Annika Saukkoriipi

Using Multilocus Sequence Data To Define the Pneumococcus

We investigated the genetic relationships between serotypeable pneumococci and nonserotypeable presumptive pneumococci using multilocus sequence typing (MLST) and partial sequencing of the pneumolysin gene (ply). Among 121 nonserotypeable presumptive pneumococci from Finland, we identified isolates of three classes: those with sequence types (STs) identical to those of serotypeable pneumococci, suggesting authentic pneumococci in which capsular expression had been downregulated or lost; isolates that clustered among serotypeable pneumococci on a tree based on the concatenated sequences of the MLST loci but which had STs that differed from those of serotypeable pneumococci in the MLST database; and a more diverse collection of isolates that did not cluster with serotypeable pneumococci. The latter isolates typically had sequences at all seven MLST loci that were 5 to 10% divergent from those of authentic pneumococci and also had distinct and divergent ply alleles. These isolates are proposed to be distinct from pneumococci but cannot be resolved from them by optochin susceptibility, bile solubility, or the presence of the ply gene. Complete resolution of pneumococci from the related but distinct population is problematic, as recombination between them was evident, and a few isolates of each population possessed alleles at one or occasionally more MLST loci from the other population. However, a tree based on the concatenated sequences of the MLST loci in most cases unambiguously distinguished whether a nonserotypeable isolate was or was not a pneumococcus, and the sequence of the ply gene fragment was found to be useful to resolve difficult cases.

The role of respiratory viral infections among children hospitalized for community-acquired pneumonia in a developing country.

We report an investigation for 16 bacteria and viruses among 184 children hospitalized with pneumonia in Salvador, Brazil. Etiology was established in 144 (78%) cases. Viral, bacterial, and mixed infections were found in 110 (60%), 77 (42%), and 52 (28%) patients, respectively. Rhinovirus (21%) and Streptococcus pneumoniae (21%) were the most common pathogens. Our results demonstrate the importance of viral and pneumococcal infections among those patients.

A Successful, Diverse Disease-Associated Lineage of Nontypeable Pneumococci That Has Lost the Capsular Biosynthesis Locus

ABSTRACT Streptococcus pneumoniae strains which fail to produce a polysaccharide capsule are commonly isolated from carriage and disease contexts. Here we use a multilocus approach to distinguish genuine nontypeable pneumococci from closely related nontypeable streptococcal isolates in a data set of 121 untypeable pneumococci from nasopharyngeal swabs and middle ear fluid of Finnish children and demonstrate that 70 of these belong to a pneumococcal lineage which has lost its capsular locus. Strains of this relatively old lineage include sequence types 344, 448, and 449. Comparison with the multilocus sequence typing database shows that strains of this lineage have spread intercontinentally and have been isolated from carriage, mucosal, and invasive disease. Furthermore we note a particular association of this nontypeable lineage with outbreaks of conjunctivitis. The diversification and geographic spread of this lineage suggest that loss of capsule is not inconsistent with long-term persistence and raise questions about the capsules role in pneumococcal transmission.

Procalcitonin is useful in identifying bacteraemia among children with pneumonia.

Abstract Empirical antibiotic use is prescribed in managing children with pneumonia worldwide. We assessed the usefulness of procalcitonin (PCT) and interferon-alpha (IFN-α) in differentiating viral from bacterial pneumonia. Among 159 hospitalized children, pneumonia was diagnosed based on clinical complaints plus pulmonary infiltrate. Aetiology was investigated for 9 viruses and 4 atypical and 3 typical bacteria. PCT and IFN-α were measured in the serum sample collected on admission. Eight patients had bacteraemic infections, 38 had non-bacteraemic typical infections, and 19 patients had atypical bacterial infections. Viral and unknown aetiology was established in 57 (36%) and 34 (21%) cases, respectively. Three patients with bacterial infection without collected blood culture were excluded. IFN-α (IU/ml) was detectable in 20 (13%) cases. The difference among median PCT values of the bacteraemic (4.22; 1.56–7.56), non-bacteraemic typical bacterial (1.47; 0.24–4.07), atypical bacterial (0.18; 0.06–1.03) and only viral (0.65; 0.11–2.22) subgroups was significant (p = 0.02). PCT was ≥2 ng/ml in 52 (33%) cases. The presence of IFN-α was associated with PCT <2 ng/ml (90% vs. 64%, p = 0.02). The negative predictive value (95% confidence interval) of PCT ≥2 ng/ml was 95% (89–100%), 89% (78–100%), 93% (85–100%) for differentiation of bacteraemic from viral, atypical bacterial and non-bacteraemic typical bacterial infection, respectively, and 58% (49–68%) for differentiation between bacterial and viral infection. PCT may be useful in identifying bacteraemia among children hospitalized with community-acquired pneumonia. IFN-α was uncommonly detected.

Pneumococcal carriage is more common in asthmatic than in non-asthmatic young men.

Introduction:  The aim was to investigate the prevalence of oropharyngeal carriage of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Neisseria meningitidis and beta‐haemolytic streptococci among asthmatic and non‐asthmatic young Finnish men and to identify putative risk factors.

