Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa

Gut Colonization With Antibiotic-Resistant Escherichia coli Pathobionts Leads to Disease Severity in Ulcerative Colitis

BACKGROUND

Escherichia coli is a Gram-negative commensal of human gut. Surprisingly, the role of E. coli in the pathogenesis of ulcerative colitis (UC) has not been explored until now.

METHODS

Human gut microbiota composition and meta-gut resistome were evaluated using metagenomics. Antibiotic susceptibility of E. coli isolates against different class of antibiotics was investigated. Further, the genome sequence analysis of E. coli isolates was performed to gain insight into the antimicrobial resistance (AMR) mechanism and virulence factors. Gut proteome of UC and non-UC was examined to understand the effect of resistant bacteria on host physiology.

RESULTS

In UC patients, meta-gut resistome was found to be dominated by AMR genes (829) compared to healthy controls (HC) [518]. The metagenome study revealed a higher prevalence of AMR genes in the rural population (378 in HC; 607 in UC) compared to the urban (340 in HC; 578 in UC). Approximately, 40% of all E. coli isolates were multi-drug resistant (MDR), with higher prevalence in UC (43.75%) compared to HC (33.33%). Up-regulated expression of antimicrobial human proteins (lactotransferrin, azurocidin, cathepsin G, neutrophil elastase, and neutrophil defensin 3) and inflammatory mediator (Protein S100-A9 and Protein S100-A8) suggest microbial infection in UC gut.

CONCLUSIONS

In addition to the conventional culturomics method, a multi-omics strategy provides deeper insights into the disease etiology, emergence of MDR pathobionts, and their roles in the disruption of the healthy gut environment in UC patients.

Keeping up with the pathogens: improved antimicrobial resistance detection and prediction from Pseudomonas aeruginosa genomes

BACKGROUND

Antimicrobial resistance (AMR) is an intensifying threat that requires urgent mitigation to avoid a post-antibiotic era. Pseudomonas aeruginosa represents one of the greatest AMR concerns due to increasing multi- and pan-drug resistance rates. Shotgun sequencing is gaining traction for in silico AMR profiling due to its unambiguity and transferability; however, accurate and comprehensive AMR prediction from P. aeruginosa genomes remains an unsolved problem.

METHODS

We first curated the most comprehensive database yet of known P. aeruginosa AMR variants. Next, we performed comparative genomics and microbial genome-wide association study analysis across a Global isolate Dataset (n = 1877) with paired antimicrobial phenotype and genomic data to identify novel AMR variants. Finally, the performance of our P. aeruginosa AMR database, implemented in our AMR detection and prediction tool, ARDaP, was compared with three previously published in silico AMR gene detection or phenotype prediction tools-abritAMR, AMRFinderPlus, ResFinder-across both the Global Dataset and an analysis-naïve Validation Dataset (n = 102).

RESULTS

Our AMR database comprises 3639 mobile AMR genes and 728 chromosomal variants, including 75 previously unreported chromosomal AMR variants, 10 variants associated with unusual antimicrobial susceptibility, and 281 chromosomal variants that we show are unlikely to confer AMR. Our pipeline achieved a genotype-phenotype balanced accuracy (bACC) of 85% and 81% across 10 clinically relevant antibiotics when tested against the Global and Validation Datasets, respectively, vs. just 56% and 54% with abritAMR, 58% and 54% with AMRFinderPlus, and 60% and 53% with ResFinder. ARDaP's superior performance was predominantly due to the inclusion of chromosomal AMR variants, which are generally not identified with most AMR identification tools.

CONCLUSIONS

Our ARDaP software and associated AMR variant database provides an accurate tool for predicting AMR phenotypes in P. aeruginosa, far surpassing the performance of current tools. Implementation of ARDaP for routine AMR prediction from P. aeruginosa genomes and metagenomes will improve AMR identification, addressing a critical facet in combatting this treatment-refractory pathogen. However, knowledge gaps remain in our understanding of the P. aeruginosa resistome, particularly the basis of colistin AMR.

