Insertion Sequence IS26 Reorganizes Plasmids in Clinically Isolated Multidrug-Resistant Bacteria by Replicative Transposition

ABSTRACTCarbapenemase-producingEnterobacteriaceae(CPE), which are resistant to most or all known antibiotics, constitute a global threat to public health. Transposable elements are often associated with antibiotic resistance determinants, suggesting a role in the emergence of resistance. One insertion sequence, IS26, is frequently associated with resistance determinants, but its role remains unclear. We have analyzed the genomic contexts of 70 IS26 copies in several clinical and surveillance CPE isolates from the National Institutes of Health Clinical Center. We used target site duplications and their patterns as guides and found that a large fraction of plasmid reorganizations result from IS26replicative transpositions, including replicon fusions, DNA inversions, and deletions. Replicative transposition could also be inferred for transposon Tn4401, which harbors the carbapenemaseblaKPCgene. Thus, replicative transposition is important in the ongoing reorganization of plasmids carrying multidrug-resistant determinants, an observation that carries substantial clinical and epidemiological implications for understanding how such extreme drug resistance phenotypes evolve.IMPORTANCEAlthough IS26is frequently reported to reside in resistance plasmids of clinical isolates, the characteristic hallmark of transposition, target site duplication (TSD), is generally not observed, raising questions about the mode of transposition for IS26. The previous observation of cointegrate formation during transposition implies that IS26transposes via a replicative mechanism. The other possible outcome of replicative transposition is DNA inversion or deletion, when transposition occurs intramolecularly, and this would also generate a specific TSD pattern that might also serve as supporting evidence for the transposition mechanism. The numerous examples we present here demonstrate that replicative transposition, used by many mobile elements (including IS26and Tn4401), is prevalent in the plasmids of clinical isolates and results in significant plasmid reorganization. This study also provides a method to trace the evolution of resistance plasmids based on TSD patterns.

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Combating multidrug‐resistant bacteria by integrating a novel target site penetration and receptor binding assay platform into translational modeling

Clinical Pharmacology & Therapeutics ◽

10.1002/cpt.2205 ◽

2021 ◽

Author(s):

Yinzhi Lang ◽

Nirav R. Shah ◽

Xun Tao ◽

Stephanie M. Reeve ◽

Jieqiang Zhou ◽

...

Keyword(s):

Receptor Binding ◽

Binding Assay ◽

Multidrug Resistant ◽

Target Site ◽

Resistant Bacteria ◽

Multidrug Resistant Bacteria ◽

Receptor Binding Assay ◽

Novel Target ◽

Translational Modeling

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Detection of Antibiotic-Resistant Bacteria, Resistance Determinants, and Mobile Elements in Surface Waters in Lebanon

10.1101/2021.02.12.21251645 ◽

2021 ◽

Author(s):

Jennifer Moussa ◽

Edmond Abboud ◽

Sima Tokajian

Keyword(s):

Surface Water ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Population Mobility ◽

Antibiotic Resistant Bacteria ◽

Antibiotic Resistant ◽

E Coli ◽

Resistance Determinants ◽

Bacterial Contaminants ◽

Plasmid Analysis

AbstractThe prevalence of antibiotic-resistant bacteria in surface water in Lebanon is a growing concern and understanding the mechanisms of the spread of resistance determinants is essential. We aimed at studying the occurrence of resistant organisms and determinants in surface water sources in Lebanon and understanding their mobilization and transmission. Water samples were collected from five major rivers in Lebanon. 91 isolates were recovered out of which 25 were multidrug-resistant (MDR) and accordingly were further characterized. Escherichia coli and Klebsiella pneumoniae were the most commonly identified MDR isolates. Conjugation assays coupled with in silico plasmid analysis were performed and validated using PCR-based replicon typing (PBRT) to identify and confirm incompatibility groups and the localization of β-lactamase encoding genes. E. coli EC23 carried a blaNDM-5 gene on a conjugative, multireplicon plasmid, while blaCTX-M-15 and blaTEM-1B were detected in the majority of the MDR isolates. Different ST types were identified including the highly virulent E. coli ST131. Our results showed a common occurrence of bacterial contaminants in surface water and an increase in the risk for the dissemination of resistance determinants exacerbated with the ongoing intensified population mobility in Lebanon and the widespread lack of wastewater treatment.

