Showing papers by "Ruichao Li published in 2019"

Antibiotic adjuvants: an alternative approach to overcome multi-drug resistant Gram-negative bacteria.

Abstract: Antibiotic resistance in Gram-negative pathogens has emerged and constituted a global crisis, thereby novel antibiotics and other anti-infective strategies are urgently needed. However, the growing...

Emergence of IncX3 Plasmid-Harboring blaNDM-5 Dominated by Escherichia coli ST48 in a Goose Farm in Jiangsu, China.

Abstract: Twelve carbapenem-resistant E. coli strains were obtained from goose farms in Jiangsu, China. These isolates were resistant to multiple antimicrobials, and positive for the blaNDM-5. The carbapenem-resistance of all strains mediated by blaNDM-5 were successfully conjugated to E. coli J53. S1-PFGE and WGS results showed blaNDM-5 was located on IncX3 conjugative plasmids with a size of ca. 46kb. All blaNDM-5-bearing IncX3 plasmids shared the same genetic context almost identical to pNDM_MGR194-blaNDM-5 and pNDM-QD28-blaNDM-5 reported in India and China, respectively. The twelve strains belonged to three STs, in which the dominant type of E. coli isolated from breeding goose farm carrying blaNDM-5 was ST48. The emergence of blaNDM-5-bearing strains in goose farms and the clonal transmission of E. coli within the breeding goose farm highlighted the potential reservoir of carbapenemase genes in waterfowl farming system, which may further contaminate environments and pose a threat to public health. Comprehensive surveillance of carbapenem-resistant bacteria in goose farms warrants further study to evaluate the underlying risks.

Emergence of a hybrid plasmid derived from IncN1-F33:A−:B− and mcr-1-bearing plasmids mediated by IS26

Abstract: Objectives To characterize the complete sequences of four plasmids in MCR-1-producing clinical Escherichia coli strain D72, and to depict the formation mechanism and characteristics of the cointegrate plasmid derived from the pD72-mcr1 and pD72-F33 plasmids. Methods The genetic profiles of plasmids in strain D72 and its transconjugant were determined by conjugation, S1-PFGE, Southern hybridization, WGS analysis and PCR. Plasmid sequences were analysed with bioinformatic tools. The traits of the fusion plasmid were characterized by cointegration, stability and conjugation assays. Results Strain D72, belonging to ST1114, contained four plasmids, including mcr-1-carrying pD72-mcr1, blaCTX-M-55-carrying pD72-F33, blaTEM-238-bearing pD72-IncP and pD72-IncX1 carrying aph(3')-Ia, qnrS2 and floR. A single plasmid, pD72C, in the transconjugant was found to be larger than any plasmid in the original strain D72. Sequence analysis showed that pD72C was the fusion product of pD72-mcr1 and pD72-F33, and the recombinant event involved an intermolecular replicative mechanism. Plasmid fusion occurred at a frequency of 1.75 × 10-4 cointegrates per transconjugant. The fusion plasmid presented a high stability and conjugation frequency of 8.00 × 10-3. Conclusions To our knowledge, this is the first report of the IS26-mediated fusion of an IncN1-F33:A-:B- plasmid and an mcr-1-carrying phage-like plasmid, providing evidence for the important role of IS26 in the recombination of plasmids. The biological advantages of the fusion plasmid indicated that the fusion event presumably plays a potential role in the dissemination of mcr-1.

Bacterial metabolism-inspired molecules to modulate antibiotic efficacy.

Abstract: The decreasing antibiotic susceptibility of bacterial pathogens calls for novel antimicrobial therapies. Traditional screening pathways based on drug-target interaction have gradually reached the stage of diminishing returns. Thus, novel strategies are urgently needed in the fight against antibiotic-refractory bacteria, particularly for tolerant bacteria. Recently, evidence has accumulated demonstrating that microbial changes caused by bacterial metabolic processes significantly modulate antibiotic killing. A better understanding of these bacterial metabolic processes is indicating a need to screen novel metabolic modulators as potential antibiotic adjuvants. In this review, we describe the state of our current knowledge about how these bacterial metabolism-inspired molecules affect antibiotic efficacy, including potentiation and inhibition activity. In addition, the challenges faced and prospects for bringing them into clinic are also discussed. These examples may provide candidates or targets for the development of novel antibiotic adjuvants.

Co-occurrence of two tet(X) variants in an Empedobacter brevis of shrimp origin.

Abstract: Emerging novel resistance mechanisms pose a great public health concern.….

Identification of a novel hybrid plasmid coproducing MCR-1 and MCR-3 variant from an Escherichia coli strain.

