Genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant ST235 isolates of Pseudomonas aeruginosa

Multiple regional outbreaks caused by global and local VIM-producing Klebsiella pneumoniae clones in Poland, 2006-2019

PURPOSE

This study was aimed at comprehensive genomic analysis of VIM-type carbapenemase-producing Klebsiella pneumoniae species complex (KpSC) in Poland.

METHODS

All non-duplicate 214 VIM-producing KpSC isolates reported in Poland in 2006-2019 were short-read sequenced and re-identified by the average nucleotide identity scoring. Their clonality/phylogeny was assessed by cgMLST and SNP in comparison with genomes from international databases. Serotypes, VIM-encoding integrons, resistomes, virulomes and plasmid replicons were identified by various bioinformatic tools. Structures of plasmids and genomic islands with VIM integrons were analysed for representative long-read sequenced isolates.

RESULTS

The KpSC isolates were the second most prevalent VIM-positive Enterobacterales (23.1%) in Poland in 2006-2019, following Enterobacter spp. (40.1%). Their significance emerged in 2014 and then grew consequently, owing to eight regional outbreaks of K. pneumoniae sequence types (STs) ST437, ST147, ST15, ST277 and ST392. These carried different VIM integrons, mainly In238 and In916 types, located on IncFIB + IncHI2 (pNDM-MAR)-, IncA- or IncM-like plasmids, or clc-type integrative and conjugative elements. Despite relatedness of the outbreak clusters to isolates from other countries, e.g. Greece, Spain, Slovakia or Germany, most of them have apparently emerged on site by horizontal acquisition of resistance determinants from other species, including Enterobacter spp. and Pseudomonas spp.

CONCLUSIONS

This work shows dynamic epidemiology of VIM-producing organisms, driven by a mix of circulation of different VIM-encoding elements, and parallel clonal spread of multiple organisms.

Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons

Antimicrobial resistance (AMR) gene cassettes comprise an AMR gene flanked by short recombination sites (attI and attC or attC and attC). Integrons are genetic elements able to capture, excise and shuffle these cassettes, providing 'adaptation on demand', and can be found on both chromosomes and plasmids. Understanding the patterns of integron diversity may help to understand the epidemiology of AMR genes. As a case study, we examined the clinical resistance gene bla GES-5, an integron-associated class A carbapenemase first reported in Greece in 2004 and since observed worldwide, which to our knowledge has not been the subject of a previous global analysis. Using a dataset comprising all de-duplicated NCBI contigs containing bla GES-5 (n=104), we developed a pangenome graph-based workflow to characterize and cluster the diversity of bla GES-5-associated integrons. We demonstrate that bla GES-5-associated integrons on plasmids are different to those on chromosomes. Chromosomal integrons were almost all identified in Pseudomonas aeruginosa ST235, with a consistent gene cassette content and order. We observed instances where insertion sequence IS110 disrupted attC sites, which might immobilize the gene cassettes and explain the conserved integron structure despite the presence of intI1 integrase promoters, which would typically facilitate capture or excision and rearrangement. The plasmid-associated integrons were more diverse in their gene cassette content and order, which could be an indication of greater integrase activity and 'shuffling' of integrons on plasmids.

VIM-type metallo-β-lactamase (MBL)-encoding genomic islands in Pseudomonas spp. in Poland: predominance of clc-like integrative and conjugative elements (ICEs)

OBJECTIVES

To characterize VIM-type metallo-β-lactamase (MBL)-encoding genomic islands (GIs) in Pseudomonas aeruginosa and P. putida group isolates from Polish hospitals from 2001-2015/16.

METHODS

Twelve P. aeruginosa and 20 P. putida group isolates producing VIM-like MBLs were selected from a large collection of these based on epidemiological and typing data. The organisms represented all major epidemic genotypes of these species spread in Poland with chromosomally located blaVIM gene-carrying integrons. The previously determined short-read sequences were complemented by long-read sequencing in this study. The comparative structural analysis of the GIs used a variety of bioinformatic tools.

RESULTS

Thirty different GIs with blaVIM integrons were identified in the 32 isolates, of which 24 GIs from 26 isolates were integrative and conjugative elements (ICEs) of the clc family. These in turn were dominated by 21 variants of the GI2/ICE6441 subfamily with a total of 19 VIM integrons, each inserted in the same position within the ICE's Tn21-like transposon Tn4380. The three other ICEs formed a novel ICE6705 subfamily, lacking Tn4380 and having different VIM integrons located in another site of the elements. The remaining six non-ICE GIs represented miscellaneous structures. The presence of various integrons in the same ICE sublineage, and of the same integron in different GIs, indicated circulation and recombination of the integron-carrying genetic platforms across Pseudomonas species/genotypes.

CONCLUSIONS

Despite the general diversity of the blaVIM-carrying GIs in Pseudomonas spp. in Poland, a clear predominance of broadly spread and rapidly evolving clc-type ICEs was documented, confirming their significant role in antimicrobial resistance epidemiology.

The type III secretion system facilitates systemic infections of Pseudomonas aeruginosa in the clinic

IMPORTANCE

The identification of decisive virulence-associated genes in highly pathogenic P. aeruginosa isolates in the clinic is essential for diagnosis and the start of appropriate treatment. Over the past decades, P. aeruginosa ST463 has spread rapidly in East China and is highly resistant to β-lactams. Given the poor clinical outcome caused by this phenotype, detailed information regarding its decisive virulence genes and factors affecting virulence expression needs to be deciphered. Here, we demonstrate that the T3SS effector ExoU has toxic effects on mammalian cells and is required for virulence in the murine bloodstream infection model. Moreover, a functional downstream SpcU is required for ExoU secretion and cytotoxicity. This work highlights the potential role of ExoU in the pathogenesis of disease and provides a new perspective for further research on the development of new antimicrobials with antivirulence ability.

