We characterised 80 Staphylococcus aureus strains isolated from human patients with SSTIs at a rural hospital in Ethiopia. Susceptibility to antibiotic of all strains was tested. The MLST method was ...used to type and a phylogenetic analysis was conducted employing the sequences of 7 housekeeping genes. PCR amplification was used to investigate the presence of the following virulence genes in all strains: hla (α-haemolysin), tstH (toxic shock syndrome toxin), luk PV (Panton-Valentine leukocidin), fnbA (fibronectin binding protein A) and mecA (methicillin resistance). Most of the strains were resistant to penicillin and ampicillin, but only 3 strains were resistant to oxacillin, and 1 of them was a true MRSA. The MLST results showed a high diversity of sequence types (ST), 55% of which were new, and ST152 was the most prevalent. A phylogeny study showed that many of the new STs were phylogenetically related to other previously described STs, but bore little relationship to the only ST from Ethiopia described in the database. Virulence gene detection showed a high prevalence of strains encoding the hla, fnbA and pvl genes (98.77%, 96.3% and 72.84%, respectively), a low prevalence of the tst gene (13.58%) and a markedly low prevalence of MRSA (1.25%). S. aureus strains isolated from patients in a rural area in Ethiopia showed low levels of antibiotic resistance, except to penicillin. Moreover, this study reveals new STs in Eastern Africa that are phylogenetically related to other previously described STs, and confirm the high prevalence of the pvl gene and the low prevalence of MRSA on the continent.
A limited number of longitudinal studies have examined the symptoms associated with long-COVID-19. We conducted an assessment of symptom onset, severity and patient recovery, and determined the ...percentage of patients who experienced reinfection up to 2 years after the initial onset of the disease. Our cohort comprises 377 patients (>=18 years) with laboratory-confirmed COVID-19 in a secondary hospital (Madrid, Spain), throughout March 3-16, 2020. Disease outcomes and clinical data were followed-up until August 12, 2022. We reviewed the evolution of the 253 patients who had survived as of April 2020 (67.1%). Nine died between April 2020 and August 2022. A multivariate regression analysis performed to detect the risk factors associated with long-COVID-19 revealed that the increased likelihood was associated with chronic obstructive lung disease (OR 14.35, 95% CI 1.89-109.09; 'p' = 0.010), dyspnea (5.02, 1.02-24.75; 'p' = 0.048), higher LDH (3.23, 1.34-7.52; 'p' = 0.006), and lower D-dimer levels (0.164, 0.04-0.678; 'p' = 0.012). Reinfected patients ('n' = 45) (47.8 years; 39.7-67.2) were younger than non-reinfected patients (64.1 years; 48.6-74.4)) ('p' < 0.001). Patients who received a combination of vaccines exhibited fewer symptoms (44.4%) compared to those who received a single type of vaccine (77.8%) ('p' = 0.048). Long-COVID-19 was detected in 27.05% (66/244) of patients. The early detection of risk factors helps predict the clinical course of patients with COVID-19. Middle-aged adults could be susceptible to reinfection, highlighting the importance of prevention and control measures regardless of vaccination status.
•The new antigen test is an indispensable tool in the control of the pandemic due to its adequate sensitivity and specificity.•The implementation of the point of care technique in primary care is ...feasible and has good results.•Results of the antigen techniques are determined by an onset of symptoms inferior to five days and a CT below 27 in PCR.
RT-qPCR is the current recommended laboratory method to diagnose SARS-CoV-2 acute infection, several factors such as requirement of special equipment, time consuming, high cost and skilled staff limit the use of these techniques. A more rapid and high-throughput method is essential.
We analyzed clinical data and nasopharyngeal samples, collected during September 2020, from patients attended at the emergency department of a secondary hospital and in two primary healthcare centers in Madrid. The performance of the Panbio™ COVID-19 AG Rapid Test Device for the detection of SARS-CoV-2 antigen was compared to RT-qPCR.
255 nasopharyngeal swabs, including 150 from the emergency department and 105 from primary helthcare centers, were tested. 184 patients were symptomatic (72.1 %). Amongst the 60 positive RT-qPCR samples, 40 were detected by the rapid antigen test, given an overall sensitivity of 73.3 %. All the samples detected positive with the rapid antigen test were also positive with RT-qPCR. The median cycle threshold was 23.28 (IQR 18.5–30.16). Patients with less than seven days onset of symptoms showed a higher viral load, and sensitivity for rapid antigen test (86.5 %), compared to those with more days (sensitivity of 53.8 %)(p < 0.004).