Abstract: Objectives To characterize the genome of an Escherichia coli harbouring both mcr-1 and mcr-3.19 on a hybrid plasmid and the underlying transmission mechanisms. Methods Broth microdilution was used to perform antimicrobial susceptibility testing. Conjugation assays and S1-PFGE were used to assess the transferability of mcr genes. Resistance genotypes and genetic contexts were investigated, based on WGS data from the Illumina and MinION platforms. Inverse PCR was performed to test the mcr-3.19-bearing circular intermediate. Bioinformatic tools were used to further characterize the hybrid plasmid. Results E. coli CP53 was identified as harbouring both mcr-1 and mcr-3.19 on a 231 859 bp hybrid plasmid pCP53-mcr1_3 containing IncFIA, IncHI1A, IncHI1B and IncN replicons. The genetic structures of mcr-1 and mcr-3.19 were similar to those reported in other mcr-1 and mcr-3.19-bearing plasmids, which suggested that recombination between mcr-bearing plasmids had been mediated by ISs. However, the MDR plasmid pCP53-mcr1_3 cannot transfer via conjugation. Furthermore, another three plasmids were identified in the isolate, two of which encoded resistance genes. In640 duplication between two MDR plasmids was observed. An MDR-region recombination existed in E. coli CP53. A core structure consisting of mcr-3-dgkA existed in mcr-3-bearing plasmids reported, to date. Circular intermediates were observed for mcr-1 and mcr-3.19 regions. Conclusions A novel mcr-3.19 was identified along with mcr-1 contained in a hybrid plasmid. This finding suggested that evolution of mcr genes among various plasmids was being driven by mobile elements. Molecular surveillance of mcr gene co-occurrence warrants further investigation to evaluate the public health risk.

Characterization of a Multidrug-Resistant Porcine Klebsiella pneumoniae Sequence Type 11 Strain Coharboring bla KPC-2 and fosA3 on Two Novel Hybrid Plasmids.

Abstract: The occurrence of carbapenemase-producing Enterobacteriaceae (CPE) poses a considerable risk for public health. The gene for Klebsiella pneumoniae carbapenemase-2 (KPC-2) has been reported in many countries worldwide, and KPC-2-producing strains are mainly of human origin. In this study, we identified two novel hybrid plasmids that carry either blaKPC-2 or the fosfomycin resistance gene fosA3 in the multiresistant K. pneumoniae isolate K15 of swine origin in China. The blaKPC-2-bearing plasmid pK15-KPC was a fusion derivative of an IncF33:A−:B− incompatibility group (Inc) plasmid and chromosomal sequences of K. pneumoniae (CSKP). A 5-bp direct target sequence duplication (GACTA) was identified at the boundaries of the CSKP, suggesting that the integration might have been due to a transposition event. The blaKPC-2 gene on pK15-KPC was in a derivative of ΔTn6296-1. The multireplicon fosA3-carrying IncN-IncR plasmid pK15-FOS also showed a mosaic structure, possibly originating from a recombination between an epidemic fosA3-carrying pHN7A8-like plasmid and a pKPC-LK30-like IncR plasmid. Stability tests demonstrated that both novel hybrid plasmids were stably maintained in the original host without antibiotic selection but were lost from the transformants after approximately 200 generations. This is apparently the first description of a porcine sequence type 11 (ST11) K. pneumoniae isolate coproducing KPC-2 and FosA3 via pK15-KPC and pK15-FOS, respectively. The multidrug resistance (MDR) phenotype of this high-risk K. pneumoniae isolate may contribute to its spread and its persistence. IMPORTANCE The global dissemination of carbapenem resistance genes is of great concern. Animals are usually considered a reservoir of resistance genes and an important source of human infection. Although carbapenemase-producing Enterobacteriaceae strains of animal origin have been reported increasingly, blaKPC-2-positive strains from food-producing animals are still rare. In this study, we first describe the isolation and characterization of a carbapenem-resistant Klebsiella pneumoniae ST11 isolate, strain K15, which is of pig origin and coproduces KPC-2 and FosA3 via two novel hybrid plasmids. Furthermore, our findings highlight that this ST11 Klebsiella pneumoniae strain K15 is most likely of human origin and could be easily transmitted back to humans via direct contact or food intake. In light of our findings, significant attention must be paid to monitoring the prevalence and further evolution of blaKPC-2-carrying plasmids among the Enterobacteriaceae strains of animal origin.

Characterization of the stability and dynamics of Tn6330 in an Escherichia coli strain by nanopore long reads.

