Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae

Insights into incompatible plasmids in multidrug-resistant Raoultella superbugs

The emergence of multidrug-resistant (MDR) Raoultella isolates is linked to the acquisition of antibiotic resistance genes (ARGs) with plasmids playing a pivotal role in this process. While plasmid-mediated transmission of ARGs in Raoultella has been extensively reported, limited attention has been given to genetically dissecting the modular structures of plasmids. This study aims to elucidate the genomic features of novel incompatible plasmids in MDR Raoultella by presenting 13 complete plasmid sequences from four isolates, along with an analysis of 16 related plasmids from GenBank. These 29 plasmids were classified into five distinct groups: IncFII single-replicon plasmids, dual-replicon plasmids containing the IncFII replicon, IncHI plasmids, IncR plasmids, and IncX8 plasmids. A new incompatible group, IncFIIp23141-CTXM, was identified, alongside five newly designated Inc groups based on previously determined sequences, namely IncFIIpKPC2_EC14653, IncFIIpCP020359, IncFIIpCP024509, IncFIIpKOX-137, and IncFIIpKDO1. Furthermore, this research marks the first report of four Inc groups of plasmids within Raoultella, namely IncFIIp23141-CTXM plasmid, IncFIIpKPC2_EC14653 plasmid, IncX8 plasmid, and IncFIIpCP020359: IncFIB-7.1 dual-replicon plasmid. Moreover, novel mobile genetic elements, including two unit transposons (Tn6806 and Tn6891), one IS-based transposition unit (Tn6561), and four insertion sequences (ISRor6, ISRor7, ISRor8, and ISRor9) were discovered. Notably, this is the first report of mcr-9 in clinical Raoultella strains. At least 49 ARGs conferring resistance against 11 different categories of antimicrobials were identified on these 13 plasmids. Overall, this research deepens the understanding of incompatible plasmids in Raoultella, serving as a reference for exploring antibiotic resistance profiles and plasmid diversity in MDR Raoultella.

Genomic analysis of IMP-8-producing Enterobacter hormaechei with a novel plasmid pK432-IMP

BACKGROUND

Carbapenem-resistant Enterobacter cloacae (CR-ECC) complex has posed significant challenges to the clinical treatment of infections, and Enterobacter hormaechei (E. hormaechei) is the most commonly identified nosocomial pathogen of CR-ECC.

METHODS

Carbapenemases were detected by the immunocolloidal gold technique. The minimum inhibitory concentration (MIC) values were determined by VITEK2. The genome sequence of strain K432 was obtained and analysed.

RESULTS

We isolated the IMP-8-producing E. hormaechei strain K432 from a patient's urine specimen in a Chinese hospital, which exhibited resistance to multiple antibiotics, including ceftazidime, piperacillin/tazobactam, aztreonam, imipenem, meropenem, ciprofloxacin, levofloxacin, minocycline, and trimethoprim/sulfamethoxazole. The genome of strain K432 was composed of the chromosome cK432 (4863 kb) and 3 plasmids: pK432-IMP (45.8 kb), pK432-TEM (75.6 kb), and pK432-NR (4.8 kb). In K432, six drug-resistant genes were detected, including blaACT-7 and fosA on cK432, blaIMP-8, and qnrS1 on pK432-IMP, blaSFO-1, and blaTEM-1 on pK432-TEM. The pK432-IMP belonged to a novel incompatibility group, and pK432-TEM was an incompatibility (Inc) R plasmid. Both of these two plasmids shared similar conserved backbone regions with their reference plasmids, respectively. However, the single accessory regions in these two plasmids were different from their reference plasmids, indicating that new recombination and integration events had occurred in K432.

CONCLUSIONS

This study provides a comprehensive understanding of the genomic characterization of K432 and identified a novel plasmid for IMP transmission. Further investigation and surveillance are warranted for pK432-IMP-type plasmid. While routine monitoring of MDR E. hormaechei strains is necessary in China.

Replicon-Based Typing About IncG Plasmids and Molecular Characterization of Five IncG Plasmids Carrying Carbapenem Resistance Gene bla KPC-2

Purpose

To investigate the genetic diversity of IncG plasmids, we have proposed a typing scheme based on replicon repA and performed comparative genomic analysis of five IncG plasmids from China.

