scholarly journals Genomic analysis of multidrug-resistant clinical Enterococcus faecalis isolates for antimicrobial resistance genes and virulence factors from the western region of Saudi Arabia

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Muhammad Farman ◽  
Muhammad Yasir ◽  
Rashad R. Al-Hindi ◽  
Suha A. Farraj ◽  
Asif A. Jiman-Fatani ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Antimicrobial Resistance ◽  
Enterococcus Faecalis ◽  
Virulence Factors ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Western Region ◽  
Antimicrobial Resistance Genes ◽  
The Western Region

Multiple-Antibiotic Resistance of Enterococcus faecalis and Enterococcus faecium from Cecal Contents in Broiler Chicken and Turkey Flocks Slaughtered in Canada and Plasmid Colocalization of tetO and ermB Genes

2011 ◽  
Vol 74 (10) ◽  
pp. 1639-1648 ◽  
Author(s):  
CINDY-LOVE TREMBLAY ◽  
ANN LETELLIER ◽  
SYLVAIN QUESSY ◽  
MARTINE BOULIANNE ◽  
DANIELLE DAIGNAULT ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Enterococcus Faecalis ◽  
Resistance Genes ◽  
Enterococcus Faecium ◽  
Broiler Chicken ◽  
Multidrug Resistant ◽  
Poultry Meat ◽  
Antimicrobial Resistance Genes ◽  
High Level ◽  
Level Resistance

This study was conducted to characterize the antimicrobial resistance determinants and investigate plasmid colocalization of tetracycline and macrolide genes in Enterococcus faecalis and Enterococcus faecium from broiler chicken and turkey flocks in Canada. A total of 387 E. faecalis and E. faecium isolates were recovered from poultry cecal contents from five processing plants. The percentages of resistant E. faecalis and E. faecium isolates, respectively, were 88.1 and 94% to bacitracin, 0 and 0.9% to chloramphenicol, 0.7 and 14.5% to ciprofloxacin, 72.6 and 80.3% to erythromycin, 3.7 and 41% to flavomycin, 9.6 and 4.3% (high-level resistance) to gentamicin, 25.2 and 17.1% (high-level resistance) to kanamycin, 100 and 94% to lincomycin, 0 and 0% to linezolid, 2.6 and 20.5% to nitrofurantoin, 3 and 27.4% to penicillin, 98.5 and 89.7% to quinupristin-dalfopristin, 7 and 12.8% to salinomycin, 46.7 and 38.5% (high-level resistance) to streptomycin, 95.6 and 89.7% to tetracycline, 73 and 75.2% to tylosin, and 0 and 0% to vancomycin. One predominant multidrug-resistant phenotypic pattern was identified in both E. faecalis and E. faecium (bacitracin, erythromycin, lincomycin, quinupristin-dalfopristin, tetracycline, and tylosin). These isolates were further examined by PCR and sequencing for the genes encoding their antimicrobial resistance. Various combinations of vatD, vatE, bcrR, bcrA, bcrB, bcrD, ermB, msrC, linB, tetM, and tetO genes were detected, and ermB, tetM, and bcrB were the most common antimicrobial resistance genes identified. For the first time, plasmid extraction and hybridization revealed colocalization of tetO and ermB genes on a ca. 11-kb plasmid in E. faecalis isolates, and filter mating experiments demonstrated its transferability. Results indicate that the intestinal enterococci of healthy poultry, which can contaminate poultry meat at slaughter, could be a reservoir for quinupristin-dalfopristin, bacitracin, tetracycline, and macrolide resistance genes.

