About

Jonathan M. Holmes, MD, is the Head of Ophthalmology and Vision Science and a Professor in the Department of Ophthalmology and Vision Science at the University of Arizona College of Medicine. He holds degrees including BM and BCh, which are equivalent to an MD, from Oxford University Medical School. His professional practice is based at 655 N. Alvernon Way, Suite 204, Tucson, AZ. Dr. Holmes's work focuses on ophthalmology and vision science, contributing to the academic and clinical advancement of the field through his leadership and research activities.

Research topics

• Ophthalmology
• Medicine
• Surgery
• Pediatrics
• Optometry
• Internal medicine
• Psychology
• Developmental psychology
• Psychiatry

Selected publications

• Artificial intelligence for detection and staging of Alzheimer’s disease using retinal images

  Cochrane Database of Systematic Reviews · 2026-05-21

  article

  OBJECTIVES: This is a protocol for a Cochrane Review (diagnostic). The objectives are as follows: To determine the diagnostic accuracy of AI algorithm-based retinal image reading for detecting referral-requiring Alzheimer's disease in adults who have behavioral symptoms or cognitive decline in the primary care setting. Secondary objectives Where data are available, we will investigate heterogeneity by incorporating covariates in a metaregression.

  PublisherDOI

• Microbial Keratitis in Southern Arizona

  Ophthalmic Research · 2026-03-30

  articleOpen accessSenior author

  Introduction There is a paucity of data on microbial keratitis in the Southwestern United States, specifically Southern Arizona. Understanding demographic factors and causative organisms will help design future treatments and preventative measures. Methods A retrospective chart review was conducted on all cases (>17 years old) of microbial keratitis at Banner University Medical Center Tucson, Arizona from September 1, 2017 to August 31, 2022. Reported frequencies of social, demographic, ocular factors, and isolated organisms. We used Fisher's exact tests to compare findings with latest census data. Results We identified 272 eyes in 268 patients. Compared with census data, demographic factors overrepresented in microbial keratitis were: unemployment (50.4%) and homelessness (8.2%). Drug use was identified in 22.4% of patients. Associated factors were contact lens wear (33.1%) and preceding ocular trauma (14.7%). Among eyes associated with contact lens use, 49 (54.4%) were worn overnight. Of 203 eyes with culture results, 152 (74.9%) yielded a positive microbial culture; 96.5% bacterial and 3.4% fungal. Gram-positive bacteria were found in 54.7%, most commonly Staphylococcus epidermidis (16.7%). The most common Gram-negative isolate was Pseudomonas aeruginosa (12.8%). Conclusion In Southern Arizona, microbial keratitis is particularly associated with drug use, unemployment, and homelessness. Contact lens use and overnight wear were common, warranting education on safe practices. Positive fungal cultures were rare. Each factor deserves consideration for societal intervention, to reduce the burden of microbial keratitis in Southern Arizona, and should be evaluated as potential risk factors in other communities. Overall culture results may influence choice of initial therapy.

  PublisherOA PDFDOI

• Serial lung ultrasound in predicting the need for surfactant and respiratory course in preterm infants—multicentre observational study (SLURP)

