Discovery of a Streptococcus pneumoniae serotype 33F capsular polysaccharide locus that lacks wcjE and contains a wcyO pseudogene.

As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs by microarray that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated '33F-1'). We investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its potential impact on serotyping results. Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the wzg, wzh, wzd, wze, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This finding adds to the understanding of molecular epidemiology of pneumococcal serotype diversity, which is poorly understood in low and middle-income countries

Silica Desiccant Packets for Storage and Transport of <i>Streptococcus pneumoniae</i> and Other Clinically Relevant Species

<div><p>Bacterial isolates are often transported between laboratories for research and diagnostic purposes. Silica desiccant packets (SDPs), which are inexpensive and do not require freezing, were evaluated for storage and recovery of bacterial isolates. Conditions such as inoculum size, swab type and temperature of storage were investigated using ten <i>Streptococcus pneumoniae</i> isolates. The optimized protocol was then tested using 49 additional <i>S. pneumoniae</i> isolates representing 40 serogroups. Overall, <i>S. pneumoniae</i> growth was considered satisfactory (>100 colony forming units) for 98/109 (89.9%) and 20/20 (100%) swabs after 14 days at room temperature or 28 days at 4° C, respectively. Storage in SDPs did not impact on the ability of <i>S. pneumoniae</i> isolates to be subsequently serotyped. When the survival of nine other clinically relevant bacterial species was tested, seven were viable after 28 days at room temperature, the exceptions being <i>Neisseria gonorrhoeae</i> and <i>Haemophilus influenzae</i>. SDPs are suitable for transport and short-term storage of bacterial species including <i>S. pneumoniae</i>.</p> </div

Prevention of young infant infections using oral azithromycin in labour in Fiji (Bulabula MaPei): study protocol of a randomised control trial

Introduction Infections are a leading cause of neonatal mortality globally and can be transmitted from mother-to-child vertically or horizontally. Fiji has higher rates of serious neonatal infections and infant skin and soft tissue infections (SSTIs) than high-income countries. Research from the Gambia found that a single dose of oral azithromycin in labour decreased bacterial carriage and infections in mothers and infants, particularly infant skin infections. The Bulabula MaPei clinical trial evaluates the safety and efficacy of a single dose of azithromycin in labour in reducing the incidence of maternal and infant SSTIs and other infections and the impact on bacterial carriage. It will also describe the effect of azithromycin on antimicrobial (AMR) resistance, the maternal and infant microbiome, and infant dysbiosis.Methods and analysis We are conducting a blinded, placebo-controlled randomised clinical trial administering 2 g of oral azithromycin, or placebo, given to healthy, pregnant women (≥18 years) in labour in Suva, Fiji. The primary outcome is the cumulative incidence of SSTIs in infants by 3 months of age. Secondary outcomes include the incidence of other infant and maternal infections, and safety and tolerability of azithromycin in mother and infant. Following informed consent, 2110 pregnant women will be randomised in a 1:1 ratio, with all study staff and participants masked to group allocation. Mother/infant pairs will be followed up for 12 months over six visits collecting clinical data on infections, antimicrobial use, safety and anthropometrics, in addition to nasopharyngeal, oropharyngeal, rectovaginal and vaginal swabs, maternal breastmilk and infant stool samples, in order to compare bacterial carriage, AMR rates and microbiome. Recruitment for Bulabula MaPei started in June 2019.Ethics and dissemination This trial was approved and is being conducted according to the protocol approved by The Royal Children’s Hospital Human Research Ethics Committee, Australia, and the Fiji National Health Research and Ethics Review Committee. The findings of this study will be disseminated in peer-reviewed journals and presented at conferences.Trial registration number NCT03925480

Nasopharyngeal carriage prevalence (%) of <i>S</i>. <i>pneumoniae</i>, <i>H</i>. <i>influenzae</i>, <i>M</i>. <i>catarrhalis</i>, and <i>S</i>. <i>aureus</i> in Indonesian children aged 12–24 months.

<p>Results are shown by region (Bandung, Padang, and Lombok). Error bars represent 95%CI.</p

Median density in log₁₀ genome equivalents/ml of pneumococcus (SP), <i>H</i>. <i>influenzae</i> (HI), and <i>M</i>. <i>catarrhalis</i> (MC) when found with (+) or without (-) another species.

<p>Median density in log₁₀ genome equivalents/ml of pneumococcus (SP), <i>H</i>. <i>influenzae</i> (HI), and <i>M</i>. <i>catarrhalis</i> (MC) when found with (+) or without (-) another species.</p

Characteristics of study participants.

<p>Characteristics of study participants.</p

The twenty most common pneumococcal serotypes identified in nasopharyngeal swabs collected from Indonesian children aged 12–24 months, shown by region (Bandung, Padang, and Lombok).

<p>* indicates serotypes included in PCV10 and ⁺ indicates the additional three serotypes included in PCV13.</p