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.

scholarly journals Characteristics of High-Level Aminoglycoside-Resistant Enterococcus faecalis Isolated from Bulk Tank Milk in Korea

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1724
Author(s):  
Hyo Jung Kang ◽  
Sunghyun Yoon ◽  
Koeun Kim ◽  
Young Ju Lee
Keyword(s):  
Antimicrobial Resistance ◽  
Enterococcus Faecalis ◽  
Virulence Factors ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Management Program ◽  
Bulk Tank Milk ◽  
Antimicrobial Resistance Genes ◽  
Bulk Tank ◽  
High Level

Enterococci, which are considered environmental mastitis-causing pathogens, have easily acquired aminoglycoside-resistant genes that encode various aminoglycoside-modifying enzymes (AME). Therefore, this study was conducted to compare the distribution of high-level aminoglycoside-resistant (HLAR) and multidrug-resistant (MDR) Enterococcus faecalis (E. faecalis) bacteria isolated from bulk tank milk in four dairy companies in Korea. Moreover, it analyzed the characteristics of their antimicrobial resistance genes and virulence factors. Among the 301 E. faecalis bacteria studied, 185 (61.5%) showed HLAR with no significant differences among the dairy companies. Furthermore, 129 (69.7%) of the 185 HLAR E. faecalis showed MDR without significant differences among companies. In contrast, HLAR E. faecalis from companies A, B, and C were significantly higher in resistance to the four classes than those in company D, which had the highest MDR ability against the three antimicrobial classes (p < 0.05). In addition, in the distribution of AME genes, 72 (38.9%) and 36 (19.5%) of the isolates carried both aac(6′)Ie-aph(2″)-la and ant(6)-Ia genes, and the ant (6)-Ia gene alone, respectively, with significant differences among the companies (p < 0.05). In the distribution of virulence genes, the ace (99.5%), efa A (98.9%), and cad 1 (98.4%) genes were significantly prevalent (p < 0.05). Thus, our results support that an advanced management program by companies is required to minimize the dissemination of antimicrobial resistance and virulence factors.

scholarly journals Genomic Investigation of Antimicrobial-Resistant Salmonella enterica Isolates From Dead Chick Embryos in China

2021 ◽  
Vol 12 ◽  
Author(s):  
Mohammed Elbediwi ◽  
Yanting Tang ◽  
Dawei Shi ◽  
Hazem Ramadan ◽  
Yaohui Xu ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Chick Embryo ◽  
Virulence Factors ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Multidrug Resistant ◽  
Henan Province ◽  
Health Concern ◽  
Antimicrobial Resistance Genes ◽  
Genomic Characterization

Salmonella spp. is recognized as an important zoonotic pathogen. The emergence of antimicrobial resistance in Salmonella enterica poses a great public health concern worldwide. While the knowledge on the incidence and the characterization of different S. enterica serovars causing chick embryo death remains obscure in China. In this study, we obtained 45 S. enterica isolates from 2,139 dead chick embryo samples collected from 28 breeding chicken hatcheries in Henan province. The antimicrobial susceptibility assay was performed by the broth microdilution method and the results showed that 31/45 (68.8%) isolates were multidrug-resistant (≥3 antimicrobial classes). Besides the highest resistance rate was observed in the aminoglycoside class, all the isolates were susceptible to chloramphenicol, azithromycin, and imipenem. Furthermore, genomic characterization revealed that S. Enteritidis (33.33%; 15/45) was a frequent serovar that harbored a higher number of virulence factors compared to other serovars. Importantly, genes encoding β-lactamases were identified in three serovars (Thompson, Enteritidis, and Kottbus), whereas plasmid-mediated quinolone resistance genes (qnrB4) were detected in certain isolates of S. Thompson and the two S. Kottbus isolates. All the examined isolates harbored the typical virulence factors from Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2). Additionally, a correlation analysis between the antimicrobial resistance genes, phenotype, and plasmids was conducted among Salmonella isolates. It showed strong positive correlations (r &lt; 0.6) between the different antimicrobial-resistant genes belonging to certain antimicrobial classes. Besides, IncF plasmid showed a strong negative correlation (r &gt; −0.6) with IncHI2 and IncHI2A plasmids. Together, our study demonstrated antimicrobial-resistant S. enterica circulating in breeding chicken hatcheries in Henan province, highlighting the advanced approach, by using genomic characterization and statistical analysis, in conducting the routine monitoring of the emerging antimicrobial-resistant pathogens. Our findings also proposed that the day-old breeder chicks trading could be one of the potential pathways for the dissemination of multidrug-resistant S. enterica serovars.

