commensal microbe found in the human gut microenvironment; however, some strains cause diseases like diarrhea, urinary tract infections, and meningitis. E. coli's two-component systems (TCSs) modulate target gene expression, especially related to virulence, pathogenesis, and antimicrobial peptides, in response to environmental stimuli. Thus, it is of utmost importance to understand the transcriptional regulation of TCSs to infer bacterial environmental adaptation and disease pathogenicity. Utilizing a combinatorial approach integrating RNA sequencing (RNA-seq), independent component analysis, chromatin immunoprecipitation coupled with exonuclease treatment (ChIP-exo), and data mining, we suggest five different modes of TCS transcriptional regulation. Our data further highlight noncognate inducers of TCSs, which emphasizes the cross-regulatory nature of TCSs in E. coli and suggests that TCSs may have a role beyond their cognate functionalities. In summary, these results can lead to an understanding of the metabolic capabilities of bacteria and correctly predict complex phenotype under diverse conditions, especially when further incorporated with genome-scale metabolic models.

Molecular evaluation of quorum quenching potential of vanillic acid against Yersinia enterocolitica through transcriptomic and in silico analysis

Introduction. Yersinia enterocolitica is one of the leading food-borne entero-pathogens causing various illnesses ranging from gastroenteritis to systemic infections. Quorum sensing (QS) is one of the prime mechanisms that control the virulence in Y. enterocolitica .

Hypothesis/Gap Statement. Vanillic acid inhibits the quorum sensing and other virulence factors related to Y. enterocolitica . It has been evaluated by transcriptomic and Insilico analysis. Therefore, it can be a prospective agent to develop a therapeutic combination against Y. enterocolitica .

Aim. The present study is focused on screening natural anti-quorum-sensing agents against Y. enterocolitica . The effect of selected active principle on various virulence factors was evaluated.

Methodology. In total, 12 phytochemicals were screened by swarming assay. MATH assay, EPS and surfactant production assay, SEM analysis, antibiotic and blood sensitivity assay were performed to demonstrate the anti-virulence activity. Further, RNA sequencing and molecular docking studies were carried out to substantiate the anti-QS activity.

Results. Vanillic acid (VA) has exhibited significant motility inhibition, thus indicating the anti-QS activity with MQIC of 400 µg ml−1 without altering the cell viability. It has also inhibited the violacein production in Chromobacterium violaceum ATCC 12472, which further confirms the anti-QS activity. VA has inhibited 16 % of cell-surface hydrophobicity (CSH), 52 % of EPS production and 60 % of surfactant production. Moreover, it has increased the sensitivity of Y. enterocolitica towards antibiotics. It has also made the cells upto 91 % more vulnerable towards human immune cells. The transcriptomic analysis by RNA sequencing revealed the down regulation of genes related to motility, virulence, chemotaxis, siderophores and drug resistance. VA treatment has also positively regulated the expression of several stress response genes. In furtherance, the anti-QS potential of VA has been validated with QS regulatory protein YenR by in silico molecular simulation and docking study.

Conclusion. The present study is possibly the first attempt to demonstrate the anti-QS and anti-pathogenic potential of VA against Y. enterocolitica by transcriptomic and in silico analysis. It also deciphers that VA can be a promising lead to develop biopreservative and therapeutic regimens to treat Y. enterocolitica infections.

Adaptation of Arginine Synthesis among Uropathogenic Branches of the Escherichia coli Phylogeny Reveals Adjustment to the Urinary Tract Habitat

Uropathogenic Escherichia coli (UPEC) is the most common cause of human urinary tract infection (UTI). Population bottlenecks during early stages of UTI make high-throughput screens impractical for understanding clinically important later stages of UTI, such as persistence and recurrence. As UPEC is hypothesized to be adapted to these later pathogenic stages, we previously identified 29 genes evolving under positive selection in UPEC. Here, we found that 8 of these genes, including argI (which is involved in arginine biosynthesis), are important for persistence in a mouse model of UTI. Deletion of argI and other arginine synthesis genes resulted in (i) arginine auxotrophy and (ii) defects in persistent UTI. Replacement of a B2 clade argI with a non-B2 clade argI complemented arginine auxotrophy, but the resulting strain remained attenuated in its ability to cause persistent bacteriuria. Thus, argI may have a second function during UTI that is not related to simple arginine synthesis. This study demonstrates how variation in metabolic genes can impact virulence and provides insight into the mechanisms and evolution of bacterial virulence.