The rapid antigen test evaluated in this study showed a high sensitivity and specificity in samples obtained during the first week of symptoms and with high viral loads. This assay seems to be an effective strategy for controlling the COVID-19 pandemic for the rapid identification and isolation of SARS-CoV-2 infected patients.
•Alltest lateral flow immunoassay is reliable to diagnose SARS-CoV-2 infection.•This immunoassay showed a specificity of 100 % and a sensitivity of 64 %.•The sensitivity increased up to 88 % from 14 ...days after symptoms onset.•Alltest is useful in patients with suspected SARS-CoV-2 pneumonia but negative PCR.•The test was positive in 89 % of patients with pneumonia and negative PCR.
SARS-CoV-2 infection diagnosis is challenging in patients from 2 to 3 weeks after the onset of symptoms, due to the low positivity rate of the PCR. Serologic tests could be complementary to PCR in these situations. The aim of our study was to analyze the diagnostic performance of one serologic rapid test in COVID-19 patients.
We evaluated a lateral flow immunoassay (AllTest COVID-19 IgG/IgM) which detects IgG and IgM antibodies. We validated the serologic test using serum samples from 100 negative patients (group 1) and 90 patients with COVID-19 confirmed by PCR (group 2). Then, we prospectively evaluated the test in 61 patients with clinical diagnosis of pneumonia of unknown etiology that were negative for SARS-CoV-2 by PCR (group 3).
All 100 patients from group 1 were negative for the serologic test (specificity = 100 %). Regarding group 2 (PCR-positive), the median time from their symptom onset until testing was 17 days. For these 90 group-2 patients, the test was positive for either IgM or IgG in 58 (overall sensitivity = 64.4 %), and in patients tested 14 days or more after the onset of symptoms, the sensitivity was 88.0 %. Regarding the 61 group-3 patients, median time after symptom onset was also 17 days, and the test was positive in 54 (88.5 % positivity).
Our study shows that Alltest lateral flow immunoassay is reliable as a complement of PCR to diagnose SARS-CoV-2 infection after 14 days from the onset of symptoms and in patients with pneumonia and negative PCR for SARS-CoV-2.
•CerTest and Panbio Ag-RDTs are reliable to diagnose SARS-CoV-2 infection.•Their sensitivity was over 90 % for samples with a Ct≤25.•Their sensitivity was over 84 % within 5 days after the onset of ...symptoms.•Specificity of both assays was 100 %. Agreement between them was excellent.•Agreement with PCR was also excellent for samples with Ct≤25.
Antigen rapid diagnostic tests (Ag-RDT) have been developed as reliable tools to control the SARS-CoV-2 pandemic. The objective of our study was to evaluate the diagnostic performance of two Ag-RDTs.
We evaluated CerTest SARS-CoV-2 Ag One Step Card Test and Panbio COVID-19 Ag Rapid Test Device Ag-RDTs. We included 320 nasopharyngeal samples: 150 PCR negative samples to assess the specificity and 170 PCR positive samples to evaluate the sensitivity. We also evaluated their sensitivity according to cycle threshold (Ct) values and the time from the onset of symptoms. Tests were compared using the McNemar’s test and agreement was evaluated using the kappa score (k).
Both Ag-RDTs showed a specificity of 100 %. Overall sensitivity was 53.5 % for CerTest and 60.0 % for Panbio. For samples with Ct≤ 25, sensitivity was 94.0 % for CerTest and 96.4 % for Panbio (p = 0.500). Regarding samples with Ct>25, sensitivity was 14.0 % for CerTest and 24.4 % for Panbio (p = 0.004). Sensitivity for samples within the first 5 days after the onset of symptoms were 84.8 % for CerTest and 91.3 % for Panbio (p = 0.250) and notably decreased for samples taken after the fifth day. Both Ag-RDTs showed an excellent agreement between them (agreement = 96.7 %, k = 0.920). Agreement with PCR was also excellent for high viral load samples (Ct<25) for CerTest (98.0 %, k = 0.954) and Panbio (98.8 %, k = 0.973).
CerTest SARS-CoV-2 and Panbio COVID-19 Ag showed excellent performance and agreement results for samples with high viral loads (Ct ≤ 25) or samples taken within the first 5 days after the onset of symptoms.
