Lack of defense systems drives Enterococcus easily evolved into lysogens

2019 ◽  
Author(s):  
Shengyi Han ◽  
JianHua Zhou ◽  
Lina Ma ◽  
Chengxiu Ma ◽  
Qiaoying Zeng ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Potential Contribution ◽  
Systematic Analysis ◽  
Evolutionary Origins ◽  
Distribution Potential ◽  
Foreign Genes ◽  
The Relationship

Abstract Background: Enterococcus are important opportunistic pathogens that readily acquire foreign genes and could be easily lysogenized by phages. But no comparative genomic analysis of Enterococcus prophages had been undertaken to date. The prophage distribution, potential contribution and the relationship with Enterococcus defensive system remain unclear. Result: This study presents a comparative analysis of 563 putative prophages identified in 107 chromosomes and 301 plasmids of Enterococcus. Our result suggested that lysogens are highly prevalent in Enterococcus and Enterococcus genomes have more prophages than other bacteria, the number of prophages are related with strains pathogenicity, groups and isolated regions, and the prophages distribution present phylogeographic pattern. By analyzing the prophages characteristic, it is found that prophages can be divided into many clusters, but most of prophages have distant genetic relationship with sequenced phages and remain unreported; Prophages integrated into chromosomes and plasmids have different evolutionary origins, and show different genomes size, GC% and genes characteristic. It should be noted that all antibiotic resistance genes are carried by plasmids prophages and E. faecium plasmid prophages play important roles in transmission of vancomycin resistance genes through plasmid conjugation transfer and phages transduction. By investigating and statistical analyzing the relationship between major defend systems and the number of prophages, it indicated that R-M system often absent in Enterococcus, orphan CRISPR array prevalent in most of Enterococcus, and the presence of CRISPR-spacers and the absence of prophages in lysogen is inversely related. Conclusion: To our knowledge, this is the first systematic analysis of Enterococcus prophages distribution, potential contribution and phylogeny, and elucidate the relationship between defense system and lysogeny in Enterococcus. This information helps to understand how prophages affect its hosts diversity, fitness and evolution.

scholarly journals Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Seung Woo Ahn ◽  
Se Hee Lee ◽  
Uh Jin Kim ◽  
Hee-Chang Jang ◽  
Hak-Jong Choi ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
University Hospital ◽  
Comparative Genomic ◽  
Toxin Gene ◽  
Rrna Gene ◽  
Clostridioides Difficile

Abstract Background Clostridioides difficile infection (CDI) is an infectious nosocomial disease caused by Clostridioides difficile, an opportunistic pathogen that occurs in the intestine after extensive antibiotic regimens. Results Nine C. difficile strains (CBA7201–CBA7209) were isolated from nine patients diagnosed with CDI at the national university hospital in Korea, and the whole genomes of these strains were sequenced to identify their genomic characteristics. Comparative genomic analysis was performed using 51 reference strains and the nine isolated herein. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that all 60 C. difficile strains belong to the genus Clostridioides, while core-genome tree indicated that they were divided into five groups, which was consistent with the results of MLST clade analysis. All strains were confirmed to have a clindamycin antibiotic resistance gene, but the other antibiotic resistance genes differ depending on the MLST clade. Interestingly, the six strains belonging to the sequence type 17 among the nine C. difficile strains isolated here exhibited unique genomic characteristics for PaLoc and CdtLoc, the two toxin gene loci identified in this study, and harbored similar antibiotic resistance genes. Conclusion In this study, we identified the specific genomic characteristics of Korean C. difficile strains, which could serve as basic information for CDI prevention and treatment in Korea.

scholarly journals Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1025
Author(s):  
Shaohua Zhao ◽  
Cong Li ◽  
Chih-Hao Hsu ◽  
Gregory H. Tyson ◽  
Errol Strain ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Bacterial Infections ◽  
Genomic Analysis ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Comparative Genomic ◽  
Salmonella Infections ◽  
Antimicrobial Resistance Genes ◽  
Salmonella Pathogenicity Islands ◽  
Shed Light

Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.

scholarly journals High-Level Aminoglycoside Resistance in Human Clinical Klebsiella pneumoniae Complex Isolates and Characteristics of armA-Carrying IncHI5 Plasmids

2021 ◽  
Vol 12 ◽  
Author(s):  
Xueya Zhang ◽  
Qiaoling Li ◽  
Hailong Lin ◽  
Wangxiao Zhou ◽  
Changrui Qian ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Conjugative Plasmid ◽  
Comparative Genomic ◽  
Aminoglycoside Resistance ◽  
Life Threatening ◽  
Aminoglycoside Resistance Genes ◽  
High Level