Identification of cpxS mutational resistome in Pseudomonas aeruginosa

Pseudomonas aeruginosa easily produces drug-resistant mutants. A large number of mutational resistome genes exist in the genome of P. aeruginosa. In this study, whole genome sequencing analysis of a multidrug-resistant P. aeruginosa strain isolated by in vitro antibiotic treatment showed a mutation in the cpxS gene. Random mutagenesis of cpxS was conducted and introduced into the PA14ΔcpxS strain. Numerous CpxS mutants, including 14 different single amino acid substitutions, were identified, which led to reduced antibiotic susceptibility. Moreover, some of them were also present in the published genomes of P. aeruginosa isolates. Around cpxS, a gene coding for a putative sensor kinase, the nearest gene coding for a response regulator is cpxR in the genome of P. aeruginosa. Deletion of cpxR restored antibiotic susceptibility in the above cpxS mutant strains. As an extension of our previous work, where the expression of the mexAB-oprM operon is directly activated by CpxR in P. aeruginosa, in this study, we showed that the expression of the mexA promoter was increased in the above cpxS mutant strains in a cpxR-dependent manner, and mexA is prerequisite for the reduced antibiotic susceptibility. Therefore, we propose that the putative sensor kinase CpxS, together with CpxR, comprises a two-component regulatory system regulating the expression of the mexAB-oprM operon in P. aeruginosa. Our work indicates that cpxS, as a novel member of mutational resistome, plays important roles on the development of multidrug resistance in P. aeruginosa.

Prioritization of Critical Factors for Surveillance of the Dissemination of Antibiotic Resistance in Pseudomonas aeruginosa: A Systematic Review

Pseudomonas aeruginosa is the primary opportunistic human pathogen responsible for a range of acute and chronic infections; it poses a significant threat to immunocompromised patients and is the leading cause of morbidity and mortality for nosocomial infections. Its high resistance to a diverse array of antimicrobial agents presents an urgent health concern. Among the mechanisms contributing to resistance in P. aeruginosa, the horizontal acquisition of antibiotic resistance genes (ARGs) via mobile genetic elements (MGEs) has gained recognition as a substantial concern in clinical settings, thus indicating that a comprehensive understanding of ARG dissemination within the species is strongly required for surveillance. Here, two approaches, including a systematic literature analysis and a genome database survey, were employed to gain insights into ARG dissemination. The genome database enabled scrutinizing of all the available sequence information and various attributes of P. aeruginosa isolates, thus providing an extensive understanding of ARG dissemination within the species. By integrating both approaches, with a primary focus on the genome database survey, mobile ARGs that were linked or correlated with MGEs, important sequence types (STs) carrying diverse ARGs, and MGEs responsible for ARG dissemination were identified as critical factors requiring strict surveillance. Although human isolates play a primary role in dissemination, the importance of animal and environmental isolates has also been suggested. In this study, 25 critical mobile ARGs, 45 critical STs, and associated MGEs involved in ARG dissemination within the species, are suggested as critical factors. Surveillance and management of these prioritized factors across the One Health sectors are essential to mitigate the emergence of multidrug-resistant (MDR) and extensively resistant (XDR) P. aeruginosa in clinical settings.

Abundant diversity of accessory genetic elements and associated antimicrobial resistance genes in pseudomonas aeruginosa isolates from a single Chinese hospital

OBJECTIVES

Pseudomonas aeruginosa has intrinsic antibiotic resistance and the strong ability to acquire additional resistance genes. However, a limited number of investigations provide detailed modular structure dissection and evolutionary analysis of accessory genetic elements (AGEs) and associated resistance genes (ARGs) in P. aeruginosa isolates. The objective of this study is to reveal the prevalence and transmission characteristics of ARGs by epidemiological investigation and bioinformatics analysis of AGEs of P. aeruginosa isolates taken from a Chinese hospital.

METHODS

Draft-genome sequencing was conducted for P. aeruginosa clinical isolates (n = 48) collected from a single Chinese hospital between 2019 and 2021. The clones of P. aeruginosa isolates, type 3 secretion system (T3SS)-related virulotypes, and the resistance spectrum were identified using multilocus sequence typing (MLST), polymerase chain reaction (PCR), and antimicrobial susceptibility tests. In addition, 17 of the 48 isolates were fully sequenced. An extensive modular structure dissection and genetic comparison was applied to AGEs of the 17 sequenced P. aeruginosa isolates.

RESULTS

From the draft-genome sequencing, 13 STs were identified, showing high genetic diversity. BLAST search and PCR detection of T3SS genes (exoT, exoY, exoS, and exoU) revealed that the exoS+/exoU- virulotype dominated. At least 69 kinds of acquired ARGs, involved in resistance to 10 different categories of antimicrobials, were identified in the 48 P. aeruginosa isolates. Detailed genetic dissection and sequence comparisons were applied to 25 AGEs from the 17 isolates, together with five additional prototype AGEs from GenBank. These 30 AGEs were classified into five groups -- integrative and conjugative elements (ICEs), unit transposons, Inc_pPBL16 plasmids, Inc_p60512-IMP plasmids, and Inc_pPA7790 plasmids.

CONCLUSION

This study provides a broad-scale and deeper genomics understanding of P. aeruginosa isolates taken from a single Chinese hospital. The isolates collected are characterized by high genetic diversity, high virulence, and multiple drug resistance. The AGEs in P. aeruginosa chromosomes and plasmids, as important genetic platforms for the spread of ARGs, contribute to enhancing the adaptability of P. aeruginosa in hospital settings.