Urinary tract infections (UTIs) are predominantly caused by uropathogenic Escherichia coli (UPEC). UPEC pathogenesis requires passage through a severe population bottleneck involving intracellular bacterial communities (IBCs) that are clonal expansions of a single invading UPEC bacterium in a urothelial superficial facet cell. IBCs occur only during acute pathogenesis. The bacteria in IBCs form the founder population that develops into persistent extracellular infections. Only a small fraction of UPEC organisms proceed through the IBC cycle, regardless of the inoculum size. This dramatic reduction in population size precludes the utility of genomic mutagenesis technologies for identifying genes important for persistence. To circumvent this bottleneck, we previously identified 29 positively selected genes (PSGs) within UPEC and hypothesized that they contribute to virulence. Here, we show that 8 of these 29 PSGs are required for fitness during persistent bacteriuria. Conversely, 7/8 of these PSG mutants showed essentially no phenotype in acute UTI. Deletion of the PSG argI leads to arginine auxotrophy. Relative to the other arg genes, argI in the B2 clade (which comprises most UPEC strains) of E. coli has diverged from argI in other E. coli clades. Replacement of argI in a UPEC strain with a non-UPEC argI allele complemented the arginine auxotrophy but not the persistent bacteriuria defect, showing that the UPEC argI allele contributes to persistent infection. These results highlight the complex roles of metabolic pathways during infection and demonstrate that evolutionary approaches can identify infection-specific gene functions downstream of population bottlenecks, shedding light on virulence and the genetic evolution of pathogenesis.

Complete Genome Sequences of Leclercia sp. W6 and W17 Isolated from a Gastric Cancer Patient

Leclercia sp. W6 and W17, which belong to the Enterobacteriaceae, were isolated from a stomach sample from a 78-year-old female gastric cancer patient, and genomic sequencing and analysis were performed. The genome of Leclercia sp. W6 consists of one chromosome with a size of 4,945,486 bp, while that of Leclercia sp. W17 contains one chromosome and two plasmids with a total size of 5,125,645 bp. Average nucleotide identity (ANI) calculations indicated that strains W6 and W17 exhibited similarities < 91.0% to other strains within the Enterobacteriaceae, except for six Leclercia strains. Phylogenomic analysis based on core-genome showed that strains W6 and W17 belong to the genus Leclercia, and phylogenetic analysis based on ANI values revealed that strains W6 and W17 formed an independent clade from those six Leclercia strains. Furthermore, comparative genomic analysis revealed that strains W6 and W17 had 5086 orthologous clusters (OCs) in their pan-genomes, and 59 exclusive OCs which were absent in their closest relatives. Genomic annotations revealed that the genomes of strains W6 and W17 encoded genes related to multidrug resistance clusters, multiple antibiotic resistance loci, and multidrug efflux pumps and had an identical urease gene cluster and a dissimilatory nitrate reduction pathway. Bioinformatic analyses indicated that strains W6 and W17 represented a novel species within the genus Leclercia. Genomic annotations revealed that these strains encoded genes related to multidrug resistance, nitrate reduction, and urease activity, which contribute to gastric malignant transformation. This will broaden our knowledge of the genetic mechanisms of the Enterobacteriaceae and help improve the clinical conditions of gastric cancer patients.

Influence of zinc on CTX-M-1 β-lactamase expression in Escherichia coli

OBJECTIVE

Zinc oxide is used to prevent post-weaning diarrhoea in pigs as an alternative to antimicrobial growth promoters. This study aims to determine if the use of zinc oxide selects for extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and affects the expression of bla_CTX-M-1 in E. coli.

METHODS

Using an in vitro faecal micro-cosmos model, the selective properties of zinc were investigated using an E. coli strain with bla_CTX-M-1 encoded by a natural IncI1 resistance plasmid (MG1655/pTF2) and another strain where the same gene was located on the chromosome (MG1655::bla_CTX-M-1). The micro-cosmos was seeded with faecal material containing an increasing concentration of zinc (0-8 mM). Outcome measurements consisted of colony-forming units (CFU) of the inoculated ESBL E. coli and naturally occurring coliforms as determined by plate counting on MacConkey with and without 5 mg/L cefotaxime as well as total viable bacteria determined on Luria agar without cefotaxime. Expression of bla_CTX-M-1 under the experimental zinc concentrations was determined by quantitative polymerase chain reaction.