Methods

p30860-KPC, p116965-KPC, pA1705-KPC, pA1706-KPC and pNY5520-KPC total in five IncG plasmids from clinical isolates of Pseudomonas and Enterobacteriaceae, respectively, were fully sequenced and were compared with the previously collected reference plasmid p10265-KPC.

Results

Based on phylogeny, IncG-type plasmids are divided into IncG-I to IncG-VIII, the five plasmids belong to IncG-VIII. A detailed sequence comparison was then presented that the IncG plasmid involved accessory region I (Tn5563a/b/c/d/e), accessory region II (ISpa19), and accessory region III (bla KPC-2-region). Expect for the pNY5520-KPC, the rest of the plasmids had the same backbone structure as the reference one. Within the plasmids, insertion sequences Tn5563d and Tn5563e were identified, a novel unknown insertion region was found in Tn5563b/c/d/e. In addition, Tn6376b and Tn6376c were newly designated in the study.

Conclusion

The data presented here including a typing scheme and detailed genetic comparison which provide an insight into the diversification and evolution history of IncG plasmids.

Genetic Characteristics of Novel IncpSE5381-aadB Plasmids, Integrative and Mobilizable Elements, and Integrative and Conjugative Elements in Pseudomonas aeruginosa

Purpose

Pseudomonas aeruginosa is a common causative bacteria in nosocomial infections. This study aims to describe the structure and evolutionary characteristics of mobile genetic elements (MGEs) carrying antibiotic resistance genes (ARGs) from P. aeruginosa and to conduct bioinformatics and comparative genomic analysis to provide a deeper understanding of the genetic characteristics and diversity of MGEs in P. aeruginosa.

Methods

Fifteen clinical isolates of P. aeruginosa from China were collected and sequenced in this study, and 15 novel MGEs were identified. Together with four MGEs from GenBank, a total of 19 MGEs were used to perform detailed modular structure dissection and sequence comparison. Then, the biological experiments were carried out to verify the biological characteristics of these isolates and MEGs.

Results

The novel MGEs identified in this study displayed diversification in modular structures, which showed complex mosaic natures. The seven types of 19 MGEs included in this study were divided into three groups: i) novel MGEs (firstly identified in this study): four IncpSE5381-aadB plasmids and three Tn7495-related integrative and mobilizable elements (IMEs); ii) newly defined MGEs (firstly designated in this study, but with previously determined sequences): four Tn7665-related IMEs; iii) novel transposons with reference prototypes identified in this study: two Tn6417-related integrative and conjugative elements (ICEs), two IS-based transposition units, two Tn501-related unit transposons, two Tn1403-related unit transposons. At least 36 ARGs involved in resistance to 11 different classes of antimicrobials and heavy metals were identified. Additionally, three novel blaOXA variants were identified. Antimicrobial susceptibility testing showed that these variants were resistant to some β-lactamase antibiotics and blaOXA-1204 was additionally resistant to cephalosporins.

Conclusion

The continuous evolution of ARG-carrying MGEs during transmission, leading to the emergence of novel MGEs or ARGs, which facilitates the spread of antibiotic resistance in P. aeruginosa and enhances the diversity of transmission modes of bacterial resistance.

Uncovering the hidden threat: The widespread presence of chromosome-borne accessory genetic elements and novel antibiotic resistance genetic environments in Aeromonas

The emergence of antibiotic-resistant Aeromonas strains in clinical settings has presented an escalating burden on human and public health. The dissemination of antibiotic resistance in Aeromonas is predominantly facilitated by chromosome-borne accessory genetic elements, although the existing literature on this subject remains limited. Hence, the primary objective of this study is to comprehensively investigate the genomic characteristics of chromosome-borne accessory genetic elements in Aeromonas. Moreover, the study aims to uncover novel genetic environments associated with antibiotic resistance on these elements. Aeromonas were screened from nonduplicated strains collected from two tertiary hospitals in China. Complete sequencing and population genetics analysis were performed. BLAST analysis was employed to identify related elements. All newly identified elements were subjected to detailed sequence annotation, dissection, and comparison. We identified and newly designated 19 chromosomal elements, including 18 integrative and mobilizable elements (IMEs) that could be classified into four categories: Tn6737-related, Tn6836-related, Tn6840-related, and Tn6844a-related IMEs. Each class exhibited a distinct pattern in the types of resistance genes carried by the IMEs. Several novel antibiotic resistance genetic environments were uncovered in these elements. Notably, we report the first identification of the blaOXA-10 gene and blaVEB-1 gene in clinical A. veronii genome, the first presence of a tetA(E)-tetR(E) resistance gene environment within the backbone region in IMEs, and a new mcr-3.15 resistance gene environment. The implications of these findings are substantial, as they provide new insights into the evolution, structure, and dissemination of chromosomal-borne accessory elements.