Molecular Characteristics and Genetic Analysis of Extensively Drug-Resistant Isolates with different Tn3 Mobile Genetic Elements

Extensively drug-resistant (XDR) bacteria are the main caues for causing clinical infectious diseases. Our aim was to distinguish the present molecular epidemiological situation of XDR Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli isolates recovered from local hospitals in Changzhou. Antibiotic susceptibility and phenotypic analysis, multilocus sequence typing and Pulsed Field Gel Electrophoresis were performed to trace these isolates. Resistant phenotype and gene analysis from 29 XDR strains demonstrated that they mainly included TEM, CTX-M-1/2, OXA-48, and KPC products. A. baumannii strains belonged to sequence type (ST) ST224, and carrying the bla_CTX-M-2/TEM gene. The quinolone genes aac(6')-ib-cr and qnrB were carrying only in A. baumannii and E.coli. Three (2.3%) of these strains were found to contain the bla_NDM-1 or bla_NDM-5 gene. A new genotype of K. pneumoniae was found as ST2639. Epidemic characteristics of the XDR clones showed that antibiotic resistance genes distributed unevenly in different wards in Changzhou's local hospitals. With the sequencing of bla_NDM carrying isolates, the plasmids often carrying a highly conservative Tn3-relavent mobile genetic element. The especially coupled insert sequence ISKox3 may be a distinctive resistance gene transfer loci. The genotypic diversity variation of XDRs suggested that tracking and isolating the sources of antibiotic resistance especially MBL-encoding genes such as bla_NDM-will help manage the risk of infection by these XDRs.

Worldwide Dissemination of blaKPC Gene by Novel Mobilization Platforms in Pseudomonas aeruginosa: A Systematic Review

The dissemination of blaKPC-harboring Pseudomonas aeruginosa (KPC-Pa) is considered a serious public health problem. This study provides an overview of the epidemiology of these isolates to try to elucidate novel mobilization platforms that could contribute to their worldwide spread. A systematic review in PubMed and EMBASE was performed to find articles published up to June 2022. In addition, a search algorithm using NCBI databases was developed to identify sequences that contain possible mobilization platforms. After that, the sequences were filtered and pair-aligned to describe the blaKPC genetic environment. We found 691 KPC-Pa isolates belonging to 41 different sequence types and recovered from 14 countries. Although the blaKPC gene is still mobilized by the transposon Tn4401, the non-Tn4401 elements (NTEKPC) were the most frequent. Our analysis allowed us to identify 25 different NTEKPC, mainly belonging to the NTEKPC-I, and a new type (proposed as IVa) was also observed. This is the first systematic review that consolidates information about the behavior of the blaKPC acquisition in P. aeruginosa and the genetic platforms implied in its successful worldwide spread. Our results show high NTEKPC prevalence in P. aeruginosa and an accelerated dynamic of unrelated clones. All information collected in this review was used to build an interactive online map.

Characterization of an atypical but widespread type IV secretion system for transfer of the integrative and conjugative element (ICEclc) in Pseudomonas putida

Conjugation of DNA relies on multicomponent protein complexes bridging two bacterial cytoplasmic compartments. Whereas plasmid conjugation systems have been well documented, those of integrative and conjugative elements (ICEs) have remained poorly studied. We characterize here the conjugation system of the ICEclc element in Pseudomonas putida UWC1 that is a model for a widely distributed family of ICEs. By in frame deletion and complementation, we show the importance on ICE transfer of 22 genes in a 20-kb conserved ICE region. Protein comparisons recognized seven homologs to plasmid type IV secretion system components, another six homologs to frequent accessory proteins, and the rest without detectable counterparts. Stationary phase imaging of P. putida ICEclc with in-frame fluorescent protein fusions to predicted type IV components showed transfer-competent cell subpopulations with multiple fluorescent foci, largely overlapping in dual-labeled subcomponents, which is suggestive for multiple conjugation complexes per cell. Cross-dependencies between subcomponents in ICE-type IV secretion system assembly were revealed by quantitative foci image analysis in a variety of ICEclc mutant backgrounds. In conclusion, the ICEclc family presents an evolutionary distinct type IV conjugative system with transfer competent cells specialized in efficient transfer.

Genomic Analysis of Carbapenem-Resistant Comamonas in Water Matrices: Implications for Public Health and Wastewater Treatments

