scholarly journals Genetic Relatedness of 5-Year Isolates of Clostridioides difficile Polymerase Chain Reaction Ribotype 017 Strains in a Hospital

Antibiotics ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1229
Author(s):  
Jieun Kim ◽  
Mi-Ran Seo ◽  
Bongyoung Kim ◽  
Jinyeong Kim ◽  
Mi-Hyun Bae ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Antibiotic Resistance ◽  
Genetic Relatedness ◽  
Geometric Mean ◽  
The Other ◽  
Chain Reaction ◽  
Clostridioides Difficile ◽  
Polymerase Chain ◽  
Resistance Rates ◽  
Hospital Acquired

The objective of this study was to analyse the genetic relatedness of Clostridioides difficile polymerase chain reaction ribotype 017 (RT017) strains from patients with hospital-acquired C. difficile infection (HA-CDI) in a hospital with a high RT017 prevalence. From 2009 to 2013, 200 RT017 strains (26.8%) were collected from 745 HA-CDI patient isolates. They comprised 64 MLVA types, and 197 (98.5%) strains were genetically related to 5 clonal complexes (CCs). The largest cluster, CC-A, included 163 isolates of 40 MLVA types. CC-A accounted for 20% of RT017 strains in 2009 and sharply increased to 94.9% in 2010, 94% in 2011, 86.2% in 2012, and 73.5% in 2013. The other 4 CCs included 20 isolates with 7 MLVA types. The resistance rates of antimicrobials were as follows: clindamycin 100%, moxifloxacin 99%, rifaximin 88.5%, and vancomycin 1%. All isolates were susceptible to metronidazole and piperacillin/tazobactam. Comparing antibiotic resistance among CCs, the geometric mean of the minimum inhibitory concentrations of moxifloxacin, vancomycin, and piperacillin/tazobactam were significantly higher for CC-A isolates than for the other CCs. RT017 clones constantly evolved over the 5 years studied with regard to genetic relatedness. The levels of antibiotic resistance may contribute to the persistence of organisms in the institution.

scholarly journals Multiplex polymerase chain reaction detection of Streptococcus pneumoniae and Haemophilus influenzae and their antibiotic resistance in patients with community-acquired pneumonia from southwest Iran

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ahmad Farajzadeh Sheikh ◽  
Robab Rahimi ◽  
Hossein Meghdadi ◽  
Ameneh Alami ◽  
Morteza Saki
Keyword(s):  
Polymerase Chain Reaction ◽  
Antibiotic Resistance ◽  
Multiplex Polymerase Chain Reaction ◽  
Culture Method ◽  
Community Acquired Pneumonia ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Sensitivity Specificity ◽  
Resistance Rates ◽  
Accuracy Rates

Abstract Background This study aimed to evaluate the occurrence of Streptococcus pneumoniae and Haemophilus influenzae in sputum of patients with community-acquired pneumonia (CAP) using culture and multiplex polymerase chain reaction (M-PCR) methods and to survey the antibiotic resistance patterns of aforesaid isolates. Result In total, 23.9 % (n = 22/92) of sputum samples showed positive results in the culture method. S. pneumoniae and H. influenzae were isolated from 15 (16.3 %) and 7 (7.6%) samples, respectively. Using M-PCR, 44 (47.8 %) samples were positive for S. pneumoniae and H. influenzae. Of these, S. pneumoniae and H. influenzae were detected in 33 (35.8%) and 11 (11.9%) of the sputum samples, respectively. The sensitivity, specificity, and accuracy rates of PCR in detection of S. pneumoniae in comparison with culture method were 100, 76.6, and 83.6%, respectively. While, the sensitivity, specificity, and accuracy rates of PCR in detection of H. influenzae in comparison with culture method were 100, 95.3, and 95.8%, respectively. Out of 11 isolates of H. influenzae, two strains confirmed as H. influenzae type b (Hib) and 3 isolates were type f. However, 6 isolates were non-typable. The co-trimoxazole and amoxicillin/clavulanate were the less effective antibiotics against S. pneumonia and H. influenzae, respectively. Ceftriaxone with 13.3% resistance rates was the most effective antibiotic against S. pneumoniae, while, clarithromycin, ceftriaxone, and gentamicin with resistance rates of 28.6% for each one were the most effective chemicals against H. influenzae isolates. Conclusion In this study, the prevalence of S. pneumoniae was more than H. influenzae using culture and M-PCR methods. The M-PCR provided better efficiency in detecting the bacterial agents in CAP patients compared to culture method. This method can improve the early detection of pathogens contributed to CAP. The drug resistant S. pneumoniae and H. influenzae indicated the need to develop a codified monitoring program to prevent further spread of these strains.

