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Mr Matheson says the Scottish government wants to press on with the implementation of the deals and to introduce regional growth deals for Ayrshire, Moray and Borderlands.

The minister says the government's economic strategy sets out the vision for sustainable economic growth.

He says it will use public procurement to create more opportunities for Scotland's businesses.

The infrastructure secretary points to the first minister's programme for government , externalwith the pledge to increase annual investment in infrastructure by £1.5bn higher by the end of the next parliament than in 2019-20.

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Last January we reported Scotland's City Region Deals had "significant" problems that need to be addressed, according to MSPs.

The economic growth projects were focused on Aberdeen, Inverness, Glasgow and Edinburgh.

Holyrood's Local Government and Communities Committee said objectives needed to be clearer.

The then Economy Secretary Keith Brown said "inclusive economic growth" was being delivered but that the report would be considered.

The City Region Deals offer more than £3bn of investment in Scotland, with the UK and Scottish governments collaborating on the projects with local councils.

Read more here.

Infrastructure Secretary Michael Matheson says the Scottish government wants to ensure city region deals cover 100% of Scotland.

Despite encouraging noises from some UK minister, we await a commitment from them for this, he adds.

The combined investment both governments will make over the next decade will bring significant benefits, Mr Matheson tells the chamber.

The minister highlights the deals now cover of all Scotland's cities.

Image source, Scottish Parliament

The Scottish government will now lead a debate entitled 'City Deal and Regional Economic Partnership'.

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Tory MSP Adam Tomkins asks what detailed positive proposals for a deal to solve the crisis have the SNP brought to the prime minister in the last week.

Ms Hyslop insists that for over two years the SNP have offered the compromise position of remaining in the customs union and single market.

She warns "the clock is ticking" and goes on to say "we need to stop the clock".

External Affairs Secretary Fiona Hyslop says the prime minister has not taken on board the "crushing" defeat of her deal in the Commons.

Her offer of an enhanced role for devolved administrations lacks credibility, Ms Hyslop adds.

The Scottish government will continue to do all it can to protect Scotland's interest, the minister says, and will continue pressing for an extension of article 50.

Ms Hyslop welcomes the scrapping of the fee for EU settlement status applications but insists they should not have to apply to retain rights they already have.

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MPs are putting forward plans to change the outcome of Brexit ahead of a vote next week on the PM's amended deal.

Theresa May said on Monday she was focused on altering the backstop - the "insurance policy" designed to avoid a hard border on the island of Ireland.

But Labour leader Jeremy Corbyn said the prime minister was in denial about the level of opposition to her deal.

Among the MPs' six amendments are plans to prevent a no-deal Brexit and to extend the deadline for leaving the EU.

But more amendments to change her next steps could be added in the coming days.

MPs are due to vote on Mrs May's proposals for Brexit on 29 January.

• Kuenssberg: Why are MPs putting forward amendments?
• Nick Watt: May boxed into her comfort zone
• Cameron warned over 'stupid' Brexit vote
• Theresa May scraps £65 fee for EU citizens to stay in UK
• Read more here

SNP MSP Bruce Crawford asks for the Scottish government's response to the prime minister’s latest statement on how she plans to proceed with the Brexit withdrawal agreement.

The health secretary says there are two further patients with fungal infections at the QEUH not connected to the one being discussed today.

Ms Freeman says two patients are being treated and the source of the infections are being pursued and she commits to update members in due course.

Labour MSP Anas Sarwar welcomes the review and seeks assurance that it will be independent.

The health secretary confirms it will be, but discussions need to be had on how the review will be carried out.

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Tory MSP Annie Wells asks what other concerns have been raised to the cabinet secretary in regards to the QEUH.

Ms Wells also calls for the review to be fully transparent.

The health secretary says there have been issues around water hygiene, external cladding, the ventilation system, glazing failures and now the most recent incident.

SNP MSP Alex Neil - who called for an inquiry at the weekend - says the health board must ensure effective, timeous and transparent communications when outbreaks of this kind occur.

Ms Freeman confirms there is ongoing communication with the families of patietns who died or with staff at the hopsital.

But she adds that in order to be sure of the facts, there will be times when she or the health board cannot respond to certain questions.

Image source, NHS GGC

Ms Lennon says the people of Scotland will feel it is absolutely extraordinary there has been a situation where pigeons and infections can kill patients.

The health board has struggled over the weekend over this, says the Labour MSP and she adds this is just the latest in a catalogue of troubles for the board.

She asks what support is being given to the families of the deceased and what is being done to prevent this happening again.

The health secretary insists concerns raised two years ago were acted on by the board, with spikes put in to deal with pigeons.

This is a new instance, she says, adding that investigating the source of this infection traced it to one plant room on the 12th floor of the building, where invisible to the naked eye was a small break in the wall.

Excrement was found there only by smoke detection and work carries on to find out how the infection was transmitted to the patients, she says.

Ms Freeman accepts there are concerns about the QEUH and that is why she has agreed a review to look at the design and construction of the building.

Ms Lennon offers sympathies to the families of the patients who died.

She says over the weekend there was "a complete lack of clarity" from Greater Glasgow and Clyde Health Board and no information from the government.

An outpatient reportedly wrote to the Scottish government about a pigeon infestation in the hospital in March, the Labour MSP adds.

Ms Freeman reiterates she is confident the health board has taken all steps to maintain patient safety.

She highlights the time it takes to confirm facts in the case, including identifying the precise infection.

Regarding the letter, she says the Scottish government has a robust system of recording all communication to ministers and a thorough search of that system was conducted, but not record was found.

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Health Secretary Jeane Freeman says in November the bacteria cryptococcus was identified in one patient who sadly later died, but the bacteria was not a contributory factor.

In December a post-mortem of a child who had passed away confirmed cryptococcus was both present and a contributory factor in their death.

Prophylaxis antifungal treatment has been given to vulnerable patients, she explains.

Ms Freeman says after her visit to the QEUH she is confident the health board have taken all the steps they should to ensure patient safety.

She tells the chamber she has asked Healthcare Environment Inspectorate to fully review this incident.

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There is to be a full investigation into the construction and design of Glasgow's Queen Elizabeth University Hospital.

Health Secretary Jeane Freeman ordered the inquiry after it emerged two patients had died after contracting a rare infection linked to pigeon droppings.

Last year a number of children with cancer were treated after a bacterial infection was identified in drains.

Ms Freeman says external experts will be appointed to lead the investigation with the findings to be made public.

At the weekend it emerged that two patients who had died at the hospital had contracted a cryptococcus fungal infection, which is linked to pigeon droppings.

The health board said one of the patients was elderly and had died from an unrelated cause. The factors contributing to the death of the other patient are being investigated.

• The troubled past of the QEUH

Labour MSP Monica Lennon asks for the government's response is to reports that two patients have died at the Queen Elizabeth University Hospital after contracting a fungal infection, and what advice has been issued to NHS boards on this matter.

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Pastor Rob McArthur from River Church in Banff delivers today's time for reflection.