Comamonas spp. are Gram-negative bacteria that catabolize a wide range of organic and inorganic substrates. Comamonas spp. are abundant in aquatic and soil environments, including wastewater, and can cause opportunistic infections in humans. Because of their potential in wastewater bioaugmentation and bioremediation strategies, the identification of Comamonas species harboring genes encoding carbapenemases and other clinically important antibiotic resistance genes warrant further investigation. Here, we present an analysis of 39 whole-genome sequences comprising three Comamonas species from aquatic environments in South Australia that were recovered on media supplemented with carbapenems. The analysis includes a detailed description of 33 Comamonas denitrificans isolates, some of which carried chromosomally acquired bla_GES-5, bla_OXA, and aminoglycoside resistance (aadA) genes located on putative genomic islands (GIs). All bla_GES-5- and bla_OXA-containing GIs appear to be unique to this Australian collection of C. denitrificans. Notably, most open reading frames (ORFs) within the GIs, including all antimicrobial resistance (AMR) genes, had adjacent attC sites, indicating that these ORFs are mobile gene cassettes. One C. denitrificans isolate carried an IncP-1 plasmid with genes involved in xenobiotic degradation and response to oxidative stress. Our assessment of the sequences highlights the very distant nature of C. denitrificans to the other Comamonas species and its apparent disposition to acquire antimicrobial resistance genes on putative genomic islands. IMPORTANCE Antimicrobial resistance (AMR) poses a global public health threat, and the increase in resistance to "last-resort drugs," such as carbapenems, is alarming. Wastewater has been flagged as a hot spot for AMR evolution. Comamonas spp. are among the most common bacteria in wastewater and play a role in its bioaugmentation. While the ability of Comamonas species to catabolize a wide range of organic and inorganic substrates is well documented, some species are also opportunistic pathogens. However, data regarding AMR in Comamonas spp. are limited. Here, through the genomic analyses of 39 carbapenem-resistant Comamonas isolates, we make several key observations, including the identification of a subset of C. denitrificans isolates that harbored genomic islands encoding carbapenemase bla_GES-5 or extended-spectrum β-lactamase bla_OXA alleles. Given the importance of Comamonas species in potential wastewater bioaugmentation and bioremediation strategies, as well as their status as emerging pathogens, the acquisition of critically important antibiotic resistance genes on genomic islands warrants future monitoring.

Carbapenem Resistance Determinants Acquired through Novel Chromosomal Integrations in Extensively Drug-Resistant Pseudomonas aeruginosa

Two novel bla_DIM-1- or bla_IMP-1-containing genomic islands (GIs) were discovered by whole-genome sequence analyses in four extensively drug-resistant (XDR) Pseudomonas aeruginosa isolates from inpatients at a tertiary hospital in Ghana. The strains were of sequence type 234 (ST234) and formed a phylogenetic clade together with ST111, which is recognized as a global high-risk clone. Their carbapenem resistance was encoded by two Tn402-type integrons, In1592 (bla_DIM-1) and In1595 (bla_IMP-1), both carrying complete tni mobilization modules. In1595 was bound by conserved 25-bp inverted repeats (IRs) flanked by 5-bp direct repeats (DRs) associated with target site duplication. The integrons were embedded in two GIs that contained cognate integrases and were distinguished by a lower GC content than the chromosomal average. PAGI-97A (52.659 bp; In1592), which encoded a P4-type site-specific integrase of the tyrosine recombinase family in its 3′ border, was integrated into tRNA-Pro(ggg) and bracketed by a 49-bp perfect DR created by 3′-end target duplication. GIs with the same structural features, but diverse genetic content, were identified in 41/226 completed P. aeruginosa genomes. PAGI-97B (22,636 bp; In1595), which encoded an XerC/D superfamily integrase in its 5′ border, was inserted into the small RNA (sRNA) PrrF1/PrrF2 locus. Specific insertions into this highly conserved locus involved in iron-dependent regulation, all leaving PrrF1 intact, were identified in an additional six phylogenetically unrelated P. aeruginosa genomes. Our molecular analyses unveiled a hospital-associated clonal dissemination of carbapenem-resistant ST234 P. aeruginosa in which the XDR phenotype resulted from novel insertions of two GIs into specific chromosomal sites.

Novel Chromosome-Borne Accessory Genetic Elements Carrying Multiple Antibiotic Resistance Genes in Pseudomonas aeruginosa

Pseudomonas aeruginosa is noted for its intrinsic antibiotic resistance and capacity of acquiring additional resistance genes. In this study, the genomes of nine clinical P. aeruginosa isolates were fully sequenced. An extensive genetic comparison was applied to 18 P. aeruginosa accessory genetic elements (AGEs; 13 of them were sequenced in this study and located within P. aeruginosa chromosomes) that were divided into four groups: five related integrative and conjugative elements (ICEs), four related integrative and mobilizable elements (IMEs), five related unit transposons, and two related IMEs and their two derivatives. At least 45 resistance genes, involved in resistance to 10 different categories of antibiotics and heavy metals, were identified from these 18 AGEs. A total of 10 β-lactamase genes were identified from 10 AGEs sequenced herein, and nine of them were captured within class 1 integrons, which were further integrated into ICEs and IMEs with intercellular mobility, and also unit transposons with intracellular mobility. Through this study, we identified for the first time 20 novel MGEs, including four ICEs Tn6584, Tn6585, Tn6586, and Tn6587; three IMEs Tn6853, Tn6854, and Tn6878; five unit transposons Tn6846, Tn6847, Tn6848, Tn6849, and Tn6883; and eight integrons In1795, In1778, In1820, In1784, In1775, In1774, In1789, and In1799. This was also the first report of two resistance gene variants bla_CARB-53 and catB3s, and a novel ST3405 isolate of P. aeruginosa. The data presented here denoted that complex transposition and homologous recombination promoted the assembly and integration of AGEs with mosaic structures into P. aeruginosa chromosomes.

Mobile Carbapenemase Genes in Pseudomonas aeruginosa

Carbapenem-resistant Pseudomonas aeruginosa is one of the major concerns in clinical settings impelling a great challenge to antimicrobial therapy for patients with infections caused by the pathogen. While membrane permeability, together with derepression of the intrinsic beta-lactamase gene, is the global prevailing mechanism of carbapenem resistance in P. aeruginosa, the acquired genes for carbapenemases need special attention because horizontal gene transfer through mobile genetic elements, such as integrons, transposons, plasmids, and integrative and conjugative elements, could accelerate the dissemination of the carbapenem-resistant P. aeruginosa. This review aimed to illustrate epidemiologically the carbapenem resistance in P. aeruginosa, including the resistance rates worldwide and the carbapenemase-encoding genes along with the mobile genetic elements responsible for the horizontal dissemination of the drug resistance determinants. Moreover, the modular mobile elements including the carbapenemase-encoding gene, also known as the P. aeruginosa resistance islands, are scrutinized mostly for their structures.

