Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus urealyticus from Diverse Hosts
Abstract
:1. Introduction
2. Materials and Methods
2.1. Media
2.2. S. cohnii Isolates
2.3. Genome Sequence and Assembly
2.4. Bioinformatics
3. Results
3.1. Phylogenomic Analyses Identify Three Lineages
3.2. Lineage Association with Host and Virulence
- YNSA55: China, human, survey of S. aureus, no disease state recorded
- NCTC11041: Homo sapiens skin, no disease
- FDAARGOS-538: Homo sapiens, clinical isolate
- H62: air, environmental
- Acroc: human skin, no disease state recorded
- RD01, RD04, RD09: Bacteria were isolated from multiple surfaces in washrooms on a university campus in Alberta, Canada.
- Hu-01: China Homo sapiens, skin swab, no disease
- G22B2: Homo sapiens, gall bladder
- 57: Homo sapiens, blood; opportunistic pathogen isolated from human patient
- 532: Homo sapiens, catheter; opportunistic pathogen isolated from human patient
- MUWRP0921: human UTI
- FDAARGOS_334: Homo sapiens, clinical isolate
- P3-SID1418: human skin, toe web space
- FDAARGOS_744: Homo sapiens, clinical isolate
- NBRC_109766: unknown
- RIT614: smartphone
- Nsq225: human, linezolid-resistant clinical isolate
- Nsq226: human, linezolid-resistant clinical isolate
- 3636: human oral infection
3.3. Horizontal Transfer between Lineages
3.4. Lineage Specific Polypeptides
3.5. Lineage Diagnostic qPCR
3.6. S. cohnii Plasmids
3.7. Genetic Diversity in BCO Infections
4. Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
Research Assurance
References
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Isolate | Colony Color | |||||
---|---|---|---|---|---|---|
Number | Exp | Bird | WGS | Lineage | CO | CS |
1637 | 29 | 10A | yes | 1 | p | l |
1649 | 29 | 10A | yes | 1 | t | t |
1662 | 29 | 10B | 1 | p | l | |
1667 | 29 | 10B | yes | 2 | w | l |
1670 | 29 | 10B | 1 | t | t | |
1638 | 29 | 11A | yes | 1 | p | l |
1650 | 29 | 11A | 1 | t | t | |
1651 | 29 | 11B | 1 | t | t | |
1652 | 29 | 12B | 1 | t | t | |
1653 | 29 | 13A | 1 | t | t | |
1654 | 29 | 13B | 1 | t | t | |
1663 | 29 | 13B | yes | 1 | p | l |
1655 | 29 | 14A | 1 | t | t | |
1656 | 29 | 14B | 1 | t | t | |
1657 | 29 | 2A | 1 | t | t | |
1658 | 29 | 2A | yes | 1 | p | l |
1659 | 29 | 3B | yes | 1 | p | l |
1664 | 29 | 3B | yes | 2 | w | l |
1644 | 29 | 5B | 1 | t | t | |
1645 | 29 | 6A | yes | 1 | t | t |
1636 | 29 | 6B | 1 | p | l | |
1646 | 29 | 6B | 1 | t | t | |
1661 | 29 | 9A | yes | 1 | p | l |
1665 | 29 | 9A | yes | 2 | w | l |
1669 | 29 | 9A | 1 | t | t | |
1639 | 29 | 9B | 1 | p | l | |
1648 | 29 | 9B | 1 | t | t | |
1666 | 29 | 9B | yes | 2 | w | l |
1697 | 30 | 2 | yes | 2 | t | t |
1725 | 30 | 3 | yes | 2 | t | t |
1711 | 30 | 4 | yes | 2 | w | l |
1701 | 30 | 6 | yes | 1 | t | t |
1728 | 30 | 8 | yes | 2 | p | l |
1714 | 30 | 10 | yes | 2 | p | l |
1715 | 30 | 10 | yes | 2 | p | l |
Lineage | n | 1 | 2 | 3 | m |
---|---|---|---|---|---|
1 | 56 | 0.99012 ± 0.00771 | 0.92023 ± 0.00566 | 0.92526 ± 0.00333 | 0.94591 ± 0.00196 |
2 | 40 | 0.99290 ± 0.00591 | 0.96082 ± 0.00171 | 0.94935 ± 0.00025 | |
3 | 23 | 0.99558 ± 0.00368 | 0.97667 ± 0.00216 | ||
m | 5 | 0.99996 ± 0.00004 |
Sn | 1 | 2 | 3 | ||
---|---|---|---|---|---|
n | 4 | 4 | 1 | 4 | |
POCP | Sn | 93.9 ± 1.8 | 84.2 ± 1.4 | 85.4 ± 1.6 | 84.0 ± 0.7 |
1 | 90.4 ± 2.3 | 88.5 ± 1.5 | 89.2 ± 1.6 | ||
2 | NA | 88.2 ± 0.6 | |||
3 | 95.3 ± 2.0 | ||||
ANI | Sn | 0.997 ± 0.0015 | 0.857 ± 0.0007 | 0.879 ± 0.0459 | 0.859 ± 0.0012 |
1 | 0.990 ± 0.0036 | 0.919 ± 0.0003 | 0.925 ± 0.0015 | ||
2 | NA | 0.961 ± 0.0004 | |||
3 | 0.997 ± 0.0017 |
Trait | Gene Count | |||
---|---|---|---|---|
Bonferroni p < 0.05 | Odds Ratio | 100% Specificity and Sensitivity | ||
>4.4 | <0.24 | |||
Lineage 1 | 1756 | 857 | 899 | 84 |
Lineage 2 | 1716 | 867 | 849 | 14 |
Lineage 3 | 1311 | 707 | 604 | 13 |
Human | 333 | 195 | 138 | 0 |
Mammal | 7 | 0 | 7 | 0 |
Avian | 7 | 7 | 0 | 0 |
Chicken | 17 | 17 | 0 | 0 |
Animal | 166 | 37 | 129 | 0 |
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House, L.C.; Hasan, A.; Asnayanti, A.; Alrubaye, A.A.K.; Pummill, J.; Rhoads, D. Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus urealyticus from Diverse Hosts. Microorganisms 2024, 12, 1549. https://doi.org/10.3390/microorganisms12081549
House LC, Hasan A, Asnayanti A, Alrubaye AAK, Pummill J, Rhoads D. Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus urealyticus from Diverse Hosts. Microorganisms. 2024; 12(8):1549. https://doi.org/10.3390/microorganisms12081549
Chicago/Turabian StyleHouse, L. Caroline, Amer Hasan, Andi Asnayanti, Adnan A. K. Alrubaye, Jeff Pummill, and Douglas Rhoads. 2024. "Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus urealyticus from Diverse Hosts" Microorganisms 12, no. 8: 1549. https://doi.org/10.3390/microorganisms12081549