Molecular Analysis of Carbapenem and Aminoglycoside Resistance Genes in Carbapenem-Resistant Pseudomonas aeruginosa Clinical Strains: A Challenge for Tertiary Care Hospitals

Carbapenem-resistant Pseudomonas aeruginosa (P. aeruginosa) strains have become a global threat due to their remarkable capability to survive and disseminate successfully by the acquisition of resistance genes. As a result, the treatment strategies have been severely compromised. Due to the insufficient available data regarding P. aeruginosa resistance from Pakistan, we aimed to investigate the resistance mechanisms of 249 P. aeruginosa strains by antimicrobial susceptibility testing, polymerase chain reaction for the detection of carbapenemases, aminoglycoside resistance genes, extended-spectrum beta-lactamases (ESBLs), sequence typing and plasmid typing. Furthermore, we tested silver nanoparticles (AgNPs) to evaluate their in vitro sensitivity against antimicrobial-resistant P. aeruginosa strains. We observed higher resistance against antimicrobials in the general surgery ward, general medicine ward and wound samples. Phenotypic carbapenemase-producer strains comprised 80.7% (201/249) with 89.0% (179/201) demonstrating genes encoding carbapenemases: blaNDM-1 (32.96%), blaOXA48 (37.43%), blaIMP (7.26%), blaVIM (5.03%), blaKPC-2 (1.12%), blaNDM-1/blaOXA48 (13.97%), blaOXA-48/blaVIM (1.68%) and blaVIM/blaIMP (0.56%). Aminoglycoside-modifying enzyme genes and 16S rRNA methylase variants were detected in 43.8% (109/249) strains: aac(6')-lb (12.8%), aac(3)-lla (12.0%), rmtB (21.1%), rmtC (11.0%), armA (12.8%), rmtD (4.6%), rmtF (6.4%), rmtB/aac(3)-lla (8.2%), rmtB/aac(6')-lla (7.3%) and rmtB/armA (3.6%). In total, 43.0% (77/179) of the strains coharbored carbapenemases and aminoglycoside resistance genes with 83.1% resistant to at least 1 agent in 3 or more classes and 16.9% resistant to every class of antimicrobials tested. Thirteen sequence types (STs) were identified: ST235, ST277, ST234, ST170, ST381, ST175, ST1455, ST1963, ST313, ST207, ST664, ST357 and ST348. Plasmid replicon types IncFI, IncFII, IncA/C, IncL/M, IncN, IncX, IncR and IncFIIK and MOB types F11, F12, H121, P131 and P3 were detected. Meropenem/AgNPs and Amikacin/AgNPs showed enhanced antibacterial activity. We reported the coexistence of carbapenemases and aminoglycoside resistance genes among carbapenem-resistant P. aeruginosa with diverse clonal lineages from Pakistan. Furthermore, we highlighted AgNP's potential role in handling future antimicrobial resistance concerns.

Recent Advances and Techniques for Identifying Novel Antibacterial Targets

BACKGROUND

With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly.

METHODS

In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification.

RESULTS

Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well.

CONCLUSION

The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.

Comparison of Lactiplantibacillus plantarum isolates from the gut of mice supplemented with different types of nutrients: a genomic and metabolomic study

Many studies have focused on the influence of dietary supplements on gut microbiota composition, but limited research have reported their effects on specific bacterial species in the gut. Lactiplantibacillus plantarum is one of the most widely studied probiotics, with a wide range of sources and good environmental adaptability. In this study, in order to elucidate the adaptation strategies of L. plantarum to the gut of mice supplemented with carbohydrates, peptides and minerals, whole genome resequencing and intracellular metabolites detection were performed, and high-frequency mutant genes and differential metabolites were screened. The results suggested different types of dietary supplements do have different effects on L. plantarum from the gut of mice. Additionally, KEGG annotation unveiled that the effects of these dietary supplements on the gene level of L. plantarum primarily pertained to environmental information processing, while the differential metabolites were predominantly associated with metabolism. This study provided new perspectives on the adaptive mechanism of L. plantarum in response to the host's gut environment, suggesting that the diversity of the genome and metabolome of L. plantarum was correlated with dietary supplements. Furthermore, this study offered useful guidance in the effective utilization of dietary supplements.

Effects of the order of exposure to antimicrobials on the incidence of multidrug-resistant Pseudomonas aeruginosa

Multidrug-resistant Pseudomonas aeruginosa (MDRP) is one of the most important pathogens in clinical practice. To clarify the mechanisms contributing to its emergence, we isolated MDRPs using the P. aeruginosa PAO1, the whole genome sequence of which has already been elucidated. Mutant strains resistant to carbapenems, aminoglycosides, and new quinolones, which are used to treat P. aeruginosa infections, were isolated; however, none met the criteria for MDRPs. Then, PAO1 strains were exposed to these antimicrobial agents in various orders and the appearance rate of MDRP varied depending on the order of exposure; MDRPs more frequently appeared when gentamicin was applied before ciprofloxacin, but were rarely isolated when ciprofloxacin was applied first. Exposure to ciprofloxacin followed by gentamicin increased the expression of MexCD-OprJ, an RND-type multidrug efflux pump, due to the NfxB mutation. In contrast, exposure to gentamicin followed by ciprofloxacin resulted in more mutations in DNA gyrase. These results suggest that the type of quinolone resistance mechanism is related to the frequency of MDRP and that the risk of MDRP incidence is highly dependent on the order of exposure to gentamicin and ciprofloxacin.

Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment

Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.

Degradation effectiveness of hexachlorohexane (ϒ-HCH) by bacterial isolate Bacillus cereus SJPS-2, its gene annotation for bioremediation and comparison with Pseudomonas putida KT2440

The contamination of Hexachlorohexane (Lindane) in soil and water has toxic effects due to its persistent nature. In our study, an indigenous HCH (gamma isomer) degrading bacterium viz Bacillus cereus SJPS-2 was isolated from Yamuna river water using enrichment culture method. The growth curve indicated that Bacillus cereus SJPS-2 was able to degrade ϒ-HCH effectively with 80.98% degradation. Further, process was improved by using immobilization using alginate beads which showed enhanced degradation (89.34%). Interestingly, in presence of fructose, the ϒ-HCH degradation was up to 79.24% with exponential growth curve whereas the degradation was only 5.61% in presence of glucose revealing diauxic growth curve. Furthermore, The FTIR results confirmed the potential lindane degradation capability of Bacillus cereus SJPS-2 and the bonds were recorded at wavelengths viz. 2900-2500 cm-¹, 3300-2800 cm-¹ and 785-540 cm-¹. Similarity, the GC studies also reconfirmed the degradation potential with retention time (RT) of ethyl acetate and lindane was 2.12 and 11.0 respectively. Further, we studied the metabolic pathway involved for lindane utilization in Bacillus cereus using KEGG-KASS and functional gene annotation through Rapid Annotation using Subsystems Technology (RAST) resulted in the annotation of the lin genes (lin A, lin B, lin C, lin X, lin D, lin E) and respective encoding enzymes. The comparative ϒ-HCH degradation potential of B. cereus and P. putida KT2440 was also evaluated. The island viewer showed the different colors on circular genome indicate the coordinates of genomic islands resulted with some common genomic islands (GEIs) between both bacteria indicating the possibility of horizontal gene transfer at contaminated site or natural environment. These genomic islands (GEIs) contribute in the rearrangement genetic material or to evolve bacteria in stress conditions, as a result the metabolic pathways evolve by formation of catabolic genes. This study establishes the potential of Bacillus cereus SJPS-2 for effectual ϒ-HCH degradation.

Rapid fluoroquinolone resistance detection in Pseudomonas aeruginosa using mismatch amplification mutation assay-based real-time PCR

Background. Antimicrobial resistance (AMR) is an ever-increasing global health concern. One crucial facet in tackling the AMR epidemic is earlier and more accurate AMR diagnosis, particularly in the dangerous and highly multi-drug-resistant ESKAPE pathogen, Pseudomonas aeruginosa .

Objectives. We aimed to develop two SYBR Green-based mismatch amplification mutation assays (SYBR-MAMAs) targeting GyrA T83I (gyrA248) and GyrA D87N, D87Y and D87H (gyrA259). Together, these variants cause the majority of fluoroquinolone (FQ) AMR in P. aeruginosa .

Methods. Following assay validation, the gyrA248 and gyrA259 SYBR-MAMAs were tested on 84 Australian clinical P. aeruginosa isolates, 46 of which demonstrated intermediate/full ciprofloxacin resistance according to antimicrobial susceptibility testing.

Results. Our two SYBR-MAMAs correctly predicted an AMR phenotype in the majority (83%) of isolates with intermediate/full FQ resistance. All FQ-sensitive strains were predicted to have a sensitive phenotype. Whole-genome sequencing confirmed 100 % concordance with SYBR-MAMA genotypes.

Conclusions. Our GyrA SYBR-MAMAs provide a rapid and cost-effective method for same-day identification of FQ AMR in P. aeruginosa . An additional SYBR-MAMA targeting the GyrB S466Y/S466F variants would increase FQ AMR prediction to 91 %. Clinical implementation of our assays will permit more timely treatment alterations in cases where decreased FQ susceptibility is identified, leading to improved patient outcomes and antimicrobial stewardship.