Novel Molecular Markers Linked to Pseudomonas aeruginosa Epidemic High-Risk Clones

The population structure of Pseudomonas aeruginosa is panmictic-epidemic in nature, with the prevalence of some high-risk clones. These clones are often linked to virulence, antibiotic resistance, and more morbidity. The clonal success of these lineages has been linked to acquisition and spread of mobile genetic elements. The main aim of the study was to explore other molecular markers that explain their global success. A comprehensive set of 528 completely sequenced P. aeruginosa genomes was analyzed. The population structure was examined using Multilocus Sequence Typing (MLST). Strain relationships analysis and diversity analysis were performed using the geoBURST Full Minimum Spanning Tree (MST) algorithm and hierarchical clustering. A phylogenetic tree was constructed using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm. A panel of previously investigated resistance markers were examined for their link to high-risk clones. A novel panel of molecular markers has been identified in relation to risky clones including armR, ampR, nalC, nalD, mexZ, mexS, gyrAT83I, gyrAD87N, nalCE153Q, nalCS46A, parCS87W, parCS87L, ampRG283E, ampRM288R, pmrALeu71Arg, pmrBGly423Cys, nuoGA890T, pstBE89Q, phoQY85F, arnAA170T, arnDG206C, and gidBE186A. In addition to mobile genetic elements, chromosomal variants in membrane proteins and efflux pump regulators can play an important role in the success of high-risk clones. Finding risk-associated markers during molecular surveillance necessitates applying more infection-control precautions.

Tn6603, a Carrier of Tn5053 Family Transposons, Occurs in the Chromosome and in a Genomic Island of Pseudomonas aeruginosa Clinical Strains

Transposons of the Pseudomonasaeruginosa accessory gene pool contribute to phenotype and to genome plasticity. We studied local P. aeruginosa strains to ascertain the encroachment of mer-type res site hunter transposons into clinical settings and their associations with other functional modules. Five different Tn5053 family transposons were detected, all chromosomal. Some were solitary elements; one was in res of Tn1013^#, a relative of a reported carrier of int-type res site hunters (class 1 integrons), but most were in res of Tn6603, a new Tn501-related transposon of unknown phenotype. Most of the Tn6603::Tn elements, and some Tn6603 and Tn6603::Tn elements found in GenBank sequences, were at identical sites in an hypothetical gene of P. aeruginosa genomic island PAGI-5v. The island in clonally differing strains was at either of two tRNA^Lys loci, suggesting lateral transfer to these sites. This observation is consistent with the membership of the prototype PAGI-5 island to the ICE family of mobile genetic elements. Additionally, the res site hunters in the nested transposons occupied different positions in the Tn6603 carrier. This suggested independent insertion events on five occasions at least. Tn5053 family members that were mer-/tni-defective were found in Tn6603- and Tn501-like carriers in GenBank sequences of non-clinical Pseudomonas spp. The transposition events in these cases presumably utilized tni functions in trans, as can occur with class 1 integrons. We suggest that in the clinical context, P. aeruginosa strains that carry Tn6603 alone or in PAGI-5v can serve to disseminate functional res site hunters; these in turn can provide the requisite trans-acting tni functions to assist in the dissemination of class 1 integrons, and hence of their associated antibiotic resistance determinants.

Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235

Genotyping of 2,882 Pseudomonas aeruginosa isolates that had been collected during the last 40 years identified the ExoU-positive lineages PA14 (ST253) and ST235 as the second and third most frequent clones in the P. aeruginosa population. Both clones were approximately 2-fold more frequently detected in animate habitats than in soil or aquatic habitats. While ST253 clone isolates were causing mainly acute and chronic infections in humans, ST235 isolates had been preferentially collected from hospitalized patients with severe acute infections, particularly, keratitis, urinary tract infections, burn wounds, and ventilator-associated pneumonia. The two major exoU clones differed substantially in the composition and flexibility of the accessory genome and by more than 8,000 amino acid sequences. Pronounced sequence variation between orthologs was noted in genes encoding elements of secretion systems and secreted effector molecules, including the type III secretion system, indicating the modes of action of the different clones. When comparing representatives of the two clones in batch culture, the PA14 strain orchestrated the quorum sensing circuitry for the expression of pathogenic traits and stopped growing in batch culture when it entered the stationary phase, but the quorum sensing-deficient ST235 strain expressed high type III secretion activity and continued to grow and to divide. In summary, unrestricted growth, high constitutive type III secretion activity, and facilitated uptake of foreign DNA could be major features that have made ST235 a global high-risk clone associated with poor outcomes of acute nosocomial infections.IMPORTANCE The ubiquitous and metabolically versatile environmental bacterium Pseudomonas aeruginosa can cause infections in a wide variety of hosts, including insects, plants, animals, and humans. P. aeruginosa is one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens that are the major cause of nosocomial infections in the United States and are a threat all over the world because of their capacity to become increasingly resistant to all available antibiotics. Most experimental work on P. aeruginosa has been performed with reference strains PAO1 and PA14, providing deep insight into key metabolic and regulatory pathways thought to be applicable to all P. aeruginosa strains. However, this comparative study on the two most common exoU-positive clones taught us that there are major lineages in the population such as the global high-risk clone ST235 that exhibit uncommon traits of lifestyle, genome mobility, and pathogenicity distinct from those in our knowledge gained from the studies with the reference strains.

