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Streptococcus pneumoniae (pneumococcus) is a leading cause of infections worldwide. Disease is preceded by asymptomatic colonization of the upper respiratory tract. Classical culture-based methods (CCBM) suggest that colonization in the elderly is lytA and piaB. Positive samples were molecular serotyped. Use of qPCR improved detection of pneumococci in oropharyngeal samples compared to CCBM: from 0.7% to 10.4% (p vs. 5.4% in the nursing homes; and 4.3% vs. 4.7% in the family homes). Twenty-one serotypes/serogroups were detected by qPCR compared to 14 by CCBM. In conclusion, use of qPCR suggests that pneumococcal carriage in Portuguese elderly is approximately 10%, and unveiled a large pool of serotypes. These results are important to understand progression to disease and impact of pneumococcal vaccines in the elderly.

Methicillin-resistant Staphylococcus aureus (MRSA) has long been known as a major cause of hospital-acquired (HA-MRSA) infections worldwide. For the past twenty years, an increasing number of studies have described its emergence in the community as well. In Portugal, a country with a high-prevalence of HA-MRSA, there are only limited data available on the epidemiology of MRSA in the community. We studied the prevalence of S. aureus and MRSA colonization among healthy adults in Portugal. Between February 2015 and December 2016, a longitudinal study was conducted in which 87 adults aged 25–50 years old were followed for six months. For each participant nasopharyngeal, oropharyngeal and saliva samples were obtained monthly and, in some cases, weekly. A total of 1,578 samples (n = 526 for each sampling site) were examined for the presence of S. aureus and MRSA by classical culture-based methods. Fifty-seven adults (65.5%) carried S. aureus at least once during the six months period of the study: 19.5% were persistent S. aureus carriers and 46.0% were intermittent carriers. Carriage rates per sampling site were 20.5% in nasopharynx, 18.3% in oropharynx, and 13.5% in saliva. Simultaneous screening of the three sampling sites increased detection of S. aureus, which overall occurred in 34.4% of the 526 sampling time-points. No MRSA were isolated. In conclusion, this study adds novel information about the MRSA scenario in the Portuguese community. Our results indicate that, in Portugal, MRSA does not seem to circulate among healthy adults without risk factors and therefore this age group does not constitute, at the current time, a reservoir of MRSA in the community.

In Portugal, the 13-valent pneumococcal conjugate vaccine (PCV13) was commercially available between 2010 and 2015, following a decade of private use of PCV7. We evaluated changes on serotype distribution and antimicrobial susceptibility of pneumococci carried by children living in two regions of Portugal (one urban and one rural). Three epidemiological periods were defined: pre-PCV13 (2009-2010), early-PCV13 (2011-2012), and late-PCV13 (2015-2016). Nasopharyngeal samples (n = 4,232) were obtained from children 0-6 years old attending day-care centers. Private use of PCVs was very high in both regions (>75%). Pneumococcal carriage remained stable and high over time (62.1%, 62.4% and 61.6% (p = 0.909) in the urban region; and 59.8%, 62.8%, 59.5% (p = 0.543) in the rural region). Carriage of PCV7 serotypes remained low (5.3%, 7.8% and 4.3% in the urban region; and 2.5%, 3.7% and 4.8% in the rural region). Carriage of PCV13 serotypes not targeted by PCV7 decreased in both the urban (16.4%, 7.3%, and 1.6%; p < 0.001) and rural regions (13.2%, 7.8%, and 1.9%; p < 0.001). This decline was mostly attributable to serotype 19A (14.1%, 4.4% and 1.3% in the urban region; and 11.1%, 3.6% and 0.8% in the rural region, both p < 0.001). Serotype 3 declined over time in the urban region (10.1%, 4.4%, 0.8%; p < 0.001) and had no obvious trend in the rural region (4.2%, 6.7%, 2.4%; p = 0.505). Serotype 6C decreased in both regions while serotypes 11D, 15A/B/C, 16F, 21, 22F, 23A/B, 24F, 35F, and NT were the most prevalent in the late-PCV13 period. Intermediate resistance to penicillin and non-susceptibility to erythromycin decreased significantly in both regions (19.5%, 13.3%, and 9.3%; and 25.4%, 25.9%, and 13.4%; both p < 0.001, respectively in the urban region; and 12.4%, 11.1%, and 2.8% (p < 0.001); and 15.3%, 14.7%, and 9.2% (p = 0.037), respectively, in the rural region). In conclusion, private use of PCV13 led to significant changes on the pneumococcal population carried by children in Portugal.

