A summary of the U.S. Marine Recruit Assessment Program (RAP) procedures and survey from 2003 to 2021

The Recruit Assessment Program (RAP) is a cross-sectional, baseline survey of U.S. Marine recruits administered at Marine Corps Recruit Depot, San Diego. This report presents RAP study procedures and survey content that was administered to 229,015 participants between 2003 and 2021. Self-reported data were collected on recruit demographics, physical and mental health, adverse life experiences, lifestyle and risky behaviors, and substance use. In 2013, the survey was updated to remove questions with other linkable and reliable sources and those with low completion rates and low relevance to Marine health research; the removal of these items allowed for the addition of instrument measures for major depression, post-traumatic stress disorder, anger, and resilience with no significant change to overall survey length. Average completion rates are approximately 95%. Multiple studies have shown the utility of RAP data collected thus far as a robust data repository of pre-service health and behavioral measures.

The Neuromusculoskeletal Epidemiological Outcome (NEO) matrix: An innovative injury classification based on anatomical location and primary tissue type.

INTRODUCTION: The purpose of this paper is to propose the Neuromusculoskeletal Epidemiological Outcome (NEO) Matrix, an injury classification based on anatomical location and primary tissue type to classify NMSKI of the trunk and extremities in orthopaedic and sports medicine epidemiological research. MATERIALS AND METHODS: In the proposed NEO matrix, NMSKI diagnosis (International Classification of Disease) codes are classified by the anatomical complex affected. These regional anatomical complexes are frequently employed in orthopaedic and sports medicine disciplines in biomechanical and clinical research. The complexes are arranged from distal to proximal in the lower extremity, inferior to superior in the trunk and head, and proximal to distal in the upper extremity. Injuries are characterized by the primary tissue type affected (Osseous; Articular; Musculotendinous; Neural; Non-specific) based on classified using International Classification of Disease codes. DISCUSSION: The expected patterns of impairment and healing rates of bone, cartilage, ligaments, muscles, tendons, and neural structures vary considerably by the tissue type based on the differences in function, perfusion, and metabolic physiology. Using knowledge of the function of the tissues, expected minimum healing times, and expected sequelae of residual body system impairments, an estimation of morbidity and expected recovery times can be made. While heterogeneity is certainly expected due to varying pathomechanics involved and intrinsic and environmental factors, the NEO matrix classifies the ICD diagnosis codes in framework that qualifies the expected patterns of impairment based on the body system type. CONCLUSION: The NEO matrix provides an alternative approach for characterizing NMSKI in epidemiological research.

Environmental Chemicals Altered in Association With Deployment for High Risk Areas.

OBJECTIVE: A study was conducted using serum samples and high-resolution metabolomics (HRM) to test for changes in abundance of environmental chemicals in deployment in high-risk areas (Balad, Iraq; Bagram, Afghanistan). METHODS: Pre and Post-deployment serum samples for deployment (cases) and matched controls stationed domestically were analyzed by HRM and bioinformatics for the relative abundance of 271 environmental chemicals. RESULTS: Of the 271 chemicals, 153 were measurable in at least 80% of the samples in one of the pre- or post-deployment groups. Several pesticides and other chemicals were modestly elevated post-deployment in the Control as well as the Bagram and Balad samples. Similarly, small decreases were seen for some chemicals. CONCLUSION: These results using serum samples show that for the 271 environmental chemicals studied, 56% were detected and small differences occurred with deployment to high-risk areas.

Metabolome-Wide Association Study of Deployment to Balad, Iraq or Bagram, Afghanistan.

OBJECTIVE: To use high-resolution metabolomics (HRM) to identify metabolic changes in military personnel associated with deployment to Balad, Iraq, or Bagram, Afghanistan. METHODS: Pre- and post-deployment samples were obtained from the Department of Defense Serum Repository (DoDSR). HRM and bioinformatics were used to identify metabolic differences associated with deployment. RESULTS: Differences at baseline (pre-deployment) between personnel deployed to Bagram compared with Balad or Controls included sex hormone and keratan sulfate metabolism. Deployment to Balad was associated with alterations to amino acid and lipid metabolism, consistent with inflammation and oxidative stress, and pathways linked to metabolic adaptation and repair. Difference associated with deployment to Bagram included lipid pathways linked to cell signaling and inflammation. CONCLUSIONS: Metabolic variations in pre- and post-deployment are consistent with deployment-associated responses to air pollution and other environmental stressors.