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Structural characterization of scorpion peptides and their bactericidal activity against clinical isolates of multidrug-resistant bacteria

PLoS ONE ◽

10.1371/journal.pone.0222438 ◽

2019 ◽

Vol 14 (11) ◽

pp. e0222438 ◽

Cited By ~ 5

Author(s):

Catherine Cesa-Luna ◽

Jesús Muñoz-Rojas ◽

Gloria Saab-Rincon ◽

Antonino Baez ◽

Yolanda Elizabeth Morales-García ◽

...

Keyword(s):

Structural Characterization ◽

Bactericidal Activity ◽

Multidrug Resistant ◽

Clinical Isolates ◽

Resistant Bacteria ◽

Multidrug Resistant Bacteria

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Resistance determinants and their genetic context in enterobacteria from a longitudinal study of pigs reared under various husbandry conditions

Applied and Environmental Microbiology ◽

10.1128/aem.02612-20 ◽

2021 ◽

Author(s):

Dominic Poulin-Laprade ◽

Jean-Simon Brouard ◽

Nathalie Gagnon ◽

Annie Turcotte ◽

Alexandra Langlois ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Efflux Pump ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Production Cycle ◽

Antimicrobial Use ◽

Resistance Determinants ◽

Extended Spectrum ◽

Antimicrobial Resistance Genes ◽

The Impact

Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. Cefotaxime-resistant bacteria were quantified and isolated from feed, feces, manures and carcasses of pigs reared with penicillin-using or antibiotic-free husbandries. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays. The extended spectrum β-lactamase (ESBL) phenotype was more frequent in isolates originating from antibiotic-free animals, while the bacteria isolated from penicillin-using animals were on average resistant to a greater number of antibiotics. The ESBL-encoding genes identified were blaCTX-M-1, blaCTX-M-15 and blaCMY-2 and they co-localised on plasmids with various genes encoding resistance to ß-lactams, co-trimoxazole, phenicols and tetracycline, all antibiotics used in pig production. Groups of genes conferring the observed resistance and the mobile elements disseminating multidrug resistance were determined. The observed resistance to ß-lactams was mainly due to the complementary actions of penicillin-binding proteins, an efflux pump and ß-lactamases. Most resistance determinants were shared by animals raised with or without antimicrobials. This suggests a key contribution of indigenous enterobacteria maternally transmitted along the sow lineage, regardless of antimicrobial use. It is unclear if the antimicrobial resistance observed in the enterobacteria populations of the commercial pig herds studied were present before the use of antibiotics, or the extent to which historical antimicrobial use exerted a selective pressure defining the resistant bacterial populations in farms using penicillin prophylaxis. Importance: Antimicrobial resistance is a global threat that needs to be fought on numerous fronts along the One Health continuum. Vast quantities of antimicrobials are used in agriculture to ensure animal welfare and productivity, and are arguably a driving force for the persistence of environmental and food-borne resistant bacteria. This study evaluated the impact of conventional, organic and other antibiotic-free husbandry practices on the frequency and nature of antimicrobial resistance genes and multidrug resistant enterobacteria. It provides knowledge about the relative contribution of specific resistance determinants to observed antibiotic resistance. It also showed the clear co-selection of genes coding for extended-spectrum beta-lactamases and genes coding for the resistance to antibiotics commonly used for prophylaxis or in curative treatments in pig operations.

