Publications by authors named "Zhenpeng Li"

57 Publications

Prevalence of 16S rRNA Methylation Enzyme Gene in From Outpatients and Food.

Front Microbiol 2021 25;12:663210. Epub 2021 May 25.

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

is the primary cause of community-acquired foodborne infections, so its resistance to antimicrobials, such as aminoglycosides, is a public health issue. Of concern, aminoglycoside resistance in is increasing rapidly. Here, we performed a retrospective study evaluating the prevalence of harboring -mediated aminoglycoside resistance in community-acquired infections and in food or environmental sources. The prevalence rates of -harboring strains were 1.1/1,000 (13/12,095) and 8.7/1,000 (32/3,687) in outpatient and food/environmental isolates, respectively. All the -harboring strains were resistant to multiple drugs, including fluoroquinolone and/or extended-spectrum cephalosporins, and most (34/45) belonged to serovar Indiana. The gene of these strains were all carried on plasmids, which spanned five replicon types with IncHI2 being the dominant plasmid type. All the -carrying plasmids were transferable into and recipients. The conjugation experiment results revealed that the -harboring . Indiana strains had a relatively higher ability to acquire -carrying plasmids. The low similarity of their pulsed field gel electrophoresis patterns indicates that the -harboring strains were unlikely to have originated from a single epidemic clone, suggesting broad spread. Furthermore, the genetic backgrounds of -harboring strains isolated from outpatients exhibited higher similarity to those isolated from poultry than to those isolated from swine, suggesting that poultry consumption maybe an infection source. These findings highlight an urgent need to monitor the prevalence and transmission of -harboring , especially Indiana, to better understand the potential public health threat and prevent the further spread of these strains.
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http://dx.doi.org/10.3389/fmicb.2021.663210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8186500PMC
May 2021

The Type II Secretory System Mediates Phage Infection in .

Front Cell Infect Microbiol 2021 16;11:662344. Epub 2021 Apr 16.

State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

Attachment and specific binding to the receptor on the host cell surface is the first step in the process of bacteriophage infection. The lytic phage VP2 is used in phage subtyping of the biotype El Tor of the O1 serogroup; however, its infection mechanism is poorly understood. In this study, we aimed to identify its receptor on . The outer membrane protein EpsD in the type II secretory system (T2SS) was found to be related to VP2-specific adsorption to , and the T2SS inner membrane protein EpsM had a role in successful VP2 infection, although it was not related to adsorption of VP2. The tail fiber protein gp20 of VP2 directly interacts with EpsD. Therefore, we found that in , in addition to the roles of the T2SS as the transport apparatus of cholera toxin secretion and filamentous phage release, the T2SS is also used as the receptor for phage infection and probably as the channel for phage DNA injection. Our study expands the understanding of the roles of the T2SS in bacteria.
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http://dx.doi.org/10.3389/fcimb.2021.662344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8101328PMC
July 2021

Severe Case of Rickettsiosis Identified by Metagenomic Sequencing, China.

Emerg Infect Dis 2021 05;27(5):1530-1532

A case of Rickettsia sibirica subspecies sibirica BJ-90 infection in China was identified by metagenomic analysis of an eschar biopsy specimen and confirmed by nested PCR. Seroprevalence of spotted fever group Rickettsia was ≈17.4% among the local population. This report highlights the threat of rickettsioses to public health in the Qinghai-Tibet Plateau.
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http://dx.doi.org/10.3201/eid2705.203265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8084477PMC
May 2021

Curcumin-loaded core-shell biopolymer nanoparticles produced by the pH-driven method: Physicochemical and release properties.

Food Chem 2021 Sep 26;355:129686. Epub 2021 Mar 26.

Hangzhou College of Commerce, Zhejiang Gongshang University, Hangzhou, 311508, China.

In this study, core-shell biopolymer nanoparticles were fabricated for the encapsulation and delivery of curcumin using a pH-driven method. The influences of the coating composition on the physicochemical properties and curcumin release characteristics of the core-shell nanoparticles were studied. Fourier transform infrared spectroscopy and X-ray diffraction analyses indicated that curcumin was encapsulated in an amorphous state inside the nanoparticles. Particle size and ζ-potential measurements indicated that the biopolymer nanoparticles were relatively stable under different environmental conditions: long term storage, heating, pH changes and salt. The DPPH radical scavenging activity of the curcumin was increased after encapsulation within the nanoparticles, whereas the gastrointestinal release of curcumin was prolonged. These results were attributed to the ability of alginate and NaCas to form a thick layer around the nanoparticles, which increased the steric and electrostatic repulsion between them, as well as inhibiting the release of curcumin.
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http://dx.doi.org/10.1016/j.foodchem.2021.129686DOI Listing
September 2021

Development of -Symmetric Chiral Spirocyclic Phase-Transfer Catalysts: Synthesis and Application to Asymmetric Alkylation of Glycinate Schiff Base.

Org Lett 2021 Apr 26;23(8):2890-2894. Epub 2021 Mar 26.

College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.

A class of -symmetric chiral spirocyclic phase-transfer catalysts based on tetramethyl-1,1'-spirobiindane scaffold was synthesized from commercially available bisphenol A in 12 steps with 22-25% total yields, which features a more rigid and stable backbone and smaller dihedral angles and can be easily modified. These catalysts show high catalytic performance in the asymmetric alkylation of -butyl glycinate Schiff base at only 2 mol % catalyst loading, giving the target products with up to 92% yield and 98% ee.
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http://dx.doi.org/10.1021/acs.orglett.1c00535DOI Listing
April 2021

Development of a Rapid and Fully Automated Multiplex Real-Time PCR Assay for Identification and Differentiation of and on the BD MAX Platform.

Front Cell Infect Microbiol 2021 25;11:639473. Epub 2021 Feb 25.

