Dataset Information

Comparing conventional, biochemical and genotypic methods for accurate identification of Klebsiella pneumoniae in Sudan.

ABSTRACT: Klebsiella pneumoniae is recognized as one of the most important healthcare-associated pathogens worldwide due to its tendency to develop antibiotic resistance and cause fatal outcomes. Bacterial identification methods such as culture and biochemical tests are routinely used with limited accuracy in many low- and middle-income countries, including Sudan. The aim of this study was to test the accuracy of identification of K. pneumoniae in Khartoum, Sudan. Two hundred and fifty K. pneumoniae isolates were collected and identified using conventional phenotypic methods, biochemically using API 20E and genotypically by amplification of 16S-23S rDNA and sequencing of rpoB, gapA and pgi. Only 139 (55.6?%) of the isolates were confirmed as K. pneumoniae genotypically by PCR and 44.4?% were identified as non- K. pneumoniae . The results demonstrate that the identification panels used by the hospitals were inaccurately identifying K. pneumonia and led to overestimation of the prevalence of this organism. The current identification methods used in Khartoum hospitals are highly inaccurate, and therefore we recommend the use of a comprehensive biochemical panel or molecular methods, when possible, for accurate identification of K. pneumoniae .

SUBMITTER: Osman EA

PROVIDER: S-EPMC7470312 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparing conventional, biochemical and genotypic methods for accurate identification of Klebsiella pneumoniae in Sudan.

Osman Einas A EA El-Amin Nagwa N Adrees Emad A E EAE Al-Hassan Leena L Mukhtar Maowia M

Access microbiology 20200210 3

Klebsiella pneumoniae is recognized as one of the most important healthcare-associated pathogens worldwide due to its tendency to develop antibiotic resistance and cause fatal outcomes. Bacterial identification methods such as culture and biochemical tests are routinely used with limited accuracy in many low- and middle-income countries, including Sudan. The aim of this study was to test the accuracy of identification of K. pneumoniae in Khartoum, Sudan. Two hundred and fifty K. ...[more]

PMID: 32974573

Similar Datasets

Project description:Klebsiella pneumoniae is not only a major hospital-acquired pathogen but also an important food-borne pathogen that can cause septicaemia, liver abscesses, and diarrhea in humans. The phenotypic and genotypic characteristics of K. pneumoniae in retail foods have not been thoroughly investigated in China. The objective of this study was to characterize K. pneumoniae isolates through biotyping, serotyping, determination of virulence factors, antibiotic resistance testing, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), and (GTG)5-PCR molecular typing. From May 2013 to April 2014, a total of 61 K. pneumoniae isolates were collected from retail foods in China. Using API 20E test strips, five different biotype profiles were identified among these isolates. The majority of isolates belonged to biochemical profile "5215773" (50 isolates, 80.6%). The capsular serotypes of the 61 K. pneumoniae isolates and one reference strain were determined by PCR. Of the seven capsular serotypes tested, four different capsular serotypes were identified. Serotypes K1, K20, K57, and K2 were detected in two, three, two, and one isolates, respectively. Serotypes K3, K5, and K54 were not detected. The presence of 11 virulence genes was assessed by PCR. The most common virulence genes were fimH (85.5%), ureA (79.0%), wabG (77.4%), uge (56.5%), and kfuBC (29.0%). ERIC-PCR and (GTG)5-PCR molecular typing indicated high genetic diversity among K. pneumoniae isolates. We identified 60 different ERIC patterns and 56 distinct (GTG)5 patterns. Genotypic results indicated that isolates carrying similar virulence factors were generally genetically related. Some isolates from the same geographic area have a closer relationship. The isolates showed high levels of resistance to ampicillin (51/62, 82.2%). Resistance to streptomycin (11/62, 17.7%) and piperacillin (10/62, 16.1%) was also common. The presence of virulent and antibiotic-resistant K. pneumoniae in foods poses a potential health hazard for consumers. Our findings highlight the importance of surveillance of K. pneumoniae in foods.