  European Journal of Pediatrics · 2025-05-23 · 5 citations

  articleOpen access

  Lung ultrasound (LUS) scores may predict surfactant need early and the progression of the respiratory course in preterm infants. The objective of this study is to report the diagnostic value of LUS scores performed by operators of varying levels of experience to predict the need for surfactant in preterm infants. A prospective observational study was conducted across 3 UK-based neonatal intensive care units. Preterm infants ≤ 34 weeks on non-invasive respiratory support within 3 h of birth were included. Ten lung zones were scored serially, first within the first 3 h of life, then at 12-24-h intervals (a total of four scans). All scans were performed by the local team members with formal training on LUS and varying levels of expertise. All the LUS videos were scored by an expert investigator who was blinded to clinical details. Written retrospective parental consents were obtained. We recruited 83 preterm infants ≤ 34 weeks (May 2023 to June 2024). A total of 325 LUS scans were performed by 27 clinical staff. The median birth gestational age and birth weight were 31 weeks and 1515 g, respectively. Twenty-eight (34%) babies received surfactants. The first LUS using a 6-zone method within 3 h of life predicted surfactant need and bronchopulmonary dysplasia with an AUC of 0.80 for both outcomes, offering sensitivity (79% and 73%) and specificity (75% and 76%), respectively. CONCLUSIONS: LUS performed by operators of varying levels of experience within the first 3 h of life is a reliable tool for predicting surfactant need in preterm infants ≤ 34 weeks. TRIAL REGISTRATION: ClinicalTrials.gov ( https://clinicaltrials.gov/ ): NCT05782569. WHAT IS KNOWN: • There are considerable variations in the selection criteria of preterm infants for surfactant administration. • Lung ultrasound score has been shown to predict the need for surfactant early and the progression of respiratory course in preterm infants. WHAT IS NEW: • LUS performed within 3 h of life by operators of varying levels of experience and interpreted by expert predicted the need for surfactant deficiency in preterm infants. • Our research with a structured training programme enabled novice operators to perform LUS and achieve reasonable competency.

  PublisherOA PDFDOI

• Understanding the demographic, clinical biochemistry and health care data associated with malnutrition in the UK Clinical Practice Research Datalink (CPRD), to support development of The EAMIT Tool (East Anglian Malnutrition Identification Tool)

  Proceedings of The Nutrition Society · 2025-08-01

  articleOpen access

  Malnutrition is a common but underrecognized clinical problem associated with sarcopenia, frailty, fragility fractures, and multiple long-term conditions (1) . Malnutrition increases treatment costs, hospital stays, and secondary care recovery. Current methods of identifying malnutrition rely on direct measures of weight loss and BMI which are often less used and so malnutrition is often missed (2) . As the first step in developing a digital application the EAMIT (East Anglian Malnutrition Identification Tool) for identifying malnutrition, using factors recorded in routine clinical healthcare data, including combinations of demographic factors, health care data (e.g. medications) and clinical biochemistry (e.g. CRP), we examined the data for these factors in the CPRD (2) . Individuals screened with the MUST tool (Malnutrition Universal Screening Tool), older than 65 years, and a matched set of people according to age, sex and GP practice were identified within the CPRD Aurum datalink (Feasbility Study reference FS_002595). Four groups were examined for demographic, health care and clinical biochemistry variables according to MUST screening category result: 1) low risk of malnutrition, 2) medium risk 3) high risk (MUST_H), 4) matched unscreened individuals (MUST_0), and either medians (IQR) or percentage of individuals per group were calculated. The percentage of people over 85Y was 47% in in the MUST_H group, versus 43% in MUST_0. Median, IQR BMI ranged from MUST_0 26.3 kg/m 2 (23.1-29.8) to 18.3 kg/m 2 (16.7-20.9) in MUST_H. Median weight loss was -5.9% in MUST_H compared with 0.1% in MUST_ 0. As expected, 50% of people in MUST_H had a BMI <18.5 kg/m 2 compared with 1% in MUST_0, though the percentage of missing values for BMI was 72%-80% in MUST categories, and 50% in MUST_0. The median number of GP visits (year before screening) was 12 (IQR 6-20) per year in MUST_H compared with 8 (IQR 4-16) in MUST_0. Number of people prescribed 5+ medications was 25% higher in MUST_H than MUST_0. Clinical biochemistry data differed by group. The percentage with low albumin (<35g/L) was 6.5% in MUST_0 compared with 22.8% in MUST_H, iron deficiency as low Hb [<120g g/l (women); <130g/l (men)] ranged from 18% in MUST_0 to 36% in MUST_H. CRP, median IQR, was higher in MUST_H (7; 3-25) compared with MUST_0 (5;2-10). Gradients were found across categories of MUST, and between matched individuals, of greater age, lower BMI, greater percentage of weight loss, lower concentrations of haemoglobin and albumin and higher concentrations of CRP. The number of medications and visits to GPs increased according to category of MUST screening. The proportion of missing BMI data indicates the need to develop a new tool but sufficient demographic, health care and clinical biochemistry data exists within the CPRD database to continue developing an algorithm for identifying risk of malnutrition in the community.