The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution

Mobile genetic elements (MGEs), such as plasmids and integrative and conjugative elements (ICEs), are main drivers for the spread of antibiotic resistance (AR). Coevolution between bacteria and plasmids shapes the transfer and stability of plasmids across bacteria. Although ICEs outnumber conjugative plasmids, the dynamics of ICE-bacterium coevolution, ICE transfer rates, and fitness costs are as yet largely unexplored. Conjugative plasmids and ICEs are both transferred by type IV secretion systems, but ICEs are typically immune to segregational loss, suggesting that the evolution of ICE-bacterium associations varies from that of plasmid-bacterium associations. Considering the high abundance of ICEs among bacteria, ICE-bacterium dynamics represent a promising challenge for future research that will enhance our understanding of AR spread in human pathogens.

Molecular Characteristics of GES-Type Carbapenemase-Producing Pseudomonas aeruginosa Clinical Isolates from Long-Term Care Facilities and General Hospitals in South Korea

Since carbapenems have been used for the treatment of infections in medical settings, multidrug-resistant Pseudomonas aeruginosa containing resistance for carbapenems has become a major cause of nosocomial infections worldwide. Information on carbapenemase-producing P. aeruginosa isolates at community hospitals, including long-term care facilities and general hospitals, has rarely been reported in South Korea. The aims of this study were to describe the characteristics of seven carbapenemase-producing P. aeruginosa isolates recovered from two long-term care facilities in South Korea. The carbapenemase genes were identified by PCR and sequencing. Strain typing was assessed by pulsed field gel electrophoresis and multilocus sequence typing (MLST) analysis. Isolates with a genomic island and class I integron surrounding bla_GES-type were confirmed by the PCR mapping method. Of seven GES-type carbapenemase-producing P. aeruginosa isolates, the bla_GES-24 gene was detected in six isolates, and the bla_GES-5 gene was detected in one isolate. The epidemiological relatedness of the seven isolates carrying bla_GES-24 and bla_GES-5 showed >81% similarity. Five isolates carrying bla_GES-24 were sequence type 155 (ST155) by MLST, followed by one ST244 isolate carrying bla_GES-24 and one ST308 isolate carrying bla_GES-5. bla_GES-type genes were embedded in two different class I integrons in a genomic island-15-like region. Our results indicate the possible spread of carbapenemase-producing P. aeruginosa and present a current threat of antimicrobial resistance in community hospitals.

Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands

Riemerella anatipestifer is a gram-negative bacterium that leads to severe contagious septicemia in ducks, turkeys, chickens, and wild waterfowl. Here, a pan-genome with 32 R. anatipestifer genomes is re-established, and the mathematical model is calculated to evaluate the expansion of R. anatipestifer genomes, which were determined to be open. Average nucleotide identity (ANI) and phylogenetic analysis preliminarily clarify intraspecies variation and distance. Comparative genomic analysis of R. anatipestifer found that horizontal gene transfer events, which provide an expressway for the recruitment of novel functionalities and facilitate genetic diversity in microbial genomes, play a key role in the process of acquiring and transmitting antibiotic-resistance genes in R. anatipestifer. Furthermore, a new antibiotic-resistance gene cluster was identified in the same loci in 14 genomes. The uneven distribution of virulence factors was also confirmed by our results. Our study suggests that the ability to acquire foreign genes (such as antibiotic-resistance genes) increases the adaptability of R. anatipestifer, and the virulence genes with little mobility are highly conserved in R. anatipestifer.

Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution

Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.

Identification of a Novel Plasmid Lineage Associated With the Dissemination of Metallo-β-Lactamase Genes Among Pseudomonads

Acquisition of metallo-β-lactamases (MBLs) represents one of most relevant resistance mechanisms to all β-lactams, including carbapenems, ceftolozane and available β-lactamase inhibitors, in Pseudomonas spp. VIM-type enzymes are the most common acquired MBLs in Pseudomonas aeruginosa and, to a lesser extent, in other Pseudomonas species. Little is known about the acquisition dynamics of these determinants, that are usually carried on integrons embedded into chromosomal mobile genetic elements. To date, few MBL-encoding plasmids have been described in Pseudomonas spp., and their diversity and role in the dissemination of these MBLs remains largely unknown. Here we report on the genetic features of the VIM-1-encoding plasmid pMOS94 from P. mosselii AM/94, the earliest known VIM-1-producing strain, and of related elements involved in dissemination of MBL. Results of plasmid DNA sequencing showed that pMOS94 had a modular organization, consisting of backbone modules associated with replication, transfer and antibiotic resistance. Plasmid pMOS94, although not typable according to the PBRT scheme, was classifiable either in MOB_F11 or MPF_T plasmid families. The resistance region included the class I integron In70, carrying bla _{V IM-1}, in turn embedded in a defective Tn402-like transposon. Comparison with pMOS94-like elements led to the identification of a defined plasmid lineage circulating in different Pseudomonas spp. of clinical and environmental origin and spreading different MBL-encoding genes, including bla _IMP-63, bla _BIM, and bla _{V IM}-type determinants. Genetic analysis revealed that this plasmid lineage likely shared a common ancestor and had evolved through the acquisition and recombination of different mobile elements, including the MBL-encoding transposons. Our findings provide new insights about the genetic diversity of MBL-encoding plasmids circulating among Pseudomonas spp., potentially useful for molecular epidemiology purposes, and revealed the existence and persistence of a successful plasmid lineage over a wide spatio-temporal interval, spanning over five different countries among two continents and over 20-years.