Project description:Despite the high success rates of preformed metal crowns (PMCs) in children no randomized clinical trials compare methods of placement and none describe its use in Africa. Our aim was to compare survival and cost-effectiveness of PMCs placed by conventional techniques (CT) and biological Hall techniques (HT) using a prospective randomized control trial in a general dental practice from Khartoum. One hundred and nine and 103 PMCs were placed in randomly selected children (5-8years) with 1-2 carious primary molars using HT and CT respectively and followed for 2 years. Socioeconomic status, periodontal health, occlusion, anxiety, and procedure time were compared using student t-test. Kaplan-Meier survival rates and incremental cost effectiveness ratio (ICER) were compared between CT and HT. CT and HT groups were similar for age, gender, socio-economic status. Survival rates were high (over 90%) for both study arms and not statistically different (p>0.05). Anxiety scores were significantly higher in CT arm after 12 months compared to HT (p<0.001). Clinically, gingival and plaque indices were similar between groups (p>0.05) but occlusions were raised in nearly all subjects in the HT arm (p<0.05). Periodontal health improved, and occlusions adjusted over time in both arms. There were 3 (2.7%) and 6 (5.8%) minor failures, 7 (6.4%) and 6 (5.8%) major failures in HT and CT arms respectively. Mean procedure time was lower in HT (9.1 min) than CT (33.9 min); p<0.001. Mean PMC cost was US$2.45 and US$7.81 for HT and CT respectively. The ICER was US$136.56 more for each PMC placed by CT per life year. We show that PMCs have high survival outcomes in disadvantaged populations similar to results from developed countries. As HT can be carried out by less experienced dental operators and therapists, this biological approach provides a promising cost-effective option to manage caries in developing countries with limited resources. Trial registration: The trial is registered at clinicaltrials.gov. ClinicalTrial.gov Trial Registration: NCT03640013.

Project description:Background:Klebsiella pneumoniae has been a leading healthcare-acquired infection (HAI) agent worldwide for decades. However, the epidemiological characteristics of K. pneumoniae in lung cancer patients with respiratory infection are unclear. Here, we characterized the frequency of K. pneumoniae in lung cancer patients with respiratory infection in a cancer hospital in China and determined the antibiotic resistance profile, virulence phenotype and clonal relationships among these K. pneumoniae strains. Methods:The clinical data of lung cancer patients with respiratory infection from September 2017 to October 2018 were retrospectively evaluated. Microbiological methods, antimicrobial susceptibility tests, pulsed-field gel electrophoresis (PFGE), polymerase chain reaction (PCR) assays, Sanger sequencing and Galleria mellonella larvae infection model were used in this study. Results:During the study period, a total of 47 lung cancer patients with respiratory infection caused by bacteria were identified, among 27 patients were identified as positive for K. pneumoniae and the positive rate was 57.45%. Among 37 nonduplicate K. pneumoniae strains from these 27 patients, 19 isolates (51.4%) were classified as multidrug resistant (MDR) with high-level resistance to, at least one agent in three or more antibiotic categories, including polymyxin B and tigecycline. Sixteen of the 37 strains (43.2%) were hypermucoviscous isolates. Extended spectrum ?-lactamases-producing K. pneumoniae strains consisted of two dominant PFGE types. Furthermore, the assessment of virulence potential using a G. mellonella larvae infection model showed that K. pneumoniae isolated from these patients exhibited a high virulence level. Conclusion:Our data showed that K. pneumoniae is the most critical cause of lung infection in patients with lung cancer in this hospital. The various drug resistance and virulence backgrounds of K. pneumoniae may make this clinical center a breeding ground for superbugs. It is paramount to enhance surveillance of K. pneumoniae strains and take control measures.

Dataset Information

Comparing conventional, biochemical and genotypic methods for accurate identification of Klebsiella pneumoniae in Sudan.

Publications

Comparing conventional, biochemical and genotypic methods for accurate identification of <i>Klebsiella pneumoniae</i> in Sudan.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets