Evaluation of Rapid SARS-CoV-2 Antigen Detection as a Single Diagnostic Test and When Combined with C-Reactive Protein Level or Neutrophil to Lymphocyte Ratio in Suspected COVID-19 Subjects.

Background Rapid antigen detection tests of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) play a crucial role in the control of the current coronavirus disease 2019 (COVID-19) pandemic. Data about the real diagnostic performance of such tests is still insufficient and hence their evaluation is of high priority. Objectives The aim of this study was to evaluate the diagnostic performance of BIOCREDIT COVID-19 antigen test alone and in combination with either C-reactive protein (CRP) or neutrophil/lymphocyte ratio (NLR) in comparison to real-time quantitative polymerase chain reaction (RT-qPCR). Additionally, we investigated the selection criteria of the suspect for best performance of the antigen test. Materials and Methods Paired nasopharyngeal (NP) swabs were collected from 200 suspected COVID-19 subjects for SARS-CoV-2 RNA by RT-qPCR and for antigen detection by BIOCREDIT test. Simultaneously, for all suspect, clinical presentations were recorded as well as CRP level and NLR were determined. Results Among 200 tested NP swabs, 125 (62.5%) were RT-PCR positive. Overall sensitivity, specificity and accuracy of BIOCREDIT test were 34.4, 98.7, and 58.5%, respectively. Sensitivity of the BIOCREDIT test was higher in COVID-19 suspect, with high viral load (100%), severely ill (56.2%), with fever alone (40%), elevated CRP (41.1%), and high NLR (36.2%). In combination with NLR or CRP, sensitivity of BIOCREDIT test increased to 89.4 and 81.6%, respectively, while its specificity decreased to 67 and 59%, respectively. Conclusion The overall low sensitivity of BIOCREDIT/COVID-19 antigen test does not permit its use as a single diagnostic test for COVID-19. However, its use should be restricted only if it is combined with either CRP or NLR in suspect with certain criteria.

Effect of the Different Plasmid-Mediated AmpC Beta-Lactamase Genotypes on the Phenotypic Detection of ESBL in Enterobacteriaceae Isolates.

BACKGROUND: Increasingly, Enterobacteriaceae isolates that are positive for the extended-spectrum-beta-lactamase (ESBL) by phenotypic screening tests yield a negative result when tested with the reference Clinical and Laboratory Standards Institute (CLSI) ESBL confirmatory test. The aim is to determine to what extent the different plasmid AmpC (pAmpC) genotypes could affect the CLSI ESBL confirmatory test for detection of the ESBL phenotype in ESBL/pAmpC co-producers. METHODS: A total of 253 Enterobacteriaceae isolates were screened for ESBL and AmpC production according to CLSI guidelines. Out of 186 ESBL and AmpC-screen-positive isolates, 96 isolates were selected for ESBL confirmation by the combined disc diffusion test (CDDT) as well as for detection of the most common ESBL and pAmpC encoding-genes by multiplex PCR. RESULTS: Out of the 96 ESBL/AmpC-screen-positive isolates, all (100%) were positive for at least one of the investigated ESBL genes, and 88 (91.7%) were positive for any of the investigated pAmpC genes. CDDT correctly identified ESBL phenotype more frequently in non-pAmpC carriers than pAmpC carriers (75% vs. 52.3%). CIT alone-containing isolates were associated more with non-confirmed ESBL phenotype rather than confirmed ESBL phenotype (76.2% vs. 30.4%, p < 0.001), especially when co-harbored blaCTXM alone (76.9% vs. 33.3%, p < 0.001) or both blaCTXM/blaSHV genes (100% vs. 0%). On the other hand, DHA-carrying isolates were more associated with confirmed ESBL phenotype than with non-confirmed ESBL phenotype when co-harboring either blaCTXM alone (47.6% vs. 0%, p < 0.001) or blaCTXM/blaSHV genes (100% vs. 0%, p = 0.022) or blaCTX-M/blaTEM genes (100% vs. 0%, p = 0.03). CONCLUSIONS: For ESBL/pAmpC co-producers of Enterobacteriaceae, CDDT results vary with the type of pAmpC genes and with different ESBL/pAmpC genotype combinations. Therefore, the ESBL-screening test is more sensitive than the CDDT in detecting ESBL phenotype among ESBL/pAmpC coproducers of Enterobacteriaceae.