Associations of Benzo(ghi)perylene and Heptachlorodibenzo-p-dioxin in Serum of Service Personnel Deployed to Balad, Iraq, and Bagram, Afghanistan Correlates With Perturbed Amino Acid Metabolism in Human Lung Fibroblasts.

OBJECTIVE: A study was conducted to identify metabolic-related effects of benzo(ghi)perylene (BghiP) and 1,2,3,4,6,7,8-heptachlorodibenzo-p-dioxin (HpCDD), on primary human fibroblasts to verify biological associations previously found in occupational health research. METHODS: Human lung fibroblasts were exposed to BghiP or HpCDD and extracts were analyzed with a metabolome-wide association study to test for pathways and metabolites altered relative to controls. Gene expression was measured by quantitative-real time polymerase chain reaction. RESULTS: Metabolic perturbations in amino-acid, oxidative stress, and fatty-acid pathways were observed for BghiP and HpCDD. HpCDD but not BghiP exposure increased gene expression of the amino acid transporters SLC7A5 and SLC7A11. CONCLUSIONS: Exposure to polycyclic aromatic hydrocarbons (PAH) or dioxins perturbs amino acid pathways at physiologically relevant concentrations with different mechanisms. These findings imply an effect on central homeostatic systems by environmental exposures which could have implications on disease susceptibility.

Integrative Network Analysis Linking Clinical Outcomes With Environmental Exposures and Molecular Variations in Service Personnel Deployed to Balad and Bagram.

OBJECTIVE: To develop a computational approach to link clinical outcomes with environmental exposures and molecular variations measured in Department of Defense (DOD) serum-repository samples. METHODS: International Classification of Diseases, Ninth Division codes which corresponded to cardiopulmonary symptoms for service personnel were selected to test for associations with deployment-related inhalation hazards and metabolomics, micro-RNA, cytokine, plasma markers, and environmental exposure analyses for corresponding samples. xMWAS and Mummichog were used for integrative network and pathway analysis. RESULTS: Comparison between 41 personnel exhibiting new cardio-pulmonary diagnoses after deployment start-date to 25 personnel exhibiting no symptoms identified biomarkers associated with cardiopulmonary conditions. Integrative network and pathway analysis showed communities of clinical, molecular, and environmental markers associated with fatty acid, lipid, nucleotide, and amino acid metabolism pathways. CONCLUSIONS: The current proof of principle study establishes a computational framework for integrative analysis of deployment-related exposures, molecular responses, and health outcomes.

Benzo[a]pyrene Perturbs Mitochondrial and Amino Acid Metabolism in Lung Epithelial Cells and Has Similar Correlations With Metabolic Changes in Human Serum.

OBJECTIVE: A study was conducted to identifymetabolic-related effects of benzo[a]pyrene (BaP) on human lung epithelial cells and validate these findings using human sera. METHODS: Human lung epithelial cells were treated with BaP, and extracts were analyzed with a global metabolome-wide association study (MWAS) to test for pathways and metabolites altered relative to vehicle controls. RESULTS: MWAS results showed that BaP metabolites were among the top metabolites differing between BaP-treated cells and controls. Pathway enrichment analysis further confirmed that fatty acid, lipid, and mitochondrial pathways were altered by BaP. Human sera analysis showed that lipids varied with BaP concentration. BaP associations with amino acid metabolism were found in both models. CONCLUSIONS: These findings show that BaP has broad metabolic effects, and suggest that air pollution exacerbates disease processes by altered mitochondrial and amino acid metabolism.

Neuropsychiatric Outcomes After Mefloquine Exposure Among U.S. Military Service Members.

Mefloquine was widely prescribed to U.S. military service members until 2009 when use was limited to personnel with contraindications to doxycycline and no contraindications to mefloquine. The need to estimate the occurrence of neuropsychiatric outcomes (NPOs) in service members prescribed mefloquine warranted a comprehensive evaluation of this issue. Active component service members filling a prescription for mefloquine, doxycycline, or atovaquone/proguanil (A/P) between January 1, 2008 and June 30, 2013, were included in the analysis. The risk of developing incident NPOs and the risk of subsequent NPOs among subjects with a history of the condition were assessed. A total of 367,840 individuals were evaluated (36,538 received mefloquine, 318,421 received doxycycline, and 12,881 received A/P). Among deployed individuals prescribed mefloquine, an increased risk of incident anxiety was seen when compared with doxycycline recipients (incidence rate ratio [IRR] = 1.12 [1.01-1.24]). Among nondeployed mefloquine recipients, an increased risk of posttraumatic stress disorder (PTSD) was seen when compared with A/P recipients (IRR = 1.83 [1.07-3.14]). An increased risk of tinnitus was seen for both deployed and nondeployed mefloquine recipients compared with A/P recipients (IRR = 1.81 [1.18-2.79]), 1.51 (1.13-2.03), respectively). Six percent of the mefloquine cohort had an NPO in the year before receiving mefloquine. When comparing individuals with a prior neuropsychiatric history to those without, the ratio of relative risks for adjustment disorder, anxiety, insomnia, and PTSD were higher (not statistically significant) for mefloquine compared with doxycycline. These findings emphasize the continued need for physicians prescribing mefloquine to conduct contraindication screening.

Assessing Health Outcomes After Environmental Exposures Associated With Open Pit Burning in Deployed US Service Members.

OBJECTIVE: This study assessed the long-term health impact of environmental exposures associated with open pit burning in deployed US service members. METHODS: Two hundred individuals deployed to Balad, Iraq, and Bagram, Afghanistan, with known exposure to open pits, were matched to 200 non-deployed service members. Both cohorts were observed for adverse health outcomes after returning from deployment. RESULTS: Slight increased risks were observed for respiratory diseases in the Bagram cohort (adj RR: 1.259), and for cardiovascular disease in the Balad cohort (adj RR: 1.072), but the findings were not significant. The combined deployed cohort showed lower risks for adverse health outcomes, suggesting a healthy deployer effect. CONCLUSIONS: In conclusion, this study did not find significantly increased risks for selected health outcomes after burn pit exposure during deployment among two deployed cohorts compared with a non-deployed cohort.

Metabolic Pathways and Networks Associated With Tobacco Use in Military Personnel.

OBJECTIVE: The aim of this study is to use high-resolution metabolomics (HRM) to identify metabolic pathways and networks associated with tobacco use in military personnel. METHODS: Four hundred deidentified samples obtained from the Department of Defense Serum Repository were classified as tobacco users or nonusers according to cotinine content. HRM and bioinformatic methods were used to determine pathways and networks associated with classification. RESULTS: Eighty individuals were classified as tobacco users compared with 320 nonusers on the basis of cotinine levels at least 10 ng/mL. Alterations in lipid and xenobiotic metabolism, and diverse effects on amino acid, sialic acid, and purine and pyrimidine metabolism were observed. Importantly, network analysis showed broad effects on metabolic associations not simply linked to well-defined pathways. CONCLUSIONS: Tobacco use has complex metabolic effects that must be considered in evaluation of deployment-associated environmental exposures in military personnel.

Deployment-Associated Exposure Surveillance With High-Resolution Metabolomics.

OBJECTIVE: The aim of this study was to assess the suitability of high-resolution metabolomics (HRM) for measure of internal exposure and effect biomarkers from deployment-related environmental hazards. METHODS: HRM provides extensive coverage of metabolism and data relevant to a broad spectrum of environmental exposures. This review briefly describes the analytic platform, workflow, and recent applications of HRM as a prototype environmental exposure surveillance system. RESULTS: Building upon techniques available for contemporary occupational medicine and exposure sciences, HRM methods are able to integrate external exposures, internal body burden of environmental agents, and relevant biological responses with health outcomes. CONCLUSIONS: Systematic analysis of existing Department of Defense Serum Repository samples will provide a high-quality, cross-sectional reference dataset for deployment-associated exposures while at the same time establishing a foundation for precision medicine.

