Molecular detection and genotypic characterisation of Streptococcus pneumoniae isolated from children in Malaysia

Abstract

Streptococcus pneumoniae (S. pneumoniae) is one of the main causative agents of pneumococcal diseases. To date, more than 90 distinct serotypes have been identified. Implementation of vaccines has caused a drastic reduction in vaccine-serotype pneumococcal diseases but increase in cases due to non-vaccine serotype has been observed in Malaysia. However, further investigation on different serotype incidence in Malaysia is needed and the rate of pneumococcal vaccination for new-born babies in Malaysia remains low. The recent emergence of drug-resistant S. pneumoniae (DRSP) has also been a global concern, especially penicillin resistance. This study determined the serotypes of S. pneumoniae strains (n = 95) isolated from nasopharyngeal specimens from children admitted to UMMC from 2013 to 2015. In accordance with previous studies, PCR result showed 40% of NT isolates were successfully typed as 3 less common serotypes, namely 9N/L, 17A, and 23B. The repetitive-element PCR (REP-PCR) result revealed genetic variations among the strains whereby five major clusters were observed at the similarity of 80% by clustering analysis based on fingerprint data. Penicillin-binding proteins (pbps) of selected isolates were studied by PCR and sequencing. Three strains with ≤19-mm diameter zone for Oxacillin Disc Diffusion (ODD) test previously were recorded to have mutation on all pbp1a, pbp2b, and pbp2x with MIC of 4 µg/ml, which were penicillin-intermediate resistance according to the CLSI breakpoints.

Identification and molecular characterization of penicillin‐nonsusceptible Streptococcus pneumoniae isolates recovered from invasive infections in a pre‐pneumococcal vaccine era

“…The results showed 16 and 42 amino acid substitutions in the STMK conserved motif of PBP1a (Thr 371 → Ala) and PBP2x (Thr 338 → Ala), respectively. Moreover, we found no substitution in the three conserved motifs of PBP2b , being in agreement with the results of Talebi et al 28 and in contrast with the results reported by Ling Goh et al 29 . In addition, the findings indicate that 20.7% of the PNSP isolates reveal no alterations in three conserved motifs of PBPs.…”

Carriage of upper respiratory tract pathogens in rural communities of Sarawak, Malaysian Borneo

“…Whilst our study found 33.3% of carried S. pneumoniae serotypes to be PCV13 VT and 14.3% PCV10 VT, studies from Peninsula Malaysia showed a higher proportion of S. pneumoniae VT carriage, with up to 69.5% being PCV13 VT and 40.6% being PCV10 and PCV7 VT [34,35]. Certainly, VT S. pneumoniae cause the majority of pneumococcal disease in Peninsular Malaysia with 66.3% of RTI in children being caused by PCV13 VT and 60% by PCV10 VT [36]. As PCV13 serotypes 1, 6B, 14, 19F, 19A are commonly associated with disease in Malaysia [10,37], the carriage of 6B and 14 (which was in children) here is of interest for public health, particularly as these serotypes are included in both PCV10 and PCV13.…”

“…AMR is an increasing issue across Asia; multidrug resistant S. pneumoniae and K. pneumoniae are of particular concern [17,36,39,40]. In Malaysia, antibiotics are commonly prescribed for the treatment of URT infections, although inappropriate antibiotic choice and dosage have been shown in up to 40% of cases.…”

β-Lactam Resistance in Upper Respiratory Tract Pathogens Isolated from a Tertiary Hospital in Malaysia

“…We observed the most frequent mutations at Thr-371-Ala/Ser (STMK motif) and Pro-432-Thr (adjacent to SRN motif) in PBP1a, corresponding to the common mutation sites in penicillin non-susceptible S. pneumoniae [22,23]. The block mutation identified at amino acid positions 574-577 in PBP1a has been previously associated with intermediate-to high-level penicillin resistance [24,25].…”

“…pneumoniae and H. influenzae strains with non-susceptible phenotypes for ampicillin were examined for potential amino acid substitution in the genes encoding for penicillinbinding proteins (pbp1a, pbp2b, and pbp2x in S. pneumoniae and ftsI, also known as pbp3, in H. influenzae). The primer sequences and PCR conditions for the amplification of pbp and ftsI genes were adapted from published studies [12,22,63]. The PCR products were then purified using MEGAquick-spin™ Plus Total Fragment DNA Purification Kit (iNtRON Biotechnology, South Korea), and sent for sequencing by a commercial sequencing service provider (First BASE Laboratories, Malaysia).…”