Emerging Options for the Diagnosis of Bacterial Infections and the Characterization of Antimicrobial Resistance

Precise and rapid identification and characterization of pathogens and antimicrobial resistance patterns are critical for the adequate treatment of infections, which represent an increasing problem in intensive care medicine. The current situation remains far from satisfactory in terms of turnaround times and overall efficacy. Application of an ineffective antimicrobial agent or the unnecessary use of broad-spectrum antibiotics worsens the patient prognosis and further accelerates the generation of resistant mutants. Here, we provide an overview that includes an evaluation and comparison of existing tools used to diagnose bacterial infections, together with a consideration of the underlying molecular principles and technologies. Special emphasis is placed on emerging developments that may lead to significant improvements in point of care detection and diagnosis of multi-resistant pathogens, and new directions that may be used to guide antibiotic therapy.

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Characterization of cefotaxime resistant Escherichia coli isolated from broiler farms in Ecuador

10.1101/462994 ◽

2018 ◽

Author(s):

Christian Vinueza-Burgos ◽

David Ortega-Paredes ◽

Cristian Narváez ◽

Lieven De Zutter ◽

Jeannete Zurita

Keyword(s):

Antimicrobial Resistance ◽

Latin American ◽

Production Systems ◽

Diffusion Method ◽

Poultry Production ◽

Disk Diffusion Method ◽

E Coli ◽

Resistance Patterns ◽

Latin American Countries

AbstractAntimicrobial resistance (AR) is a worldwide concern. Up to a 160% increase in antibiotic usage in food animals is expected in Latin American countries. The poultry industry is an increasingly important segment of food production and contributor to AR. The objective of this study was to evaluate the prevalence, AR patterns and the characterization of relevant resistance genes in Extended Spectrum β-lactamases (ESBL) and AmpC E. coli from large poultry farms in Ecuador. Sampling was performed from June 2013 to July 2014 in 6 slaughterhouses that slaughter broilers from 115 farms totaling 384 flocks. Each sample of collected caeca was streaked onto TBX agar supplemented with cefotaxime (3 mg/l). In total, 176 isolates were analyzed for antimicrobial resistance patterns by the disk diffusion method and for blaCTX-M, blaTEM, blaCMY, blaSHV, blaKPC, and mcr-1 by PCR and sequencing. ESBL and AmpC E. coli were found in 362 flocks (94.3%) from 112 farms (97.4%). We found that 98.3% of the isolates were multi-resistant to antibiotics. Low resistance was observed for ertapenem and nitrofurantoin. The most prevalent ESBL genes were the blaCTX-M (90.9%) blaCTX-M-65, blaCTX-M-55 and blaCTX-M-3 alleles. Most of the AmpC strains presented the blaCMY-2 gene. Three isolates showed the mcr-1 gene. Poultry production systems represent a hotspot for antimicrobial resistance in Ecuador, possibly mediated by the extensive use of antibiotics. Monitoring this sector in national and regional plans of antimicrobial resistance surveillance should therefore be considered.

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Restriction endonuclease characterization of resistant plasmids in Enterobacteriaceae isolated from children in the Sudan

Epidemiology and Infection ◽

10.1017/s0950268800030892 ◽

1989 ◽

Vol 103 (3) ◽

pp. 487-496 ◽

Cited By ~ 1

Author(s):

P. Shears ◽

G. Suliman ◽

C. A. Hart

Keyword(s):

Antimicrobial Resistance ◽

Restriction Endonuclease ◽

Restriction Enzymes ◽

Surveillance Systems ◽

High Prevalence ◽

Resistance Patterns ◽

Reproducible Method ◽

Restriction Endonuclease Digest

SUMMARYThe investigation of plasmid similarity is an important component in the surveillance of antimicrobial resistance and in the detection of epidemic plasmids. The use of restriction endonucleases in the classification of transferable, multiply-resistant plasmids from faecal Enterobacteriaceae isolated at the Children's Emergency Hospital, Khartoum was investigated. Twenty-four transconjugant plasmids, coding for 11 different resistance patterns, each of molecular weight 62 MDa. were studied using four restriction enzymes;PstI,EcoR I,HindIII andAraII. Fifteen different digest profiles were obtained. Restriction profiles discriminated between plasmids with differing resistance patterns and demonstrated homology of plasmids with common resistance patterns. Restriction endonuclease digest patterns provide a potentially rapid and reproducible method of plasmid classification, that could contribute towards surveillance systems in tropical countries with a high prevalence of antimicrobial resistance.