scholarly journals Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance inKlebsiella pneumoniae, an urgent threat to public health

2015 ◽  
Vol 112 (27) ◽  
pp. E3574-E3581 ◽  
Author(s):  
Kathryn E. Holt ◽  
Heiman Wertheim ◽  
Ruth N. Zadoks ◽  
Stephen Baker ◽  
Chris A. Whitehouse ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Distinct Species ◽  
Invasive Disease ◽  
Multidrug Resistant ◽  
Human Infection ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes

Klebsiella pneumoniaeis now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections.K.pneumoniaeis ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure ofK.pneumoniae, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework forK.pneumoniaebased on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting ofK.pneumoniaeinto three distinct species, KpI (K.pneumoniae), KpII (K.quasipneumoniae), and KpIII (K.variicola). Further, forK.pneumoniae(KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We showK.pneumoniaehas a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasiveK.pneumoniaeinfections; our data provide the whole-genome framework against which to track the emergence of such threats.

scholarly journals Serotype distribution, antimicrobial susceptibility, antimicrobial resistance genes and virulence genes of Salmonella isolated from a pig slaughterhouse in Yangzhou, China

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Quan Li ◽  
Jian Yin ◽  
Zheng Li ◽  
Zewei Li ◽  
Yuanzhao Du ◽  
...  
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Antimicrobial Susceptibility ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Resistance Rate ◽  
Economic Losses ◽  
Production Chain ◽  
Antimicrobial Resistance Genes

AbstractSalmonella is an important food-borne pathogen associated with public health and high economic losses. To investigate the prevalence and the characteristics of Salmonella in a pig slaughterhouse in Yangzhou, a total of 80 Salmonella isolates were isolated from 459 (17.43%) samples in 2016–2017. S. Derby (35/80, 43.75%) was the most prevalent, followed by S. Rissen (16/80, 20.00%) and S. Newlands (11/80, 13.75%). The highest rates of susceptibility were observed to cefoxitin (80/80, 100.0%) and amikacin (80/80, 100.0%), followed by aztreonam (79/80, 98.75%) and nitrofurantoin (79/80, 98.75%). The highest resistance rate was detected for tetracycline (65/80, 81.25%), followed by ampicillin (60/80, 75.00%), bactrim (55/80, 68.75%), and sulfisoxazole (54/80, 67.50%). Overall, 91.25% (73/80) of the isolates were resistant to at least one antibiotic, while 71.25% (57/80) of the isolate strains were multidrug resistant in the antimicrobial susceptibility tested. In addition, 86.36% (19/22) of the 22 antimicrobial resistance genes in the isolates were identified. Our data indicated that the resistance to certain antimicrobials was significantly associated, in part, with antimicrobial resistance genes. Furthermore, 81.25% (65/80) isolates harbored the virulence gene of mogA, of which 2 Salmonella Typhimurium isolates carried the mogA, spvB and spvC virulence genes at the same time. The results showed that swine products in the slaughterhouse were contaminated with multidrug resistant Salmonella commonly, especially some isolates carry the spv virulence genes. The virulence genes might facilitate the dissemination of the resistance genes to consumers along the production chain, suggesting the importance of controlling Salmonella during slaughter for public health.