Competitive SNP-LAMP probes for rapid and robust single-nucleotide polymorphism detection

In this work, we developed a simple and robust assay to rapidly detect SNPs in nucleic acid samples. Our approach combines loop-mediated isothermal amplification (LAMP)-based target amplification with fluorescent probes to detect SNPs with high specificity. A competitive "sink" strand preferentially binds to non-SNP amplicons and shifts the free energy landscape to favor specific activation by SNP products. We demonstrated the broad utility and reliability of our SNP-LAMP method by detecting three distinct SNPs across the human genome. We also designed an assay to rapidly detect highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants from crude biological samples. This work demonstrates that competitive SNP-LAMP is a powerful and universal method that could be applied in point-of-care settings to detect any target SNP with high specificity and sensitivity. We additionally developed a publicly available web application for researchers to design SNP-LAMP probes for any target sequence of interest.

Ciprofloxacin induced antibiotic resistance in Salmonella Typhimurium mutants and genome analysis

Antibiotic resistance of Salmonella species is well reported. Ciprofloxacin is the frontline antibiotic for salmonellosis. The repeated exposure to ciprofloxacin leads to resistant strains. After 20 cycles of antibiotic exposure, resistant bacterial clones were evaluated. The colony size of the mutants was small and had an extended lag phase compared to parent strain. The whole genome sequencing showed 40,513 mutations across the genome. Small percentage (5.2%) of mutations was non-synonymous. Four-fold more transitions were observed than transversions. Ratio of < 1 transition vs transversion showed a positive selection for antibiotic resistant trait. Mutation distribution across the genome was uniform. The native plasmid was an exception and 2 mutations were observed on 90 kb plasmid. The important genes like dnaE, gyrA, iroC, metH and rpoB involved in antibiotic resistance had point mutations. The genome analysis revealed most of the metabolic pathways were affected.

Resistance mechanisms and genetic relatedness among carbapenem-resistant Pseudomonas aeruginosa isolates from three major hospitals in Hanoi, Vietnam (2011-15)

Background

MDR bacteria including carbapenem-resistant Pseudomonas aeruginosa are recognized as an important cause of hospital-acquired infections worldwide. This investigation seeks to determine the molecular characterization and antibiotic resistance genes associated with carbapenem-resistant P. aeruginosa.

Methods

We conducted WGS and phylogenetic analysis of 72 carbapenem-resistant P. aeruginosa isolated from hospital-acquired infection patients from August 2011 to March 2015 in three major hospitals in Hanoi, Vietnam.

Results

We identified three variants of IMP gene, among which bla_IMP-15 was the most frequent (n = 34) in comparison to bla_IMP-26 (n = 2) and bla_IMP-51 (n = 12). We observed two isolates with imipenem MIC >128 mg/L that co-harboured bla_IMP-15 and bla_DIM-1 genes and seven isolates (imipenem MIC > 128 mg/L) with a bla_KPC-1 gene from the same hospital. MLST data shows that these 72 isolates belong to 18 STs and phylogenetic tree analysis has divided these isolates into nine groups.

Conclusions

Our results provide evidence that not only bla_IMP-26 but other IMP variants such as bla_IMP-15 and bla_IMP-51 genes and several STs (ST235, ST244, ST277, ST310, ST773 and ST3151) have been disseminating in healthcare settings in Vietnam. In addition, we report the emergence of two isolates belonging to ST1240 and ST3340 that harboured two important carbapenemase genes (bla_IMP-15 and bla_DIM-1) and seven isolates belonging to ST3151 of P. aeruginosa that carried the bla_KPC-1 gene in Vietnam, which could potentially cause serious restricted availability of treatment options in healthcare settings.

Insight into phenotypic and genotypic differences between vaginal Lactobacillus crispatus BC5 and Lactobacillus gasseri BC12 to unravel nutritional and stress factors influencing their metabolic activity

The vaginal microbiota, normally characterized by lactobacilli presence, is crucial for vaginal health. Members belonging to L. crispatus and L. gasseri species exert crucial protective functions against pathogens, although a total comprehension of factors that influence their dominance in healthy women is still lacking. Here we investigated the complete genome sequence and comprehensive phenotypic profile of L. crispatus strain BC5 and L. gasseri strain BC12, two vaginal strains featured by anti-bacterial and anti-viral activities. Phenotype microarray (PM) results revealed an improved capacity of BC5 to utilize different carbon sources as compared to BC12, although some specific carbon sources that can be associated to the human diet were only metabolized by BC12, i.e. uridine, amygdalin, tagatose. Additionally, the two strains were mostly distinct in the capacity to utilize the nitrogen sources under analysis. On the other hand, BC12 showed tolerance/resistance towards twice the number of stressors (i.e. antibiotics, toxic metals etc.) with respect to BC5. The divergent phenotypes observed in PM were supported by the identification in either BC5 or BC12 of specific genetic determinants that were found to be part of the core genome of each species. The PM results in combination with comparative genome data provide insights into the possible environmental factors and genetic traits supporting the predominance of either L. crispatus BC5 or L. gasseri BC12 in the vaginal niche, giving also indications for metabolic predictions at the species level.

