A tragic Listeria illness and the search for the cause

On July 24, 2024, John Trahar tested positive for Listeria, while in the ICU. John’s sample was genetically linked, by Whole Genome Sequencing, to a cluster of Listeria associated with potatoes from Mexico.

Figure: SNP-tree of sequences of REP strain uploaded to the public sequence repository at 
NCBI.

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

A week later, on July 22, 2024, John was intubated and sedated in the ICU, where he remained for five weeks, fighting for his life against bacterial meningitis caused by Listeria. 

When John was first admitted to ICU, he had been hospitalized for a week with symptoms; it took another three days of testing to determine that Listeria was the cause of his illness. John was on a ventilator and multiple IV drips to keep him alive in the ICU. He was comatose and unresponsive for at least a week. At one point, he was so swollen with fluids and meds, he could not even close his eyes. 

After approximately five weeks in the ICU, John was transferred to a rehab hospital for long term acute care (LTAC). He was minimally responsive to his family for the first several months in LTAC. He remained unable to move, speak, swallow, or see without double vision. He developed pressure wounds that required serious care , including a specialized bed. He remained on the IV antibiotic drip for 12 weeks, until blood tested determined that the bacteria had been killed; however, the massive effects of the infection included multiple abscesses in his brainstem and cerebellum, and his brain was left swollen and inflamed. 

John remained on the ventilator until the end of November 2024. He was only able to sit in a wheelchair, propped with pillows for 30 minutes at a time. John started to receive PT, OT, and speech therapy. During this time, John encountered multiple infections including UTIs, bronchitis, and pinkeye. 

John spent eight months at the rehab hospital and continued to improve very slowly and to regain some strength. But the damage was apparent, as his wife details: 

He made gains in communication, but it became apparent that his cognitive perception and personality were affected by the damage from the Listeria infection. It is devastating to see your loved one suffer so much and devastating on a whole different level to try to help and have them hallucinating that you are someone else and there to harm them. To see my husband, my partner in life, have every part of his body and mind affected  is something I will never unsee or unfeel. 

In March 2025, John was transferred to skilled nursing, but it quickly became apparent that this was not the proper level of care for him. In three weeks at the facility, EMS was called for John three times; twice, he had pulled out his own trach tube because it had become clogged with secretions and he could not breathe, and once because he had fallen and none of the nurses could lift him. John’s mental health deteriorated as well, with him saying he felt neglected and like he was left there to die. Subsequently, due to a lack of nursing care, John ended up in the ICU with pneumonia, where he stayed for 10 days and, once again, nearly died. He was discharged back to the rehab hospital, to start the cycle all over again—LTAC, rehab, and then insurance pushing him out the door to skilled nursing. His wife writes: 

I worry and research constantly about where John can be placed and the level of care I can get for him. He requires assistance to  walk, bathe, dress or take care of himself. He is on a feeding tube because he cannot swallow without aspirating. He has tracheostomy that may be permanent as well as the feeding tube. He can speak but is very difficult to understand initially, as half of his face remains paralyzed. He cannot write due to loss of fine motor skills, and he can only read with difficulty due to double vision. He was recently diagnosed with Cerebellar Cognitive Affective Syndrome, for which there is not treatment and no cure. John’s long-term memory remains intact, but his short-term memory, emotional regulation, and impulse control are all affected. 

John has never made it home since being admitted to hospital care last July. He may never make it home, as his medical needs, both physical and mental, remain complex. John is a beloved, successful, vibrant, healthy, intelligent and opinionated man who headed up a family and a business. John is the Chief Creative Officer, CEO, and founding member, of our business. Coming to terms with the changes in our business structure and making sure we are still providing the same levels of thinking and execution has been a nearly full-time job, beyond managing John’s care. Thankfully, John’s thoughtful leadership prior to his sudden disappearance gave us an effective blueprint to keep going and maintaining our level of performance, but to say that this time has been stressful is frankly the understatement of the year.  I only sleep because I’m too mentally exhausted to stay awake at a certain point. 

Essentially, our entire life has been dominated and completely turned upside down by John’s illness since he was admitted. I have struggled to be a parent to our 15-year-old son while my hours (literally and mentally) are dominated by managing John’s care. I worry for my son’s mental health while trying to maintain my own and to be an engaged and involved mom. 

The version of the husband, father, brother, friend, uncle, and boss we all knew, loved and depended on is gone. A shadow version of John remains in place, and because of the complexity of his medical needs, we don’t know for how long. It has been harrowing to watch him suffer for the better part of a year now. He has said he wished he had died last July. What does one even say to that? At the time I was so grateful  that John lived… but seeing how miserable he is now, I don’t feel grateful at all. I feel that my best friend and husband John did die then, and I am a widow to a living person… and that is a truly awful place to exist for both of us.