Genomic epidemiology and heterogeneity of Providencia and their blaNDM-1-carrying plasmids

Providencia as an opportunistic pathogen can cause serious infection, and moreover the emergence of multi-drug-resistant Providencia strains poses a potentially life-threatening risk to public health. However, a comprehensive genomic study to reveal the population structure and dissemination of Providencia is still lacking. In this study, we conducted a genomic epidemiology analysis on the 580 global sequenced Providencia isolates, including 257 ones sequenced in this study (42 ones were fully sequenced). We established a genome sequence-based species classification scheme for Providencia, redefining the conventional 11 Providencia species into seven genocomplexes that were further divided into 18 genospecies, providing an extensively updated reference for Providencia species discrimination based on the largest Providencia genome dataset to date. We then dissected the profile of antimicrobial resistance genes and the prevalence of multi-drug-resistant Providencia strains among these genocomplexes/genospecies, disclosing the presence of diverse and abundant antimicrobial resistance genes and high resistance ratios against multiple classes of drugs in Providencia. We further dissected the genetic basis for the spread of blaNDM-1 in Providencia. blaNDM-1 genes were mainly carried by five incompatible (Inc) groups of plasmids: IncC, IncW, IncpPROV114-NR, IncpCHS4.1-3, and IncpPrY2001, and the last three were newly designated in this study. By tracking the spread of blaNDM-1-carrying plasmids, IncC, IncpPROV114-NR, IncpCHS4.1-3, and IncpPrY2001 plasmids were found to be highly involved in parallel horizontal transfer or vertical clonal expansion of blaNDM-1 among Providencia. Overall, our study provided a comprehensive genomic view of species differentiation, antimicrobial resistance prevalence, and plasmid-mediated blaNDM-1 dissemination in Providencia.

A Wohlfahrtiimonas chitiniclastica with a novel type of blaVEB-1-carrying plasmid isolated from a zebra in China

Background

Wohlfahrtiimonas chitiniclastica is an emerging fly-borne zoonotic pathogen, which causes infections in immunocompromised patients and some animals. Herein, we reported a W. chitiniclastica BM-Y from a dead zebra in China.

Methods

The complete genome sequencing of BM-Y showed that this isolate carried one chromosome and one novel type of blaVEB-1-carrying plasmid. Detailed genetic dissection was applied to this plasmid to display the genetic environment of blaVEB-1.

Results

Three novel insertion sequence (IS) elements, namely ISWoch1, ISWoch2, and ISWoch3, were found in this plasmid. aadB, aacA1, and gcuG were located downstream of blaVEB-1, composing a gene cassette array blaVEB-1-aadB-aacA1-gcuG bracketed by an intact ISWoch1 and a truncated one, which was named the blaVEB-1 region. The 5'-RACE experiments revealed that the transcription start site of the blaVEB-1 region was located in the intact ISWoch1 and this IS provided a strong promoter for the blaVEB-1 region.

Conclusion

The spread of the blaVEB-1-carrying plasmid might enhance the ability of W. chitiniclastica to survive under drug selection pressure and aggravate the difficulty in treating infections caused by blaVEB-1-carrying W. chitiniclastica. To the best of our knowledge, this is the first report of the genetic characterization of a novel blaVEB-1-carrying plasmid with new ISs from W. chitiniclastica.