Antibiogram profile and virulence signatures of Pseudomonas aeruginosa isolates recovered from selected agrestic hospital effluents

Hospital wastewater (HWW) harbours diverse microbial species and a miscellany of genome that would facilitate the emergence of novel pathogen upon genome integration that manifests novel traits in infectious pathogens. The study aimed to determine the antibiogram, and virulence signatures of Pseudomonas aeruginosa (P. aeruginosa) recovered from selected agrestic hospital effluents in Eastern Cape, South Africa. Thirty-six (36) wastewater samples were collected from selected hospital drains between February 2018 and April 2018, processed and analyzed by culture-dependent methods for the isolation of P. aeruginosa. The identity confirmation of isolates was achieved by amplification of oprl and oprL genes. Antibiogram was done using standard disk diffusion technique of Kirby-Bauer as approved by CLSI 2018 guidelines. Virulence signatures (lasA, lasB, toxA, popB) among isolates were analysed using polymerase chain reaction. A total of 54 P. aeruginosa isolates were confirmed by amplification of oprl and oprL genes in the hospital wastewater effluent samples. The isolates showed a 100% susceptibility to gentamicin, amikacin and imipenem antimicrobial agents. Ceftazidime recorded the most resistance (63%) against the isolates studied. Other antibiotics had a resistance range of 7% and 35%. The MAR index among the isolates revealed a range of 0.23 and 0.38. ToxA virulence gene was detected in all isolates while popB, lasB, lasA were detected in 82%, 75% and 54% of the isolates. This study reveals P. aeruginosa isolates with virulence traits and some strains showing multiple antibiotic resistance. The multiple antibiotic resistance index (MARI) of ≥ 0.2 indicates that the some isolates may have emerged from high-risk sources, thus projecting a risk to public health. However, with the high sensitivity pattern observed among the studied isolates, most of the antibiotics used in the susceptibility tests are not at peril. Hence, the use of these antibiotics is encouraged for treatment of infection attributed to P. aeruginosa. It is also pertinent to initiate strict control and rigid antibiotics therapeutic policy with surveillance programmes for multidrug-resistant pathogens to forestall the development and transmission of resistance traits in the pathogens.

Split light up aptamers as a probing tool for nucleic acids

Aptamers that bind non-fluorescent dyes and increase their fluorescence can be converted to fluorescent sensors. Here, we discuss and provide guidance for the design of split (binary) light up aptameric sensors (SLAS) for nucleic acid analysis. SLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. The two strands hybridize to the analyzed DNA or RNA sequence and form a dye-binding pocket, followed by dye binding, and increase in its fluorescence. SLAS can detect nucleic acids in a cost-efficient label-free format since it does not require conjugation of organic dyes with nucleic acids. SLAS design is preferable over monolith fluorescent sensors due to simpler assay optimization and improved selectivity. RNA-based SLAS can be expressed in cells and used for intracellular monitoring and imaging biological molecules.

Evaluation of targeted next-generation sequencing for detection of equine pathogens in clinical samples

Equine infectious disease outbreaks may have profound economic impact, resulting in losses of millions of dollars of revenue as a result of horse loss, quarantine, and cancelled events. Early and accurate diagnosis is essential to limit the spread of infectious diseases. However, laboratory detection of infectious agents, especially the simultaneous detection of multiple agents, can be challenging to the clinician and diagnostic laboratory. Next-generation sequencing (NGS), which allows millions of DNA templates to be sequenced simultaneously in a single reaction, is an ideal technology for comprehensive testing. We conducted a proof-of-concept study of targeted NGS to detect 62 common equine bacterial, viral, and parasitic pathogens in clinical samples. We designed 264 primers and constructed a bioinformatics tool for the detection of targeted pathogens. The designed primers were able to specifically detect the intended pathogens. Results of testing 27 clinical samples with our targeted NGS assay compared with results of routine tests (assessed as a group) yielded positive percent agreement of 81% and negative percent agreement of 83%, overall agreement of 81%, and kappa of 0.56 (moderate agreement). This moderate agreement was likely the result of low sensitivity of some primers. However, our NGS assay successfully detected multiple pathogens in the clinical samples, including some pathogens missed by routine techniques.

