Sample pooling for SARS-CoV-2 RT-PCR screening.

OBJECTIVE: To evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of coronavirus disease 2019 (COVID-19) by using different commercial platforms for nucleic acid extraction and amplification. METHODS: A total of 3519 nasopharyngeal samples received at nine Spanish clinical microbiology laboratories were processed individually and in pools (342 pools of ten samples and 11 pools of nine samples) according to the existing methodology in place at each centre. RESULTS: We found that 253 pools (2519 samples) were negative and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples), we found discordant results when compared to their correspondent individual samples, as follows: in 22 of 29 pools (28 samples), minor discordances were found; for seven pools (7 samples), we found major discordances. Sensitivity, specificity and positive and negative predictive values for pooling were 97.10% (95% confidence interval (CI), 94.11-98.82), 100%, 100% and 99.79% (95% CI, 99.56-99.90) respectively; accuracy was 99.80% (95% CI, 99.59-99.92), and the kappa concordant coefficient was 0.984. The dilution of samples in our pooling strategy resulted in a median loss of 2.87 (95% CI, 2.46-3.28) cycle threshold (Ct) for E gene, 3.36 (95% CI, 2.89-3.85) Ct for the RdRP gene and 2.99 (95% CI, 2.56-3.43) Ct for the N gene. CONCLUSIONS: We found a high efficiency of pooling strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA testing across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity and positive and negative predictive values.

Direct, indirect and total effectiveness of bivalent HPV vaccine in women in Galicia, Spain.

Bivalent human papillomavirus (HPV) vaccine was incorporated into the childhood vaccination calendar in Galicia, Spain in 2008. The objectives of this study were to estimate direct, indirect and total effectiveness of HPV vaccine and to identify sexual habits changes in the post-vaccination period in Galicia, Spain.Endocervical scrapings of 745 women attending 7 Health Areas of the Galician Public Health Service were collected in the post-vaccination period, from 2014-2017. Two groups were studied: women born between 1989 and 1993 (n = 397) and women born in 1994 or later (n = 348). Twelve high-risk human papillomavirus (HR-HPV) genotypes were detected by Cobas® 4800 HPV test (Roche Diagnostics, Mannheim, Germany). The Linear Array® HPV Genotyping Test (Roche Diagnostics) was used for HR-HPV genotype detection other than HPV 16/18. Information about sexual habits was collected by a self-filled questionnaire. Post-vaccination data were compared to previously published pre-vaccination data obtained between 2008 and 2010 in Galicia from women of the same age (18-26 years old, n = 523). The Stata 14.2 software was employed for statistical analyses.Data from 392 unvaccinated and 353 vaccinated women were compared. For unvaccinated and vaccinated women, HPV 16/18 prevalence was 9.2% and 0.8%, respectively, and HPV 31/33/45 prevalence was 8.4% and 1.1%, respectively. Direct, indirect and total effectiveness of the HPV vaccine were (%, 95% CI): 94 (72-99), 30 (-11-56) and 95 (79-99), respectively, for HPV 16/18 and 83 (46-94), -10 (-88-33) and 84 (54-94), respectively, for HPV 31/33/45. The number of women with first intercourse before 17 years old and 3 or more sexual partners along life was higher in the post-vaccination period (p < 0.05). A positive impact of bivalent HPV vaccine was observed, both on direct and cross protection. Sexual habits could have changed in the post-vaccination period.

Colorectal neoplasm in cases of Clostridium septicum and Streptococcus gallolyticus subsp. gallolyticus bacteraemia.

BACKGROUND: Bacteremia with Clostridium septicum (CS) and Streptococcus gallolyticus subsp. gallolyticus (SGG) have both been associated with colorectal neoplasms (CRN) and colonoscopic examination is advised, however the differences and similarities in colorectal findings are not well known. METHODS: This is a multicenter, comparative study of patients with CS bacteremia [44 of 664 cases (6.6%) of Clostridium spp.] and SGG bacteremia [257 of 596 cases (44.2%) of S. bovis group], carried out in three hospitals from Spain. Clinical findings related to bacteremia and associated CRN were collected. RESULTS: The main sources of infection were abdominal (77.7%) for CS bacteremia and endovascular (75%) for SGG bacteremia. CS bacteremia was more often associated with malignancies, (72.6% vs. 19.4%) and neutropenia (29.5% vs. 3.1%), and was more acute, with shock at presentation (63.6% vs. 3.9%) and higher 30-day mortality (47.7% vs. 9.7%) compared to SGG (P<0.05 for all). Both, patients with CS and SGG bacteremia often had concomitant CRN (43.1% vs. 49.8%) and most of them presented as occult CRN (73.7% vs. 91.4%; P=0.02). CS cases more often had invasive carcinomas (94.7% vs. 19.5%), location of CRN in the right colon (73.7% vs. 23.4%), larger tumor size (median 7 vs. 1.5cm), and a higher overall CRN related mortality rate (68.4% vs. 7.8%) compared to SGG cases (P<0.05 for all). CONCLUSIONS: Both, CS and SGG bacteremia are associated with occult CRN. CS cases more often had advanced carcinomas than SGG cases, suggesting a distinct temporal association with CRN.

Streptococcus bovis septic arthritis and osteomyelitis: A report of 21 cases and a literature review.