Background Limited information is available on pneumococcal colonization among adults. We studied pneumococcal carriage dynamics in healthy adults using high-sensitivity approaches. Methods Eighty-seven adults (25–50 years old) were followed for 6 months in Portugal. Nasopharyngeal, oropharyngeal, and saliva samples were obtained monthly; pneumococcal carriers were also sampled weekly. Carriage was investigated by quantitative polymerase chain reaction (targeting lytA and piaB) and culture. Positive samples were serotyped. Results Approximately 20% of the adults were intermittent carriers; 10% were persistent carriers (>4 months). Pneumococcal acquisition and clearance rates were 16.5 (95% confidence interval [CI], 11.2–24.2) and 95.9 (95% CI, 62.3–145.0) cases/1000 person-weeks, respectively. Living with children increased pneumococcal acquisition (hazard ratio, 9.7 [95% CI, 2.6–20.5]; P Conclusions The pneumococcal carrier state in healthy adults is more dynamic than generally assumed: Acquisition is frequent and duration of carriage is often long. This suggests that some adults may act as reservoirs of pneumococci and hence, depending on the social structure of a community, the magnitude of herd effects potentially attainable through children vaccination may vary. These findings are important when designing strategies to prevent pneumococcal disease in adults.

In Portugal, the 7-valent pneumococcal conjugate vaccine (PCV7) was not introduced in the national immunization plan but was commercially available between 2001 and 2010. We studied serotype distribution and antibiotic susceptibility of Streptococcus pneumoniae carried by children in 2009 and 2010. Vaccination with PCV7 was extracted from children's immunization bulletins and information on recent antimicrobial consumption was obtained through a questionnaire. For comparison, we included data from previous studies conducted since 1996: 1996-1999, 2001-2003, 2006-2007. Pneumococci were isolated from nasopharyngeal samples of 1092 children up to six years old attending day-care in an urban area. Among these, 76% (819/1070) were vaccinated and 62% (677/1092) carried pneumococci. In 2009-2010, serotype replacement was extensive. Carriage of PCV7 serotypes was 4.9% and 5.8%, in 2009 and 2010, respectively, with the majority being of serotype 19F (carried by 4.3% and 4.6% of all participants, respectively). Colonization by serotype 19F was associated with vaccine status (7.7% (19/248) of non-vaccinees vs. 3.5% (29/818) of PCV7-vaccinees, p=0.010). Carriage of serotype 19A was high in 2009 and 2010 (8.6% of all participants) consistent with values already observed in 2007; carriage of serotype 6A was

The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in the community in Portugal is not completely understood. To evaluate S. aureus and MRSA carriage among the elderly, we conducted a large cross-sectional study between April 2010 and December 2012. A total of 3,361 adults over 60 years of age were screened for S. aureus nasopharyngeal and oropharyngeal carriage. MRSA were characterized by staphylococcal cassette chromosome mec (SCCmec) typing, spa typing, multilocus sequence typing (MLST), and tested for the presence of Panton-Valentine leukocidin (PVL). Risk factors for MRSA carriage were identified by multiple logistic regression analysis. The prevalence of S. aureus and MRSA carriage among the elderly was 20.1 % and 1.8 %, respectively. The risk of being an MRSA carrier was higher among the elderly living in retirement homes [odds ratio (OR) = 2.90, 95 % confidence interval (CI): 1.48-5.48] and those that had been hospitalized in the previous year (OR = 2.64, 95 % CI: 1.47-4.58). Among the 62 MRSA isolates, 64.5 % were multidrug-resistant and none carried PVL. Most MRSA (82.3 %) were related to three hospital-associated (HA-MRSA) clones disseminated in Portugal: ST105-II (New York/Japan clone; 43.5 %), ST5-IVc (Pediatric clone; 19.4 %), and ST22-IVh (EMRSA-15 clone; 19.4 %). The New York/Japan and Pediatric clones were significantly associated with carriers living in retirement homes, while the EMRSA-15 clone was associated with carriers that had been hospitalized. We conclude that the elderly population in Portugal is essentially free of MRSA. Given the current European societal challenges for a healthy active aging, these results are of importance to healthcare professionals and public authorities to decide on strategies to promote health in this age group.