The aim of our study was to evaluate the diagnostic performance of two antigen rapid diagnostic tests (Ag‐RDTs) to diagnose severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection. We ...evaluated Panbio and SD‐Biosensor Ag‐RDTs. We employed 186 polymerase chain reaction (PCR) negative samples to evaluate the specificity and 170 PCR positive samples to assess the sensitivity. We evaluated their sensitivity according to Cycle threshold (C
t) values and days post onset of symptoms (d.p.o.). Tests were compared using the McNemar's test. Agreement was evaluated using the kappa score. Specificity was 100% for Panbio and 97.3% for SD‐Biosensor. Sensitivity for samples with C
t ≤ 20 was 100% for both assays and for samples with C
t = 20–25 was 93.0% (Panbio) and 95.3% (SD‐Biosensor) (p = 1.000). Sensitivity decreased for samples wit C
t = 25–30 (Panbio: 41.3%, SD‐Biosensor: 52.2%, p = 0.125) and samples with C
t ≥ 30 (Panbio: 5.0%, SD‐Biosensor: 17.5%, p = 0.063). Sensitivity within seven d.p.o. was 87.7% for Panbio and 90.4% for SD‐Biosensor and notably decreased after seven d.p.o. Agreement with PCR was excellent for high viral load samples (C
t ≤ 25): Panbio, 98.9%, kappa = 0.974; SD‐Biosensor, 97.4%, kappa = 0.940. Agreement between Ag‐RDTs was excellent (94.9%, kappa = 0.882). Panbio and SD‐Biosensor Ag‐RDTs showed excellent agreement and diagnostic performance results for samples with high viral loads (C
t ≤ 25) or samples within seven d.p.o.
Highlights
Panbio and SD‐Biosensor Ag‐RDTs are reliable to diagnose SARS‐CoV‐2 infection.
They showed high specificity: 100% (Panbio) and 97.3% (SD‐Biosensor).
Sensitivity for samples with Ct ≤ 20 was 100% and for samples with Ct ≤ 25 was over 93%.
Their sensitivity was over 87% within 7 days after symptoms onset. Agreement between them was excellent (agreement = 94.9%, kappa = 0.882).
•The six immunoassays are reliable to detect antibodies against SARS-CoV-2.•LFAs using S and N protein as antigens achieved the highest sensitivity.•One Step LFA, Dia.Pro ELISA, Elecsys and COV2T ...CLIAs showed 100 % specificity.•These four assays showed sensitivity over 97 % from 14 days after the onset of symptoms.•These four assays showed excellent agreement with kappa scores (k) > 0.9.
Serologic techniques can serve as a complement to diagnose SARS-CoV-2 infection. The objective of our study was to compare the diagnostic performance of six immunoassays to detect antibodies against SARS-CoV-2: three lateral flow immunoassays (LFAs), one ELISA and two chemiluminescence assays (CLIAs).
We evaluated three LFAs (Alltest, One Step and SeroFlash), one ELISA (Dia.Pro) and two CLIAs (Elecsys and COV2T). To assess the specificity, 60 pre-pandemic sera were used. To evaluate the sensitivity, we used 80 serum samples from patients with positive PCR for SARS-CoV-2. Agreement between techniques was evaluated using the kappa score (k).
All immunoassays showed a specificity of 100 % except for SeroFlash (96.7 %). Overall sensitivity was 61.3 %, 73.8 %, 67.5 %, 85.9 %, 88.0 % and 92.0 % for Alltest, One Step, SeroFlash, Dia.Pro, Elecsys and COV2T, respectively. Sensitivity increased throughout the first two weeks from the onset of symptoms, reaching sensitivities over 85 % from 14 days for all LFAs, being One Step the most sensitive (97.6 %), followed by SeroFlash (95.1 %). Dia.Pro, Elecsys and COV2T showed sensitivities over 97 % from 14 days, being 100 % for COV2T. One Step showed the best agreement results among LFAs, showing excellent agreement with Dia.Pro (agreement = 94.2 %, k = 0.884), COV2T (99.1 %, k = 0.981) and Elecsys (97.3 %, k = 0.943). Dia.Pro, COV2T and Elecsys also showed excellent agreement between them.
One Step, Dia.Pro, Elecsys and COV2T obtained the best diagnostic performance results. All these techniques showed a specificity of 100 % and sensitivities over 97 % from 14 days after the onset of symptoms, as well as excellent levels of agreement.