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Evaluation of the impact of antimicrobial use protocols in PRRS virus infected swine on phenotypic antimicrobial resistance patterns

Applied and Environmental Microbiology ◽

10.1128/aem.00970-21 ◽

2021 ◽

Author(s):

Carissa A. Odland ◽

Roy Edler ◽

Noelle R. Noyes ◽

Scott A. Dee ◽

Joel Nerem ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Longitudinal Studies ◽

Bacterial Infections ◽

Population Level ◽

Control Group ◽

Antimicrobial Use ◽

Treatment Groups ◽

Resistance Patterns ◽

The Impact ◽

Over Time

A longitudinal study was conducted to assess the impact of different antimicrobial exposures of nursery-phase pigs on patterns of phenotypic antimicrobial resistance in fecal indicator organisms throughout the growing phase. Based on practical approaches used to treat moderate to severe PRRSV-associated secondary bacterial infections, two antimicrobial protocols of differing intensity of exposure [44.1 and 181.5 animal-treatment days per 1000 animal days at risk (ATD)] were compared with a control group with minimal antimicrobial exposure (2.1 ATD). Litter-matched pigs (n = 108) with no prior antimicrobial exposure were assigned randomly to the treatment groups. Pen fecal samples were collected nine times during the wean-to-finish period and cultured for Escherichia coli and Enterococcus spp. Antimicrobial susceptibility testing was conducted using NARMS gram-negative and gram-positive antibiotic panels. Despite up to 65-fold difference in ATD, few and modest differences were observed between groups and over time. Resistant patterns at marketing overall remained similar to those observed at weaning, prior to any antimicrobial exposures. Those differences observed could not readily be reconciled with the patterns of antimicrobial exposure. Resistance of E. coli to streptomycin was higher in the group exposed to 44.1 ATD, but no aminoglycosides were used. In all instances where resistance differed between time points, the higher resistance occurred early in the trial prior to any antimicrobial exposures. These minimal impacts on AMR despite substantially different antimicrobial exposures point to the lack of understanding of the drivers of AMR at the population level and the likely importance of factors other than antimicrobial exposure. IMPORTANCE Despite a recognized need for more longitudinal studies to assess the effects of antimicrobial use on resistance in food animals, they remain sparse in the literature, and most longitudinal studies of pigs have been observational. The current experimental study had the advantages of greater control of potential confounding, precise measurement of antimicrobial exposures which varied markedly between groups and tracking of pigs until market age. Overall, resistance patterns were remarkably stable between the treatment groups over time, and the differences observed could not be readily reconciled with the antimicrobial exposures, indicating the likely importance of other determinants of AMR at the population level.

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Regional Dissemination of a Carbapenemase-encoding Plasmid: Plasmidome analysis Reveals Diverse Adaptations of Carbapenemase-Producing Enterobacteriaceae

10.21203/rs.3.rs-34719/v1 ◽

2020 ◽

Author(s):

Ryuichiro Abe ◽

Yukihiro Akeda ◽

Yo Sugawara ◽

Dan Takeuchi ◽

Yuki Matsumoto ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Bacterial Infections ◽