Accessory genome of the multi-drug resistant ocular isolate of Pseudomonas aeruginosa PA34

Bacteria can acquire an accessory genome through the horizontal transfer of genetic elements from non-parental lineages. This leads to rapid genetic evolution allowing traits such as antibiotic resistance and virulence to spread through bacterial communities. The study of complete genomes of bacterial strains helps to understand the genomic traits associated with virulence and antibiotic resistance. We aimed to investigate the complete accessory genome of an ocular isolate of Pseudomonas aeruginosa strain PA34. We obtained the complete genome of PA34 utilising genome sequence reads from Illumina and Oxford Nanopore Technology followed by PCR to close any identified gaps. In-depth genomic analysis was performed using various bioinformatics tools. The susceptibility to heavy metals and cytotoxicity was determined to confirm expression of certain traits. The complete genome of PA34 includes a chromosome of 6.8 Mbp and two plasmids of 95.4 Kbp (pMKPA34-1) and 26.8 Kbp (pMKPA34-2). PA34 had a large accessory genome of 1,213 genes and had 543 unique genes not present in other strains. These exclusive genes encoded features related to metal and antibiotic resistance, phage integrase and transposons. At least 24 genomic islands (GIs) were predicated in the complete chromosome, of which two were integrated into novel sites. Eleven GIs carried virulence factors or replaced pathogenic genes. A bacteriophage carried the aminoglycoside resistance gene (AAC(3)-IId). The two plasmids carried other six antibiotic resistance genes. The large accessory genome of this ocular isolate plays a large role in shaping its virulence and antibiotic resistance.

Genome plasticity favours double chromosomal Tn4401b-blaKPC-2 transposon insertion in the Pseudomonas aeruginosa ST235 clone

BACKGROUND

Pseudomonas aeruginosa Sequence Type 235 is a clone that possesses an extraordinary ability to acquire mobile genetic elements and has been associated with the spread of resistance genes, including genes that encode for carbapenemases. Here, we aim to characterize the genetic platforms involved in resistance dissemination in blaKPC-2-positive P. aeruginosa ST235 in Colombia.

RESULTS

In a prospective surveillance study of infections in adult patients attended in five ICUs in five distant cities in Colombia, 58 isolates of P. aeruginosa were recovered, of which, 27 (46.6%) were resistant to carbapenems. The molecular analysis showed that 6 (22.2%) and 4 (14.8%) isolates harboured the blaVIM and blaKPC-2 genes, respectively. The four blaKPC-2-positive isolates showed a similar PFGE pulsotype and belonged to ST235. Complete genome sequencing of a representative ST235 isolate shows a unique chromosomal contig of 7097.241 bp with eight different resistance genes identified and five transposons: a Tn6162-like with ant(2″)-Ia, two Tn402-like with ant(3″)-Ia and blaOXA-2 and two Tn4401b with blaKPC-2. All transposons were inserted into the genomic islands. Interestingly, the two Tn4401b copies harbouring blaKPC-2 were adjacently inserted into a new genomic island (PAGI-17) with traces of a replicative transposition process. This double insertion was probably driven by several structural changes within the chromosomal region containing PAGI-17 in the ST235 background.

CONCLUSION

This is the first report of a double Tn4401b chromosomal insertion in P. aeruginosa, just within a new genomic island (PAGI-17). This finding indicates once again the great genomic plasticity of this microorganism.

Carbapenemases on the move: it's good to be on ICEs

Background

The evolution and spread of antibiotic resistance is often mediated by mobile genetic elements. Integrative and conjugative elements (ICEs) are the most abundant conjugative elements among prokaryotes. However, the contribution of ICEs to horizontal gene transfer of antibiotic resistance has been largely unexplored.

Results

Here we report that ICEs belonging to mating-pair formation (MPF) classes G and T are highly prevalent among the opportunistic pathogen Pseudomonas aeruginosa, contributing to the spread of carbapenemase-encoding genes (CEGs). Most CEGs of the MPF_G class were encoded within class I integrons, which co-harbour genes conferring resistance to other antibiotics. The majority of the integrons were located within Tn3-like and composite transposons. Conserved attachment site could be predicted for the MPF_G class ICEs. MPF_T class ICEs carried the CEGs within composite transposons which were not associated with integrons.

Conclusions

The data presented here provides a global snapshot of the different CEG-harbouring ICEs and sheds light on the underappreciated contribution of these elements to the evolution and dissemination of antibiotic resistance on P. aeruginosa.

Electronic supplementary material

The online version of this article (10.1186/s13100-018-0141-4) contains supplementary material, which is available to authorized users.

Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites

The large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P. aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P. aeruginosa isolated from two different infection types and countries.

Mobile Genetic Elements Associated with Antimicrobial Resistance

Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.

Unravelling the genome of a Pseudomonas aeruginosa isolate belonging to the high-risk clone ST235 reveals an integrative conjugative element housing a blaGES-6 carbapenemase

Objectives

In Pseudomonas aeruginosa, the blaGES-6 carbapenemase gene was previously associated with an In1076 class I integron. Here, we conducted a genome-based analysis and explored the genetic platform associated with the mobility of this gene.

Methods

WGS of a blaGES-6-harbouring P. aeruginosa isolate (FFUP_PS_690) was performed with Illumina HiSeq, de novo assembly was performed using SPAdes and subsequent bioinformatic analysis was performed concerning antibiotic resistance genes, virulence features and mobile genetic elements.

Results

The FFUP_PS_690 isolate belongs to the ST235 high-risk clone and houses a novel integrative conjugative element (ICE), hereby named ICEPae690. This clc-like ICE comprises the blaGES-6-harbouring In1076 integron and specific modules. An ExoU island A variant was also identified.