Antimicrobial Resistance and Virulence of Enterococcus faecalis Isolated from Retail Food†

2008 ◽  
Vol 71 (4) ◽  
pp. 760-769 ◽  
Author(s):  
LORI L. McGOWAN-SPICER ◽  
PAULA J. FEDORKA-CRAY ◽  
JONATHAN G. FRYE ◽  
RICHARD J. MEINERSMANN ◽  
JOHN B. BARRETT ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Enterococcus Faecalis ◽  
Virulence Factors ◽  
Tetracycline Resistance ◽  
Grocery Stores ◽  
Erythromycin Resistance ◽  
Significance Level ◽  
Antimicrobial Resistance Genes ◽  
Overall Resistance ◽  
Retail Food

Although enterococci are considered opportunistic nosocomial pathogens, their contribution to foodborne illnesses via dissemination through retail food remains undefined. In this study, prevalence and association of antimicrobial resistance and virulence factors of 80 Enterococcus faecalis isolates from retail food items were investigated. The highest rates of resistance were observed for lincomycin (73 of 80 isolates, 91%) and bacitracin (57 of 80 isolates, 71%), and lower rates of resistance (≤40%) were found for chloramphenicol, ciprofloxacin, erythromycin, flavomycin, gentamicin, kanamycin, nitrofurantoin, penicillin, and tylosin. Overall resistance to antimicrobials was low for most isolates tested. Of the virulence factors tested, the majority of isolates were positive for ccf (78 of 80 isolates, 98%), efaAfs (77 of 80, 96%), and cpd (74 of 80, 93%). Isolates also commonly contained cob (72 of 80 isolates, 90%) and gelE (68 of 80, 85%). Very few isolates contained cylMBA (12 of 80 isolates [15%] for cylM and 9 of 80 isolates [11%] for both cylB and cylA) and efaAfm (2 of 80 isolates, 3%). Positive statistical associations (significance level of 0.05) were found between agg and tetracycline resistance, cylM and erythromycin resistance, and gelE and efaAfs and lincomycin resistance. The presence of the cylB and cylA alleles also was positively correlated with bacitracin and tetracycline resistance. Negative correlations were observed between many of the virulence attributes and resistance to ciprofloxacin, erythromycin, flavomycin, gentamicin, kanamycin, and tylosin. These data suggest that both positive and negative associations exist between antimicrobial resistance genes and virulence factors in E. faecalis isolates from foods commonly purchased from grocery stores.

scholarly journals Multidrug-Resistant Streptococcus agalactiae Strains Found in Human and Fish with High Penicillin and Cefotaxime Non-Susceptibilities

2020 ◽  
Vol 8 (7) ◽  
pp. 1055
Author(s):  
Carmen Li ◽  
Dulmini Nanayakkara Sapugahawatte ◽  
Ying Yang ◽  
Kam Tak Wong ◽  
Norman Wai Sing Lo ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Streptococcus Agalactiae ◽  
Novel Mutation ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Healthcare Facilities ◽  
Surveillance Studies ◽  
Penicillin Binding Proteins ◽  
Antimicrobial Resistance Genes

Penicillin non-susceptible Streptococcus agalactiae (PEN-NS GBS) has been increasingly reported, with multidrug-resistant (MDR) GBS documented in Japan. Here we identified two PEN-NS GBS strains during our surveillance studies: one from a patient’s wound and the other from a tilapia. The patient’s GBS (H21) and fish GBS (F49) were serotyped and tested for antibiotic susceptibility. Whole-genome sequencing was performed to find the sequence type, antimicrobial resistance genes, and mutations in penicillin-binding proteins (PBPs) and fluoroquinolone (FQ) resistance genes. H21 and F49 belonged to ST651, serotype Ib, and ST7, serotype Ia, respectively. H21 showed PEN and cefotaxime minimum inhibitory concentrations (MICs) of 2.0 mg/L. F49 showed PEN MIC 0.5 mg/L. H21 was MDR with ermB, lnuB, tetS, ant6-Ia, sat4a, and aph3-III antimicrobial resistance genes observed. Alignment of PBPs showed the combination of PBP1B (A95D) and 2B mutations (V80A, S147A, S160A) in H21 and a novel mutation in F49 at N192S in PBP2B. Alignment of FQ-resistant determinants revealed mutation sites on gyrA, gyrB, and parC and E in H21. To our knowledge, this is the first report of GBS isolates with such high penicillin and cefotaxime MICs. This raises the concern of emergence of MDR and PEN-NS GBS in and beyond healthcare facilities.

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