Characterization of Three Novel IMP Metallo-β-Lactamases, IMP-89, IMP-91, and IMP-96, and Diverse blaIMP-Carrying Accessory Genetic Elements from Chinese Clinical Isolates

Three novel imipenemase (IMP)-type metallo-β-lactamases (MBLs), referred to as IMP-89, IMP-91, and IMP-96, were detected in three clinical isolates from China. Antimicrobial susceptibility tests indicated these novel enzymes were resistant to most β-lactams, and IMP-96 with a Ser262Gly mutation had higher activity against meropenem than its point mutant. We then collected sequence data on all 91 available IMP variants for phylogenetic analysis. To further analyze the genetic environment of blaIMP, an extensive comparison was applied to nine accessory genetic elements (AGEs), including six sequenced blaIMP-carrying AGEs in this study and three others from GenBank. These nine AGEs were divided into three groups: three IncpJBCL41 plasmids, Tn6417 and its two derivatives, and three Tn6879-related integrative and conjugative elements (ICEs). All blaIMP genes in this study were captured by class 1 integrons. In the integrons, blaIMP genes usually coexisted with other resistance genes, which further impeded clinical antibacterial treatment. The emergence of new IMP variants and the diversity and complexity of their genetic environment make the prevention and control of drug-resistant strains critical, requiring serious attention from clinical and public health management departments. IMPORTANCE The spread of IMP-type MBLs has increased dramatically in recent years. We discovered three novel IMP variants from three clinical isolates in China. We summarized the classification and evolutionary relationship of all available IMP variants. Moreover, we detailed the genetic characteristics of blaIMP-carrying accessory genetic elements in five clinical isolates. Given the risk of rapid and extensive spread of blaIMP genes, we suggest that continuous surveillance is crucial to combat the acquisition and transmission of blaIMP genes by bacteria, which can impede clinical therapy effectiveness.

Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis

Although polymerase chain reaction (PCR) amplification and sequencing of the bacterial 16S rDNA region has numerous scientific applications, it does not provide DNA methylation information. Herein, we propose a simple extension for bisulfite sequencing to investigate 5-methylcytosine residues in the bacterial 16S rDNA region from clinical isolates or flora. Multiple displacement amplification without DNA denaturation was used to preferentially pre-amplify single-stranded bacterial DNA after bisulfite conversion. Following the pre-amplification, the 16S rDNA region was analyzed using nested bisulfite PCR and sequencing, enabling the simultaneous identification of DNA methylation status and sequence data. We used this approach (termed sm16S rDNA PCR/sequencing) to identify novel methylation sites and a methyltransferase (M. MmnI) in Morganella morganii and different methylation motifs among Enterococcus faecalis strains from small volumes of clinical specimens. Further, our analysis suggested that M. MmnI may be correlated to erythromycin resistance. Thus, sm16S rDNA PCR/sequencing is a useful extension method for analyzing the DNA methylation of 16S rDNA regions in a microflora, providing additional information not provided by conventional PCR. Given the relationship between DNA methylation status and drug resistance in bacteria, we believe this technique can be effectively applied in clinical sample testing.

Genetic Characterization of Four Groups of Chromosome-Borne Accessory Genetic Elements Carrying Drug Resistance Genes in Providencia

Purpose

The aim of this study was to gain a deeper genomics and bioinformatics understanding of diversification of accessory genetic elements (AGEs) in Providencia.

Methods

Herein, the complete genome sequences of five Providencia isolates from China were determined, and seven AGEs were identified from the chromosomes. Detailed genetic dissection and sequence comparison were applied to these seven AGEs, together with additional 10 chromosomal ones from GenBank (nine of them came from Providencia).

Results

These 17 AGEs were divided into four groups: Tn6512 and its six derivatives, Tn6872 and its two derivatives, Tn6875 and its one derivative, and Tn7 and its four derivatives. These AGEs display high-level diversification in modular structures that had complex mosaic natures, and particularly different multidrug resistance (MDR) regions were presented in these AGEs. At least 52 drug resistance genes, involved in resistance to 15 different categories of antimicrobials and heavy metal, were found in 15 of these 17 AGEs.

Conclusion

Integration of these AGEs into the Providencia chromosomes would contribute to the accumulation and distribution of drug resistance genes and enhance the ability of Providencia isolates to survive under drug selection pressure.