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

and are common diarrheal pathogens of great public health concern. A multiplex TaqMan-based real-time PCR assay was developed on the BD MAX platform; this assay can simultaneously detect and differentiate and directly from human fecal specimens. The assay includes two reactions. One reaction, BDM-VC, targets the gene , the cholera toxin (CT) coding gene , the O1 serogroup specific gene , and the O139 serogroup specific gene of . The other, BDM-VP, targets the gene and the toxin coding genes and of . In addition, each reaction contains a sample process control. When evaluated with spiked stool samples, the detection limit of the BD MAX assay was 195-780 CFU/ml for and 46-184 CFU/ml for , and the amplification efficiency of all genes was between 95 and 115%. The assay showed 100% analytical specificity, using 63 isolates. The BD MAX assay was evaluated for its performance compared with conventional real-time PCR after automated DNA extraction steps, using 164 retrospective stool samples. The overall percent agreement between the BD MAX assay and real-time PCR was ≥ 98.8%; the positive percent agreement was 85.7% for , 100% for /, and lower (66.7%) for because of a false negative. This is the first report to evaluate the usage of the BD MAX open system in detection and differentiation of and directly from human samples.
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http://dx.doi.org/10.3389/fcimb.2021.639473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7947656PMC
July 2021

Case Report: Identification of SARS-CoV-2 in Cerebrospinal Fluid by Ultrahigh-Depth Sequencing in a Patient With Coronavirus Disease 2019 and Neurological Dysfunction.

Front Med (Lausanne) 2021 22;8:629828. Epub 2021 Feb 22.

Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China.

We reported that the complete genome sequence of SARS-Coronavirus-2 (SARS-CoV-2) was obtained from a cerebrospinal fluid (CSF) sample by ultrahigh-depth sequencing. Fourteen days after onset, seizures, maxillofacial convulsions, intractable hiccups and a significant increase in intracranial pressure developed in an adult coronavirus disease 2019 patient. The complete genome sequence of SARS-CoV-2 obtained from the cerebrospinal fluid indicates that SARS-CoV-2 can invade the central nervous system. In future, along with nervous system assessment, the pathogen genome detection and other indicators are needed for studying possible nervous system infection of SARS-CoV-2.
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http://dx.doi.org/10.3389/fmed.2021.629828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7937706PMC
February 2021

Rapid Identification of Plasmid Replicon Type and Coexisting Plasmid-Borne Antimicrobial Resistance Genes by S1-Pulsed-Field Gel Electrophoresis-Droplet Digital Polymerase Chain Reaction.

Foodborne Pathog Dis 2021 05 4;18(5):298-305. Epub 2021 Mar 4.

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

Bacterial drug resistance is a significant food safety problem and public health threat. Plasmids carrying drug resistance genes may result in the rapid spread of resistance among different bacteria, hosts, and environments; therefore, antibiotic resistance monitoring and continuing research into the mechanisms of drug resistance are urgently needed. Southern blotting with probes for antibiotic resistance genes and even next-generation sequencing have been used previously to detect plasmid-borne resistance genes, but these approaches are complex and time-consuming. The next-generation sequencing requires strict laboratory conditions and bioinformatics analysis ability. In this study, we developed a simplified and sensitive method to detect plasmid-borne antimicrobial resistance genes and plasmid replicon types. strains carrying plasmids of three different replicon types that contained and two ESBL-producing genes were used to verify the new method. The plasmids harbored by the strains were separated by S1 nuclease treatment and pulsed-field gel electrophoresis (PFGE), then recovered and used as the templates for droplet digital polymerase chain reaction (ddPCR) to identify target genes. The target genes were present in significantly higher copy numbers on the plasmids than the background noise. These results were consistent with the plasmid sequencing results. This S1-PFGE-ddPCR method was less time-consuming to perform than Southern blot and complete plasmid sequencing. Therefore, this method represents a time-saving alternative for detecting plasmid-borne genes, and is likely to be a valuable tool for detecting coexisting plasmid-borne drug resistance genes.
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http://dx.doi.org/10.1089/fpd.2020.2865DOI Listing
May 2021

Comparison of the Multiple Platforms to Identify Various Species.

Front Microbiol 2020 18;11:625961. Epub 2021 Jan 18.

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

We compared several identification methods for genus members, including traditional biochemical testing, multiplex-PCR amplification, mass spectrometry identification, whole-genome sequencing, multilocus phylogenetic analysis (MLPA), and , and - gene sequencing. Isolates ( = 62) belonging to the genus, which were came from the bacterial bank in the laboratory, were used to assess the identification accuracy of the different methods. Whole-genome sequencing showed that the spp. isolates comprised ( = 21), ( = 18), ( = 8), ( = 7), ( = 5), ( = 2), and ( = 1). Using the whole-genome sequencing results as the standard, the consistency of the other methods was compared with them. The results were 46.77% (29/62) for biochemical identification, 83.87% (52/62) for mass spectrometric identification, 67.74% (42/62) for multiplex-PCR, 100% (62/62) for MLPA typing, 72.58% for , and 59.68% for and -. MLPA was the most consistent, followed by mass spectrometry. Therefore, in the public health laboratory, both MLPA and whole-genome sequencing methods can be used to identify various species. However, rapid and relatively accurate mass spectrometry is recommended for clinical lab.
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http://dx.doi.org/10.3389/fmicb.2020.625961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7848130PMC
January 2021

Application of whey protein isolate fibrils in encapsulation and protection of β-carotene.

Food Chem 2021 Jun 30;346:128963. Epub 2020 Dec 30.

School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China.

