Search

Background: Streptococcus pneumoniae causes invasive pneumococcal disease (IPD) in adults. The introduction of pneumococcal conjugate vaccines (PCVs) has reduced vaccine serotypes but has also led to the rise of non-vaccine serotypes. The aim of this study was to analyse pneumococcal lineages and their association with recent changes in IPD among adults in Spain., Methods: Data from adult IPD cases (≥18 years) were collected from six Spanish hospitals in 2019-2021. Strains were serotyped, tested for antibiotic susceptibility and subjected to whole genome sequencing (WGS). Findings were compared with data from previous periods (2008-2016)., Results: A total of 655 IPD episodes were examined. Pneumonia was the main focus (515/655), and 366 episodes occurred in adults over 64 years. Although IPD incidence decreased during COVID-19 pandemic, the burden of disease caused by PCV13 serotypes was significant. Notably, serotype 3 persisted (GPSC12-ST180 and GPSC83-ST260), and a new serotype 4 lineage emerged (GPSC162-ST13022). Among non-PCV13 serotypes, serotype 8 expanded (GPSC3-ST53) and a new serotype 12 F lineage emerged (GPSC55-ST8060). Most serotypes presented a dominant Global Pneumococcal Sequencing Cluster (GPSC) like GPSC16-ST67 of 9 N or GPSC19-ST433 of 22 F. Nevertheless, some GPSCs were associated with several serotypes, the most numerous were GPSC3 (serotypes 8, 11 A, and 33 F) and GPSC6 (serotypes 11 A and 14). The overall penicillin non-susceptibility rate was 17.0 %, 14.6 % resistance for meningitis and 1.6 % for pneumonia (15.1 % susceptible at increased exposure [SIE]). Serotypes 11 A and 14 (GPSC6-ST156/6521) and 19 A (GPSC1-ST320) had penicillin MICs above 1 mg/L. Acquired resistance genes associated with macrolide and/or tetracycline resistance were present in 19.4 % of isolates, particularly among serotypes 6 C (GPSC47-ST386/4310) and 19 A (GPSC1-ST320)., Conclusions: The burden of PCV13 serotypes in adult IPD remains significant, and serotype 3 is the primary contributor. However, the rise of stable lineages associated with non-PCV13 serotypes, particularly 8, 9 N, and 22 F highlights a shifting epidemiology. The persistence of multidrug-resistant lineages, such as GPSC6-ST156 and GPSC1-ST320, emphasizes the need for continued surveillance. Vaccination of high-risk adults with current and broader coverage PCVs would help to control the burden of pneumonia and IPD among adults., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Sara Calvo-Silveria declares that the Project was partially funded by PFIS predoctoral grant number FI22/00279. José Yuste declares grants or contracts paid to his institution from MSD, Pfizer and Meiji. Support for attending meetings and/or travel from MSD and Pfizer. Participation on a Data Safety Monitoring Board or Advisory Board from GSK, MSD and Pfizer. Carmen Ardanuy declares funding to the institution from Instituto de Salud Carlos III through PI18/0339; PI21/1000 and INT22/0096; CB06/06/0037. Grants or contracts paid to her institution from MSD, Pfizer and Menarini. Payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from MSD. Support for attending meetings and/or travel from MSD and Pfizer., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Objective: To analyse relevant changes in incidence, clinical and microbiological characteristics of nocardiosis over the last 24 years at the current institution., Materials and Methods: The clinical records of patients with nocardiosis (2006-2018) were reviewed and then compared with a previous cohort (1995-2006). Nocardia isolates were identified by 5'-end-16S-rRNA-gene-PCR targeting the first 500 bp of the gene and sequencing. Susceptibility tests were determined by broth microdilution (CLSI guidelines)., Results: Forty-two patients (64.3% male) with nocardiosis were evaluated in the recent cohort: 51.2% had COPD, 43.9% were on corticosteroid therapy and 31.7% had cancer. The incidence of nocardiosis varied from 6.3 to 7.1/100,000 admissions (p = 0.62). There was a decrease in HIV patients (27% vs. 4.9%, p = 0.01) and solid organ transplantation (SOT) recipients (18.9% vs. 2 .4%, p = 0.01). Cases with pulmonary involvement had increased (70.3% vs. 90.5%, p = 0.04). Nocardia species were similar but the most common were N. cyriacigeorgica (32.4% vs. 40.5%, p = 0.49) and N. farcinica (24.3% vs. 14.3%, p = 0.39). Antibiotic resistance remained stable: cotrimoxazole (10.8% vs. 5.7%, p = 0.68), imipenem (5.4% vs. 5.6%, p = 1.0); amikacin and linezolid were 100% active. No differences were found in breakthrough nocardiosis (21.6% vs. 9.8%, p = 0.21) or related mortality (21.6% vs. 21.4%, p = 1.0). The multivariate analysis confirmed that nocardiosis caused by N. farcinica is a risk factor for poor outcome (p = 0.045)., Conclusions: Nocardiosis incidence has remained stable. It mainly affected elderly patients with chronic respiratory conditions and those on corticosteroid treatment. Infections in HIV and SOT patients have practically disappeared. Pulmonary involvement remains the most common area to be affected. Nocardiosis caused by N. farcinica is apparently a risk factor for poor clinical outcome., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Objective: An early reduction of adult invasive pneumococcal disease (IPD) was observed after the 13-valent pneumococcal conjugate vaccine (PCV13) introduction for children in Spain. We analysed the epidemiology of adult IPD in the late-PCV13 period., Methods: This was a prospective multicentre study of adult IPD involving six hospitals. Strains were serotyped, genotyped and studied for antimicrobial susceptibility. The late-PCV13 period was compared with the pre- and early-PCV13 periods., Results: A total of 2197 episodes were collected-949 in 2008-2009, 609 in 2012-2013 and 639 in 2015-2016. The initial decrease of IPD observed (from 12.3/100 000 to 8.1/100 000; 2008-2009 versus 2012-2013) plateaued in 2015-2016 (8.3/100 000). IPD due to PCV13 serotypes decreased (from 7.7 to 3.5 to 2.3/100 000; p < 0.05), whereas IPD caused by non-PCV13 serotypes increased (from 4.5 to 4.6 to 6.0/100 000; p < 0.05). The most frequent serotypes in the late-PCV13 period were: 8 (15.1%), 3 (10.5%), 12F (7.9%) and 9N (5.4%). These serotypes were related to major genotypes: CC53 (59.8%) and CC404 (30.4%) for serotype 8, CC180 (64.1%) and CC260 (28.1%) for serotype 3, CC989 (91.7%) for serotype 12F and CC67 (84.8%) for serotype 9N. Penicillin-non-susceptibility (21.2%) was associated with serotypes 11A (CC156), 14 (CC156) and 19A (CC320), and macrolide-resistance was related to serotypes 24F and 19A. Rates of pneumococcal meningitis remained stable throughout the periods (ranges 0.9, 0.8 and 1.0/100 000)., Conclusions: The initial decrease of adult IPD observed after PCV13 introduction for children has been balanced by the rise of non-PCV13 serotypes. The spread of antibiotic-resistant lineages related to non-PCV13 serotypes (11A and 24F) could be a threat for the treatment of serious pneumococcal diseases., (Copyright © 2019 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)