Seasonal patterns of viral and bacterial infections among children hospitalized with community-acquired pneumonia in a tropical region

Abstract Community-acquired pneumonia (CAP) is a common cause of morbidity among children. Evidence on seasonality, especially on the frequency of viral and bacterial causative agents is scarce; such information may be useful in an era of changing climate conditions worldwide. To analyze the frequency of distinct infections, meteorological indicators and seasons in children hospitalized for CAP in Salvador, Brazil, nasopharyngeal aspirate and blood were collected from 184 patients aged <5 y over a 21-month period. Fourteen microbes were investigated and 144 (78%) cases had the aetiology established. Significant differences were found in air temperature between spring and summer (p = 0.02) or winter (p < 0.001), summer and fall (p = 0.007) or winter (p < 0.001), fall and winter (p = 0.002), and on precipitation between spring and fall (p = 0.01). Correlations were found between: overall viral infections and relative humidity (p = 0.006; r = 0.6) or precipitation (p = 0.03; r = 0.5), parainfluenza and precipitation (p = 0.02; r = −0.5), respiratory syncytial virus (RSV) and air temperature (p = 0.048; r = −0.4) or precipitation (p = 0.045; r = 0.4), adenovirus and precipitation (p = 0.02; r = 0.5), pneumococcus and air temperature (p = 0.04; r = −0.4), and Chlamydia trachomatis and relative humidity (p = 0.02; r = −0.5). The frequency of parainfluenza infection was highest during spring (32.1%; p = 0.005) and that of RSV infection was highest in the fall (36.4%; p < 0.001). Correlations at regular strength were found between several microbes and meteorological indicators. Parainfluenza and RSV presented marked seasonal patterns.

Pneumococcal carriage is more common in asthmatic than in non-asthmatic young men

Introduction:  The aim was to investigate the prevalence of oropharyngeal carriage of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Neisseria meningitidis and beta‐haemolytic streptococci among asthmatic and non‐asthmatic young Finnish men and to identify putative risk factors.

Nasopharyngeal carriage of Streptococcus pneumoniae and pneumococcal urine antigen test in healthy elderly subjects

Abstract Background: Children frequently carry Streptococcus pneumoniae (pneumococcus) in their nasopharynx, even when healthy. Lower carriage rates have been reported in adults and only sparse data are available for the elderly. We sampled healthy elderly subjects for nasopharyngeal carriage to assess the prevalence of pneumococcal carriage using various assays. Methods: A deep nasopharyngeal swab sample was taken from 590 healthy elderly subjects aged ≥ 65 y. The samples were stored in STGG (skim milk–tryptone–glucose–glycerol) medium and cultured directly and after incubation in enrichment broth using routine identification methods. Real-time polymerase chain reaction (PCR) assays specific for pneumolysin and pneumococcal surface antigen A genes was performed on the same samples. Urine was also collected and assayed using the commercial Binax Streptococcus pneumoniae NOW urine antigen test. Results: The prevalence of pneumococcal carriage in healthy elderly persons was 1.5% for encapsulated pneumococci and 5.3% for all presumptive pneumococci. The use of the enrichment broth did not increase the yield of positives. PCR assays gave higher numbers of positives, but pneumolysin PCR in particular gave probable false-positive results. Only 1 urine antigen test was positive, and this was in a person not carrying pneumococcus. Conclusions: Nasopharyngeal carriage of pneumococci in the elderly was rare. Identification of presumptive pneumococci in culture requires further confirmation, e.g. by serotyping. The urine antigen test was not affected by concurrent carriage. Low carriage prevalence suggests that encapsulated pneumococci detected in a respiratory tract sample during sickness may be the true cause of disease, since contamination from asymptomatic nasopharyngeal carriage seems unlikely.

Effect of xylitol and other carbon sources on Streptococcus pneumoniae biofilm formation and gene expression in vitro

Kurola P, Tapiainen T, Sevander J, Kaijalainen T, Leinonen M, Uhari M, Saukkoriipi A. Effect of xylitol and other carbon sources on Streptococcus pneumoniae biofilm formation and gene expression in vitro. APMIS 2010; 119: 135–42.

All Known Human Rhinovirus Species Are Present in Sputum Specimens of Military Recruits During Respiratory Infection

Human rhinoviruses (HRV) are known to cause common cold as well as more complicated respiratory infections. HRV species -A, -B and -C have all been associated with lower respiratory infections and exacerbations of asthma. However, the type distribution of strains connected to different kinds of lower respiratory conditions is not clearly known. We have analysed the presence of HRV in sputum specimens derived from military recruits with and without pre-diagnosed asthma at times of acute respiratory infection (CIAS Study, 2004–2005). The analysis was performed with HRV and HEV real-time RT-PCR assays. Subsequently we studied type distribution of HRV strains by genetic typing in the VP4/VP2 genomic region. In total 146 (38.8%) specimens were HRV-positive and 36 (9.3%) HEV-positive. No difference was found in HRV detection between the asthmatic vs. non-asthmatic patients. Most of the genetically typed strains, 18 (62.1%), belonged to HRV-A, while HRV-B strains constituted five (17.2%) of the HRV-positive strains. HRV-C strain was typed four times from the HRV-positive cases and a HEV-D strain twice. We further typed six HEV positive strains in the partial VP1 region. Three of these belonged to HRV-A and three to HEV-D. HRV-A strains were discovered throughout the study period, while HRV-C strains originated from winter and spring specimens. Interestingly, four out of five typed HRV-B strains originated from the summer season specimens.