  PublisherOA PDFDOI

• Needs and experiences of families after a sudden unexplained death in childhood: a qualitative study

  BMJ Paediatrics Open · 2025-08-01 · 1 citations

  articleOpen access

  BACKGROUND: Sudden unexplained death in childhood (SUDC) is a rare and devastating experience for families. In the UK, multi-agency investigation by police, health and social care of sudden, unexpected child deaths is a statutory requirement aiming to identify full causes for deaths. Families should be allocated bereavement keyworkers for support throughout the investigative process which can take several months. Previous research has focused on multi-agency investigation of sudden infant deaths, with little known about parents' experiences for deaths of older children. METHODS: Bereaved parents of children in the UK, aged 1 to 17 years who died from SUDC during 2018-2022, were recruited through SUDC-UK charity and their mailing list and word of mouth. Semi-structured interviews were conducted in 2023. Interview transcripts underwent thematic analysis. RESULTS: Interviews were conducted with parents from 20 families across England, Scotland and Northern Ireland in 2023. Four key themes were identified: the importance of keyworkers, trauma-informed communication, proactivity from professionals and provision of medical screening for families. Keyworkers were valued by parents, but only 12/20 families had keyworkers allocated. Communication and language were important; families were often distressed by unexpected telephone calls particularly relating to post-mortem results. Parents felt they had to be proactive explaining about SUDC to professionals who lacked knowledge of the condition. Parents wanted medical screening to be proactively offered for their families. CONCLUSIONS: Every family must receive swift, proactive, knowledgeable communication from professionals, during and beyond the investigation into their child's sudden unexpected death. This will help them through the process and mitigate the impact of poor communication on their grief. While all parents expressed that they wanted to find out why their child died, they also identified key improvements to the consistency and effectiveness of the investigation process.

  PublisherOA PDFDOI

• Workplace Stratification and Racial Health Disparities

  National Bureau of Economic Research · 2025-02-01

  reportOpen access

  To what extent is a worker's relative rank within their workplace a determinant of health status, conditional on income?We provide the first US-based evidence on the relationship between relative workplace rank and health status for the near population of workers in one US state.Using a new linkage of commercial all-payer health insurance data to administrative earnings records for workers in Utah from 2013-2015, we quantify the impact of relative workplace rank on health status, the incidence of specific chronic diseases, and racial health disparities.We show that about 70% of SES-health gradient that is commonly interpreted as an income gradient actually operates through relative rank.For an average worker, moving from the 90th to the 10th percentile of withinfirm rank holding fixed income, age, location, and health insurance characteristics is associated with a 16.5% increase in morbidity.The racial segregation of jobs in the US leads minority workers to be overrepresented in lower-ranked jobs within firms, which in turn exacerbates racial health disparities.

  PublisherDOI

• Effects of Age at Surgery and Laterality of Cataract on Visual Acuity 5 Years after Surgery in Infants Left Aphakic

  Ophthalmology · 2025-06-27

  articleOpen access
  PublisherOA PDFDOI

• Ophthalmic outcomes five years after lensectomy among children with Down syndrome

  Journal of American Association for Pediatric Ophthalmology and Strabismus · 2025-07-28

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Visual Outcomes and Complications Over 5 Years Following Lensectomy for Childhood Traumatic Cataract