Genomic epidemiology of carbapenemase-producing Klebsiella pneumoniae in china

The rapid spread of carbapenemase-producing Klebsiella pneumoniae (cpKP) poses serious threats to public health, however, the underlying genetic basis for its dissemination is still unknown. We conducted a comprehensive genomic epidemiology analysis on 420 cpKP isolates collected from 70 hospitals in 24 provinces of China during 2009-2017 by short-/long-read sequencing. The results showed that most cpKP isolates were categorized into clonal group 258 (CG258), in which ST11 was the dominant clone. Phylogenetic analysis revealed three major clades including the top one of Clade 3 for CG258 cpKP isolates. Additionally, carbapenemase gene analysis indicated that bla_KPC was dominant in the cpKP isolates, and most bla_KPC genes were located in five major incompatibility (Inc) groups of bla_KPC-harboring plasmids. Importantly, three advantageous combinations of host-bla_KPC-carrying plasmids (Clade 3.1 + 3.2-IncFII_pHN7A8, Clade 3.1 + 3.2-IncFII_pHN7A8:IncR, and Clade 3.3-IncFII_pHN7A8:Inc_pA1763-KPC) were identified to confer cpKP isolates the advantages in both genotypes (strong correlation/co-evolution) and phenotypes (resistance/growth/competition) to facilitate the nationwide spread of ST11/CG258 cpKP. Intriguingly, Bayesian skyline analysis illustrated that the three advantageous combinations might be directly associated with the strong population expansion during 2007-2008 and subsequent maintenance of the population of ST11/CG258 cpKP after 2008. We then examined drug resistance profiles of these cpKP isolates and proposed combination treatment regimens for CG258/non-CG258 cpKP infections. Thus, the findings of our systematical analysis shed light on the molecular epidemiology and genetic basis for the dissemination of ST11/CG258 cpKP in China, and much emphasis should be given to the close monitoring of advantageous cpKP-plasmid combinations.

VIM-encoding IncpSTY plasmids and chromosome-borne integrative and mobilizable elements (IMEs) and integrative and conjugative elements (ICEs) in Pseudomonas

BACKGROUND

The carbapenem-resistance genes bla_VIM are widely disseminated in Pseudomonas, and frequently harbored within class 1 integrons that reside within various mobile genetic elements (MGEs). However, there are few reports on detailed genetic dissection of bla_VIM-carrying MGEs in Pseudomonas.

METHODS

This study presented the complete sequences of five bla_VIM-2/-4-carrying MGEs, including two plasmids, two chromosomal integrative and mobilizable elements (IMEs), and one chromosomal integrative and conjugative element (ICE) from five different Pseudomonas isolates.

RESULTS

The two plasmids were assigned to a novel incompatibility (Inc) group Inc_pSTY, which included only seven available plasmids with determined complete sequences and could be further divided into three subgroups Inc_pSTY-1/2/3. A detailed sequence comparison was then applied to a collection of 15 MGEs belonging to four different groups: three representative Inc_pSTY plasmids, two Tn6916-related IMEs, two Tn6918-related IMEs, and eight Tn6417-related ICEs and ten of these 15 MGEs were first time identified. At least 22 genes involving resistance to seven different categories of antibiotics and heavy metals were identified within these 15 MGEs, and most of these resistance genes were located within the accessory modules integrated as exogenous DNA regions into these MGEs. Especially, eleven of these 15 MGEs carried the bla_VIM genes, which were located within 11 different concise class 1 integrons.

CONCLUSION

These bla_VIM-carrying integrons were further integrated into the above plasmids, IMEs/ICEs with intercellular mobility. These MGEs could transfer between Pseudomonas isolates, which resulted in the accumulation and spread of bla_VIM among Pseudomonas and thus was helpful for the bacteria to survival from the stress of antibiotics. Data presented here provided a deeper insight into the genetic diversification and evolution of VIM-encoding MGEs in Pseudomonas.

IncFIB-4.1 and IncFIB-4.2 Single-Replicon Plasmids: Small Backbones with Large Accessory Regions

Purpose

To establish a typing scheme for IncFIB replicon and to dissect genomic features of IncFIB-4.1/4.2 single-replicon plasmids.