scholarly journals Development of a Genoserotyping Method for Salmonella Infantis Detection on the Basis of Pangenome Analysis

2020 ◽  
Vol 9 (1) ◽  
pp. 67
Author(s):  
Seung-Min Yang ◽  
Jiwon Baek ◽  
Eiseul Kim ◽  
Hyeon-Be Kim ◽  
Seyoung Ko ◽  
...  
Keyword(s):  
Public Health ◽  
Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Cost Effective ◽  
The Other ◽  
Gene Marker ◽  
Diagnostic Assay ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Substantial Economic Burden

In recent years, Salmonella Infantis has become a predominant serovariant in clinical and poultry isolates, thereby imposing a substantial economic burden on both public health and the livestock industry. With the aim of coping with the steep increase in serovar Infantis prevalence, a polymerase chain reaction (PCR)-based rapid and accurate diagnostic assay was developed in this study through pangenome profiling of 60 Salmonella serovars. A gene marker, SIN_02055, was identified, which is present in the S. Infantis genome but not in the pangenome of the other serovars. Primers specific to SIN_02055 were used to accurately detect serovar Infantis, and to successfully differentiate Infantis from the other 59 serovars in real-time PCR with a R2 of 0.999 and an efficiency of 95.76%. The developed method was applied to 54 Salmonella strains belonging to eight dominant serovars, and distinguished Infantis from the other seven serovars with an accuracy of 100%. The diagnostic primer set also did not show false positive amplification with 32 strains from eight non-Salmonella bacterial species. This cost-effective and rapid method can be considered an alternative to the classic serotyping using antisera.

scholarly journals Feasibility and safety of a symptom-based strategy to discontinue infection control precautions for patients hospitalised with COVID-19 – a retrospective study

2021 ◽  
Author(s):  
Gaël Grandmaison ◽  
Marine Baumberger ◽  
Charlotte Pellaud ◽  
Véronique Erard ◽  
Christian Chuard
Keyword(s):  
Polymerase Chain Reaction ◽  
Retrospective Study ◽  
Infection Control ◽  
Median Time ◽  
Median Number ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Clinical Criteria ◽  
Polymerase Chain ◽  
Hospital Acquired

Background: Various recommendations exist concerning the discontinuation of contact and droplet precautions (CDP) for patients hospitalised with coronavirus disease 2019 (COVID-19). Some are based on repeated negative real-time polymerase chain reaction (RT-PCR) results, whereas other are based on clinical criteria. The feasibility and safety of these recommendations are poorly documented. Method: We conducted a retrospective study to assess the feasibility and safety of a symptom-based strategy to discontinue CDP for patients hospitalised with COVID-19. We reviewed the clinical charts of all symptomatic patients hospitalised in our institution with RT-PCR-confirmed COVID-19 to assess the application of a symptom-based strategy for the implementation and discontinuation of CDP. The patients with discontinuation of CDP in accordance with the symptom-based strategy were cross-referenced with patients with potential hospital-acquired COVID-19 in order to assess the safety of this strategy. Results: Among the 147 patients included in our study, our symptom-based strategy was respected in 95 cases (64.6%). Discontinuation of CDP in accordance with the recommendations occurred in 39 patients (26.5%). After the discontinuation of CDP, patients remained hospitalised for a median time of 18 days, with exposure to a median number of three patients, resulting in a total number of 588 days ‘patient-day-exposition’. No hospital-acquired COVID-19 was detected in contact patients. Discussion: The use of a symptom-based strategy to discontinue CDP is applicable and safe. This symptom-based strategy was applicable regardless of patient’s age or COVID-19 severity.

scholarly journals Occurrence of virulent multidrug-resistantEnterococcus faecalisandEnterococcus faeciumin the pigs, farmers and farm environments in Malaysia

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5353 ◽  
Author(s):  
Shiang Chiet Tan ◽  
Chun Wie Chong ◽  
Cindy Shuan Ju Teh ◽  
Peck Toung Ooi ◽  
Kwai Lin Thong
Keyword(s):  
Polymerase Chain Reaction ◽  
Antibiotic Resistance ◽  
Environmental Factors ◽  
Environmental Samples ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Peninsular Malaysia ◽  
Chain Reaction ◽  
Swine Farms ◽  
Polymerase Chain

