Viral pathogens of acute gastroenteritis in Egyptian children: role of the parechovirus.

BACKGROUND AND AIM: Human parechovirus (HPeV) has emerged as a pathogen associated with acute gastroenteritis (AGE). AIM: To detect the presence of HPeV in the stool samples from Egyptian children with AGE seeking care and the possibility of its co-infection with other enteric viruses. METHODOLOGY: One hundred stool samples were collected from children attending Mansoura University Children's Hospital with AGE. HPeV and astrovirus were detected by reverse transcriptase-polymerase chain reaction (RT-PCR). At the same time, detection of rotavirus antigen and norovirus was achieved by enzyme-linked immunosorbent assay and rapid immunochromatographic method, respectively. RESULTS: The most frequently detected virus was rotavirus (39%), followed by norovirus (27%), HPeV (19%), and astrovirus (12%). Interestingly, the single infection with HPeV was 5%. Among the 19 HPeV positive samples, the co-infection of HPeV with other enteric viruses was detected in 9(43.9%) for rotavirus, 7(36.8%) for norovirus, 2(10.5%) for astrovirus, in 3(15.8%) for rotavirus and norovirus and 1(5.3%) for norovirus and astrovirus. Regarding the clinical presentation, there was no significant difference between children infected with HPeV alone and those infected with viruses other than HPeV alone; fever (p = 0.3), vomiting (p = 0.12), abdominal pain (p = 0.12), and grades of severity (P = 0.82). HPeV alone infected children were of mild severity (60%), and their main presenting symptom was fever (60%). CONCLUSIONS: Detection of HPeV as a single viral pathogen in the stool of some children with AGE showed that this virus could be a causative agent of AGE in Egyptian children. Therefore, HPeV could be included as one of the viruses screened for AGE diagnosis in children in Egypt.

Molecular Study of Nodulation Division Genes and Integron Genes in Acinetobacter baumannii.

BACKGROUND: Acinetobacter is an opportunistic bacterial pathogen, primarily associated with hospital-acquired infections. Antibiotic resistance in Acinetobacter is mainly mediated by efflux systems. This study aimed to identify the prevalence of adeA, adeI, adeJ, and adeY genes in Acinetobacter baumannii (A. baumannii) by PCR, assess the presence of integron genes by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and relate the presence of these genes to antimicrobial resistance of the clinically isolated A. baumannii. METHODS: The study included identification of Acinetobacter spp. and antimicrobial antibiotic susceptibility. PCR was performed for adeA, adeI, adeJ, and adeY genes. Detection of Integron (Intl) system was performed by PCR followed by restriction fragment length polymorphism (PCR-RFLP). RESULTS: The frequency of Ade genes among isolates were 66%, 62%, 60%, and 2% for AdeJ, AdeI, AdeA, and AdeY genes, respectively. The intI gene was detected in 10% of the isolates. There was a statistically significant difference in resistance to amikacin, gentamicin, and tetracycline between A. baumanii positive. The most frequent association was between AdeJ, AdeA, and AdeI (31%). CONCLUSIONS: Our study highlighted the high prevalence of AdeJ, AdeI, and AdeA in A. baumannii. Integron gene was detected with considerable frequency. There was a statistically significant association of these genes with resistance to aminoglycosides and tetracycline.

Study of MicroRNA-124 in Patients with Lupus Nephritis.

BACKGROUND: Lupus nephritis is associated with a six-fold increase in mortality compared with the general population. MicroRNAs studies revealed that increased MicroRNA -21 and MicroRNA -155 levels represent risk factors for active LN patients. MicroRNAs can be used as biomarkers in the diagnosis of clinical stages of LN. OBJECTIVES: The present study aimed to determine the level of miR-124 in patients with lupus nephritis by reverse transcriptase real-time polymerase chain reaction compared to healthy control and correlate its levels with biochemical findings in those patients. METHODS: The study was a case-control study that included fifty patients with lupus nephritis in addition to fifty healthy controls. Blood samples from the participants were subjected to the determination of serological markers of SLE. Moreover, real-time PCR was used for the determination of miR-124. RESULTS: The comparison of Micro-RNA124 between patients and control subjects revealed a statistically significant decrease in Micro-RNA124 in patients (1.193 ± 0.56) compared to the control (3.36 ± 0.50, p <0.001); the comparison of the level of MicroRNA 124 in the patients with different clinical and serological findings of SLE revealed a significant decrease in the level of MicroRNA 124 in patients with muscular findings (1.02 ± 0.5) compared to the patients with negative manifestations (1.47 ± 0.5, p =0.005). CONCLUSION: In the present study, a comparison of MicroRNA-124 in LN patients with different stages compared to normal control showed a statistically significant decrease in Micro-RNA124 in patients with lupus nephritis p <0.001 with significant correlation to the patients' different clinical and serological findings of SLE. Therefore, it may be used as a new noninvasive therapeutic approach to monitor response to therapy, predict relapses, and identify the degree of the activity of the disease or the progression to the chronic stage.

Prevalence of extended-spectrum beta-lactamase and molecular detection of blaTEM, blaSHV, and blaCTX-M genotypes among gram-negative Bacilli isolates from hospital acquired infections in pediatrics, one institutional study.

BACKGROUND: Gram-negative bacilli represents an important pathogen in hospital-acquired infections (HAIs) worldwide. The emergence of antibiotic resistance in these pathogens warrants attention for the proper management of infections. Extended-spectrum beta-lactamase (ESBL) resistance represents a major therapeutic problem in infections due to Gram-negative bacilli. The present study aimed to study the extended-spectrum beta-lactamase genes blaTEM, blaSHV, and blaCTX-M by multiplex polymerase reaction in isolated Gram-negative bacilli from HAIs in pediatric patients. METHODS: The study included one hundred-five isolates of Gram-negative bacilli from pediatric patients with different types of HAIs. The isolates were subjected to full microbiological identification, antibiotics susceptibility by disc diffusion method, the phenotypic study of ESBL, and the genetic study of ESBL genes by multiplex PCR. RESULTS: Fifty isolates of Gram-Negative bacilli showed ESBL activity by a phenotypic study by double disc diffusion method (50/105). All ESBL producers' isolates were positive by PCR for ESBL genes. The most frequent gene was blaTEM (64%), followed by blaSHV (30%) and CTX-M (22%). Mixed genes were found in 4 isolates (8%) for blaTEM and blaSHV, blaTEM and CTX-M. There was a significant association between PCR for ESBL genes and phenotypic ESBL detection (P = 0.001). There was significant detection of ESBL genes in E. coli (28%), followed by Enterobacter spp. (26%), Klebsiella spp. (24%), Serratia (14%), Pseudomonas spp. (6%) and Proteus (2%), P = 0.01. There Seventy percent of isolates positive for ESBL production had an insignificant association between MDR and PCR for ESBL genes (P = 0.23). CONCLUSION: The present study highlights the prevalence of ESBL activity among clinical isolates of Gram-negative bacilli isolated from hospital-acquired infections in pediatric patients. The most common gene responsible for this activity was blaTEM gee followed by blaSHV and blaCTX-M. There was a high prevalence of multiple antibiotic resistance among isolates with ESBL activity. The finding of the present study denotes the importance of screening extended beta-lactamase among Gram-negative bacilli associated with HAIs in pediatric patients.

Extended-Spectrum ß-Lactamase-Producing Escherichia coli and Virulence Genes in Pediatric Patients with Health-Care Urinary Tract Infections.

INTRODUCTION: Healthcare-associated urinary tract infection (UTI) represents a significant health problem, especially in infants and young children. The most common pathogen associated with this infection is Escherichia coli (E. coli). OBJECTIVE: The present study aimed to detect the frequency of virulence genes among clinical isolates of E. coli isolated from healthcare-associated urinary tract infections in children and the correlation between these virulence genes and the presence of the blaCTX gene. METHODS: The study included one hundred clinical isolates of E. coli isolated from healthcareassociated urinary tract infections in children in intensive care units. The isolates were subjected to antibiotics sensitivity by disc diffusion method and detection of extended-spectrum beta-lactamase by double disc diffusion method. In addition, multiplex polymerase chain reaction (PCR) was used to detect some virulence genes, and PCR was used to detect the blaCTX-M gene. RESULTS: E. coli producing ESBL by double discs method was identified in 74 isolates. blaCTX-M gene detection by PCR was identified among 38 isolates representing 51.4% of ESBL-producing E. coli. There was a significant association between ESBL and blaCTX-M Gene, P = 0.0001. The frequency of the studied virulence genes by multiplex PCR in the isolated E. coli was 66% for the Fim gene, 75% for the Aer gene, 68% for the FliC gene, 53% for each of IucD gene and Usp gene, 40% for pap gene, 35% for each of AFA and ironN genes and 17% for sfa gene. None of the isolated E. coli had the Cdt gene. There was a significant association between the presence of the FimH gene (P = 0.0001), Pap gene (P = 0.05), sfa (P = 0.026), Afa gene (P = 0.018), and aer gene (P = 0.035) and the presence of the blaCTX-M gene in the isolated E. coli. CONCLUSION: The present study highlights the presence of virulence genes and blaCTX-M gene in uropathogenic E. coli isolated from pediatric patients with healthcare-associated urinary tract infections. There was an association between the blaCTX-M gene and virulence genes FimH, pap, sfa, Afa, and aer. Various distributions of the studied genes with a high frequency of fimbria are flic genes. Moreover, the ESBL had high frequency in E. coli with the presence of blaCTX-M in about one-third of the isolates.

Molecular Study of Integrase Gene I and Integrase Gene II in Clinical Isolates of Pseudomonas aeruginosa.

BACKGROUND: The presence of the class I integron gene is associated with the emergence of multiple drug resistance (MDR) phenotype in Pseudomonas aeruginosa (P. aeruginosa) isolates. AIM: The objectives of this research were to study the prevalence of integrase genes I (Intel I) and integrase genes II (Intel II) in clinical isolates of P. aeruginosa and its association with antibiotic resistance in these isolates. METHODS: The study was a retrograde cross-sectional study that was carried out on 150 clinical isolates of P. aeruginosa isolated from patients with healthcare-associated infections. The isolates were subjected to biochemical identification and antibiotic sensitivity study by discs diffusion test. Intel I & Intel II genes were detected by polymerase chain reaction (PCR). RESULTS: Intel I gene was present in 48% of the isolates, and Intel II was present in 1.3% of the isolates. Intel I gene was detected at a statistically significant high rate in MDR- P. aeruginosa (76.9%, P=0.001) compared to non-MDR- P. aeruginosa (3.4%), while intel II had a statistically insignificant increase in MDR- P. aeruginosa (1.1%, P=1.00) compared to non-MDR-P. aeruginosa (1.7%). Both Intl I/Intl II genes were detected in 2.2% of MDR-P. aeruginosa isolates and were absent in non- MDR-P. aeruginosa isolates with statistically insignificant difference (P=1.00). P. aeruginosa isolates with Intel I gene had an increase in antibiotic resistance pattern to the used antibiotics discs. However, this increase had statistically significant rates only for gentamicin (63.9%, P≤0.001), meropenem (47.2%, P=0.009), trimethoprim/sulfamethoxazole (37.5%, P=0.013) and imipenem (44.4%, P=0.025). CONCLUSION: The present study highlights the high prevalence of the Intel I gene in clinical isolates of P. aeruginosa, while the Intel II gene was less prevalent in these isolates. There was a significant association between the prevalence of the Intel I gene and the MDR phenotype of P. aeruginosa and resistance to gentamicin, meropenem, trimethoprim/sulfamethoxazole, and imipenem. These findings need future evaluation in a higher number of clinical isolates of P. aeruginosa.

Study of single nucleotide polymorphism of vascular endothelium factor in patients with differentiated thyroid cancer.

BACKGROUND: Genetic alterations and high levels of the vascular endothelial growth factor (VEGF) are presumptive risk factors for differentiated thyroid cancer (DTC). OBJECTIVE: This work aims to study the presence of - 634G/C polymorphism of vascular endothelial growth factor (rs2010963) and its' serum level in patients with DTC and comparing these results with those of the control subjects. MATERIAL AND METHOD: The study was a retrograde case-control study that included seventy patients with DTCin addition to seventy apparently healthy control subjects. Blood sample was taken and subjected to study of - 634G/C VEGF polymorphism (rs2010963) by real time PCR and measurement of its' plasma level by immunoassay kit (ELISA). RESULTS: Regarding genotyping of VEGFA - 634G/C (rs2010963) polymorphism, there was significant increase in CG and GG genotypes (28.6%, 18.6% respectively) among patients compared to control subjects (20.0%, 4.3% respectively) and significant increase in CC genotype in control subjects (75.7%) compared to patients (52.9%), P = 0.001. The VEGF mean ± SD level was significantly elevated in patients compared to control subjects (1215.81 ± 225.78 versus 307.16 ± 91.81, P = 0.006). Moreover, there was significant increase in VEGF levels in patients with CG and GG genotypes (1295.9 ± 68.74, 1533.08 ± 109.95, respectively) compared to patients with CC genotype (1061 163.25), P = 0.001). CONCLUSION: There was significant increase in GG and CG genotypes in patients with DTC compared to control subjects which may suggest a predisposing role for these genotypes in development of DTC. Moreover, there was significant increase in serum level of vascular endothelial growth factor in patients with GG and CG genotypes which may reflect the mechanism of these genotypes in development of DTC.

Molecular Study of Adenovirus Genotypes 40 and 41 in Children with Acute Gastroenteritis.

