Comparison of contemporary invasive and non-invasive Streptococcus pneumoniae isolates reveals new insights into circulating anti-microbial resistance determinants.

2023-11-15

Higgs, Charlie

Kumar, Lamali Sadeesh

Stevens, Kerrie

Strachan, Janet

Korman, Tony

Horan, Kristy

Daniel, Diane

Russell, Madeline

McDevitt, Christopher A

Sherry, Norelle L

Stinear, Timothy P

Howden, Benjamin P

Gorrie, Claire L

Streptococcus pneumoniae

antibiotic resistance

genomics

Journal Article

0000-0001-7364-7380

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0000-0002-6155-8353

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0000-0003-1596-4841

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0000-0003-0150-123X

0000-0003-0237-1473

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10.1128/aac.00785-23

Streptococcus pneumoniae is a major human pathogen with a high burden of disease. Non-invasive isolates (those found in non-sterile sites) are thought to be a key source of invasive isolates (those found in sterile sites) and a reservoir of anti-microbial resistance (AMR) determinants. Despite this, pneumococcal surveillance has almost exclusively focused on invasive isolates. We aimed to compare contemporaneous invasive and non-invasive isolate populations to understand how they interact and identify differences in AMR gene distribution. We used a combination of whole-genome sequencing and phenotypic anti-microbial susceptibility testing and a data set of invasive (n = 1,288) and non-invasive (n = 186) pneumococcal isolates, collected in Victoria, Australia, between 2018 and 2022. The non-invasive population had increased levels of antibiotic resistance to multiple classes of antibiotics including beta-lactam antibiotics penicillin and ceftriaxone. We identified genomic intersections between the invasive and non-invasive populations and no distinct phylogenetic clustering of the two populations. However, this analysis revealed sub-populations overrepresented in each population. The sub-populations that had high levels of AMR were overrepresented in the non-invasive population. We determined that WamR-Pneumo was the most accurate in silico tool for predicting resistance to the antibiotics tested. This tool was then used to assess the allelic diversity of the penicillin-binding protein genes, which acquire mutations leading to beta-lactam antibiotic resistance, and found that they were highly conserved (≥80% shared) between the two populations. These findings show the potential of non-invasive isolates to serve as reservoirs of AMR determinants.

link

Antimicrobial Agents and Chemotherapy 2023-11-15; 67(11)

Antimicrobial Agents and Chemotherapy

1098-6596