BACKGROUND: The Streptococcus bovis group (SBG) is a well-known cause of endocarditis, but its role in osteoarticular infections (OAIs) has not been well described. METHODS: We analyzed all patients with OAIs by SBG diagnosed in our hospital (1988-2014). We selected those cases with septic arthritis and osteomyelitis, as defined according to clinical, microbiological, and imaging studies. Identification of the strains was performed by using the API 20 Strep and the GP card of the Vitek 2 system, and confirmed the identification by molecular methods. In addition, we reviewed the literature to select all cases of OAI by SBG during the period 1980-2015. RESULTS: From the 83 cases of OAI included in the analysis (21 from our center and 62 from the literature review), 59 were osteomyelitis (57 of them spondylodiscitis) and 24 were arthritis (2 with associated spondylodiscitis). The mean age was 66.9 years, and 79.2% of the patients were men. Endocarditis (IE) was associated with 59% of the cases and this association was greater for osteomyelitis than for arthritis (78.9% vs. 13.6%; P = 0.001). OAI was a presenting symptom in 63% of the cases of IE. Colonoscopy was performed in 64 cases, which detected colorectal neoplasm (CRN) in 46 patients (71.8%), almost all asymptomatic. Some 69.5% of these neoplasm were carcinomas or advanced adenomas. The blood cultures were positive in 78.3% cases. In 45 cases, the S. bovis species was identified; in 82.2% of the cases the cause was Streptococcus gallolyticus subsp. gallolyticus. The mortality was 7.2%, which in no case was attributable to the OAI. CONCLUSIONS: OAIs are frequently the initial manifestation of IE caused by SBG. S. gallolyticus causes most of these infections. Echocardiogram and colonoscopy are therefore mandatory, given the species' close association with IE and CRN.

The clinical epidemiology and malignancies associated with Streptococcus bovis biotypes in 506 cases of bloodstream infections.

OBJECTIVES: To determine the incidence of Streptococcus bovis (Sb) biotypes causing bacteraemia and associated malignancies. METHODS: This is a retrospective analysis of patients with Sb bacteraemia, pulled out from a prospective surveillance protocol of bacteraemia cases, in three areas of Spain (1990-2013): a cattle area (Lugo), a fishing area (Ferrol) and an urban area (Barcelona). Colonoscopy and Sb biotypes (Sb-I and Sb-II) were determined in most cases. RESULTS: 506 patients with Sb bacteraemia; mean age 68.1 (±14.1) years, and 66.2% were males. The cattle area, compared with the fishing and urban areas, had higher incidence of bacteraemia by SbI (40.29 vs 9.38 vs 6.15 cases/10(6) person-years, P < 0.001) and bacteraemia by Sb-II (29.07 vs 9.84 vs 13.37 cases/10(6) person-years, P < 0.001). The Sb-I cases (n = 224), compared with Sb-II cases (n = 270), had greater rates of endocarditis (77.6% vs 9.6%, P < 0.001) and colorectal neoplasm (CRN) (50.9% vs 16.6%, P < 0.001), and smaller rates of biliary tract infection (2.2% vs 29.6%, P < 0.001) and non-colorectal malignancy (8.9% vs 31.4%, P < 0.001). CONCLUSION: There was a link between the cattle area and higher incidence of Sb bacteraemia. Sb-I differed from Sb-II cases in clinical findings and associated malignancies. Colonoscopy is mandatory in cases of endocarditis or bacteraemia caused by Sb-I.

Association between bacteremia due to Streptococcus gallolyticus subsp. gallolyticus (Streptococcus bovis I) and colorectal neoplasia: a case-control study.

BACKGROUND: The association between bacteremia by Streptococcus gallolyticus subsp. gallolyticus (SGG) and colorectal neoplasia (CRN) is well established but the frequency of the association varies widely in different studies. We conducted a case-control study to assess the association between SGG bacteremia and CRN. METHODS: An analysis of all SGG bacteremias was performed during the period 1988-2011. The frequency of CRN in patients with SGG bacteremia was compared with the frequency of CRN in a symptomatic control group of patients matched at a 1:2 ratio for gender and age (±3 years) without S. bovis bacteremia and personal history of CRN and with increased risk of CRN (by the presence of symptoms, signs, or test suspicious of colonic pathology or by family history of CRN). RESULTS: One hundred nine cases of SGG bacteremia were detected (mean age, 66 years; 87% male). Colonoscopy was performed in 98 cases, diagnosing 69 cases of CRN: 57 adenomas (39 advanced adenomas) and 12 invasive carcinomas. Only 4 cases had suspected CRN before the blood culture. The prevalence of CRN was higher in patients with SGG bacteremia than in the 196 control patients (70% vs 32%; odds ratio [OR], 5.1; 95% confidence interval [CI], 3.0-8.6). This difference was not significant when comparing nonadvanced adenomas (19% vs 12%), but we found significant differences in advanced adenomas (40% vs 16%; OR, 3.5; 95% CI, 2.0-6.1) and invasive carcinomas (12% vs 5%; OR, 2.9; 95% CI, 1.2-6.9). CONCLUSIONS: The frequency of CRN among SGG infected patients is significantly increased compared with symptomatic age-matched controls, indicating that SGG infection is a strong indicator for underlying occult malignancy.