β-Carotene (BC) exhibits several bioactive properties, but its application is restrained due to the unstability and low biological availability. In this study, protein fibrils were prepared from whey protein isolate fibrils (WPIF), which were used as carriers to protect and deliver BC. With the extension of heating time, the molecular weight of WPI decreased gradually. WPI was hydrolyzed into peptides which self-assembled into WPIF, resulting in significant changes in secondary structure, zeta-potential, viscosity and, antioxidant capacity. The main interactions between WPIF and BC were hydrogen bonding and hydrophobic interaction. The encapsulation efficiency of WPIF was increased from 76.55% to 92.11% compared to that of untreated WPI. Moreover, the simulated gastrointestinal release showed that the cumulative release of BC encapsulated by WPIF reached the maximum in the simulated intestine. Therefore, WPIF could be a potential delivery system for water-insoluble bioactive compounds with enhanced encapsulation efficiency and protection effect.
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http://dx.doi.org/10.1016/j.foodchem.2020.128963DOI Listing
June 2021

A PolyQ Membrane Protein of Vibrio cholerae Acts as the Receptor for Phage Infection.

J Virol 2021 02 24;95(6). Epub 2021 Feb 24.

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China

Bacteriophage VP1 is a typing phage used for the phage subtyping of O1 biotype El Tor, but the molecular mechanisms of its receptor recognition and the resistance of its host to infection are mostly unknown. In this study, we aimed to identify the host receptor and its role in resistance in natural VP1-resistant strains. Generating spontaneous resistance mutations and genome sequencing mutant strains found the polyQ protein VcpQ, which carries 46 glutamine residues in its Q-rich region, to be responsible for infection by VP1. VcpQ is a membrane protein and possibly forms homotrimers. VP1 adsorbed to through VcpQ. Sequence comparisons showed that 72% of natural VP1-resistant strains have fewer glutamines in the VcpQ Q-rich stretch than VP1-sensitive strains. This difference did not affect the membrane location and oligomer of VcpQ but abrogated VP1 adsorption. These mutant VcpQs did not recover VP1 infection sensitivity in a strain with deleted. Our study revealed that the polyQ protein VcpQ is responsible for the binding of VP1 during its infection of and that glutamine residue reduction in VcpQ affects VP1 adsorption to likely be the main cause of VP1 resistance in natural resistant strains. The physiological functions of this polyQ protein in bacteria need further clarification; however, mutations in the polyQ stretch may endow with phage resistance and enhance survival against VP1 or related phages. Receptor recognition and binding by bacteriophage are the first step for its infection of bacterial cells. In this study, we found the subtyping phage VP1 uses a polyQ protein named VcpQ ( polyQ protein) as the receptor for VP1 infection. Our study reveals the receptor's recognition of phage VP1 during its adsorption and the VP1 resistance mechanism of the wild resistant strains bearing the mutagenesis in the receptor VcpQ. These mutations may confer the survival advantage on these resistant strains in the environment containing VP1 or its similar phages.
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http://dx.doi.org/10.1128/JVI.02245-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8094955PMC
February 2021

Culturing Bacteria From Fermentation Pit Muds of Baijiu With Culturomics and Amplicon-Based Metagenomic Approaches.

Front Microbiol 2020 23;11:1223. Epub 2020 Jun 23.

School of Light Industry, Beijing Technology and Business University, Beijing, China.

The Baijiu-making microbiota has an important role in the alcohol production, flavor, and character of Baijiu. 16S rRNA gene sequencing revolutionized the understanding of Baijiu-making microbiota. In this study, nine phyla, 23 classes, 49 orders, 99 families, and 201 genera were detected in pit muds (PMs) by 16S rRNA gene sequencing. Firmicutes and Bacteroidetes predominated (>99%). At the order level, Clostridiales, Bacteroidales, and Bacillales predominated (>92%). At the genus level, , , , and predominated. The pure culture of Baijiu-making prokaryotes was essential to elucidating the role of these microbes in the fermentation of Baijiu. According to the theory of microbial culturomics, a culturing approach with multiple culture conditions was adopted, combining 16S rRNA gene sequencing. We identified 215 prokaryotic strains, which were assigned to 66 species, 41 genera, four phyla, and 19 potential new species. Gas conditions were key factors in culturomics. In addition, culturomics significantly increased the number of species isolated from the fermentation PM compared with previous reports. With culturomics, the diversity spectrum of culturable bacteria in the PM was increased 273.33% at the genus level. This study confirms the complementary role of culturomics in the exploration of complex microbiota.
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http://dx.doi.org/10.3389/fmicb.2020.01223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7344326PMC
June 2020

Multilocus sequence analysis for the taxonomic updating and identification of the genus Proteus and reclassification of Proteus genospecies 5 O'Hara et al. 2000, Proteus cibarius Hyun et al. 2016 as later heterotypic synonyms of Proteus terrae Behrendt et al. 2015.

BMC Microbiol 2020 06 10;20(1):152. Epub 2020 Jun 10.

National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China.

Background: Members of the genus Proteus are mostly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species have not been elucidated to date. In this study, we developed a multilocus sequence analysis (MLSA) approach based on five housekeeping genes (HKGs) to delineate phylogenetic relationships of species within the genus Proteus.

Results: Of all 223 Proteus strains collected in the current study, the phylogenetic tree of five concatenated HKGs (dnaJ, mdh, pyrC, recA and rpoD) divided 223 strains into eleven clusters, which were representative of 11 species of Proteus. Meanwhile, the phylogenetic trees of the five individual HKGs also corresponded to that of the concatenated tree, except for recA, which clustered four strains at an independent cluster. The evaluation of inter- and intraspecies distances of HKG concatenation indicated that all interspecies distances were significantly different from intraspecies distances, which revealed that these HKG concatenations can be used as gene markers to distinguish different Proteus species. Further web-based DNA-DNA hybridization estimated by genome of type strains confirmed the validity of the MLSA, and each of eleven clusters was congruent with the most abundant Proteus species. In addition, we used the established MLSA method to identify the randomly collected Proteus and found that P. mirabilis is the most abundant species. However, the second most abundant species is P. terrae but not P. vulgaris. Combined with the genetic, genomic and phenotypic characteristics, these findings indicate that three species, P. terrae, P. cibarius and Proteus genospecies 5, should be regarded as heterotypic synonyms, and the species should be renamed P. terrae, while Proteus genospecies 5 has not been named to date.