A progressive increase in the incidence of infections caused by multidrug-resistant microorganisms is being reported. Among these resistant microorganisms, the main threats are extended-spectrum β-lactamase-, AmpC-, and carbapenemase-producing Gram-negative bacilli, methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. To address this important problem, it is essential to establish pediatric Antimicrobial Stewardship programs, perform active epidemiological surveillance and develop an adequate infection control policy. The therapeutic approach of these infections is often complex, frequently requiring antibiotics with less experience in children. In this position document made by the Spanish Association of Pediatrics and the Spanish Society of Pediatric Infectious Diseases, the epidemiology and treatment of these infections are reviewed according to the best available evidence., (Copyright © 2019 Asociación Española de Pediatría. Publicado por Elsevier España, S.L.U. All rights reserved.)

The identification of Nocardia isolates still represents a challenge for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) despite its acceptance for most bacterial and fungal isolates. In this study we evaluate the identification of Nocardia isolates using direct spotting and an updated database. Overall, 82 Nocardia isolates belonging to 13 species were identified by DNA sequence analysis of the 16S rRNA and secA1 genes. Nine of these well-characterized isolates from 6 Nocardia species were used to create an in-house library. The remaining 73 isolates were directly spotted on the target plate and on-plate protein extraction was performed. The protein spectra obtained were analyzed by MALDI-TOF MS using the BDAL database (Bruker Daltonics) updated with 6,903 MSPs or the combination of this commercial database and our in-house library. As a result, the use of the commercial database alone and in combination with the in-house library yielded 94.5% and 95.9% of correct species-level identifications, respectively, No isolate was misidentified at the genus level with either database. Besides, the use of the in-house library allowed the species-level identification of a N. otitidiscaviarum isolate that could only be identified at the genus-level with a score value <1.6 using the commercial database. In conclusion, the implementation of the direct spotting method and the in-house database provided a high rate of correct species assignment of Nocardia isolates despite the low number of isolates added. Further addition of well-characterized Nocardia isolates may ensure the rapid, accurate and inexpensive identification of most isolates encountered in the routine of the microbiology laboratory., (Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)

Staphylococcus aureus is the main pathogen responsible for bone and joint infections worldwide and is also capable of causing pneumonia and other invasive severe diseases. Panton-Valentine leukocidin (PVL) and methicillin-resistant S. aureus (MRSA) have been studied as factors related with severity in these infections. The aims of this study were to describe invasive community-acquired S. aureus (CA-SA) infections and to analyse factors related to severity of disease. Paediatric patients (aged 0-16 years) who had a CA-SA invasive infection were prospectively recruited from 13 centres in 7 European countries. Demographic, clinical and microbiological data were collected. Severe infection was defined as invasive infection leading to death or admission to intensive care due to haemodynamic instability or respiratory failure. A total of 152 children (88 boys) were included. The median age was 7.2 years (interquartile range, 1.3-11.9). Twenty-six (17%) of the 152 patients had a severe infection, including 3 deaths (2%). Prevalence of PVL-positive CA-SA infections was 18.6%, and 7.8% of the isolates were MRSA. The multivariate analysis identified pneumonia (adjusted odds ratio (aOR) 13.39 (95% confidence interval (CI) 4.11-43.56); p 0.008), leukopenia at admission (<3000/mm(3)) (aOR 18.3 (95% CI 1.3-259.9); p 0.03) and PVL-positive infections (aOR 4.69 (95% CI 1.39-15.81); p 0.01) as the only factors independently associated with severe outcome. There were no differences in MRSA prevalence between severe and nonsevere cases (aOR 4.30 (95% CI 0.68- 28.95); p 0.13). Our results show that in European children, PVL is associated with more severe infections, regardless of methicillin resistance., (Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)

In recent years, matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has proved a rapid and reliable method for the identification of bacteria and yeasts that have already been isolated. The objective of this study was to evaluate this technology as a routine method for the identification of microorganisms directly from blood culture bottles (BCBs), before isolation, in a large collection of samples. For this purpose, 1000 positive BCBs containing 1085 microorganisms have been analysed by conventional phenotypic methods and by MALDI-TOF MS. Discrepancies have been resolved using molecular methods: the amplification and sequencing of the 16S rRNA gene or the Superoxide Dismutase gene (sodA) for streptococcal isolates. MALDI-TOF predicted a species- or genus-level identification of 81.4% of the analysed microorganisms. The analysis by episode yielded a complete identification of 814 out of 1000 analysed episodes (81.4%). MALDI-TOF identification is available for clinicians within hours of a working shift, as oppose to 18 h later when conventional identification methods are performed. Moreover, although further improvement of sample preparation for polymicrobial BCBs is required, the identification of more than one pathogen in the same BCB provides a valuable indication of unexpected pathogens when their presence may remain undetected in Gram staining. Implementation of MALDI-TOF identification directly from the BCB provides a rapid and reliable identification of the causal pathogen within hours., (© 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.)

The incidence of central-line-associated bloodstream infection (CLA-BSI) is reported per 1000 days of catheter exposure, mainly in the intensive care unit (ICU), because recording exposure throughout an institution is not always feasible. Confirmation of catheter-related bloodstream infection (CR-BSI) requires specific laboratory testing that identifies the catheter as the source of infection. This information is available in microbiology laboratories and can be assessed using a denominator of 1000 admissions. We evaluated recent trends in the incidence and aetiology of CR-BSI and compared adult ICUs with the remaining areas of the hospital in a retrospective cohort analysis of all confirmed CR-BSIs. During the 8-year study period, we recorded 1208 episodes (8.2% of BSIs) of CR-BSI. After adjusting for the blood cultures drawn, a significant reduction in incidence was observed in adult ICUs (47%), where care bundles had been applied. The reduction was similar irrespective of whether CLA-BSI or CR-BSI was assessed. We recorded a significant reduction in the incidence of Staphylococcus aureus CR-BSI, and a significant increase in the incidence of CR-BSI caused by Enterococcus sp., Gram-negative microorganisms and fungi. The microbiology department may complement CLA-BSI/1000 catheter-days by providing CR-BSI when days of exposure are not available, because both figures are parallel. We demonstrated a significant reduction in the incidence of CR-BSI in recent years in the population admitted to adult ICUs but not in the remaining areas of the hospital. A shift in the aetiological spectrum of CR-BSI may be occurring., (© 2012 The Authors Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.)