Nearly one year later we are still searching for the conclusive link between John’s devastating Listeria illness and all the others ill and likely Mexican potatoes.  Question?  Where is our FDA and CDC and the State of Texas in the investigation?

Whole genome sequencing (WGS), which determines the full nucleotide sequence of a bacterium’s genetic makeup, is now the gold standard for laboratory surveillance and investigation of outbreaks of foodborne infections.

With WGS, outbreaks are detected faster when they are smaller, and more outbreaks are being solved and controlled than ever before. WGS has an unsurpassed high resolution by detecting changes at the level of the building stones of the genetic code of the bacteria. The resolution is so high that small differences might be observed within a single bacterial strain and therefore a strain by WGS is not defined by one sequence but rather by a group of highly similar sequences, e.g. differing from each other by up to 10 differences. Biologically, bacteria with similar sequences likely share a recent common ancestor. Along the same lines, it is a basic assumption in outbreak surveillance that bacteria with very similar sequences likely come from the same source even if collected over extended time periods.

Very soon after WGS was introduced in the surveillance, food safety specialists realized that outbreaks with very few cases might occur over long periods, sometimes years. The term “low and slow” was introduced to describe these outbreaks. However, even now the food safety authorities rarely actively look for these outbreaks. They investigate them when they accidently stumble into them when isolates from a food or the food environment match isolates from historical patients, or patient isolates in current outbreak investigations match seemingly sporadic cases from years ago. An example of the latter is the Listeria outbreak linked to Blue Bell ice cream in 2015. 

It is well-known that bacterial strains may persist for years in the food production systems and that such contamination has caused outbreaks. For example, a particular strain of Salmonella Enteritidis caused two outbreaks associated with almonds from California in the 1990s, which lead to the implementation of mandatory fumigation of almonds for human consumption. A strain of Salmonella Newport caused outbreaks every year in the 2000s associated with tomatoes produced in the Delmarva region. A more recent example is a strain of Shiga toxin-producing E. coli causing several outbreaks associated with produce grown in the South Western US. Scientists at the Center for Disease Control and Prevention (CDC) came up with a name, REP-strains (short of Repeating, Emerging or Persistent) for such strains. REP-strains may cause outbreaks with different food vehicles if the ultimate source is outside the food production systems (e.g. the latter E. colioutbreaks) or with just one vehicle if a specific production system has been contaminated (e.g. the Salmonella outbreaks).

After the implementation of WGS it has  been realized that some REP-strains may cause ‘low and slow’ outbreaks that are neither detected nor investigated because the outbreak signals are weak and the illnesses are too spread out in time to be caught by the detection  algorithms used by the public health authorities. This is a shame, because a REP-strain problem that looks small in a one-year time frame may be a big and significant public health issue that needs to be addressed if it persists for years. The wealth of sequence data  in the GenomeTrakr network in the public sequence repository, SRA, at the National Center for Biotechnology information (NCBI) could easily be used to detect such large “low and slow” outbreaks.

Recently, scientists discovered a REP-strain in the SRA, when working on John’s case.  They were checking sequences of Listeria monocytogenes and discovered a group of 130 highly related sequences submitted to the database between 2016 and now (Table and Figure).

These sequences showed up to 23 differences (“SNP-differences”) between them with an average of just 6 SNPs, a difference that is often seen in Listeria outbreaks. 97 sequences were from human clinical isolates in the US submitted by PulseNet USA and 33 were from potatoes (32) and an apple (1) submitted by the Mexican Service for the National Health for Food Safety and Food Quality (SENASICA) with food origin listed as USA. Distribution of sequence submissions by year is seen in the table below.

Table: Listeria isolates of REP strain submitted the public sequence repository at NCBI by year and source.

The distribution by year peaked between 2017 and 2022 from a low start. Since 2022 there has been a few infections every year. Two sequences have so far been submitted in 2025. Unfortunately, the state distribution of the clinical isolates is not provided in the database. CDC or the Food and Drug Administration (FDA) has not mentioned anything about outbreaks or outbreak investigations related to this REP-strain on their web-sites, so it is unclear if they have ever investigated it during one of the peaking years or over the whole time-period. This is odd, since the total number of cases is high and 32 of the sequences originate from a potential food source. This is surely a potential long-lasting outbreak that should be investigated. 

The resources to the CDC and FDA, particularly affecting international activities, have been drastically reduced this year. While the administration suggests these cuts address inefficiencies without compromising core functions, food safety scientists dispute this claim. Investigating the cluster with this REP-strain could provide important clues to settle this dispute testing the agencies’ capabilities in domestic and international outbreak investigation and management, highlighting the importance of maintaining robust food safety programs.

Hello, FDA, CDC and State of Texas.

Republished with permission from Bill Marler and Marler Clark. Copyright (c) Marler Clark LLP, PS. All rights reserved.

Source: https://www.marlerblog.com/case-news/a-tragic-listeria-illness-and-the-search-for-the-cause/