Conclusions: This study suggested that MLSA is a powerful method for the discrimination and classification of Proteus at the species level. The MLSA scheme provides a rapid and inexpensive means of identifying Proteus strains. The identification of Proteus species determined by the MLSA approach plays an important role in the clinical diagnosis and treatment of Proteus infection.
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http://dx.doi.org/10.1186/s12866-020-01844-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7288399PMC
June 2020

Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of .

Microorganisms 2020 Apr 13;8(4). Epub 2020 Apr 13.

National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China.

The genus is ubiquitous in marine environments and uses numerous evolutionary characteristics and survival strategies in order to occupy its niche. Here, a newly identified species, , was deeply explored to reveal a unique environmental adaptability. type strain FJ201301 shared 817 core genes with the species in the population genomic analysis, but possessed unique genes of its own. In addition, FJ201301 was predicated to carry 106 virulence-related factors, several of which were mostly found in other pathogenic species. Moreover, a comparative transcriptome analysis between the low-salt (1% NaCl) and high-salt (8% NaCl) condition was conducted to identify the genes involved in salt tolerance. A total of 913 unigenes were found to be differentially expressed. In a high-salt condition, 577 genes were significantly upregulated, whereas 336 unigenes were significantly downregulated. Notably, differentially expressed genes have a significant association with ribosome structural component and ribosome metabolism, which may play a role in salt tolerance. Transcriptional changes in ribosome genes indicate that may have gained a predominant advantage in order to adapt to the changing environment. In conclusion, to survive in adversity, has enhanced its environmental adaptability and developed various strategies to fill its niche.
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http://dx.doi.org/10.3390/microorganisms8040555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7232310PMC
April 2020

Molecular genetic analysis of an XDR Pseudomonas aeruginosa ST664 clone carrying multiple conjugal plasmids.

J Antimicrob Chemother 2020 06;75(6):1443-1452

State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China.

Objectives: A group of ST664 XDR Pseudomonas aeruginosa strains have been isolated from a burn clinic. Here we decipher their resistomes and likely mechanisms of resistance acquisition.

Methods: The complete nucleotide sequences of representative isolates were determined, by PacBio and Illumina MiSeq sequencing, and analysed for antimicrobial resistance (AMR) genes as well as sequence variations. S1-PFGE was used to determine the sizes and numbers of plasmids harboured by the isolates. Purified plasmid DNA was further sequenced by PacBio technology, closed manually and annotated by RAST. The mobility of plasmids was determined by conjugation assays.

Results: The XDR P. aeruginosa ST664 clone carries 11 AMR genes, including a blaKPC-2 gene that confers resistance to carbapenems. Most of the ST664 isolates carry three coexisting plasmids. blaKPC-2 and a cluster of three AMR genes (aadB-cmlA1-sul1) are encoded on a 475 kb megaplasmid pNK546a, which codes for an IncP-3-like replication and partitioning mechanism, but has lost the conjugative transfer system. Interestingly, however, pNK546a is mobilizable and can be transferred to P. aeruginosa PAO1 with the help of a co-residing IncP-7 conjugative plasmid. The blaKPC-2 gene is carried by an IS6100-ISKpn27-blaKPC-2-ΔISKpn6-Tn1403 mobile element, which might be brought into the ST664 clone by another co-resident IncP-1α plasmid, which is inclined to be lost. Moreover, pNK546a harbours multiple heavy metal (mercury, tellurite and silver) resistance modules.

Conclusions: To the best of our knowledge, pNK546a is the first fully sequenced blaKPC-2-carrying megaplasmid from P. aeruginosa. These results give new insights into bacterial adaptation and evolution during nosocomial infections.
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http://dx.doi.org/10.1093/jac/dkaa063DOI Listing
June 2020

High-efficiency protein delivery into transfection-recalcitrant cell types.

Biotechnol Bioeng 2020 03 20;117(3):816-831. Epub 2019 Dec 20.

State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China.

Intracellular delivery of functional proteins is of great interest for basic biological research as well as for clinical applications. Transfection is the most commonly used method, however, it is not applicable to large-scale manipulation and inefficient in important cell types implicated in biomedical applications, such as epithelial, immune and pluripotent stem cells. In this study, we explored a bacterial type III secretion system (Bac-T3SS)-mediated proteofection method to overcome these limitations. An attenuated Pseudomonas aeruginosa vector was constructed, which has features of low toxicity, high T3SS activity, and self-limiting growth. Compared to the method of transfection, the Bac-T3SS showed significantly higher efficiencies of Cre recombinase translocation and target site recombination for hard-to-transfect human cell lines. Furthermore, through the delivery of β-lactamase in live animals, we demonstrated the feasibility and biosafety of in vivo application of the Bac-T3SS. This study provided an efficient and low-cost proteofection strategy for laboratory use as well as for application in large-scale cell manipulations.
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http://dx.doi.org/10.1002/bit.27245DOI Listing
March 2020

Bacterial succession and the dynamics of flavor compounds in the Huangjiu fermented from corn.

Arch Microbiol 2020 Mar 25;202(2):299-308. Epub 2019 Oct 25.

Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China.

Huangjiu is one of the Chinese unique and traditional liquor. Corn is a kind of high yield crop in China, which has the characteristics of wide distribution, low price and high starch content. Fermenting Huangjiu with corn not only enrich Huangjiu types, but also opens up a new way for the utilization of corn. The flavor compounds and microorganisms in corn wine fermentation were studied in this study. A total of 98 volatile compounds and 8 kinds of organic acids were detected. Bacillus, Weissella, Streptomyces, Aeromonas and Blautia were the dominant bacteria. The correlation analysis between flavor compounds and bacteria showed that there were 557 correlations between major flavor compounds and bacteria. Among them, Lactococcus, Virgibacillus, Sphingobacterium and Sporolactobacillus were dominant genus of flavor producing bacteria. This study may reveal the changing rule of bacteria in Huangjiu, predict the relationship between metabolites and bacteria. In addition, this study expanded the application of corn and increased the variety of Huangjiu.
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http://dx.doi.org/10.1007/s00203-019-01748-3DOI Listing
March 2020

Co-existence of multiple distinct lineages in serotype O4:K12.