BACKGROUND: Adenovirus is a common virus associated with acute gastroenteritis in children. There are certain genotypes that are prevalent in these infections, such as genotypes 40 and 41. OBJECTIVE: The aim of the present study was to investigate the incidence of adenovirus genotypes 40 and 41 in children with acute gastroenteritis by polymerase chain reaction (PCR) and also to determine the possibility of Adenovirus co-infections with Rotavirus. METHODS: The study was a cross-sectional study that included 100 children with acute gastroenteritis. The children were subjected to full history taking and clinical examination. Stool samples from the patients were subjected to detection of adenovirus and rotavirus antigens by enzyme-linked immunosorbent assay (ELISA) and detection of adenovirus genotypes 40 and 41 by polymerase chain reaction (PCR). RESULTS: The most prevalent virus by the used methods was rotavirus antigen in the stool (35%). Adenovirus antigen detection was positive in 23% of the stool samples, with positive PCR for these samples in 22%. The ADv40 was detected in 13 samples, and ADv41 was detected in 9 samples. One positive sample by adenovirus antigen ELISA was negative by PCR for these genotypes. Mixed rotavirus and adenovirus by ELISA were detected in 7% of the children. In patients with positive adenovirus antigen by ELISA, the most common symptoms were vomiting (54.5%) and abdominal pain (45.5%). An insignificant difference between fever (P=0.94) and abdominal pain (P=0.63) was detected in children infected with adenovirus compared to patients infected with other organisms. The adenovirus was detected in 68.2% of children with acute gastroenteritis ≤ 24 months. Vomiting was significantly increased in children with adenovirus (54.5%) compared to children negative for adenovirus (23.1%-P=0.004, OR 4.0, 95%CI: 1.5-10.8). CONCLUSION: The study highlights the presence of adenovirus genotypes 40 and 41 in the stool of children with acute gastroenteritis. Combined rotavirus and adenovirus infections were detected in our study.

Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020.

Background: Sapovirus has emerged as a viral cause of acute gastroenteritis. However, there are insufficient data about the presence of this virus among children with acute gastroenteritis. The present study aimed to evaluate the presence of sapovirus in children with acute gastroenteritis by reverse transcriptase-polymerase chain reaction (RT-PCR). Methods: A cross-sectional study enrolled 100 children patients with acute gastroenteritis from outpatient clinics with excluded bacterial pathogens and parasitic infestation. A stool sample was collected from each child for laboratory examination. Each stool sample was subjected to study by direct microscopic examination, study for rotavirus by enzyme-linked immunoassay (ELISA) and the remaining sample was subjected to RNA extraction and RT- PCR for sapovirus. Results: The most frequently detected virus was rotavirus by ELISA (25%). RT-PCR detected sapovirus in 7% of the stool samples. The children with sapovirus were all from rural regions and presented mainly during the winter season in Egypt (42.9%). The main presenting symptoms were fever (71.4%) and vomiting (57.1%). None of the children with sapovirus had dehydration. Rotavirus was significantly associated with sapovirus infections in 5 patients (71.4%, P=0.01). There was an insignificant difference between symptoms of gastroenteritis in children with sapovirus and children with gastroenteritis without sapovirus as regards vomiting (P=0.7), fever (P=0.46), and abdominal pain (P=0.69). Conclusion: The present study highlights the emergence of sapovirus as a frequent pathogen associated with acute gastroenteritis in children. There is a need for a national survey program for the study of sapovirus among other pathogens associated with acute gastroenteritis for better management of such infection.

Study of Plasmid-Mediated Quinolone Resistance in Escherichia coli from Nosocomial Urinary Tract Infections.

OBJECTIVE: The aim of the present study was to study the prevalence of plasmid-mediated quinolone resistance (PMQR) genes (qnrA, qnrB, qnrC, qnrD, qnrS, qepA, oqxA, oqxB and aac) in Escherichia coli (E. coli) isolated from patients with nosocomial urinary tract infections (UTIs) and its relation to the extended-spectrum ß-lactamase (ESBL) production. ; Methods: A cross-sectional study was carried out on 200 non-duplicated isolates of E. coli isolated from patients with nosocomial UTIs. E.coli isolates were subjected to antibiotic susceptibility testing by disc diffusion method, determination of minimum inhibitory concentrations (MICs) of ciprofloxacin by Epsillometer (E) test strips, detection of ESBL production by double disc synergy method and detection of qnrA, qnrB, qnrC, qnrD, qnrS, qepA, oqxA, oqxB and aac genes by polymerase chain reaction (PCR). ; Results: The antimicrobial susceptibility testing of the isolated E. coli revealed a high frequency of resistance to ampicillin (73.5%), ceftazidime (72%) and imipenem (71.5%). The less frequent resistance was for aztreonam (21.5%), amikacin (36.5%) and gentamicin (38.5%). ESBL production was found in 131 isolates (65.5%) and phenotypic quinolone resistance was detected by MIC in 65 isolates (32.5%), with 52.3% of them showed high resistance to ciprofloxacin with an MIC more than 32 µg/ml. PMQR genes were found in 40 isolates. The frequency of the detected genes was 40%, 37.5%, 35%, 20% and 5% for qnrA, qnrS, qepA, qnrB and oqxA, respectively. Significant association was found between the presence of PMQR genes and ESBL production (P=0.0001). ; Conclusion: The study highlights the prevalence of PMQR genes in E. coli with high association with the ESBL phenotype. This finding is a sign of limited therapeutic options for E. coli.