Comparative genomics of the sequential Pseudomonas aeruginosa isolates obtained from the continuous imipenem stress evolution

Pseudomonas aeruginosa is a major opportunistic human pathogen that causes nosocomial infections, and the proportion of carbapenem resistance has recently dramatically increased in P. aeruginosa due to the overuse of them. In this study, strains G10 and G20, with minimum inhibitory concentration (MIC) of imipenem of 16 μg/ml and more than 32 μg/ml, were isolated during continuous subculture of cells exposed to stepwise increasing concentrations of imipenem, respectively. The genomes of G10 and G20 were sequenced and compared with parental strain (P. aeruginosa ATCC 27853, G0). There were 59, 59, and 58 genes involved in antibiotic resistance which were predicted in G0, G10, and G20, respectively, while 374, 366, and 363 genes involved in virulence factors were identified among these three strains. Due to the significantly different MICs of imipenem and highly similar profiles of antibiotic resistance and virulence factors related genes among three strains, the specific genetic variations that occurred were identified and compared, including single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and structural variations (SVs). The increase in the MIC of imipenem was proposed to be linked to mutations involved in polyamine biosynthesis, biofilm formation, OprD, and efflux pump functions. This study aims to clarify the underlying mechanism of imipenem resistance and provide alternative strategies for reducing resistance in P. aeruginosa. KEY POINTS: • Strains with different imipenem MIC were obtained via laboratory selection evolution. • Whole genomes of two strains with different MIC of imipenem were sequenced. • Underlying mechanism of imipenem resistance was clarified via comparative genomics.

Combining structure and genomics to understand antimicrobial resistance

Antimicrobials against bacterial, viral and parasitic pathogens have transformed human and animal health. Nevertheless, their widespread use (and misuse) has led to the emergence of antimicrobial resistance (AMR) which poses a potentially catastrophic threat to public health and animal husbandry. There are several routes, both intrinsic and acquired, by which AMR can develop. One major route is through non-synonymous single nucleotide polymorphisms (nsSNPs) in coding regions. Large scale genomic studies using high-throughput sequencing data have provided powerful new ways to rapidly detect and respond to such genetic mutations linked to AMR. However, these studies are limited in their mechanistic insight. Computational tools can rapidly and inexpensively evaluate the effect of mutations on protein function and evolution. Subsequent insights can then inform experimental studies, and direct existing or new computational methods. Here we review a range of sequence and structure-based computational tools, focussing on tools successfully used to investigate mutational effect on drug targets in clinically important pathogens, particularly Mycobacterium tuberculosis. Combining genomic results with the biophysical effects of mutations can help reveal the molecular basis and consequences of resistance development. Furthermore, we summarise how the application of such a mechanistic understanding of drug resistance can be applied to limit the impact of AMR.

Characterization of a SPM-1 metallo-beta-lactamase-producing Pseudomonas aeruginosa by comparative genomics and phenotypic analysis

Pseudomonas aeruginosa is one of the most common pathogens related to healthcare-associated infections. The Brazilian isolate, named CCBH4851, is a multidrug-resistant clone belonging to the sequence type 277. The antimicrobial resistance mechanisms of the CCBH4851 strain are associated with the presence of the bla\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$_\text {SPM-1}$$\end{document}SPM-1 gene, encoding a metallo-beta-lactamase, in combination with other exogenously acquired genes. Whole-genome sequencing studies focusing on emerging pathogens are essential to identify key features of their physiology that may lead to the identification of new targets for therapy. Using both Illumina and PacBio sequencing data, we obtained a single contig representing the CCBH4851 genome with annotated features that were consistent with data reported for the species. However, comparative analysis with other Pseudomonas aeruginosa strains revealed genomic differences regarding virulence factors and regulatory proteins. In addition, we performed phenotypic assays that revealed CCBH4851 is impaired in bacterial motilities and biofilm formation. On the other hand, CCBH4851 genome contained acquired genomic islands that carry transcriptional factors, virulence and antimicrobial resistance-related genes. Presence of single nucleotide polymorphisms in the core genome, mainly those located in resistance-associated genes, suggests that these mutations may also influence the multidrug-resistant behavior of CCBH4851. Overall, characterization of Pseudomonas aeruginosa CCBH4851 complete genome revealed the presence of features that strongly relates to the virulence and antibiotic resistance profile of this important infectious agent.

Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review

Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.

Rapid determination of carbapenem resistance by low-cost colorimetric methods: Propidium Iodide and alamar blue staining

Carbapenems are a class of β-lactam antibiotics with a broad antimicrobial activity spectrum. Owing to their sturdy structures resistant to most β-lactamases, they have been regarded as one of the last-resort antibiotics for combating multidrugresistant bacterial infections. However, the emergence of carbapenem resistance increases predominantly in nosocomial pathogens. To prevent spread of carbapenem resistance in early stages, it is imperative to develop rapid diagnostic tests that will substantially reduce the time and cost in determining carbapenem resistance. Thus, we devised a staining-based diagnostic method applicable to three different Gram-negative pathogens of Acinetobacter baumannii, Escherichia coli, and Klebsiella pneumoniae, all with the high potential to develop carbapenem resistance. Regardless of the resistance mechanisms presented by bacterial species and strains, double staining with propidium iodide (PI) and alamar blue (AB) identified resistant bacteria with an average sensitivity of 95.35%, 7 h after imipenem treatments in 343 clinical isolates. Among the three species tested, A. baumannii showed the highest diagnostic sensitivity of 98.46%. The PI and ABmediated staining method could be a promising diagnostic method with high-throughput efficacy and low cost.

Draft Genome Sequence of a Pseudomonas aeruginosa Sequence Type 3351 Strain Exhibiting High-Level Resistance to Polymyxins in a Pediatric Patient with Cystic Fibrosis in Mexico

Here, we present the draft genome sequence of a Pseudomonas aeruginosa isolate (strain CF16053) belonging to a novel sequence type (ST), ST3351, isolated from a pediatric patient with cystic fibrosis (CF). CF16053 shows high-level resistance to polymyxins associated with mutations in the pmrB gene. Biofilm, pyoverdine, exotoxin A, and type III secretion system (T3SS) genes were identified.

Here, we present the draft genome sequence of a Pseudomonas aeruginosa isolate (strain CF16053) belonging to a novel sequence type (ST), ST3351, isolated from a pediatric patient with cystic fibrosis (CF). CF16053 shows high-level resistance to polymyxins associated with mutations in the pmrB gene. Biofilm, pyoverdine, exotoxin A, and type III secretion system (T3SS) genes were identified.

Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010-2016

Background

Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017.

Results

The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. The phylogenetic tree constructed with 78 genomes including 30 genomes from Korea formed two clusters and further divided into two sub-clusters. eBURST analysis revealed two clonal complexes according to P1 typing results showing higher diversity among P1 type 2 strains.

Conclusions

The comparative whole genome approach was able to define high genetic identity, unique structural diversity, and phylogenetic associations among the 78 M. pneumoniae strains isolated worldwide.

The Collaborative Cross mouse model for dissecting genetic susceptibility to infectious diseases

Infectious diseases, also known as communicable diseases, refer to a full range of maladies caused by pathogen invasion to the host body. Host response towards an infectious pathogen varies between individuals, and can be defined by responses from asymptomatic to lethal. Host response to infectious pathogens is considered as a complex trait controlled by gene-gene (host-pathogen) and gene-environment interactions, leading to the extensive phenotypic variations between individuals. With the advancement of the human genome mapping approaches and tools, various genome-wide association studies (GWAS) were performed, aimed at mapping the genetic basis underlying host susceptibility towards infectious pathogens. In parallel, immense efforts were invested in enhancing the genetic mapping resolution and gene-cloning efficacy, using advanced mouse models including advanced intercross lines; outbred populations; consomic, congenic; and recombinant inbred lines. Notwithstanding the evident advances achieved using these mouse models, the genetic diversity was low and quantitative trait loci (QTL) mapping resolution was inadequate. Consequently, the Collaborative Cross (CC) mouse model was established by full-reciprocal mating of eight divergent founder strains of mice (A/J, C57BL/6J, 129S1/SvImJ, NOD/LtJ, NZO/HiLtJ, CAST/Ei, PWK/PhJ, and WSB/EiJ) generating a next-generation mouse genetic reference population (CC lines). Presently, the CC mouse model population comprises a set of about 200 recombinant inbred CC lines exhibiting a unique high genetic diversity and which are accessible for multidisciplinary studies. The CC mouse model efficacy was validated by various studies in our lab and others, accomplishing high-resolution (< 1 MB) QTL genomic mapping for a variety of complex traits, using about 50 CC lines (3-4 mice per line). Herein, we present a number of studies demonstrating the power of the CC mouse model, which has been utilized in our lab for mapping the genetic basis of host susceptibility to various infectious pathogens. These include Aspergillus fumigatus, Klebsiella pneumoniae, Porphyromonas gingivalis and Fusobacterium nucleatum (causing oral mixed infection), Pseudomonas aeruginosa, and the bacterial toxins Lipopolysaccharide and Lipoteichoic acid.