RESULTS

The proportion of MG1655/pTF2 of the total viable bacteria was significantly higher at high zinc concentrations (6 and 8 mM) compared with low concentrations (0-4 mM). The messenger RNA (mRNA) levels of bla_CTX-M-1 in the two ESBL strains increased at increasing zinc concentrations and varied with the growth phase.

CONCLUSION

The growth of the inoculated CTX-M-1-encoding E. coli MG1655 strains and naturally occurring coliforms was impacted differently when exposed to zinc oxide. The bla_CTX-M-1 mRNA expression levels seemed to increase with increasing zinc concentrations, but varied with growth phase, but not gene location.

Regulatory Role of the Two-Component System BasSR in the Expression of the EmrD Multidrug Efflux in Escherichia coli

Due to excessive use of antimicrobial agents in the treatment of infectious diseases, bacteria have developed resistance to antibacterial drugs and toxic compounds. The development of multidrug efflux pumps is one of the important mechanisms of bacterial drug resistance. A multidrug efflux pump, EmrD, belonging to the major facilitator superfamily of transporters, confers resistance to many antimicrobial agents. BasSR, a typical two-component signal transduction system (TCS), regulates susceptibility to the cationic antimicrobial peptide, polymyxin B, and the anionic bile detergent, deoxycholic acid, in Escherichia coli. However, whether or not the BasSR TCS affects susceptibility or resistance to other antimicrobial agents and transcription of emrD has not been reported in E. coli. In the present study, we constructed the basSR mutants of wild-type MG1655 and clinical strain APECX40 and performed antimicrobial susceptibility testing, antibacterial activity assays, real-time reverse transcription-PCR experiments and electrophoretic mobility shift assays (EMSA) to investigate the molecular mechanism by which BasSR regulates the EmrD multidrug efflux pump. Results showed that the basSR mutation increased cell susceptibility to eight antimicrobial agents, including ciprofloxacin, norfloxacin, doxycycline, tetracycline, clindamycin, lincomycin, erythromycin, and sodium dodecyl sulfate, by downregulating the transcriptional levels of emrD. Furthermore, EMSA indicated that BasR could directly bind to the emrD promoter. Therefore, this study was the first to demonstrate that BasSR activates transcription of emrD by binding directly to its promoter region, and then decreases susceptibility to various antimicrobial agents in E. coli strains, APECX40 and MG1655.

Expression of Meiothermus ruber luxS in E. coli alters the antibiotic susceptibility and biofilm formation

Quorum sensing (QS) and signal molecules used for interspecies communication are well defined in mesophiles, but there is still a plethora of microorganisms in which existence and mechanisms of QS need to be explored, thermophiles being among them. In silico analysis has revealed the presence of autoinducer-2 (AI-2) class of QS signaling molecules in thermophiles, synthesized by LuxS (AI-2 synthase), though the functions of this system are not known. In this study, LuxS of Meiothermus ruber was used for understanding the mechanism and functions of AI-2 based QS among thermophilic bacteria. The luxS gene of M. ruber was expressed in luxS^- deletion mutant of Escherichia coli. Complementation of luxS resulted in significant AI-2 activity, enhanced biofilm formation, and antibiotic susceptibility. Transcriptome analysis showed significant differential expression of 204 genes between the luxS-complemented and luxS^- deletion mutant of E. coli. Majority of the genes regulated by luxS belonged to efflux pumps. This elucidation may contribute towards finding novel alternatives against incessant antibiotic resistance in bacteria.Key Points• Expression of luxS in luxS^-E. coli resulted in increase in biofilm index. • Reduction in the MIC of antibiotics was observed after complementation of luxS. • Downregulation of efflux pump genes was observed after complementation of luxS. • Transcriptome analysis showed that 204 genes were differentially regulated significantly.

QseBC is involved in the biofilm formation and antibiotic resistance in Escherichia coli isolated from bovine mastitis

Background

Mastitis is one of the most common infectious diseases in dairy cattle and causes significant financial losses in the dairy industry worldwide. Antibiotic therapy has been used as the most effective strategy for clinical mastitis treatment. However, due to the extensive use of antibacterial agents, antimicrobial resistance (AMR) is considered to be one of the reasons for low cure rates in bovine mastitis. In addition, biofilms could protect bacteria by restricting antibiotic access and shielding the bacterial pathogen from mammary gland immune defences. The functional mechanisms of quorum sensing E. coli regulators B an d C (QseBC) have been well studied in E. coli model strains; however, whether QseBC regulates antibiotic susceptibility and biofilm formation in clinical E. coli strain has not been reported.