Molecular Study of Accessory-Gene-Regulator in Staphylococcus aureus Isolated from Sepsis in Pediatric Patients.

BACKGROUND: Pediatric sepsis due to Staphylococcus aureus (S. aureus) is associated with high morbidity and mortality. Accessory-Gene-Regulator (agr) has a role in the pathogenesis of S. aureus through controlling and regulating the expression of virulence genes. Therefore, the aim of the present study was to investigate the prevalence of genotypes of the agr system in S. aureus isolated from children with sepsis and to assess their relationship to biofilm formation and antibiotic resistance. METHODS: The study was a retrograde cross-sectional study that included 131 children with health care associated sepsis due to S. aureus. The isolated S. aureus was investigated for their ability to form biofilm by microplate method, antibiotic susceptibility pattern by disc diffusion method, and molecular determination of agr genotypes by polymerase chain reaction (PCR). RESULTS: Methicillin resistant S. aureus (MRSA) was defined by resistance to cefoxitin antibiotic disc in 70 (53.4%) of the isolates and biofilm formation was positive in 67 (58%) of the isolates. Molecular study of the agr genes revealed that 54 (41.2%), 40 (30.5%), 27 (20.6%), and 10 (7.5%) of the studied isolates had agr I, agr II, agr III, and agr IV, respectively. In comparison between MRSA and methicillin sensitive S. aureus (MSSA), there was a signif-icant increase in biofilm formation among MRSA (65.7%, p = 0.01) compared to MSSA (34.3%) and an increase in agr genotype I among MRSA (68.6%, p = 0.001) compared to agr I in MSSA (9.8%). There was a significant association with the presence of a central venous catheter (51.4%, p = 0.001) and urinary tract catheter (81.4%, p = 0.001) in children with MRSA compared to children with MSSA (21.3%, OR = 3.9, 95% CI = 1.8 - 8.5 and 36.1%, OR = 7.8, 95% CI 3.5 - 17.3, respectively). CONCLUSIONS: There was an increase in the biofilm formation among S. aureus isolated from pediatric patients with sepsis with a significant increase in MRSA. The agr group I was the main agr gene among the isolated S. aureus. Moreover, agr I was the predominant gene in MRSA isolates and was significantly associated with biofilm formation.

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.

Aerobic bacteria isolated from diabetic foot ulcers of Egyptian patients: types, antibiotic susceptibility pattern and risk factors associated with multidrug-resistant organisms.

INTRODUCTION: Diabetic foot infection (DFI) is one of the common diabetic complications. Pathogens causing DFI and their antibiotic susceptibility vary with location. Therefore, empirical antibiotic therapy should be based on the pathogens that are most likely to be present. Aim: To identify the frequent aerobic bacteria causing DFI with detection of their antibiotic susceptibility to help clinicians in our community choose the best empirical antibiotic for DFI. METHODS: Swabs were collected from 104 diabetic foot ulcers (DFUs). Aerobic bacterial cultures were done followed by bacterial identification and antibiotic susceptibility testing on VITEK® 2 system. Extended-spectrum beta-lacatamase (ESBL) detection was performed phenotypically and confirmed by multiplex-PCR for bla CTX-M, bla TEM, and bla SHV genes. RESULTS: Aerobic bacterial infection was detected in 82/104 (78.8%) of the DFUs. Gram-negative bacilli (GNB) were isolated more frequently (56.1%) than Gram-positive cocci (GPC) (43.9%). The most common single-isolated bacteria were K. pneumoniae (26.8%), S. aureus and coagulase negative staphylococci (22% for each). The only significant independent predictors of DFI with GNB or GPC were long DM duration and frequent hospitalizations, respectively. The most active antibiotics were amikacin, tigecycline and meropenem for GNB, and linezolid and vancomycin for staphylococci. Multidrug-resistance prevalence was 95.1%. ESBL was detected in 52.6% of Enterobacteriaceae; the bla CTX-M gene was the most common (90%), followed by bla TEM (65%) and bla SHV (35%). Peripheral neuropathy was the single independent predictor for DFI with ESBL producers (adjusted OR=15.5). CONCLUSIONS: There is a notable local pattern of DFI bacteriology in our community. Our findings could be valuable in developing the future empirical treatment guidelines for DFIs.