Microb Genom 2020 12 3;6(12). Epub 2019 Oct 3.

Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China.

is an important cause of foodborne gastroenteritis globally. Thermostable direct haemolysin (TDH) and the TDH-related haemolysin are the two key virulence factors in pathogenicity islands harbour the genes encoding these two haemolysins. The serotyping of is based on the combination of O and K antigens. Frequent recombination has been observed in , including in the genomic regions encoding the O and K antigens. serotype O4:K12 has caused gastroenteritis outbreaks in the USA and Spain. Recently, outbreaks caused by this serotype of have been reported in China. However, the relationships among this serotype of strains isolated in different regions have not been addressed. Here, we investigated the genome variation of the serotype O4:K12 using the whole-genome sequences of 29 isolates. We determined five distinct lineages in this strain collection. We observed frequent recombination among different lineages. In contrast, little recombination was observed within each individual lineage. We showed that the lineage of this serotype of isolated in America was different from those isolated in Asia and identified genes that exclusively existed in the strains isolated in America. Pan-genome analysis showed that strain-specific and cluster-specific genes were mostly located in the genomic islands. Pan-genome analysis also showed that the vast majority of the accessory genes in the O4:K12 serotype of were acquired from within the genus . Hence, we have shown that multiple distinct lineages exist in serotype O4:K12 and have provided more evidence about the gene segregation found in isolated in different continents.
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http://dx.doi.org/10.1099/mgen.0.000287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8116679PMC
December 2020

Nonhemolysis of epidemic El Tor biotype strains of is related to multiple functional deficiencies of hemolysin A.

Gut Pathog 2019 12;11:38. Epub 2019 Jul 12.

1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping, Beijing, 102206 China.

Background: Hemolysis of bacteria is an important phenotype used for typing and characterizing strains with specific biomarkers and even a virulence factor in bacterial pathogenesis. In , hemolysin HlyA is responsible for hemolysis of sheep red blood cells, and this hemolytic phenotype is used as a biotyping indicator and considered one of the virulence factors. At the beginning of the seventh cholera pandemic, the El Tor biotype strains of serogroup O1 were distinguished by hemolysis from the sixth pandemic O1 classical biotype strains, whereas during the following epidemics, nonhemolytic El Tor strains appeared, suggesting phenotypic and genetic variations in these strains. This study aimed to investigate the possible mechanisms involved in nonhemolysis of El Tor strains.

Results: Five sequence types of genes were found in the studied O1 El Tor strains isolated during the seventh pandemic. A 4-base deletion in caused the HlyA protein mutation and non-hemolytic phenotype. Some strains carry wildtype genes but are still non-hemolytic, and greatly reduced transcription and blocked secretion of hemolysin were observed in hemolysis tests of the subcellular components and transcription/expression analysis of .

Conclusions: Mechanisms responsible for nonhemolysis of the epidemic O1 El Tor strains are complex and not only confined to gene mutation but also deficiencies of transcription and extracellular transport of HlyA. Mutations in gene regulation and protein secretion systems of HlyA in the nonhemolytic strains should be areas of concern in future studies.
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http://dx.doi.org/10.1186/s13099-019-0316-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6626427PMC
July 2019

Genetic characteristics of pathogenic Leptospira in wild small animals and livestock in Jiangxi Province, China, 2002-2015.

PLoS Negl Trop Dis 2019 06 24;13(6):e0007513. Epub 2019 Jun 24.

Department of Microbiology and Immunology, Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.

Background: Leptospirosis is one of the most important neglected tropical bacterial diseases worldwide. However, there is limited information on the genetic diversity and host selectivity of pathogenic Leptospira in wild small mammal populations.

Methodology/principal Findings: Jiangxi Province, located in southern China, is a region highly endemic for leptospirosis. In this study, among a total of 3,531 trapped rodents dominated by Apodemus agrarius (59.7%), 330 Leptospira strains were successfully isolated from six different sites in Jiangxi between 2002 and 2015. Adding 71 local strains from humans, various kinds of livestock and wild animals in Jiangxi, a total of 401 epidemic strains were characterized using 16S rRNA gene senquencing, multilocus sequence typing (MLST) and the microscopic agglutination test (MAT). Among them, the most prevalent serogroup was Icterohaemorrhagiae (61.10%), followed by Javanica (19.20%) and Australis (9.73%); the remaining five serogroups, Canicola, Autumnalis, Grippotyphosa, Hebdomadis and Pomona, accounted for 9.97%. Species identification revealed that 325 were L. interrogans and 76 were L. borgpetersenii. Moreover, L. interrogans was the only pathogenic species in Fuliang and Shanggao and was predominant in Shangrao (95.0%); L. borgpetersenii was the most common in the remaining three sites. Twenty-one sequence types (STs) were identified. Similarly, ST1 and serogroup Icterohaemorrhagiae were most prevalent in Shangrao (86.0% and 86.4%) and Fuliang (90.4% and 90.4%), ST143 and serogroup Javanica in Shangyou (88.5% and 90.4%) and Longnan (73.1% and 73.1%), and ST105 and serogroup Australis in Shanggao (46.3% and 56.1%). Serogroup Icterohaemorhagiae primarily linked to A. agrarius (86.9%), serogroup Canicola to dogs (83.3%). There were significant differences in the distribution of leptospiral species/serogroups/STs prevalence across host species/collected locations among the 394 animal-associated strains (Fisher's exact test, p<0.001).