Aminoglycosides are important options for treating life-threatening infections. However, high levels of aminoglycoside resistance (HLAR) among Klebsiella pneumoniae isolates have been observed to be increasing frequently. In this study, a total of 292 isolates of the K. pneumoniae complex from a teaching hospital in China were analyzed. Among these isolates, the percentage of HLAR strains was 13.7% (40/292), and 15 aminoglycoside resistance genes were identified among the HLAR strains, with rmtB being the most dominant resistance gene (70%, 28/40). We also described an armA-carrying Klebsiella variicola strain KP2757 that exhibited a high-level resistance to all aminoglycosides tested. Whole-genome sequencing of KP2757 demonstrated that the strain contained one chromosome and three plasmids, with all the aminoglycoside resistance genes (including two copies of armA and six AME genes) being located on a conjugative plasmid, p2757-346, belonging to type IncHI5. Comparative genomic analysis of eight IncHI5 plasmids showed that six of them carried two copies of the intact armA gene in the complete or truncated Tn1548 transposon. To the best of our knowledge, for the first time, we observed that two copies of armA together with six AME genes coexisted on the same plasmid in a strain of K. variicola with HLAR. Comparative genomic analysis of eight armA-carrying IncHI5 plasmids isolated from humans and sediment was performed, suggesting the potential for dissemination of these plasmids among bacteria from different sources. These results demonstrated the necessity of monitoring the prevalence of IncHI5 plasmids to restrict their worldwide dissemination.

Antibiotic susceptibility profiles and frequency of resistance genes in clinical Shiga toxin-producing Escherichia coli isolates from Michigan over a 14-year period

2021 ◽  
Author(s):  
Sanjana Mukherjee ◽  
Heather M. Blankenship ◽  
Jose A. Rodrigues ◽  
Rebekah E. Mosci ◽  
James T. Rudrik ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Shiga Toxin ◽  
Antibiotic Susceptibility ◽  
Genetic Relatedness ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Mechanisms Of Resistance ◽  
Susceptibility Profiles

Background: Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen that contributes to over 250,000 infections in the US each year. Because antibiotics are not recommended for STEC infections, resistance in STEC has not been widely researched despite an increased likelihood for the transfer of resistance gene from STEC to opportunistic pathogens residing within the same microbial community. Methods: Between 2001 and 2014, 969 STEC isolates were collected from Michigan patients. Serotyping and antibiotic susceptibility profiles to clinically relevant antibiotics were determined using disc diffusion, while epidemiological data was used to identify factors associated with resistance. Whole genome sequencing was used to examine genetic relatedness and identify genetic determinants and mechanisms of resistance in the non-O157 isolates. Results: Increasing frequencies of resistance to at least one antibiotic was observed over the 14 years (p=0.01). While the non-O157 serogroups were more commonly resistant than O157 (Odds Ratio: 2.4; 95% Confidence Interval:1.43-4.05), the frequency of ampicillin resistance among O157 isolates was significantly higher in Michigan compared to the national average (p=0.03). Genomic analysis of 321 non-O157 isolates uncovered 32 distinct antibiotic resistance genes (ARGs). Although mutations in genes encoding resistance to ciprofloxacin and ampicillin were detected in four isolates, most of the horizontally acquired ARGs conferred resistance to aminoglycosides, β-lactams, sulfonamides and/or tetracycline. Conclusions: This study provides insight into the mechanisms of resistance in a large collection of clinical non-O157 STEC isolates and demonstrates that antibiotic resistance among all STEC serogroups has increased over time, prompting the need for enhanced surveillance.

scholarly journals Characterization of an IncR Plasmid with Two Copies of ISCR-Linked qnrB6 from ST968 Klebsiella pneumoniae

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Changrui Qian ◽  
Xinyi Zhu ◽  
Junwan Lu ◽  
Kai Shen ◽  
Qianqian Chen ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
The Other ◽  
Comparative Genomic ◽  
Clear Understanding ◽  
Class 1 Integron ◽  
Bacterial Chromosomes ◽  
Class 1 ◽  
Plasmid Backbone

