A tragic Listeria sickness and the seek for the trigger

On July 24, 2024, John Trahar examined optimistic for Listeria, whereas within the ICU. John’s pattern was genetically linked, by Complete Genome Sequencing, to a cluster of Listeria related to potatoes from Mexico.

Determine: SNP-tree of sequences of REP pressure uploaded to the general public sequence repository at 
NCBI.

On July 16, 2024, John Trahar was admitted to the hospital with a headache, facial drooping, dizziness, and an irregular MRI. His household feared he was having an aneurysm. 

Per week later, on July 22, 2024, John was intubated and sedated within the ICU, the place he remained for 5 weeks, combating for his life in opposition to bacterial meningitis brought on by Listeria. 

When John was first admitted to ICU, he had been hospitalized for per week with signs; it took one other three days of testing to find out that Listeria was the reason for his sickness. John was on a ventilator and a number of IV drips to maintain him alive within the ICU. He was comatose and unresponsive for at the least per week. At one level, he was so swollen with fluids and meds, he couldn’t even shut his eyes. 

After roughly 5 weeks within the ICU, John was transferred to a rehab hospital for long run acute care (LTAC). He was minimally conscious of his household for the primary a number of months in LTAC. He remained unable to maneuver, communicate, swallow, or see with out double imaginative and prescient. He developed strain wounds that required critical care , together with a specialised mattress. He remained on the IV antibiotic drip for 12 weeks, till blood examined decided that the micro organism had been killed; nevertheless, the large results of the an infection included a number of abscesses in his brainstem and cerebellum, and his mind was left swollen and infected. 

John remained on the ventilator till the tip of November 2024. He was solely in a position to sit in a wheelchair, propped with pillows for half-hour at a time. John began to obtain PT, OT, and speech remedy. Throughout this time, John encountered a number of infections together with UTIs, bronchitis, and pinkeye. 

John spent eight months on the rehab hospital and continued to enhance very slowly and to regain some power. However the harm was obvious, as his spouse particulars: 

He made good points in communication, but it surely turned obvious that his cognitive notion and persona had been affected by the harm from the Listeria an infection. It’s devastating to see the one you love endure a lot and devastating on a complete totally different stage to attempt to assist and have them hallucinating that you’re another person and there to hurt them. To see my husband, my associate in life, have each a part of his physique and thoughts affected  is one thing I’ll by no means unsee or unfeel. 

In March 2025, John was transferred to expert nursing, but it surely shortly turned obvious that this was not the correct stage of take care of him. In three weeks on the facility, EMS was known as for John thrice; twice, he had pulled out his personal trach tube as a result of it had turn into clogged with secretions and he couldn’t breathe, and as soon as as a result of he had fallen and not one of the nurses might carry him. John’s psychological well being deteriorated as effectively, with him saying he felt uncared for and like he was left there to die. Subsequently, attributable to a scarcity of nursing care, John ended up within the ICU with pneumonia, the place he stayed for 10 days and, as soon as once more, almost died. He was discharged again to the rehab hospital, to begin the cycle yet again—LTAC, rehab, after which insurance coverage pushing him out the door to expert nursing. His spouse writes: 

I fear and analysis continually about the place John could be positioned and the extent of care I can get for him. He requires help to  stroll, bathe, gown or care for himself. He’s on a feeding tube as a result of he can not swallow with out aspirating. He has tracheostomy that could be everlasting in addition to the feeding tube. He can communicate however could be very obscure initially, as half of his face stays paralyzed. He can not write attributable to lack of tremendous motor abilities, and he can solely learn with problem attributable to double imaginative and prescient. He was just lately identified with Cerebellar Cognitive Affective Syndrome, for which there’s not remedy and no remedy. John’s long-term reminiscence stays intact, however his short-term reminiscence, emotional regulation, and impulse management are all affected. 

John has by no means made it house since being admitted to hospital care final July. He could by no means make it house, as his medical wants, each bodily and psychological, stay complicated. John is a beloved, profitable, vibrant, wholesome, clever and opinionated man who headed up a household and a enterprise. John is the Chief Inventive Officer, CEO, and founding member, of our enterprise. Coming to phrases with the adjustments in our enterprise construction and ensuring we’re nonetheless offering the identical ranges of considering and execution has been a virtually full-time job, past managing John’s care. Fortunately, John’s considerate management previous to his sudden disappearance gave us an efficient blueprint to maintain going and sustaining our stage of efficiency, however to say that this time has been aggravating is frankly the understatement of the 12 months.  I solely sleep as a result of I’m too mentally exhausted to remain awake at a sure level. 

Primarily, our whole life has been dominated and utterly turned the wrong way up by John’s sickness since he was admitted. I’ve struggled to be a guardian to our 15-year-old son whereas my hours (actually and mentally) are dominated by managing John’s care. I fear for my son’s psychological well being whereas making an attempt to take care of my very own and to be an engaged and concerned mother. 

The model of the husband, father, brother, buddy, uncle, and boss all of us knew, cherished and trusted is gone. A shadow model of John stays in place, and due to the complexity of his medical wants, we don’t know for a way lengthy. It has been harrowing to look at him endure for the higher a part of a 12 months now. He has mentioned he wished he had died final July. What does one even say to that? On the time I used to be so grateful  that John lived… however seeing how depressing he’s now, I don’t really feel grateful in any respect. I really feel that my greatest buddy and husband John did die then, and I’m a widow to a residing particular person… and that could be a really terrible place to exist for each of us.

