Edit in JSFiddle

let count = 0;
const input = 'Run `npm install`, then `npm start`';

const output = input.replace(/`/g, () => {
	count++;
  if (count % 2) {
    return '<code>'
  }
  return '</code>';
});

// or if I wanted to show off my mad one-liner skillz
// const output = input.replace(/`/g, () => ++count % 2 ? '<code>' : '</code>');

document.querySelector('#output').innerHTML = output;

<div id="output"></div>

code {
  background: #eee;
  border-radius: 3px;
  padding: 3px 5px;
}