BackgroundEnterococcus faecalisandEnterococcus faeciumare ubiquitous opportunistic pathogens found in the guts of humans and farmed animals. This study aimed to determine the occurrence, antimicrobial resistance, virulence, biofilm-forming ability and genotypes ofE. faecalisandE. faeciumfrom swine farms. Correlations between the genotypes, virulotypes, antibiotic resistance, and the environmental factors such as locality of farms and farm hygiene practice were explored.MethodsE. faecalisandE. faeciumstrains were isolated from the oral, rectal and fecal samples of 140 pigs; nasal, urine and fecal samples of 34 farmers working in the farms and 42 environmental samples collected from seven swine farms located in Peninsular Malaysia. Antibiotic susceptibility test was performed using the disk diffusion method, and the antibiotic resistance and virulence genes were detected by Polymerase Chain Reaction. Repetitive Extragenic Palindromic-Polymerase Chain Reaction and Pulsed-Field Gel Electrophoresis were performed to determine the clonality of the strains. Crosstab/Chi-square test and DistLM statistical analyses methods were used to determine the correlations between the genotypes, virulence factors, antibiotic resistance, and the environmental factors.ResultsA total of 211E. faecalisand 42E. faeciumwere recovered from 140 pigs, 34 farmers and 42 environmental samples collected from seven swine farms in Peninsular Malaysia. Ninety-eight percent of the strains were multidrug-resistant (resistant to chloramphenicol, tetracycline, ciprofloxacin and erythromycin). Fifty-two percent of the strains formed biofilms. Virulence genesefa, asaI, gelE,esp,cylandacegenes were detected. Virulence genesefaandasaI were most prevalent inE. faecalis(90%) andE. faecium(43%), respectively. Cluster analyses based on REP-PCR and PFGE showed the strains were genetically diverse. Overall, the strains isolated from pigs and farmers were distinct, except for three highly similar strains found in pigs and farmers. The strains were regional- and host-specific.DiscussionThis study revealed alarming high frequencies of multidrug-resistant enterococci in pigs and swine farmers. The presence of resistance and virulence genes and the ability to form biofilm further enhance the persistence and pathogenicity of the strains. Although the overall clonality of the strains were regionals and host-specific, strains with high similarity were found in different hosts. This study reiterates a need of a more stringent regulation to ensure the proper use of antibiotics in swine husbandry to reduce the wide spread of multidrug-resistant strains.

scholarly journals Identification of Neisseria gonorrhoeae isolates with a recombinant porA gene in Scotland, United Kingdom, 2010 to 2011

2012 ◽  
Vol 17 (9) ◽  
Author(s):  
K Eastick ◽  
A Winter ◽  
S Jamdar
Keyword(s):  
Polymerase Chain Reaction ◽  
United Kingdom ◽  
Neisseria Gonorrhoeae ◽  
Sequence Type ◽  
The Other ◽  
Chain Reaction ◽  
Polymerase Chain

Three isolates of Neisseria gonorrhoeae have been identified in Scotland in 2010 and 2011, which lack sequences in the porA pseudogene commonly used as the target for confirmatory gonorrhoea polymerase chain reaction assays. Two isolates were clustered temporally and geographically and have the same sequence type and porA sequence. A similar strain was reported in Australia during early 2011. The other Scottish isolate was identified separately and is different in sequence type and porA sequence.

Identification and diagnosis of Leishmania mexicana complex isolates by polymerase chain reaction

Parasitology ◽  
1994 ◽  
Vol 109 (4) ◽  
pp. 423-433 ◽  
Author(s):  
S. Eresh ◽  
S. M. McCallum ◽  
D. C. Barker
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
The Other ◽  
South American ◽  
Kinetoplast Dna ◽  
Leishmania Mexicana ◽  
Chain Reaction ◽  
Potential Host ◽  
Oligonucleotide Primers ◽  
Polymerase Chain

SUMMARYFollowing cloning of Leishmania (L.) amazonensis kinetoplast DNA two recombinant clones were identified: one specific for L. (L.) amazonensis and the other specific for L. (L.) amazonensis and closely related isolates. DNA sequences from these clones were compared with those of other kinetoplastids and oligonucleotide primers were designed to be used in the polymerase chain reaction. A pair of these primers has been shown not only to be highly specific for L. mexicana complex isolates but can also be used to distinguish between L. (L.) mexicana and L. (L.) amazonensis isolates. These primers have been tested with water-lysed cultures, crude DNA extracts from human patients, potential host reservoirs, sandfly vectors and with cell pellets after isoenzyme characterization. The results of these tests indicate that the primers can be used specifically in the presence of excess host DNA originating from the majority of South American countries.

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