  JAMA Ophthalmology · 2025-11-06

  articleOpen access

  Importance: The long-term outcomes of surgery for pediatric traumatic cataract are not well described; understanding these outcomes would inform parental expectations. Objective: To report visual acuity (VA) outcomes and cumulative incidence of ocular complications by 5 years following lensectomy for pediatric traumatic cataract. Design, Setting, and Participants: This prospective cohort study was conducted across 32 sites in the US and Canada among 75 children undergoing lensectomy from birth to less than 13 years of age for unilateral traumatic cataract. Of 75 children, 60 had primary intraocular lens (IOL) placement; 15 were left aphakic. Data were collected from August 2012 to February 2020. Data analysis was performed from October 2022 to May 2025. Exposure: Lensectomy. Main Outcomes and Measures: The primary outcomes were best-corrected VA 5 years after lensectomy; period prevalence of strabismus and glaucoma (including cases diagnosed before lensectomy); surgery for visual axis opacification (VAO); and cumulative incidence of ocular complications by 5 years. Annual data collection was from medical record reviews through 5 years following lensectomy. Results: Among 75 participants, 28 (37%) were female, and median (range) age at lensectomy was 7.4 years (0.1-13 years). Median (IQR) best-corrected VA at 5 years (available for 37 participants [49%]) was 20/63 (20/35-20/159) in pseudophakic eyes (n = 29; mean [SD] age at surgery, 7.2 [3.0] years) and 20/258 (20/56-<20/800) in aphakic eyes (n = 8; mean [SD] age at surgery, 5.5 [4.3] years). Age-normal VA was achieved by 6 pseudophakic eyes (21%; 95% CI, 10%-38%) and 1 aphakic eye (13%; 95% CI, 2%-47%). The 5-year period prevalence of glaucoma was 9% in pseudophakic eyes (95% CI, 1%-16%) and 9% in aphakic eyes (95% CI, 0%-24%). The 5-year cumulative incidence of surgery for VAO was 47% in pseudophakic eyes (95% CI, 31%-60%) and 13% in aphakic eyes (95% CI, 0%-28%). The risk was greater in eyes that did not undergo an anterior vitrectomy (84%; 95% CI, 55%-94%) vs eyes that did (15%; 95% CI, 2%-26%) (age-adjusted hazard ratio, 11.4; 95% CI, 4.6-33.1; P < .001). Conclusions and Relevance: In this cohort study, while only half of the study participants had a 5-year follow-up visit, achieving age-normal VA was uncommon among the cohort in whom a best-corrected VA was determined. The prevalence of glaucoma at 5 years was low among those with 5-year follow-up, while nearly half of the pseudophakic eyes needed surgery for VAO supporting the need to monitor these children.

  PublisherOA PDFDOI

• Validating Rules for Defining No Improvement of Visual Acuity in Childhood Amblyopia

  Investigative Ophthalmology & Visual Science · 2025-01-02 · 1 citations

  articleOpen access

  Purpose: When treating amblyopia, it is important to define when visual acuity (VA) is no longer improving (i.e., stable) because treatment decisions may be altered based on this determination. Methods: Simulated observed VAs, incorporating measurement error, were compared with simulated true VAs to determine false-positive and false-negative rates for stable VA for six rules (using single VA or test/retest measurements, with or without averaging, over two or three visits). Four HOTV VA profiles were modeled: stable or improving VA over time with each of patching and spectacles. Results: Across six rules and two treatments, when true VA was stable, false-negative rates for stability ranged from 26% to 67%; when true VA was improving, false-positive rates for stability ranged from 0% to 38%. Single VA measurements at consecutive visits had a false-negative rate of 30% with patching and 29% with spectacles, a false-positive rate of 38% with patching and 35% with spectacles. Averaging two VA tests at each visit slightly increased the false-negative rate (35% with patching and 36% with spectacles), while reducing the false-positive rate (22% with patching and 21% with spectacles). Conclusions: Comparing false-negative and false-positive rates for stability across rules allows selection of the most appropriate rule for clinical practice or research. When considering less desirable treatments, a rule with a lower false-negative rate is preferable, whereas a rule with a lower false-positive rate would be preferred when it is important to correctly classify improving VA.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01EY012798

  NIH · $909k · 2006

• NIH Grant R01EY024333

  NIH · $3.3M · 2021

• NIH Grant U10EY018810

  NIH · $3.5M · 2014

• NIH Grant R01EY015799

  NIH · $1.5M · 2011

• NIH Grant R21EY011578

  NIH · $77k · 2002

Frequent coauthors

• David A. Leske

  295 shared

• Sarah R. Hatt

  Mayo Clinic in Arizona

  213 shared

• Eileen E. Birch

  Retina Foundation of the Southwest

  168 shared

• Michael X. Repka

  Johns Hopkins Medicine

  131 shared

• Raymond T. Kraker

  Jaeb Center for Health Research

  123 shared

• David K. Wallace

  University of Toronto

  105 shared

• Roy W. Beck

  Jaeb Center for Health Research

  103 shared

• Susan A. Cotter

  Marshall B. Ketchum University

  99 shared

Labs

• McKay LabPI