Phenotypic tests do not always unequivocally identify some species of viridans group streptococci (VGS). sodA sequence analysis is the most accurate method for identification, although it requires specialized personnel and has not been applied systematically in clinical microbiology laboratory routines. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) is emerging as a rapid alternative for bacterial identification. This study assesses the ability of MALDI-TOF and the API 20 Strep system to identify VGS isolates recovered from blood cultures using sodA sequence analysis as the reference method. All clinically significant VGS isolates recovered from blood cultures between January 2007 and January 2010 were identified by sodA sequence analysis and API 20 Strep. The strains were then tested by MALDI-TOF. Agreement between API 20 Strep/MALDI-TOF and sodA sequence analysis was determined. We examined 124 clinical isolates. Sensitivities of API 20 strep and MALDI-TOF for the species level identification of VGS isolates were, respectively, as follows: 60.5% and 73.4%. Sensitivities of API 20 strep and MALDI-TOF for the group level identification were, respectively, as follows: 70% and 94.3%. The turnaround times to identify VGS isolates by sodA sequence analysis, API 20 Strep and MALDI-TOF were 12-24, 24-48 h and 15 min, respectively. API 20 Strep cannot accurately identify all isolates of VGS. MALDI-TOF appeared to be a rapid and reliable alternative for identification of VGS strains to group level, but was not able to discriminate closely related species of certain groups., (© 2012 The Authors. Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.)

From July 2007 to June 2009, all pneumococci causing invasive pneumococcal disease in our hospital were serotyped. Antimicrobial susceptibility was determined by microdilution. Molecular typing was performed by pulsed-field gel electrophoresis and by multilocus sequence typing. Among 251 invasive pneumococci, serotype 8 was the most frequent (13.5%). All serotype 8 strains were susceptible to penicillin; however, 61.8% (21/34) were co-resistant to erythromycin, levofloxacin and tetracycline and identical to the Sweden(15A) -ST63 clone. Serotype 8 was significantly more frequent among human immunodeficiency virus (HIV)-infected patients (36.5%). The high prevalence of this non-conjugate vaccine multiresistant serotype 8 is a cause for concern mainly in HIV-infected patients., (© 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.)

A prospective cohort study including all new cases of methicillin-resistant Staphylococcus aureus (MRSA) colonization or infection in 64 Spanish hospitals during June 2003 was performed to investigate the epidemiology of MRSA in Spain. Only patients who yielded clinical MRSA-positive samples were included. Epidemiological and clinical data for a total of 370 cases were collected. Genotyping was performed using pulsed-field gel electrophoresis and multilocus sequence typing. Panton-Valentine leukocidin genes and the staphylococcal chromosomal cassette mec (SCCmec) were identified in representative isolates. MRSA was considered to be nosocomially acquired in 202 cases (55%), healthcare-associated (HCA) in 139 cases (38%), community-acquired (CA) in three cases, and of uncertain mode of acquisition in 26 (7%) cases. The pooled population-based rate was 2.31 cases/100,000 population/month, and the pooled nosocomial rate was 0.21 cases/1000 hospital stays (20.2% of S. aureus). Peripheral vascular disease, respiratory tract infections, catheter infections, bloodstream infections and crude mortality were more frequent among HCA cases, whereas neoplasia and urinary tract infections were more frequent among nosocomially acquired cases. Two clones related to the paediatric clone ST5-IV accounted for 71% of the isolates; EMRSA-16 has emerged in two different geographical areas. Only one isolate belonged to the formerly predominant Iberian clone. The three CA isolates were related to the USA300 clone. SCCmec type IV was the most frequent type in nosocomial and HCA isolates. The epidemiology of MRSA has changed in Spain; outpatients with previous healthcare contact represent a very important reservoir of MRSA, and community isolates are emerging.