Among the over 90 serotypes of Streptococcus pneumoniae described, serotypes 1, 5, and 7F account for a significant proportion of invasive disease worldwide and are now covered by the most recent 10- and 13-valent pneumococcal conjugate vaccines (PCVs). The epidemiology of these serotypes in carriage remains poorly studied because they are rarely detected. We aimed to gain insights into the epidemiology and population structure of serotypes 1, 5 and 7F carried by children in Portugal before PCV10 and PCV13 became widely used. Isolates obtained in cross-sectional studies carried out over a 15-year period (1996-2010) were retrospectively pooled and characterized. Of 5,123 pneumococci obtained, 70 were associated with serotypes 1 (n = 21), 5 (n = 7), and 7F (n = 42). The highest prevalence detected was 3.3% for serotype 1 in 2006, 1% for serotype 5 in 2009, and 3.3% for serotype 7F in 2006; Serotype 1 was associated with PMEN international clones Sweden(1)-28(ST306) and Sweden(1)-40(ST304); serotype 5 was associated with Colombia(5)-19(ST289); and serotype 7F was associated with Netherlands(7F)-39(ST191). All these isolates were fully susceptible. Most carriers of serotypes 1 (86%), 5 (86%), and 7F (91%) were older than two years but a significant association with older age was only observed for serotype 7F (p = 0.006). Evidence for cross-transmission was obtained. In conclusion, we were able to detect and characterize the rarely carried serotypes 1, 5, and 7F among healthy children in Portugal. These data will constitute an important baseline for upcoming surveillance studies aimed to establish the impact of novel PCVs targeting these serotypes in carriage.

Pneumococcal disease is frequent at the extremes of age. While several studies have looked at colonization among young children, much less is known among the elderly. We aimed to evaluate pneumococcal carriage among elderly adults living in Portugal. Between April 2010 and December 2012, nasopharyngeal and oropharyngeal swabs of adults over 60 years of age, living in an urban area (n = 1,945) or in a rural area (n = 1,416), were obtained. Pneumococci were isolated by culture-based standard procedures, identified by optochin susceptibility, bile solubility and PCR screening for lytA and cpsA, and characterized by antibiotype, serotype, and MLST. Associations between pneumococcal carriage, socio-demographic and clinical characteristics were evaluated by univariate analysis and multiple logistic regression. The global prevalence of carriage was 2.3% (95% CI: 1.8–2.8). In the multiple logistic regression analysis, smoking, being at a retirement home, and living in a rural area increased the odds of being a pneumococcal carrier by 4.4-fold (95% CI: 1.9–9.2), 2.0-fold (95% CI: 1.1–3.6) and 2.0-fold (95% CI: 1.2–3.5), respectively. Among the 77 pneumococcal isolates, 26 serotypes and 40 STs were identified. The most prevalent serotypes were (in decreasing order) 19A, 6C, 22F, 23A, 35F, 11A, and 23B, which accounted, in total, for 60.0% of the isolates. Most isolates (93.5%) had STs previously described in the MLST database. Resistance to macrolides, non-susceptibility to penicillin and multidrug resistance were found in 19.5%, 11.7%, and 15.6% of the isolates, respectively. We conclude that the prevalence of pneumococcal carriage in the elderly, in Portugal, as determined by culture-based methods, is low. Serotype and genotype diversity is high. Living in a rural area, in a retirement home, and being a smoker increased the risk of pneumococcal carriage. This study contributes to the establishment of a baseline that may be used to monitor how novel pneumococcal vaccines impact on colonization among the elderly.