- Probiotic Streptococcus Thermophilus (in yogurt) has no clear benefit (see this post)
- Anticariogenic activity of some tropical medicinal plants against Streptococcus mutans  cites G. glabra (licorice see this post), K. pandurata(chinese ginger) and P. angulata (gooseberry)
- “Triphala a tradtional herbal Ayurvedic formula”  ($22 or 454gm/ 1 pound on Amazon — Organic)
- “Magnolol(magnolia bark) had significant effects on the activities of streptococcal Gtfs.” 
- Essential oil of Curcuma longa inhibits Streptococcus mutans biofilm formation . aka Turmeric — note that it does not kill, just slows films.
- “Water extract of Syzygium aromaticum [Clove] …Ficus carica[Figs] and Oleo europaea leaves [Olive Leaf] .. inhibited growth of Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pyogenes,” 
- “Lactobacillus acidophilus LA-5 inhibited significantly more SM culture growth than most other probiotics.” 
- Vitamin D deficiency in community-acquired [Streptococcus] pneumonia: low levels of 1,25(OH)2 D are associated with disease severity .
Concerning antibiotics, there is a lot of antibiotic resistance reported.
- “A total of 2.4% (95CI%: 0.1-4.7%) of the [Streptococcus] pneumococcal strains were highly resistant to both phenoxymethylpenicillin and macrolides, whereas the highest resistance rates were to cefaclor (53.3%), followed by tetracycline (20%) and cefuroxime (12.1%).”
- “penicillin – 5.41%, erythromycin – 8.1%, clindamycin – 4.05%, amoxicillin-6.76%, tetracycline 28.38%.” 
- “The rates of resistance and reduced sensitivity of the isolates for penicillin and ampicillin were determined at 61.2% and 55.1%, respectively. However, all isolates were found to be susceptible to vancomycin” 
- “a substantial group of strains is resistant to macrolides and the majority of strains are resistant to tetracycline.” 
- Note: Wikipedia states differently (likely old studies) “Most Streptococcus milleri strains are resistant to bacitracin and nitrofurazone, and sulfonamides are totally ineffective. However, most strains studied have been shown to be susceptible to penicillin, ampicillin, erythromycin, and tetracycline.“
Rosehip and pomegranate blossom teas reduces K.pneumoniae (but do not take with antibiotics) [2017
Discuss with your medical professional, starting with licorice (especially Spezzata), then I would suggest Triphala because its long history of treating digestive disorders. Magnolia Bark and Olive leaf would be the next wave of supplements to try (remember to rotate!).
Because you are high in E.Coli (atypical for CFS), then Lactobacillus acidophilus LA-5 would likely do double duty. Lactobacillus acidophilus inhibits most E.Coli.
Concerning D-lactate excess see these two post:
Last but not least… Vitamin D3
This has slow impact. You want to move yourself into the top 10% of the “normal range”. This often means 10,000 IU/day of Vitamin D3 for a younger person. More for an older person. Amount depends on degree of malabsorption.