Murray, G. G. | Search bioRxiv

bioRxiv2023

Evidence of virulence and antimicrobial resistance in Streptococcus pneumoniae serotype 16F lineages

IntroductionDue to the emergence of non-vaccine serotypes in vaccinated populations, Streptococcus pneumoniae remains a major global health challenge despite advances in vaccine development. Serotype 16F is among the predominant non-vaccine serotypes identified among vaccinated infants in South Africa (SA). AimTo characterise lineages and antimicrobial resistance in 16F isolates obtained from South Africa and placed the local findings in a global context. MethodologyWe analysed 10923 S. pneumoniae carriage isolates obtained from infants recruited as part of a broader SA birth cohort. We inferred serotype, resistance profile for penicillin, chloramphenicol, cotrimoxazole, erythromycin and tetracycline, and Global Pneumococcal Sequence Clusters (GPSCs) from genomic data. To ensure global representation, we also included S. pneumoniae carriage and disease isolates from the Global Pneumococcal Sequencing (GPS) project database (n=19,607, collected from 49 countries across five continents, years covered (1995 - 2018), accessed on 17th March 2022). ResultsNine percent (934/10923) of isolates obtained from infants in the Drakenstein community in SA and 2% (419/19607) of genomes in the GPS dataset were serotype 16F. Serotype 16F isolates were from 28 different lineages of S. pneumoniae, with GPSC33 and GPSC46 having the highest proportion of serotype 16F isolates at 26% (346/1353) and 53% (716/1353), respectively. Serotype 16F isolates were identified globally, however, most isolates were collected from Africa. GPSC33 was associated with carriage [OR (95% CI) 0.24 (0.09 - 0.66); p=0.003], while GPSC46 was associated with disease [OR (95% CI) 19.9 (2.56 - 906.50); p=0.0004]. 10% (37/346) and 15% (53/346) of isolates within GPSC33 had genes associated with resistance to penicillin and co-trimoxazole, respectively, and 18% (128/716) of isolates within GPSC46 had genes associated with resistance to co-trimoxazole. Resistant isolates formed genetic clusters which may suggest emerging resistant lineages. DiscussionSerotype 16F lineages are common in Southern Africa. Some of these lineages are associated with disease, and resistance to penicillin and cotrimoxazole. We recommend continuous genomic surveillance to determine long term impact of serotype 16F lineages on vaccine efficacy and antimicrobial therapy globally. Investing in vaccine strategies that offer protection over a wide range of serotypes/lineages remains essential. DATA SUMMARYThe sequencing reads for the genomes analysed have been deposited in the European Nucleotide Archive and the accession numbers for each isolate are listed in Supplementary Table1. Phylogenetic tree of serotype 16F pneumococcal genomes and associated metadata are available for download and visualisation on the Microreact website: Phylogenies of seotype 16F, GPSC33 and GPSC46 are available on the Microreact serotype-16F, GPSC33 and GPSC46, respectively. IMPACT STATEMENTThis study shows that serotype 16F lineages are predominant in Southern Africa and are associated with disease and antimicrobial resistance. Although serotype 16F has been included in the newer formulation of the upcoming vaccine formulations of PCV21 and IVT-25, continuous surveillance to determine long term impact of serotype 16F lineages on vaccines and antimicrobial therapy remains essential.

genomics↗

bioRxiv2022

Absence of Staphylococcus aureus in wild populations of fish supports a spillover hypothesis

Staphylococcus aureus is a human commensal and opportunistic pathogen that can also colonise and cause disease in other animal species. In humans and livestock, where S. aureus is most studied, there is evidence that strains have different host specialisms. Recent studies have found S. aureus in many wild animals, including fish, whose physiologies and ecologies are very different to humans. However, it remains unclear whether S. aureus is adapted to and persisting within these species, or if its presence is due to repeated spillover from a source population. Distinguishing between these two scenarios is important for both public health and conservation. In this study we looked for evidence to support the hypothesis that the presence of S. aureus in fish is the result of spillover, through testing for the presence of S. aureus in fish that are isolated from likely source populations. We sampled 123 brown trout and their environment from 16 sites in the Scottish Highlands. All these sites are remote and have very low populations density of wild animal species known to carry S. aureus, but were selected to represent variable levels of exposure to humans, avian and livestock species. While our sampling methods readily detected S. aureus from the external and internal organs of a farmed fish, we did not detect S. aureus in any wild trout or their environment from any of the 16 sites. We sequenced 12 S. aureus isolates from the farmed fish. While they were all from clonal-complex 45, the genomic diversity was high enough to indicate repeated acquisition from a source population. In addition, the presence of a {varphi}Sa3 prophage containing a human immune evasion cluster indicates a recent history of these isolates within human populations. Taken together, our results support the presence of S. aureus in fish being due to spillover from other host populations, rather than the adaptation of S. aureus to aquaculture or fish populations. Given predictions that fish consumption will increase, more whole genome sequencing of S. aureus in aquaculture is needed to understand the presence of S. aureus in these environments and to mitigate the risk to fish and human health.

microbiology↗