Conclusions/significance: Our study demonstrated high genetic diversity of pathogenic Leptospira strains from wild small animals in Jiangxi from 2002 to 2015. A. agrarius was the most abundantly trapped animal reservoir, and serogroup Icterohaemorrhagiae and ST1 were the most dominant in Jiangxi. Significant geographic variation and host diversity in the distribution of dominant species, STs and serogroups were observed. Moreover, rat-to-human transmission might play a crucial role in the circulation of Leptospirosis in Jiangxi. Details of the serological and molecular characteristics circulating in this region will be essential in implementing prevention and intervention measures to reduce the risk of disease transmission in China. However, phylogenetic analysis of more Leptospira isolates should explore the impact of ecological change on leptospirosis transmission dynamics and investigate how such new knowledge might better impact environmental monitoring for disease control and prevention at a public health level.
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http://dx.doi.org/10.1371/journal.pntd.0007513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611636PMC
June 2019

Novel Prophages and a Comparative Analysis of Genomic Diversity.

Front Microbiol 2019 29;10:1184. Epub 2019 May 29.

State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases - Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.

is a major agent of foodborne diseases worldwide. Prophage plays an important role in the genetic evolution of the bacterial genome. Little is known about the genetic information about prophages in the genome of , and no pathogenic prophages have been described. In this study, we induced and described the genomes of six prophages from pathogenic for the first time. Phylogenetic analysis based on whole genome sequencing revealed that these novel phages are genetically distinct from the previously reported phages, showing considerable genetic diversity. Interestingly, the prophages induced from O:3 and O:9 showed different genomic sequences and morphology but highly conserved among the same serotype strains, which classified into two diverse clusters. The three long-tailed prophages induced from serotype O:3 were highly conserved, shared ≥99.99% identity and forming genotypic cluster A; the three prophages induced from the serotype O:9 strains formed cluster B, also shared more than 99.90% identity with one another. Cluster A was most closely related to O:5 non-pathogenic prophage PY54 (61.72% identity). The genetic polymorphism of these two kinds of prophages and highly conserved among the same serotype strains, suggested a possible shared evolutionary past for these phages: originated from distinct ancestors, and entered pathogenic as extrachromosomal genetic components during evolution when facing selective pressure. These results are critically important for further understanding of phage roles in host physiology and the pathology of disease.
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http://dx.doi.org/10.3389/fmicb.2019.01184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6548840PMC
May 2019

Identification of a small RNA that directly controls the translation of the quorum sensing signal synthase gene rhlI in Pseudomonas aeruginosa.

Environ Microbiol 2019 08 10;21(8):2933-2947. Epub 2019 Jun 10.

State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China.

The biofilm formation by Pseudomonas aeruginosa highly increases the bacterial resistance to antimicrobial agents and host immune clearance. The biofilm formation is positively regulated by two small RNAs, RsmY and RsmZ. Previously, we reported that mutation in the polynucleotide phosphorylase (PNPase) coding gene pnp increases the levels of RsmY/Z. However, in this study, we found that the biofilm formation is decreased in the pnp mutant, which is due to a defect in rhamnolipids production. The rhamnolipids production is regulated by the RhlI-RhlR quorum sensing system. We found that PNPase influences the translation of RhlI through its 5'-untranslated region (UTR) and identified that the sRNA P27 is responsible for the translational repression. In vitro translation experiments demonstrated that P27 directly represses the translation of the rhlI mRNA through its 5'UTR in an Hfq-dependent manner. Point mutations in the rhlI 5'UTR or P27, which abolish the pairing between the two RNAs restore the rhlI expression and rhamnolipids production as well as the biofilm formation in the pnp mutant. Overall, our results reveal a novel layer of regulation of the Rhl quorum sensing system by the sRNA P27.
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http://dx.doi.org/10.1111/1462-2920.14686DOI Listing
August 2019

Expanding dynamics of the virulence-related gene variations in the toxigenic Vibrio cholerae serogroup O1.

BMC Genomics 2019 May 9;20(1):360. Epub 2019 May 9.

State Key Laboratory for Infectious Disease Prevention and Control. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.

Background: Toxigenic Vibrio cholerae serogroup O1 is the causative pathogen in the sixth and seventh cholera pandemics. Cholera toxin is the major virulent factor but other virulence and virulence-related factors play certain roles in the pathogenesis and survival in the host. Along with the evolution of the epidemic strains, the virulence-related genes also experience variation, gain and loss, and lead to genetic divergence in different strains.

Results: In this study, we analyzed the virulence-related gene profiles in the toxigenic serogroup O1 strains isolated from 1923 to 2015, the genomes of which were publicly available. The virulence-related genes of the V. cholerae O1 strains were annotated based on the Virulence Factors Database (VFDB). An average of 230.1 virulence-related genes per strain were identified; significant differences in the average numbers were found between the classical and El Tor biotypes, and increasing trends in the number of virulence-related genes along with the isolation years were observed in the El Tor biotype strains. A total of 176 homologs of virulence-related genes were found from these strains, of which 25 belonged to the core genes, suggesting their conservative and necessary roles in V. cholerae pathogenesis. We described the diversities of the homologs by defining gene sequence type, and illustrated its association with gene duplication; we found that gene duplication clearly increased the complexity of the gene sequence types in the core virulence-related genes. In addition, we provided virulence-related gene profiles whose genetic characteristic depend on the isolation years from the view of gene gain and loss, variation, gene duplication and gene sequence type number.

Conclusions: Our study reveals the comprehensive variation dynamics of the virulence-related genes in toxigenic V. cholerae serogroup O1 during epidemics. The increasing trend for the virulence-related genes may suggest the evolutional advantage of strains by gaining virulence-related genes with diverse functional categories.
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http://dx.doi.org/10.1186/s12864-019-5725-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509779PMC
May 2019

Genomic comparison of serogroups O159 and O170 with other Vibrio cholerae serogroups.