To characterize the molecular structure of IncR plasmid-related sequences, comparative genomic analysis was conducted using 261 IncR plasmid backbone-related sequences. Among the sequences, 257 were IncR plasmids including the multidrug-resistance IncR plasmid pR50-74 from Klebsiella pneumoniae strain R50 of this work, and the other four were from bacterial chromosomes. The IncR plasmids were derived from different bacterial genera or species, mainly Klebsiella pneumoniae (70.82%, 182/257), Escherichia coli (11.28%, 29/257), Enterobacter cloacae (7.00%, 18/257), and Citrobacter freundii (3.50%, 9/257). The bacterial chromosomes carrying IncR plasmid backbone sequences were derived from Proteus mirabilis AOUC-001 and Klebsiella pneumoniae KPN1344, among others. The IncR backbone sequence of P. mirabilis AOUC-001 chromosome shows the highest identity with that of pR50-74. Complex class 1 integrons carrying various copies of ISCR1-sdr-qnrB6-△qacE/sul1 (ISCR1-linked qnrB6 unit) were identified in IncR plasmids. In addition to two consecutive copies of qnrB6-qacE-sul1, the other resistance genes encoded on pR50-74 are all related to mobile genetic elements, such as IS1006, IS26, and the class 1 integron. This study provides a clear understanding of the mobility and plasticity of the IncR plasmid backbone sequence and emphasizes the important role of ISCR in the recruitment of multicopy resistance genes.

scholarly journals Sequencing and Comparative Genomic Analysis of pK29, a 269-Kilobase Conjugative Plasmid Encoding CMY-8 and CTX-M-3 β-Lactamases in Klebsiella pneumoniae

2007 ◽  
Vol 51 (8) ◽  
pp. 3004-3007 ◽  
Author(s):  
Ying-Tsong Chen ◽  
Tsai-Ling Lauderdale ◽  
Tsai-Lien Liao ◽  
Yih-Ru Shiau ◽  
Hung-Yu Shu ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Conjugative Plasmid ◽  
Comparative Genomic ◽  
Antimicrobial Resistance Genes ◽  
Genomic Analyses ◽  
The Common

ABSTRACT A 269-kilobase conjugative plasmid, pK29, from a Klebsiella pneumoniae strain was sequenced. The plasmid harbors multiple antimicrobial resistance genes, including those encoding CMY-8 AmpC-type and CTX-M-3 extended-spectrum β-lactamases in the common backbone of IncHI2 plasmids. Mechanisms for dissemination of the resistance genes are highlighted in comparative genomic analyses.

scholarly journals Non-antibiotic pharmaceuticals can enhance the spread of antibiotic resistance via conjugation

2019 ◽  
Author(s):  
Yue Wang ◽  
Ji Lu ◽  
Shuai Zhang ◽  
Jie Li ◽  
Likai Mao ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Cell Membrane ◽  
Membrane Permeability ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Protein Sequencing ◽  
Cell Membrane Permeability ◽  
Lipid Lowering ◽  
Potential Contribution

AbstractAntibiotic resistance is a global threat for public health. It is widely acknowledged that antibiotics at sub-inhibitory concentrations are important in disseminating antibiotic resistance via horizontal gene transfer. While there is high use of non-antibiotic human-targeted pharmaceuticals in our societies, the potential contribution of these on the spread of antibiotic resistance has been overlooked so far. Here, we report that commonly consumed non-antibiotic pharmaceuticals, including nonsteroidal anti-inflammatories (ibuprofen, naproxen, diclofenac), a lipid-lowering drug (gemfibrozil), and a β-blocker (propanolol), at clinically and environmentally relevant concentrations, significantly accelerated the conjugation of plasmid-borne antibiotic resistance genes. We looked at the response to these drugs by the bacteria involved in the gene transfer through various analyses that included monitoring reactive oxygen species (ROS) and cell membrane permeability by flow cytometry, cell arrangement, and whole-genome RNA and protein sequencing. We found the enhanced conjugation correlated well with increased production of ROS and cell membrane permeability. We also detected closer cell-to-cell contact and upregulated conjugal genes. Additionally, these non-antibiotic pharmaceuticals caused the bacteria to have responses similar to those detected when exposed to antibiotics, such as inducing the SOS response, and enhancing efflux pumps. The findings advance our understanding of the bacterial transfer of antibiotic resistance genes, and importantly emphasize concerns of non-antibiotic human-targeted pharmaceuticals for enhancing the spread of antibiotic resistance.