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Facile Accelerated Specific Therapeutic (FAST) Platform to Counter Multidrug-Resistant Bacteria

10.1101/850313 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kristen A. Eller ◽

Thomas R. Aunins ◽

Colleen M. Courtney ◽

Jocelyn K. Campos ◽

Peter B. Otoupal ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Mammalian Cells ◽

Multidrug Resistant ◽

Clinical Isolates ◽

Resistant Bacteria ◽

New Delhi ◽

Beta Lactamase ◽

Extended Spectrum Beta Lactamase ◽

Effective Manner ◽

Intracellular Infections

ABSTRACTMultidrug-resistant (MDR) bacteria pose a grave concern to global health. This problem is further aggravated by a lack of new and effective antibiotics and countermeasure platforms that can sustain the creation of novel antimicrobials in the wake of new outbreaks or evolution of resistance to antibiotics. To address this, we have developed a Facile Accelerated Specific Therapeutic (FAST) platform that can develop effective therapies against MDR bacteria within a week. Our FAST platform combines four essential modules- design, build, test, and delivery-of drug development cycle. The design module comprises a bioinformatics toolbox that predicts sequence-specific peptide nucleic acids (PNAs) that target non-traditional pathways and genes of bacteria in minutes. The build module constitutes in-situ synthesis and validation of selected PNAs in less than four days and efficacy testing within a day. As a proof of concept, these PNAs were tested against MDR clinical isolates. Here we tested Enterobacteriaceae including carbapenem-resistant Escherichia coli, extended-spectrum beta-lactamase (ESBL) Klebsiella pneumoniae, New Delhi Metallo-beta-lactamase-1 carrying Klebsiella pneumoniae and MDR Salmonella enterica. PNAs showed significant growth inhibition for 82% of treatments, with nearly 18% of the treatments leading to more than 97% decrease. Further, these PNAs are capable of potentiating antibiotic activity in the clinical isolates despite presence of cognate resistance genes. Finally, FAST offers a novel delivery approach to overcome limited transport of PNAs into mammalian cells to clear intracellular infections. This method relies on repurposing the bacterial Type III secretion system in conjunction with a kill switch that is effective at eliminating 99.6% of an intracellular Salmonella infection in human epithelial cells. Our findings demonstrate the potential of the FAST platform in treating MDR bacteria in a rapid and effective manner.

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Analyses of Plasmids Harbouring Quinolone Resistance Determinants in Enterobacteriaceae Members

Polish Journal of Microbiology ◽

10.5604/01.3001.0010.7084 ◽

2017 ◽

Vol 66 (4) ◽

pp. 529-532

Author(s):

Bayri Erac ◽

Fethiye Ferda Yilmaz ◽

Ismail Ozturk ◽

Sabire Sohret Aydemir ◽

Mine Hosgor-Limoncu

Keyword(s):

Broad Spectrum ◽

Quinolone Resistance ◽

Clinical Isolates ◽

Conjugative Plasmid ◽

Beta Lactamase ◽

Beta Lactamases ◽

Conjugative Plasmids ◽

Resistance Determinants ◽

Resistance Plasmids ◽

Lactamase Gene

The aim of this study was to explore the plasmid characteristics of eight clinical Enterobacteriaceae strains containing extended broad spectrum beta-lactamases and plasmid-mediated quinolone resistance. Plasmids were transferred by conjugation or transformation and resistance determinants were investigated by PCR. We showed that at least one plasmid harbouring qnrB or qnrS determinant was transferred by conjugation in five isolates. QepA determinant was confirmed to be on a non-conjugative plasmid. We found at least one beta-lactamase gene in seven of the eight clinical isolates having plasmid-mediated quinolone resistance, which indicated that these two resistance determinants were mostly on the same conjugative plasmids.