Activity of imipenem/relebactam on Klebsiella pneumoniae with different mechanisms of imipenem non-susceptibility.

BACKGROUND AND OBJECTIVES: Imipenem/relebactam (IMP/R) is a newly FDA approved ß-lactam/ß-lactamase inhibitor combination. Relebactam ability to restore IMP activity could differ according to the cause of imipenem non-susceptibility. Therefore, we investigated the in-vitro activity of IMP/R against Klebsiella pneumoniae with different mechanisms of imipenem non-susceptibility. MATERIALS AND METHODS: Imipenem-nonsusceptible (IMP-NS) K. pneumoniae isolates were collected and characterized for ß-lactamase encoding genes by multiplex PCR. For IMP-NS carbapenemase-negative isolates, study of Ompk35 & Ompk36 gene expression was performed by reverse transcription-PCR while efflux pump activity was studied by minimum inhibitory concentration (MIC) reduction assay using efflux pump inhibitor. Susceptibility testing of K. pneumoniae to IMP and IMP/R were achieved by broth microdilution (BMD) method. RESULTS: During the study period, 140 isolates of IMP-NS K. pneumoniae were collected. BMD method showed that relebactam restored IMP susceptibility in 100%, 60% and 49% of isolates that only harbor AmpC, extended spectrum beta lactamase (ESBL) and carbapenemases, respectively. IMP/R was most potent against all bla KPC and 50% of bla OXA-48 _producing isolates. No demonstrable activity of IMP/R against K. pneumoniae harboring metallo-ß-lactamases (MBLs). Out of 18 isolates with IMP non-suceptibility due to porins loss with overproduction of ESBL and/or AmpC, 14 (77.7%) isolates were IMP/R susceptible. IMP/R showed no activity against isolates with only efflux pump hyperactivity. CONCLUSION: Relebactam could restore IPM activity in KPC or AmpC-producing IMP/NS K. pneumoniae but with no activity against MBL- producing isolates. Relebactam activity against isolates harbouring-bla OXA-48 or with altered Ompk35 & Ompk36 gene expression and efflux pump hyperactivity need further studies. Therefore, using IMP/R antibiotic in the treatment of infections caused by IMP/NS K. pneumoniae should be based on its molecular profile of IMP resistance to optimize the utility of IMP/R.

Colistin-heteroresistance in carbapenemase-producing Enterobacter species causing hospital-acquired infections among Egyptian patients.

OBJECTIVES: Colistin is the last resort for treating carbapenemase-producing Enterobacter. Colistin-heteroresistance is a new concern as it may cause treatment failure. Our study aimed to detect colistin-heteroresistance among carbapenemase-producing Enterobacter species causing hospital-acquired infections in patients at Mansoura University Hospitals (MUHs). METHODS: Sensitivity of recovered Enterobacter species to imipenem, meropenem and colistin was estimated by the broth dilution method. Carbapenemase production was detected with the Carba NP test and confirmed with multiplex PCR. Population analysis profile (PAP) was performed to assess colistin-heteroresistance. Enterobacter isolates with colistin MIC≤2µg/mL had subpopulations growing at colistin concentration>2µg/mL were considered heteroresistant. Isolates with subpopulations growing at colistin concentrations two times higher than MIC but ≤ 2 µg/mLwere considered heterogeneous. RESULTS: Of 115 Enterobacter isolates collected during the period of the study, 61 (53%) were cabapenem-resistant. Of these, 49 isolates (42.6%) were carbapenemase-producers, including Enterobacter cloacae complex (37; 75.5%) and Enterobacter aerogenes (12; 24.5%). The most prevalent carbapenemase gene was blaNDM (20 isolates; 40.8%). Seven isolates were colistin-resistant (7/115; 6.1%). Seventeen isolates (34.7% of carbapenemase-producers) were colistin-heteroresistant and two isolates had heterogeneous profiles. Most of these isolates were E. cloacae complex (12/17) and from bloodstream infection (10/17). The frequency of heteroresistant subpopulations ranged from 1 × 10-5 to 5.5 × 10-4. CONCLUSION: Carbapenem-resistant Enterobacter is a common resistant pathogen in the hospital setting. Colistin-heteroresistance among carbapenemase-producing Enterobacter is a growing serious medical problem as colistin is considered the last hope for treating infections caused by these multidrug-resistant pathogens.