BMC Genomics 2019 Mar 25;20(1):241. Epub 2019 Mar 25.

State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.

Background: Of the hundreds of Vibrio cholerae serogroups, O1 and O139 are the main epidemic-causing ones. Although non-O1/non-O139 serogroups rarely cause epidemics, the possibility exists for strains within them to have pathogenic potential.

Results: We selected 25 representative strains within 16 V. cholerae serogroups and examined their genomic and functional characteristics. We tentatively constructed a gene pool containing 405 homologous gene clusters, which is well organized and functions in O-antigen polysaccharide (O-PS) synthesis. Our network analysis indicate that great diversity exists in O-PS among the serogroups, and several serogroup pairs share a high number of homologous genes (e.g., O115 and O37; O170 and O139; O12 and O39). The phylogenetic analysis results suggest that a close relationship exists between serogroups O170, O89 and O144, based on neighbor-joining (NJ) and gene trees, although serogroup O159 showed an inconsistent phylogenetic relationship between the NJ tree and the gene tree, indicating that it may have undergone extensive recombination and horizontal gene transfer. Different phylogenetic structures were observed between the core genes, pan genes, and O-PS genes. The virulence gene analysis indicated that the virulence genes from all the representative strains may have their sources from four particular bacteria (Pseudomonas aeruginosa, V. vulnificus, Haemophilus somnus and H. influenzae), which suggests that V. cholerae may have exchanged virulence genes with other bacterial genera or species in certain environments. The mobile genetic element analysis indicated that O159 carries nearly complete VSP-II and partial VPI-1 and VPI-2, O170 carries partial VPI-1 and VPI-2, and several non-O1/non-O139 strains contain full or partial VPI-1 and VPI-2. Several genes showing evidence of positive selection are involved in chemotaxis, Na + resistance, or cell wall synthesis, suggestive of environmental adaptation.

Conclusions: This study reports on the newly sequenced O159 and O170 genomes and their comparisons with other V. cholerae serogroups. The complicated O-PS network of constituent genes highlights the detailed recombination mechanisms that have acted on the serogroups' genomes. The serogroups have different virulence-related gene profiles, and there is evidence of positive selection acting on other genes, possibly during adaptation to different environments and hosts.
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http://dx.doi.org/10.1186/s12864-019-5603-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434791PMC
March 2019

Epidemiologic and genomic insights on mcr-1-harbouring Salmonella from diarrhoeal outpatients in Shanghai, China, 2006-2016.

EBioMedicine 2019 Apr 21;42:133-144. Epub 2019 Mar 21.

State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China. Electronic address:

Background: Colistin resistance mediated by mcr-1-harbouring plasmids is an emerging threat in Enterobacteriaceae, like Salmonella. Based on its major contribution to the diarrhoea burden, the epidemic state and threat of mcr-1-harbouring Salmonella in community-acquired infections should be estimated.

Methods: This retrospective study analysed the mcr-1 gene incidence in Salmonella strains collected from a surveillance on diarrhoeal outpatients in Shanghai Municipality, China, 2006-2016. Molecular characteristics of the mcr-1-positive strains and their plasmids were determined by genome sequencing. The transfer abilities of these plasmids were measured with various conjugation strains, species, and serotypes.

Findings: Among the 12,053 Salmonella isolates, 37 mcr-1-harbouring strains, in which 35 were serovar Typhimurium, were detected first in 2012 and with increasing frequency after 2015. Most patients infected with mcr-1-harbouring strains were aged <5 years. All strains, including fluoroquinolone-resistant and/or extended-spectrum β-lactamase-producing strains, were multi-drug resistant. S. Typhimurium had higher mcr-1 plasmid acquisition ability compared with other common serovars. Phylogeny based on the genomes combined with complete plasmid sequences revealed some clusters, suggesting the presence of mcr-1-harbouring Salmonella outbreaks in the community. Most mcr-1-positive strains were clustered together with the pork strains, strongly suggesting pork consumption as a main infection source.

Interpretation: The mcr-1-harbouring Salmonella prevalence in community-acquired diarrhoea displays a rapid increase trend, and the ESBL-mcr-1-harbouring Salmonella poses a threat for children. These findings highlight the necessary and significance of prohibiting colistin use in animals and continuous monitoring of mcr-1-harbouring Salmonella.
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http://dx.doi.org/10.1016/j.ebiom.2019.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6491383PMC
April 2019

Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus .

Appl Environ Microbiol 2019 06 16;85(11). Epub 2019 May 16.

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China

The genus comprises a group of marine-dwelling species with worldwide distribution. Several species are regarded as causative agents of food spoilage and opportunistic pathogens of human diseases. In this study, a standard multilocus sequence analysis (MLSA) based on six protein-coding genes (, , , , , and ) was established as a rapid and accurate identification tool in 59 type strains. This method yielded sufficient resolving power in regard to enough informative sites, adequate sequence divergences, and distinct interspecies branches. The stability of phylogenetic topology was supported by high bootstrap values and concordance with different methods. The reliability of the MLSA scheme was further validated by identical phylogenies and high correlations of genomes. The MLSA approach provided a robust system to exhibit evolutionary relationships in the genus. The split network tree proposed twelve distinct monophyletic clades with identical G+C contents and high genetic similarities. A total of 86 tested strains were investigated to explore the population biology of the genus in China. The most prevalent species was , followed by , , , , and The strains frequently isolated from clinical and food samples highlighted the importance of increasing the surveillance of species. Based on the combined genetic, genomic, and phenotypic analyses, should be considered a synonym of , and should be reclassified as a synonym of The MLSA scheme based on six housekeeping genes (HKGs) (, , , , , and ) is well established as a reliable tool for taxonomic, evolutionary, and population diversity analyses of the genus in this study. The standard MLSA method allows researchers to make rapid, economical, and precise identification of strains. The robust phylogenetic network of MLSA provides profound insight into the evolutionary structure of the genus The population genetics of species determined by the MLSA approach plays a pivotal role in clinical diagnosis and routine monitoring. Further studies on remaining species and genomic analysis will enhance a more comprehensive understanding of the microbial systematics, phylogenetic relationships, and ecological status of the genus .
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http://dx.doi.org/10.1128/AEM.03126-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532039PMC
June 2019

Distribution and characteristics of SGI1/PGI2 genomic island from Proteus strains in China.