Almost one 12 months later we’re nonetheless trying to find the conclusive hyperlink between John’s devastating Listeria sickness and all of the others sick and certain Mexican potatoes.  Query?  The place is our FDA and CDC and the State of Texas within the investigation?

Complete genome sequencing (WGS), which determines the complete nucleotide sequence of a bacterium’s genetic make-up, is now the gold customary for laboratory surveillance and investigation of outbreaks of foodborne infections.

With WGS, outbreaks are detected quicker when they’re smaller, and extra outbreaks are being solved and managed than ever earlier than. WGS has an unsurpassed excessive decision by detecting adjustments on the stage of the constructing stones of the genetic code of the micro organism. The decision is so excessive that small variations could be noticed inside a single bacterial pressure and subsequently a pressure by WGS isn’t outlined by one sequence however relatively by a bunch of extremely comparable sequences, e.g. differing from one another by as much as 10 variations. Biologically, micro organism with comparable sequences possible share a current frequent ancestor. Alongside the identical strains, it’s a fundamental assumption in outbreak surveillance that micro organism with very comparable sequences possible come from the identical supply even when collected over prolonged time durations.

Very quickly after WGS was launched within the surveillance, meals security specialists realized that outbreaks with only a few instances would possibly happen over lengthy durations, typically years. The time period “low and gradual” was launched to explain these outbreaks. Nonetheless, even now the meals security authorities not often actively search for these outbreaks. They examine them after they accidently stumble into them when isolates from a meals or the meals atmosphere match isolates from historic sufferers, or affected person isolates in present outbreak investigations match seemingly sporadic instances from years in the past. An instance of the latter is the Listeria outbreak linked to Blue Bell ice cream in 2015. 

It’s well-known that bacterial strains could persist for years within the meals manufacturing methods and that such contamination has precipitated outbreaks. For instance, a selected pressure of Salmonella Enteritidis precipitated two outbreaks related to almonds from California within the Nineteen Nineties, which result in the implementation of necessary fumigation of almonds for human consumption. A pressure of Salmonella Newport precipitated outbreaks yearly within the 2000s related to tomatoes produced within the Delmarva area. A newer instance is a pressure of Shiga toxin-producing E. coli inflicting a number of outbreaks related to produce grown within the South Western US. Scientists on the Heart for Illness Management and Prevention (CDC) got here up with a reputation, REP-strains (in need of Repeating, Rising or Persistent) for such strains. REP-strains could trigger outbreaks with totally different meals automobiles if the final word supply is outdoors the meals manufacturing methods (e.g. the latter E. colioutbreaks) or with only one car if a selected manufacturing system has been contaminated (e.g. the Salmonella outbreaks).

After the implementation of WGS it has  been realized that some REP-strains could trigger ‘low and gradual’ outbreaks which can be neither detected nor investigated as a result of the outbreak alerts are weak and the diseases are too unfold out in time to be caught by the detection  algorithms utilized by the general public well being authorities. This can be a disgrace, as a result of a REP-strain downside that appears small in a one-year timeframe could also be a giant and important public well being challenge that must be addressed if it persists for years. The wealth of sequence knowledge  within the GenomeTrakr community within the public sequence repository, SRA, on the Nationwide Heart for Biotechnology info (NCBI) might simply be used to detect such giant “low and gradual” outbreaks.

Not too long ago, scientists found a REP-strain within the SRA, when engaged on John’s case.  They had been checking sequences of Listeria monocytogenes and found a bunch of 130 extremely associated sequences submitted to the database between 2016 and now (Desk and Determine).

These sequences confirmed as much as 23 variations (“SNP-differences”) between them with a median of simply 6 SNPs, a distinction that’s usually seen in Listeria outbreaks. 97 sequences had been from human medical isolates within the US submitted by PulseNet USA and 33 had been from potatoes (32) and an apple (1) submitted by the Mexican Service for the Nationwide Well being for Meals Security and Meals High quality (SENASICA) with meals origin listed as USA. Distribution of sequence submissions by 12 months is seen within the desk under.

Desk: Listeria isolates of REP pressure submitted the general public sequence repository at NCBI by 12 months and supply.

The distribution by 12 months peaked between 2017 and 2022 from a low begin. Since 2022 there was just a few infections yearly. Two sequences have thus far been submitted in 2025. Sadly, the state distribution of the medical isolates isn’t offered within the database. CDC or the Meals and Drug Administration (FDA) has not talked about something about outbreaks or outbreak investigations associated to this REP-strain on their web-sites, so it’s unclear if they’ve ever investigated it throughout one of many peaking years or over the entire time-period. That is odd, because the whole variety of instances is excessive and 32 of the sequences originate from a possible meals supply. That is absolutely a possible long-lasting outbreak that needs to be investigated. 

The sources to the CDC and FDA, notably affecting worldwide actions, have been drastically diminished this 12 months. Whereas the administration suggests these cuts handle inefficiencies with out compromising core capabilities, meals security scientists dispute this declare. Investigating the cluster with this REP-strain might present vital clues to settle this dispute testing the companies’ capabilities in home and worldwide outbreak investigation and administration, highlighting the significance of sustaining strong meals security packages.

Hey, FDA, CDC and State of Texas.