Acquisition of antimicrobial-resistant variants in repeated infections caused by Pseudomonas aeruginosa revealed by whole genome sequencing

Pseudomonas aeruginosa, responsible for serious nosocomial-acquired infections, possesses intrinsic antibiotic resistance mechanisms and commonly exhibits multidrug resistance. Here, we report the evolving resistance profiles of strains isolated from the sputum of a patient being treated for repeated P. aeruginosa infections following cancer resection. Whole genome sequencing of six isolates obtained over a 2-month period revealed two key single nucleotide polymorphisms in the mexR and gyrB genes that affected efflux pump expression and antimicrobial resistance.

Evaluation of Targeted Next-Generation Sequencing for Detection of Bovine Pathogens in Clinical Samples

The laboratory diagnosis of infectious diseases, especially those caused by mixed infections, is challenging. Routinely, it requires submission of multiple samples to separate laboratories. Advances in next-generation sequencing (NGS) have provided the opportunity for development of a comprehensive method to identify infectious agents. This study describes the use of target-specific primers for PCR-mediated amplification with the NGS technology in which pathogen genomic regions of interest are enriched and selectively sequenced from clinical samples. In the study, 198 primers were designed to target 43 common bovine and small-ruminant bacterial, fungal, viral, and parasitic pathogens, and a bioinformatics tool was specifically constructed for the detection of targeted pathogens. The primers were confirmed to detect the intended pathogens by testing reference strains and isolates. The method was then validated using 60 clinical samples (including tissues, feces, and milk) that were also tested with other routine diagnostic techniques. The detection limits of the targeted NGS method were evaluated using 10 representative pathogens that were also tested by quantitative PCR (qPCR), and the NGS method was able to detect the organisms from samples with qPCR threshold cycle (C_T) values in the 30s. The method was successful for the detection of multiple pathogens in the clinical samples, including some additional pathogens missed by the routine techniques because the specific tests needed for the particular organisms were not performed. The results demonstrate the feasibility of the approach and indicate that it is possible to incorporate NGS as a diagnostic tool in a cost-effective manner into a veterinary diagnostic laboratory.

Recent Advances in Molecular Diagnosis of Pseudomonasaeruginosa Infection by State-of-the-Art Genotyping Techniques

Pseudomonas aeruginosa is a rod-shaped Gram-negative bacterium which is notably known as a pathogen in humans, animals, and plants. Infections caused by P. aeruginosa especially in hospitalized patients are often life-threatening and rapidly increasing worldwide throughout the years. Recently, multidrug-resistant P. aeruginosa has taken a toll on humans' health due to the inefficiency of antimicrobial agents. Therefore, the rapid and advanced diagnostic techniques to accurately detect this bacterium particularly in clinical samples are indeed necessary to ensure timely and effective treatments and to prevent outbreaks. This review aims to discuss most recent of state-of-the-art molecular diagnostic techniques enabling fast and accurate detection and identification of P. aeruginosa based on well-developed genotyping techniques, e.g., polymerase chain reaction, pulse-field gel electrophoresis, and next generation sequencing. The advantages and limitations of each of the methods are also reviewed.

Differential Effect of Newly Isolated Phages Belonging to PB1-Like, phiKZ-Like and LUZ24-Like Viruses against Multi-Drug Resistant Pseudomonas aeruginosa under Varying Growth Conditions

In this study, we characterize three phages (SL1 SL2, and SL4), isolated from hospital sewage with lytic activity against clinical isolates of multi-drug resistant Pseudomonas aeruginosa (MDR-PA). The host spectrum ranged from 41% to 54%, with all three phages together covering 79% of all tested clinical isolates. Genome analysis revealed that SL1 (65,849 bp, 91 open reading frames ORFs) belongs to PB1-like viruses, SL2 (279,696 bp, 354 ORFs) to phiKZ-like viruses and SL4 (44,194 bp, 65 ORFs) to LUZ24-like viruses. Planktonic cells of four of five selected MDR-PA strains were suppressed by at least one phage with multiplicities of infection (MOIs) ranging from 1 to 10⁻⁶ for 16 h without apparent regrowth of bacterial populations. While SL2 was most potent in suppressing planktonic cultures the strongest anti-biofilm activity was observed with SL4. Phages were able to rescue bacteria-infected wax moth larvae (Galleria melonella) for 24 h, whereby highest survival rates (90%) were observed with SL1. Except for the biofilm experiments, the effect of a cocktail with all three phages was comparable to the action of the best phage alone; hence, there are no synergistic but also no antagonistic effects among phages. The use of a cocktail with these phages is therefore expedient for increasing host range and minimizing the development of phage resistance.