Abstract: Background The mcr-1 gene has been widely reported in both bacterial chromosomes and plasmids, while its stability in these genetic materials is not well understood. Objectives Our aim was to characterize the stability and dynamics of Tn6330 elements in both a plasmid and the chromosome in a single bacterial population. Methods Plasmid-borne and chromosomal Tn6330 were characterized by PCR, conjugation, S1-PFGE, stability assay, single-molecule long-read sequencing and bioinformatics analysis. Results Tn6330 was simultaneously detected in both a plasmid and the chromosome of a clinical Escherichia coli strain. The plasmid was found to comprise the IncFIB replicon and a phage-like replicon, as well as two integrons that harboured various mobile elements and resistance genes including mcr-1, floR, blaTEM-1b and strAB. Both plasmid-borne and chromosomal Tn6330 transposons could be re-organized into a circular intermediate that played a role in transmission of the mcr-1 gene. Tn6330 was found to be very stable in both the plasmid and chromosome after 30 passages of 12 h with or without colistin selective pressure. The decayed structure of Tn6330 in the genuine single DNA molecules of bacterial populations, although occurring at a very low frequency, could be detected for the first time, in which Tn6330 was degraded into a single ISApl1 element. Conclusions Long-read sequencing technology is a good tool to study the evolution and stability of genetic elements in bacteria. The ultrastability of an mcr-1-encoding element in a bacterial plasmid and chromosome renders it unlikely to be eradicated quickly by the reduced use of colistin, and factors leading to the frequent demise of Tn6330 warrant further studies.

Loss of mcr Genes Mediated by Plasmid Elimination and IS Apl1 .

Abstract: We characterized the stability of a plasmid pCP53-mcr1_3 encoding mcr-1 and mcr-3.19 with and without colistin exposure during cultural passages via S1-pulsed-field gel electrophoresis (PFGE) and nanopore MinION sequencing. Both mcr-1 and mcr-3.19 were missing in certain subclones, mediated by genetic excision (ISApl1-mcr-1-pap2), and deletions of large multidrug resistance (MDR) regions confirmed by ISApl1 and plasmid elimination. Without colistin exposure, the eradication of mcr genes is feasible, while the factors influencing the elimination processes warrant further study.

Genetic characterization of an MDR/virulence genomic element carrying two T6SS gene clusters in a clinical Klebsiella pneumoniae isolate of swine origin

Abstract: Objectives Multiresistant Klebsiella pneumoniae isolates rarely cause infections in pigs. The aim of this study was to investigate a multiresistant porcine K. pneumoniae isolate for plasmidic and chromosomal antimicrobial resistance and virulence genes and their genetic environment. Methods K. pneumoniae strain ZYST1 originated from a pig with pneumonia. Antimicrobial susceptibility testing was performed using broth microdilution. Conjugation experiments were conducted using Escherichia coli J53 as the recipient. The complete sequences of the chromosomal DNA and the plasmids were generated by WGS and analysed for the presence of resistance and virulence genes. Results The MDR K. pneumoniae ST1 strain ZYST1 contained three plasmids belonging to incompatibility groups IncFIIk5-FIB, IncI1 and IncX4, respectively. The IncFIIk5-FIB plasmid carried the resistance genes aadA2, mph(A), sul1 and aph(3')-Ia, and the IncI1 plasmid carried aadA22 and erm(B). No resistance genes were present on the IncX4 plasmid. Plasmids related to the aforementioned three plasmids were also present in other Enterobacteriaceae species from humans, animals and the environment. Bioinformatic analyses identified a chromosomal 904 kb MDR element flanked by two copies of ISKpn26. This element included virulence factors, such as a type VI secretion system (T6SS) and genes for type 1 fimbriae, the toxin-antitoxin system HipA/HipB, antimicrobial resistance genes, such as blaSHV-187, mdtk, catA and the multiple antibiotic resistance operon marRABC, and heavy metal resistance determinants, such as chrB/chrA and tehA/tehB. Conclusions This study reports a novel 904 kb MDR/virulence genomic element and three important plasmids coexisting in a clinical K. pneumoniae isolate of animal origin.

Composition of melbine and doxycycline and application thereof to preparation of medicament for bacterial infectious diseases

Abstract: The invention relates to a composition of melbine and doxycycline and application thereof to preparation of a medicament for bacterial infectious diseases. The invention explains that the melbine, asa hypoglycemic medicament for human use, can restore the sensitivity of drug-resistant bacteria to the doxycycline, and the in-vivo and in-vitro effectiveness of combined use of the melbine and the doxycycline is assessed systematically, so that the development of a novel antibiotic synergist is facilitated, and the problem that the harm of multi-drug resistant bacteria (MDR) is on the rise is alleviated.