Methods

A total of 146 representative fully sequenced IncFIB-replicon-containing plasmids were selected to construct a phylogenetic tree of repB_IncFIB sequences. A collection of nine IncFIB-4.1/4.2 single-replicon plasmids from China were fully sequenced here and compared with the first sequenced IncFIB-4.1/4.2 single-replicon plasmids from GenBank to dissect their genomic diversity.

Results

In this study, a repB sequence-based scheme was proposed for grouping IncFIB replicon into seven primary types and further into 70 subtypes. A collection of nine IncFIB-4.1/4.2 single-replicon plasmids were fully sequenced here and compared with the first sequenced IncFIB-4.1/4.2 single-replicon plasmids from GenBank. These 11 plasmids had small backbones and shared only three key backbone markers repB together with its iterons, parABC, and stbD. Each plasmid contained one large accessory region (LAR) inserted into the backbone, and these 11 LARs had significantly distinct profiles of mobile genetic elements (MGEs) and resistance/metabolism gene loci. Antibiotic resistance regions (ARRs; the antibiotic resistance gene-containing genetic elements) were found in seven of these 11 LARs. Besides resistance genes, ARRs carried unit or composite transposons, integrons, and putative resistance units. IncFIB-4.1/4.2 single-replicon plasmids were important vectors of drug resistance genes. This was the first report of three novel MGEs: In1776, Tn6755, and Tn6857.

Conclusion

Data presented here provided a deeper insight into diversity and evolution of IncFIB replicon and IncFIB-4.1/4.2 single-replicon plasmids.

A Genomic and Bioinformatics View of the Classification and Evolution of Morganella Species and Their Chromosomal Accessory Genetic Elements Harboring Antimicrobial Resistance Genes

In this study, draft-genome sequencing was conducted for 60 Chinese Morganella isolates, and furthermore, 12 of them were fully sequenced. Then, a total of 166 global sequenced Morganella isolates, including the above 60, were collected to perform average nucleotide identity-based genomic classification and core single nucleotide polymorphism-based phylogenomic analysis. A genome sequence-based species classification scheme for Morganella was established, and accordingly, the two conventional Morganella species were redefined as two complexes and further divided into four and two genospecies, respectively. At least 88 acquired antimicrobial resistance genes (ARGs) were disseminated in these 166 isolates and were prevalent mostly in the isolates from hospital settings. IS26/IS15DI, IS10 and IS1R, and Tn3-, Tn21-, and Tn7-subfamily unit transposons were frequently presented in these 166 isolates. Furthermore, a detailed sequence comparison was applied to 18 Morganella chromosomal accessory genetic elements (AGEs) from the fully sequenced 12 isolates, together with 5 prototype AGEs from GenBank. These 23 AGEs were divided into eight different groups belonging to composite/unit transposons, transposable prophages, integrative and mobilizable elements, and integrative and conjugative elements, and they harbored at least 52 ARGs involved in resistance to 15 categories of antimicrobials. Eleven of these 23 AGEs acquired large accessory modules, which exhibited complex mosaic structures and contained many antimicrobial resistance loci and associated ARGs. Integration of ARG-containing AGEs into Morganella chromosomes would contribute to the accumulation and dissemination of ARGs in Morganella and enhance the adaption and survival of Morganella under complex and diverse antimicrobial selection pressures. IMPORTANCE This study presents a comprehensive genomic epidemiology analysis on global sequenced Morganella isolates. First, a genome sequence-based species classification scheme for Morganella is established with a higher resolution and accuracy than those of the conventional scheme. Second, the prevalence of accessory genetic elements (AGEs) and associated antimicrobial resistance genes (ARGs) among Morganella isolates is disclosed based on genome sequences. Finally, a detailed sequence comparison of eight groups of 23 AGEs (including 19 Morganella chromosomal AGEs) reveals that Morganella chromosomes have evolved to acquire diverse AGEs harboring different profiles of ARGs and that some of these AGEs harbor large accessory modules that exhibit complex mosaic structures and contain a large number of ARGs. Data presented here provide a deeper understanding of the classification and evolution of Morganella species and also those of ARG-containing AGEs in Morganella at the genomic scale.