Infect Genet Evol 2019 06 27;70:123-130. Epub 2019 Feb 27.

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China; Center for Human Pathogen Collection, China CDC, Beijing, 102206, China. Electronic address:

The emergence of multidrug-resistant Salmonella genomic island 1 (SGI1) and Proteus genomic island (PGI) bearing P. mirabilis present a serious threat to public health. In this study, we screened 288 Proteus isolates recovered from seven provinces in China. Fourteen strains (4.9%) all belonged to P. mirabilis were positive for SGI1/PGI2, including twelve from clinical samples (5.3%) and two from food (3.3%). A Blastn search against GenBank and phylogenetic analyses identified eight different SGI1 variants and one PGI2 variant from the fourteen SGI1/PGI2 variants. All SGI1 variants shared a common backbone and harbored different resistance gene(s), except the sul1 gene at its multidrug-resistant (MDR) region. Among the variants, three novel SGI1 variants, designated as SGI1-PmCA11, SGI1-PmCA14 and SGI1-PmCA46, contained different gene cassettes, which were similar to sequences in plasmids or class 1 integrons of Klebsiella pneumoniae, P. mirabilis, Escherichia coli and Salmonella. Moreover, one novel PGI2, designated as PGI2-PmCA72, had an identical gene cassette to the first class 1 integron from PGI2 (GenBank accession no. MG201402.1) in P. mirabilis, but varied due to missing, replaced, inserted and inverted gene clusters. The four novel SGI1/PGI2 variants contained the cmlA5, dfrA14, bla, aadA15, bla, catB3 and dfrA16 resistance genes, which have never been reported in SGI1/PGI2 variants. Phenotypically, all fourteen SGI1/PGI2-containing strains showed multidrug resistance. All except four strains were resistant to the first, or the second and/or-third generation cephalosporins. Considering the increasing number and the emergence of new SGI1/PGI2 variants, further surveillance is needed to prevent the spreading of the MDR genomic islands among Proteus isolates from human and food.
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http://dx.doi.org/10.1016/j.meegid.2019.02.027DOI Listing
June 2019

Proteus faecis sp. nov., and Proteus cibi sp. nov., two new species isolated from food and clinical samples in China.

Int J Syst Evol Microbiol 2019 Mar 21;69(3):852-858. Epub 2019 Jan 21.

2​Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, PR China.

Eight swarming motile bacteria were isolated from food and clinical samples in China. Cells were Gram-stain-negative, facultatively anaerobic and rod-shaped (0.5-0.8×1.0-3.0 μm) with hairlike pili and flagella. The 16S rRNA and partial rpoB housekeeping gene sequence analyses indicated that the strains belong to the genus Proteusin the family Enterobacteriaceae. Of the eight strains studied, seven and a single isolate formed two separate clades in the phylogeny of Proteusspecies, indicating two separate species. Both the in silico DNA-DNA hybridization and the average nucleotide identity values between these two groups and to the type strains of the genus Proteuswere below the recommended threshold for signifying their candidature as two separate species. The DNA G+C contents of strains TJ1636 and FJ2001126-3 were 37.8 and 38.1 mol%, respectively. The major cellular fatty acids of the two novel type strains were C16:0, cyclo C17:0, summed feature 3 and summed feature 8. The results supported that the strains belong to different taxonomic positions in the genus Proteus. The isolates were named Proteus faecis sp. nov., with type strain TJ1636 (=DSM 106180=GDMCC 1.1245), and Proteuscibi sp. nov., with type strain FJ2001126-3 (=DSM 106178 =GDMCC 1.1244).
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http://dx.doi.org/10.1099/ijsem.0.003248DOI Listing
March 2019

Distribution and Genetic Characteristics of SXT/R391 Integrative Conjugative Elements in spp. From China.

Front Microbiol 2018 11;9:920. Epub 2018 May 11.

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

The genus consists of facultatively anaerobic Gram-negative bacteria, which are regarded as potential agents of food contamination and opportunistic human pathogens. Information about the distribution and genetic characteristics of SXT/R391 integrative conjugative elements (ICEs) in species is limited. Here, 91 strains collected from diverse samples in China were studied for the presence of SXT/R391 ICEs. Three positive strains, classified as , were obtained from patients and water from a local mill. In light of their close clonal relationships and high sequence similarity, a representative ICE was selected and designated ICECHN110003. The BLASTn searches against GenBank showed that ICEBan5 was most closely related to ICECHN110003, with the coverage of 76% and identity of 99%. The phylogenetic tree of concatenated core genes demonstrated that ICECHN110003 formed a distinct branch outside the cluster comprising ICEA056-1, ICECHN2410, and ICEChn1. Comparison of the genetic structures revealed that ICECHN110003 encoded uncommon genes in hotspots, such as specific type III restriction-modification system, conferring adaptive functions to the host. Based on the low coverage in the sequence analysis, independent clade in the phylogenetic tree, and unique inserted fragments in hotspots, ICECHN110003 represented a novel SXT/R391 element, which widened the list of ICEs. Furthermore, the antibiotic resistance genes , , , and in ICECHN110003 and resistance to multiple drugs of the positive isolates were detected. A cross-species transfer capability of the SXT/R391 ICEs was also discovered. In summary, it is necessary to reinforce continuous surveillance of SXT/R391 ICEs in the genus .
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http://dx.doi.org/10.3389/fmicb.2018.00920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5958206PMC
May 2018
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