Conclusions

The presence of a 'hitch-hiking' blaGES-6-harbouring In1076 integron in an ICE and an exoU-carrying genomic island highlight the potential spread of these elements through conjugation and/or clonal expansion of the ST235 lineage.

The Integrative Conjugative Element clc (ICEclc) of Pseudomonas aeruginosa JB2

Integrative conjugative elements (ICE) are a diverse group of chromosomally integrated, self-transmissible mobile genetic elements (MGE) that are active in shaping the functions of bacteria and bacterial communities. Each type of ICE carries a characteristic set of core genes encoding functions essential for maintenance and self-transmission, and cargo genes that endow on hosts phenotypes beneficial for niche adaptation. An important area to which ICE can contribute beneficial functions is the biodegradation of xenobiotic compounds. In the biodegradation realm, the best-characterized ICE is ICEclc, which carries cargo genes encoding for ortho-cleavage of chlorocatechols (clc genes) and aminophenol metabolism (amn genes). The element was originally identified in the 3-chlorobenzoate-degrader Pseudomonas knackmussii B13, and the closest relative is a nearly identical element in Burkholderia xenovorans LB400 (designated ICEclc-B13 and ICEclc-LB400, respectively). In the present report, genome sequencing of the o-chlorobenzoate degrader Pseudomonas aeruginosa JB2 was used to identify a new member of the ICEclc family, ICEclc-JB2. The cargo of ICEclc-JB2 differs from that of ICEclc-B13 and ICEclc-LB400 in consisting of a unique combination of genes that encode for the utilization of o-halobenzoates and o-hydroxybenzoate as growth substrates (ohb genes and hyb genes, respectively) and which are duplicated in a tandem repeat. Also, ICEclc-JB2 lacks an operon of regulatory genes (tciR-marR-mfsR) that is present in the other two ICEclc, and which controls excision from the host. Thus, the mechanisms regulating intracellular behavior of ICEclc-JB2 may differ from that of its close relatives. The entire tandem repeat in ICEclc-JB2 can excise independently from the element in a process apparently involving transposases/insertion sequence associated with the repeats. Excision of the repeats removes important niche adaptation genes from ICEclc-JB2, rendering it less beneficial to the host. However, the reduced version of ICEclc-JB2 could now acquire new genes that might be beneficial to a future host and, consequently, to the survival of ICEclc-JB2. Collectively, the present identification and characterization of ICEclc-JB2 provides insights into roles of MGE in bacterial niche adaptation and the evolution of catabolic pathways for biodegradation of xenobiotic compounds.

Correlation between phenotypic antibiotic susceptibility and the resistome in Pseudomonas aeruginosa

Genetic determinants of antibiotic resistance (AR) have been extensively investigated. High-throughput sequencing allows for the assessment of the relationship between genotype and phenotype. A panel of 672 Pseudomonas aeruginosa strains was analysed, including representatives of globally disseminated multidrug-resistant and extensively drug-resistant clones; genomes and multiple antibiograms were available. This panel was annotated for AR gene presence and polymorphism, defining a resistome in which integrons were included. Integrons were present in >70 distinct cassettes, with In5 being the most prevalent. Some cassettes closely associated with clonal complexes, whereas others spread across the phylogenetic diversity, highlighting the importance of horizontal transfer. A resistome-wide association study (RWAS) was performed for clinically relevant antibiotics by correlating the variability in minimum inhibitory concentration (MIC) values with resistome data. Resistome annotation identified 147 loci associated with AR. These loci consisted mainly of acquired genomic elements and intrinsic genes. The RWAS allowed for correct identification of resistance mechanisms for meropenem, amikacin, levofloxacin and cefepime, and added 46 novel mutations. Among these, 29 were variants of the oprD gene associated with variation in meropenem MIC. Using genomic and MIC data, phenotypic AR was successfully correlated with molecular determinants at the whole-genome sequence level.

Clonal Dissemination of Pseudomonas aeruginosa Sequence Type 235 Isolates Carrying blaIMP-6 and Emergence of blaGES-24 and blaIMP-10 on Novel Genomic Islands PAGI-15 and -16 in South Korea

A total of 431 Pseudomonas aeruginosa clinical isolates were collected from 29 general hospitals in South Korea in 2015. Antimicrobial susceptibility was tested by the disk diffusion method, and MICs of carbapenems were determined by the agar dilution method. Carbapenemase genes were amplified by PCR and sequenced, and the structures of class 1 integrons surrounding the carbapenemase gene cassettes were analyzed by PCR mapping. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were performed for strain typing. Whole-genome sequencing was carried out to analyze P. aeruginosa genomic islands (PAGIs) carrying the bla_IMP-6, bla_IMP-10, and bla_GES-24 genes. The rates of carbapenem-nonsusceptible and carbapenemase-producing P. aeruginosa isolates were 34.3% (148/431) and 9.5% (41/431), respectively. IMP-6 was the most prevalent carbapenemase type, followed by VIM-2, IMP-10, and GES-24. All carbapenemase genes were located on class 1 integrons of 6 different types on the chromosome. All isolates harboring carbapenemase genes exhibited genetic relatedness by PFGE (similarity > 80%); moreover, all isolates were identified as sequence type 235 (ST235), with the exception of two ST244 isolates by MLST. The bla_IMP-6, bla_IMP-10, and bla_GES-24 genes were found to be located on two novel PAGIs, designated PAGI-15 and PAGI-16. Our data support the clonal spread of an IMP-6-producing P. aeruginosa ST235 strain, and the emergence of IMP-10 and GES-24 demonstrates the diversification of carbapenemases in P. aeruginosa in Korea.

Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis

Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.