scholarly journals Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen

2020 ◽  
Author(s):  
Robin B. Guevarra ◽  
Stefan Magez ◽  
Eveline Peeters ◽  
Mi Sook Chung ◽  
Kyung Hyun Kim ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Virulence Factors ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Pantoea Agglomerans ◽  
Whole Genome ◽  
Tnf Α ◽  
Wide Range ◽  
Depth Analysis

AbstractPantoea agglomerans is a Gram-negative aerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome of P. agglomerans KM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophages in vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-α, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-α, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-α, IL-6 and NO involved solely activation of the NF-κB, IL-10 secretion was largely dependent on NF-κB and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of the P. agglomerans KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts.

scholarly journals Evolution of Antibiotic Resistance and the Relationship between the Antibiotic Resistance Genes and Microbial Compositions under Long-Term Exposure to Tetracycline and Sulfamethoxazole

2019 ◽  
Vol 16 (23) ◽  
pp. 4681 ◽  
Author(s):  
Bingbing Du ◽  
Qingxiang Yang ◽  
Ruifei Wang ◽  
Ruimin Wang ◽  
Qiang Wang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
The Core ◽  
Aerobic Wastewater Treatment ◽  
The Relationship ◽  
Bacterial Groups ◽  
Wastewater Treatment Systems

The removal of antibiotics and widespread of antibiotic resistance genes (ARGs) have received continuous attention due to the possible threats to environment. However, little information is available on the evolution of antibiotic resistance and the relationship between ARGs and microbial communities under long-term exposure to sub-inhibitory concentrations of antibiotics. In our study, two laboratory-scale anoxic-aerobic wastewater treatment systems were established and operated for 420 days to investigate the evolution of antibiotic resistance under exposure of 5 mg·L−1 tetracycline (TC) or 5 mg·L−1 TC and 1 mg·L−1 sulfamethoxazole (SMX). The average removal rates of TC and SMX were about 59% and 72%, respectively. The abundance of the main ARGs responsible for resistance to TC and SMX increased obviously after antibiotics addition, especially when TC and SMX in combination (increased 3.20-fold). The tetC and sul1 genes were the predominant genes in the development of TC and SMX resistance, in which gene sul1 had the highest abundance among all the detected ARGs. Network analysis revealed that under antibiotic pressure, the core bacterial groups carrying multiple ARGs formed and concentrated in about 20 genera such as Dechloromonas, Candidatus Accumulibacter, Aeromonas, Rubrivivax, in which intI1 played important roles in transferring various ARGs except sul3.

scholarly journals Emergence and Evolution of Multidrug-Resistant Klebsiella pneumoniae with both blaKPC and blaCTX-M Integrated in the Chromosome

2017 ◽  
Vol 61 (7) ◽  
Author(s):  
Weihua Huang ◽  
Guiqing Wang ◽  
Robert Sebra ◽  
Jian Zhuge ◽  
Changhong Yin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
De Novo ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Type I ◽  
Content Type ◽  
Antimicrobial Resistance Genes

ABSTRACT The extended-spectrum-β-lactamase (ESBL)- and Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae represent serious and urgent threats to public health. In a retrospective study of multidrug-resistant K. pneumoniae, we identified three clinical isolates, CN1, CR14, and NY9, carrying both bla CTX-M and bla KPC genes. The complete genomes of these three K. pneumoniae isolates were de novo assembled by using both short- and long-read whole-genome sequencing. In CR14 and NY9, bla CTX-M and bla KPC were carried on two different plasmids. In contrast, CN1 had one copy of bla KPC-2 and three copies of bla CTX-M-15 integrated in the chromosome, for which the bla CTX-M-15 genes were linked to an insertion sequence, ISEcp1, whereas the bla KPC-2 gene was in the context of a Tn4401a transposition unit conjugated with a PsP3-like prophage. Intriguingly, downstream of the Tn4401a-bla KPC-2-prophage genomic island, CN1 also carried a clustered regularly interspaced short palindromic repeat (CRISPR)-cas array with four spacers targeting a variety of K. pneumoniae plasmids harboring antimicrobial resistance genes. Comparative genomic analysis revealed that there were two subtypes of type I-E CRISPR-cas in K. pneumoniae strains and suggested that the evolving CRISPR-cas, with its acquired novel spacer, induced the mobilization of antimicrobial resistance genes from plasmids into the chromosome. The integration and dissemination of multiple copies of bla CTX-M and bla KPC from plasmids to chromosome depicts the complex pandemic scenario of multidrug-resistant K. pneumoniae. Additionally, the implications from this study also raise concerns for the application of a CRISPR-cas strategy against antimicrobial resistance.

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