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Discrepancy between colistin and polymyxin B susceptibility results among Escherichia coli and Klebsiella pneumoniae clinical isolates

Acta Microbiologica et Immunologica Hungarica ◽

10.1556/030.2021.01458 ◽

2021 ◽

Author(s):

Serap Süzük Yıldız ◽

Can Hüseyin Hekimoğlu ◽

Zekiye Bakkaloğlu ◽

Emine Alp

Keyword(s):

Escherichia Coli ◽

Klebsiella Pneumoniae ◽

Polymyxin B ◽

Multidrug Resistant ◽

Clinical Isolates ◽

Resistant Bacteria ◽

Major Error ◽

E Coli ◽

Microdilution Method ◽

Broth Microdilution Method

AbstractThe selection of therapeutic agent to be used for the treatment of multidrug-resistant bacteria is a major concern. Polymyxin B use has been commenced in Turkey, although its clinical breakpoint is not listed in the EUCAST. This study aimed to determine the correlation between the MIC values of polymyxin B and colistin. A total of 505 isolates, including 122 isolates of Escherichia coli and 383 isolates of Klebsiella pneumoniae were included in the present study. All the isolates were assessed for colistin and polymyxin B using the broth microdilution method. The categorical agreement in the E. coli isolates was 98.4%, and the rate of very major error was 33.3%. The categorical agreement in the K. pneumoniae isolates was 99.5%, the rate of major error was 0.36%, and the rate of very major error was 0.98%. In the evaluation of the essential agreement, 1.6% error in E. coli and 2.3% error in K. pneumoniae were observed. It was concluded that polymyxin B should never be used in the treatment of the isolates reported as colistin-resistant, and if the MIC values are above 4 mg/L in E. coli and K. pneumoniae. Our results indicate importance of reporting both polymyxin B and colistin susceptibility results of clinical isolates.

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Prevalence of trimethoprim/sulfamethoxazole resistance genes among Stenotrophomonas maltophilia clinical isolates in Egypt

Acta Microbiologica et Immunologica Hungarica ◽

10.1556/030.2021.01568 ◽

2021 ◽

Author(s):

Amel Elsheredy ◽

Azza Elsheikh ◽

Abeer Ghazal ◽

Sherine Shawky

Keyword(s):

Resistance Genes ◽

Surveillance System ◽

Stenotrophomonas Maltophilia ◽

Insertion Sequence ◽

Antimicrobial Agents ◽

Multidrug Resistant ◽

Clinical Isolates ◽

Nosocomial Pathogen ◽

Drug Of Choice

Abstract Stenotrophomonas maltophilia is an important multidrug resistant nosocomial pathogen. Trimethoprim/sulfamethoxazole (TMP/SMX) is considered the drug of choice for treatment of S. maltophilia infections, thus emerging resistance to TMP/SMX poses a serious threat. In the present study we aimed to investigate the frequency of TMP/SMX resistance genes (sul1, sul2, dfrA), and to evaluate their relatedness with integron 1 (int1), and insertion sequence common regions (ISCR) among 100 S. maltophilia from different clinical isolates in Egypt. Isolates were identified biochemically and confirmed by VITEK2. Detection of sul1, sul2, and dfrA genes, int1 and ISCR elements was performed by PCR. Among the 16 TMP/SMX resistant isolates, sul1 gene was detected in all of them, and it was associated with int1 gene presence in all resistant isolates. The sul2 gene was detected in 6 out of 16 resistant isolates (37.5%), and only 2 of the 16 resistant isolates (12.5%) harboured dfrA gene. ISCR was detected in 10 of the resistant isolates (62.5%) and in 4 of them it was associated with the presence of sul2 gene. Among the 84 TMP/SMX sensitive isolates, sul1 gene was detected in 15 (17.8%), int1 in 16 (19%) and ISCR in 6 (7.1%). None of the susceptible isolates had sul2 or dfrA genes. These findings point out an increasing frequency of TMP/SMX resistance genes among S. maltophilia clinical isolates in our region, so the adoption of prudent use of S. maltophilia antimicrobial agents and the establishment of a surveillance system are desperately needed.

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