A point-prevalence study, performed in 2002 in 143 Spanish hospitals, collected 439 isolates of Staphylococcus aureus. Of these, 134 (30.5%) were resistant to methicillin (i.e., MRSA). Susceptibility testing was performed by a microdilution method, and mecA was detected by PCR. The isolates were characterised by phage typing, pulsed-field gel electrophoresis (PFGE) after SmaI digestion, and SCCmec typing. The 134 MRSA isolates showed resistance to ciprofloxacin (93.3%), tobramycin (88.8%), erythromycin (67.9%), clindamycin (59.7%), gentamicin (42.5%), mupirocin (17.9%), rifampicin (5.2%) and trimethoprim-sulphamethoxazole (5.2%). All of the isolates were susceptible to glycopeptides. Twenty-five resistance patterns were found, of which four accounted for 66% of the isolates. Phage group III was the most frequent (41.1%). PFGE revealed 31 different patterns, with ten major clones (including two predominant clones with variable antibiotypes that accounted for 43.3% of the MRSA isolates) and 21 sporadic patterns. Two isolates belonged to two variants of the Iberian clone (ST247-MRSA-I), one to the Brazilian clone (ST239-MRSA-III), and seven to the EMRSA-16 clone (ST36-MRSA-II). SCCmecIV accounted for 70.2% of the isolates (73.9% were type IVA), while SCCmecI, SCCmecII and SCCmecIII accounted for 22.1%, 6.9% and 0.8% of isolates, respectively, with three non-typeable isolates. Isolates of SCCmecIV and SCCmecIVA were predominantly nosocomial (95.8% and 97.1%, respectively). None of the isolates produced Panton-Valentine leukocidin. Thus, two clones carrying SCCmecIV and SCCmecIVA, respectively, were predominant among nosocomial MRSA isolates throughout Spain.

A retrospective study of Streptococcus pneumoniae bacteraemia among adult patients in two large teaching hospitals in Spain identified 108 (10.6%) of 1,020 episodes as nosocomial pneumococcal bloodstream infections (NPBIs). Seventy-seven clinical records with sufficient data were available for analysis. The interval between admission and a positive blood culture was 3--135 days (median 17 days; interquartile range 8--27). The main underlying and predisposing conditions for NPBI were malignancy (31%), chronic obstructive pulmonary disease (28.6%), heart failure (16.9%), chronic renal failure (15.6%), liver cirrhosis (13%) and infection with human immunodeficiency virus (13%). Overall, 31.2% of patients developed severe sepsis, 11.7% septic shock, and 3.9% multi-organ failure. The main portals of entry were pneumonia (70.1%), meningitis (5.2%) and primary peritonitis (5.2%). Of the responsible serogroups, 78% were included in the 23-valent polysaccharide vaccine. Thirty-five (45.5%) patients died, with death considered to be related to the NPBI in 21 (27.3%) cases. Following multivariate analysis, factors that independently predicted death after adjusting for age were: ultimately fatal underlying disease (OR, 8.9; 95% CI, 0.8--94.3; p<0.001); rapidly fatal underlying disease (OR, 15.0; 95% CI, 2.8--81.3; p<0.001); heart failure (OR, 8.11; 95% CI, 1.1--60.8; p<0.03); inadequate empirical therapy (OR, 10.6; 95% CI, 1.2--97; p<0.003); a severe sepsis score (OR, 9.5; 95% CI, 1.9--47.0; p<0.001); and septic shock or multi-organ failure (OR, 63.7; 95% CI, 4.9--820.7; p<0.001). Adequate empirical therapy was an independent protective factor (OR, 0.05; 95% CI, 0.04--0.58; p<0.005), but the use of more than one antimicrobial agent was not.

Clinical isolates (496) of 10 different enterobacterial genera were studied for aerobactin excretion, colicin production and antibiotic resistance. In the case of Escherichia coli, the incidence of aerobactin-positive strains in 108 blood isolates (45%) was not significantly different from that corresponding to faecal sources (41%). Although colicin V production was much more frequently associated with aerobactin production than other colicins, colicin V was only produced by 26% of aerobactin excreters. Some strains were aerobactin-negative and colicin V producers. Aerobactin production seemed to be significantly associated with plasmidic antibiotic resistance. The production of the siderophore is described for the first time in Proteus, Serratia and Morganella strains.