Methods

In this study, we performed construction of the qseBC gene mutant, complementation of the qseBC mutant, antimicrobial susceptibility testing, antibacterial activity assays, biofilm formation assays, real-time reverse transcription PCR (RT-PCR) experiments and electrophoretic mobility shift assays (EMSAs) to investigate the role of qseBC in regulating biofilm formation and antibiotic susceptibility in the clinical E. coli strain ECDCM2.

Results

We reported that inactivation of QseBC led to a decrease in biofilm formation capacity and an increase in antibiotic susceptibility of an E. coli strain isolated from a dairy cow that suffered from mastitis. In addition, this study indicated that QseBC increased biofilm formation by upregulating the transcription of the biofilm-associated genes bcsA, csgA, fliC, motA, wcaF and fimA and decreased antibiotic susceptibility by upregulating the transcription of the efflux-pump-associated genes marA, acrA, acrB, acrD, emrD and mdtH. We also performed EMSA assays, and the results showed that QseB can directly bind to the marA promoter.

Conclusions

The QseBC two-component system affects antibiotic sensitivity by regulating the transcription of efflux-pump-associated genes. Further, biofilm-formation-associated genes were also regulated by QseBC TCS in E. coli ECDCM2. Hence, this study might provide new clues to the prevention and treatment of infections caused by the clinical E. coli strains.

Acinetobacter baumannii Efflux Pumps and Antibiotic Resistance

Acinetobacter baumannii is a nosocomial pathogen and gram-negative coccobacillus that is responsible for opportunistic infections, pneumonia, and infections of the urinary tract, bloodstream, skin, and soft tissue. This bacterium poses a major public health problem due to inducing resistance to several drugs, isolates, multidrug treatment, and occasionally pan drugs. Drug resistance is not only a major concern caused by A. baumannii but also is considered as the main challenge in many other pathogens. Several factors such as the efflux pump are associated with antibiotic resistance, biofilm production, and genetic mutations. In this review, A. baumannii is introduced in then some of the practical works conducted on the existing efflux pump are reviewed. The importance of the efflux pump is considered in this paper in relation to the antibiotic resistance and mechanisms developed for the inhibition of these pumps as well.

Genome-Wide Transposon Screen of a Pseudomonas syringae mexB Mutant Reveals the Substrates of Efflux Transporters

Bacteria express numerous efflux transporters that confer resistance to diverse toxicants present in their environment. Due to a high level of functional redundancy of these transporters, it is difficult to identify those that are of most importance in conferring resistance to specific compounds. The resistance-nodulation-division (RND) protein family is one such example of redundant transporters that are widespread among Gram-negative bacteria. Within this family, the MexAB-OprM protein complex is highly expressed and conserved among Pseudomonas species. We exposed barcoded transposon mutant libraries in isogenic wild-type and ΔmexB backgrounds in P. syringae B728a to diverse toxic compounds in vitro to identify mutants with increased susceptibility to these compounds. Mutants with mutations in genes encoding both known and novel redundant transporters but with partially overlapping substrate specificities were observed in a ΔmexB background. Psyr_0228, an uncharacterized member of the major facilitator superfamily of transporters, preferentially contributes to tolerance of acridine orange and acriflavine. Another transporter located in the inner membrane, Psyr_0541, contributes to tolerance of acriflavine and berberine. The presence of multiple redundant, genomically encoded efflux transporters appears to enable bacterial strains to tolerate a diversity of environmental toxins. This genome-wide screen performed in a hypersusceptible mutant strain revealed numerous transporters that would otherwise be dispensable under these conditions. Bacterial strains such as P. syringae that likely encounter diverse toxins in their environment, such as in association with many different plant species, probably benefit from possessing multiple redundant transporters that enable versatility with respect to toleration of novel toxicants.IMPORTANCE Bacteria use protein pumps to remove toxic compounds from the cell interior, enabling survival in diverse environments. These protein pumps can be highly redundant, making their targeted examination difficult. In this study, we exposed mutant populations of Pseudomonas syringae to diverse toxicants to identify pumps that contributed to survival in those conditions. In parallel, we examined pump redundancy by testing mutants of a population lacking the primary efflux transporter responsible for toxin tolerance. We identified partial substrate overlap for redundant transporters, as well as several pumps that appeared more substrate specific. For bacteria that are found in diverse environments, having multiple, partially redundant efflux pumps likely allows flexibility in habitat colonization.