Tuberculosis/toxoplasmosis co-infection in Egyptian patients: A reciprocal impact.

OBJECTIVE: To assess the concurrent toxoplasmosis infection in Egyptian TB patients and the impact of each infection on the other in terms of increased severity of TB or reactivation of latent Toxoplasma infection. METHODS: Three hundred suspected pulmonary TB cases were initially screened for TB using direct Ziehl Neelsen staining and Lowenstein Jensen culture of their sputa. Rifampicin resistance was detected by Xpert MTB/RIF assay. Control group of 30 age and sex-matched healthy individuals negative for TB was included for comparison. All subjects were further assessed for serum levels of anti-Toxoplasma IgG antibodies and malondialdehyde (MDA). RESULTS: Forty three confirmed TB-infected patients including 10 (23.3%) rifampicin-resistant patients were detected. Associated toxoplasmosis was found to be significantly higher among TB patients (OR = 2.709; 95% CI: 1.034-7.099; P<0.05) and among rifampicin sensitive than rifampicin resistant TB patients (OR=0.213; 95% CI: 0.048-0.951; P < 0.05). Serum levels of anti-Toxoplasma IgG antibodies and MDA were significantly higher among TB patients than the control group. Furthermore, serum level of MDA was significantly higher among TB/Toxoplasma co-infected patients as compared to toxoplasmosis free-TB patients. Strong positive correlation was detected between serum levels of anti-Toxoplasma IgG and MDA in TB patients (r = 0.75, P = 0.001). CONCLUSIONS: Among pulmonary TB Egyptian patients, there is a considerable prevalence of toxoplasmosis. Severity of pulmonary tuberculosis could be increased by Toxoplasma co-infection.

Anti-Toxoplasma antibodies in Egyptian rheumatoid arthritis patients.

OBJECTIVE: To assess seroprevalence of anti-Toxoplasma gondii antibodies; both IgG and IgM in Egyptian rheumatoid arthritis (RA) patients versus a non-RA group and to compare anti-Toxoplasma antibodies seroprevalence among RA patients receiving traditional treatment and RA patients treated with biologic drug. METHODS: 60 RA patients and 60 healthy controls were enrolled in the study. Patients were categorized into two groups: one group included 30 patients receiving disease modifying anti-rheumatic drugs (DMARDs), while the other group included 30 patients receiving biologic agent, infliximab, a TNF-α antagonist. Serum samples of all investigated persons were examined for anti-Toxoplasma antibodies. RA activity markers including rheumatoid factor, anti-cyclic citrullinated protein antibodies, C reactive protein, ESR in addition to disease activity score 28 (DAS28) of RA patients were also evaluated to explore their association with Toxoplasma seropositivity. RESULTS: Anti-Toxoplasma IgG antibodies were detected among 46/60 RA patients (76.7%) versus 29/60 controls (48.3%), (p = 0.001). Anti-Toxoplasma IgG titre was higher among RA group [median, (range) = 232.940 (8.949-653.242) IU/ml] than among controls [median, (range) = 68.820 (2.450-318.945) IU/ml], (p < 0.001). No difference was detected among RA patients either on traditional or biologic treatment regarding anti-Toxoplasma IgG antibodies. No positive anti-Toxoplasma IgM was detected. A positive correlation was detected between anti-Toxoplasma IgG titre and disease activity markers. CONCLUSION: Higher seroprevalence of anti-Toxoplasma IgG antibodies among RA patients compared to controls reflects an association between latent Toxoplasma infection and RA. Our findings support previous studies and necessitate future large-scale studies to elucidate the exact role of Toxoplasma whether a trigger of autoimmunity in RA or an effect of immunosuppression.