Single Point ◽

Complete Sequence ◽

Surveillance Study ◽

Single Point Mutation ◽

Chromosomal Integration ◽

Carbapenemase Gene ◽

Resistance Patterns ◽

Horizontal Spread

Abstract Background. The global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens human health by limiting the range of usable antibiotics even against common bacterial infections. The spread of CRE is primarily due to the transmission of carbapenemase genes located on plasmids. However, few studies have comprehensively identified regionally spreading carbapenemase-encoding plasmids because of the difficulty to determine the complete sequence of a plasmid encoding carbapenemases. In a CRE surveillance study of 1,507 patients from 43 hospitals in northern Osaka, Japan, we previously found that 12% of the patients carried CRE and 95% of CRE isolates were IMP-6 producers. This result suggested a vast horizontal spread of a clonal plasmid carrying blaIMP-6 among Enterobacteriaceae in this region. In the current study, we aimed to describe the dynamics of this regional horizontal plasmid transmission.Results. We systematically analysed the plasmids of 230 CRE isolates carrying blaIMP obtained in our previous surveillance study by using whole genome sequencing and Southern blotting. We detected a major population (187 out of 230 blaIMP-positive CRE isolates, 85.6%) that carried blaIMP-6 on the IncN plasmid pKPI-6, along with diverse minor subpopulations. Among the subpopulations, we identified a novel cluster carrying an IncF plasmid that leads to heteroresistance due to amplification of blaIMP-6, resulting in covert transmission of blaIMP-6 or occasional chromosomal integration of blaIMP-6. In addition, we detected one isolate that harboured blaIMP-1, which is identical to blaIMP-6 except for a single point mutation, on pKPI-6 and thus had acquired a broader range of antimicrobial resistance. Conclusions. Carbapenemase-encoding plasmid tracking revealed the clonal dissemination of pKPI-6 among chromosomally distinct isolates. Focusing on the mode of carbapenemase gene carriage is helpful for monitoring of horizontal spread of CRE isolates that is difficult to trace only by the comparisons of the whole genomes. A seemingly clonal horizontal dissemination of the predominant plasmid had embraced heterogenous subpopulations that contribute to diverse adaptations including covert transmission, stable chromosomal integration of blaIMP-6, or broadened antimicrobial resistance patterns, ultimately leading to treatment failure.

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Innovations in point of care testing for bacterial infections: The Longitude Prize with Daniel Berman

Video Journal of Biomedicine ◽

10.2217/vjbm-2020-0007 ◽

2020 ◽

Author(s):

Daniel Berman

Keyword(s):

Antimicrobial Resistance ◽

Diagnostic Tests ◽

Bacterial Infections ◽

Point Of Care ◽

Rapid Diagnostic Tests ◽

Public Healthcare ◽

Point Of Care Testing ◽

Set Up ◽

Insight Into

Antimicrobial resistance (AMR) is one of the most serious clinical and public healthcare challenges. In this video Daniel Berman, Nesta Challenges, provides an overview of the Longitude Prize, why the prize was set up and what the prize hopes to achieve. Daniel also provides insight into some of the rapid diagnostic tests currently in the running for the £8 million prize.

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Bacterial infections and emerging resistance in renal transplant recipients

Bangladesh Journal of Medical Science ◽

10.3329/bjms.v14i1.16306 ◽

2014 ◽

Vol 14 (1) ◽

pp. 14-21 ◽

Cited By ~ 4

Author(s):

Inam Danish Khan ◽

Ajay Kumar Sahni

Keyword(s):

Renal Transplant ◽

Antimicrobial Resistance ◽

Bacterial Infections ◽

Tertiary Care ◽

Renal Transplant Recipients ◽

Transplant Recipients ◽

Beta Lactamases ◽

Post Transplant ◽

Resistance Patterns ◽

Altered Metabolism

Objective: Renal transplantation is frequently complicated by bacterial infections in the scenario of immunosuppression, altered metabolism and interventions resulting in prolonged morbidity. Subdued clinical presentation, antimicrobial resistance and toxicity question the outcome of transplantation. This retrospective study conducted at tertiary care apex transplant centre highlights colonization, clinical infection and antimicrobial resistance patterns in Renal Transplant Recipients (RTR). Materials and methods: Infection and antimicrobial resistance patterns in 130 RTR were studied. Clinico-demographic and transplant parameters were noted. Infection screening in the post transplant period along with antimicrobial susceptibility were used to analyze data in a post transplant time frame. Results and discussion: Culture positivity timeline was dominated by post surgical infections in the first week post transplant. Urinary infections followed by blood stream infections were noted. Infection profile included simultaneous polymicrobial, prolonged and widespread infections. Multi-resistant organisms producing beta lactamases and extended spectrum beta lactamases were isolated. Conclusion: Transplant recipients remain prone to bacterial infections with multi-resistant organisms which may persist due to immunosuppression, altered metabolism and toxicity, and contribute to nosocomial hazard. Infection control may be targeted at avoidance of donor derived infections, surgical complications, epidemiologic exposures, strengthening antimicrobial prophylaxis and anti-infection engineering. Antimicrobial stewardship, outbreak and epidemic preparedness should be ensured. DOI: http://dx.doi.org/10.3329/bjms.v14i1.16306 Bangladesh Journal of Medical Science Vol.14(1) 2015 p.14-21

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