There is little information about carbapenemase-producing (CP) Citrobacter spp. We studied the molecular epidemiology and microbiological features of CP Citrobacter spp. isolates collected in Spain ...(2013-15).
In total, 119 isolates suspected of being CP by the EUCAST screening cut-off values were analysed. Carbapenemases and ESBLs were characterized using PCR and sequencing. The genetic relationship among Citrobacter freundii isolates was studied by PFGE.
Of the 119 isolates, 63 (52.9%) produced carbapenemases, of which 37 (58.7%) produced VIM-1, 20 (31.7%) produced OXA-48, 12 (19%) produced KPC-2, 2 (3.2%) produced NDM-1 and 1 (1.6%) produced VIM-2; 9 C. freundii isolates co-produced VIM-1 plus OXA-48. Fourteen isolates (22.2%) also carried ESBLs: 8 CTX-M-9 plus SHV-12, 2 CTX-M-9, 2 SHV-12 and 2 CTX-M-15. Fifty-seven isolates (90.5%) were C. freundii, 4 (6.3%) were Citrobacter koseri, 1 (1.6%) was Citrobacter amalonaticus and 1 (1.6%) was Citrobacter braakii. By EUCAST breakpoints, eight (12.7%) of the CP isolates were susceptible to the four carbapenems tested. In the 53 CP C. freundii analysed by PFGE, a total of 44 different band patterns were observed. Four PFGE clusters were identified: cluster 1 included eight isolates co-producing VIM-1 and OXA-48; blaVIM-1 was carried in a class 1 integron (intI-blaVIM-1-aacA4-dfrB1-aadA1-catB2-qacEΔ1/sul1) and blaOXA-48 was carried in a Tn1999.2 transposon.
We observed the clonal and polyclonal spread of CP Citrobacter spp. across several Spanish geographical areas. Four species of Citrobacter spp. produced up to five carbapenemase types, including co-production of VIM-1 plus OXA-48. Some CP Citrobacter spp. isolates were susceptible to the four carbapenems tested, a finding with potential clinical implications.
Staphylococcus aureus is the main causative agent of joint prosthesis infections. The decolonization of the carriers is effective in the prevention of the infections of the elective arthroplasties. ...The aim of this study is to evaluate if it is also in arthroplasties after hip fracture.
Study in patients with hip fracture who underwent joint prosthesis from January 2011 to December 2015 with a protocol of S. aureus detection-decolonization with intranasal mupirocin and chlorhexidine baths. Patients between January 2009 and December 2010 were the comparison group.
In the intervention period, the study of colonization of S. aureus was performed in 307 patients, of whom 87 were positive (28.3%). The study period was completed by 267 patients, of whom two developed S. aureus infection, compared to six of 138 in the control group (0.7% vs 4.3%, RR 0.1, p = 0.03).
In our study, S. aureus decolonization in patients with hip fracture decreased the incidence of joint prosthesis infection by this microorganism.
Most publications about prosthetic joint infections (PJI) are referred to elective prosthesis and they exclude arthroplasties due to hip fracture.
We conducted a descriptive study about prosthetic ...joint infections after joint fracture in Alcalá de Henares Hospital (Madrid) between 2009 and 2014 and we compared with elective prosthetic infections in the same period.
There were 30 PJI after hip fracture and 14 elective PJI. The incidence of infection was 4.7% in arthroplasties due to hip fracture from 1.3% in elective prosthesis (RR 3.8, p=0.005). The PJI after fracture affected older patients (82.5 years vs 71.5, p=0.006), with greater comorbidity (5.4 vs 3.6, p=0.003), higher anesthetic risk (ASA>2 70% vs 21.4%, p=0.004) and higher incidence of dementia (50% vs 0%, p=0.02). Staphylococcus aureus was the most common causative agent in both groups, but there was higher incidence of Gram negative-cases in PJI after fracture group (43.3% vs 21.4%, p no significance) and cefazolin-resistance (63.3% vs 28.6%, p=0.03). In logistic regression analysis the treatment had less chance of success in PJI after fracture than elective PJI (33.3% vs 78.6%, OR 0.09, p=0.06).
The PJI after fracture are more frequent than elective PJI, affect older patients, with poor general condition, are produced by more resistant bacteria and have worst evolution than EPJI.
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