Pilot Metabolome-Wide Association Study of Benzo(a)pyrene in Serum From Military Personnel.

OBJECTIVE: A pilot study was conducted to test the feasibility of using Department of Defense Serum Repository (DoDSR) samples to study health and exposure-related effects. METHODS: Thirty unidentified human serum samples were obtained from the DoDSR and analyzed for normal serum metabolites with high-resolution mass spectrometry and serum levels of free benzo(a)pyrene (BaP) by gas chromatography-mass spectrometry. Metabolic associations with BaP were determined using a metabolome-wide association study (MWAS) and metabolic pathway enrichment. RESULTS: The serum analysis detected normal ranges of glucose, selected amino acids, fatty acids, and creatinine. Free BaP was detected in a broad concentration range. MWAS of BaP showed associations with lipids, fatty acids, and sulfur amino acid metabolic pathways. CONCLUSION: The results show that the DoDSR samples are of sufficient quality for chemical profiling of DoD personnel.

High-Resolution Metabolomics Assessment of Military Personnel: Evaluating Analytical Strategies for Chemical Detection.

OBJECTIVE: The aim of this study was to maximize detection of serum metabolites with high-resolution metabolomics (HRM). METHODS: Department of Defense Serum Repository (DoDSR) samples were analyzed using ultrahigh resolution mass spectrometry with three complementary chromatographic phases and four ionization modes. Chemical coverage was evaluated by number of ions detected and accurate mass matches to a human metabolomics database. RESULTS: Individual HRM platforms provided accurate mass matches for up to 58% of the KEGG metabolite database. Combining two analytical methods increased matches to 72% and included metabolites in most major human metabolic pathways and chemical classes. Detection and feature quality varied by analytical configuration. CONCLUSIONS: Dual chromatography HRM with positive and negative electrospray ionization provides an effective generalized method for metabolic assessment of military personnel.

High-Resolution Metabolomics for Nutrition and Health Assessment of Armed Forces Personnel.

OBJECTIVE: The aim of this study was to test the utility of high-resolution metabolomics (HRM) for analysis of nutritional status and health indicators in military personnel. METHODS: Serum samples from 400 military personnel were obtained from the Department of Defense Serum Repository (DoDSR) and analyzed for metabolites related to nutrition and health status. Metabolic profile organization was studied using modulated modularity clustering (MMC). RESULTS: HRM provided quantitative measures of 61 metabolites across chemical classes for use as nutritional and clinical biomarkers. Levels were comparable to reported values except for arginine and glutamine, which were above and below reference ranges, respectively. MMC generated five clusters, three of which were associated and contained amino acids. The others contained lipids and mitochondria-related metabolites. CONCLUSIONS: HRM analysis of serum is suitable for real-time and/or retrospective evaluation of nutrition and health status of specific military cohorts.

The Challenges of Implementing Next Generation Sequencing Across a Large Healthcare System, and the Molecular Epidemiology and Antibiotic Susceptibilities of Carbapenemase-Producing Bacteria in the Healthcare System of the U.S. Department of Defense.

OBJECTIVE: We sought to: 1) provide an overview of the genomic epidemiology of an extensive collection of carbapenemase-producing bacteria (CPB) collected in the U.S. Department of Defense health system; 2) increase awareness of the public availability of the sequences, isolates, and customized antimicrobial resistance database of that system; and 3) illustrate challenges and offer mitigations for implementing next generation sequencing (NGS) across large health systems. DESIGN: Prospective surveillance and system-wide implementation of NGS. SETTING: 288-hospital healthcare network. METHODS: All phenotypically carbapenem resistant bacteria underwent CarbaNP® testing and PCR, followed by NGS. Commercial (Newbler and Geneious), on-line (ResFinder), and open-source software (Btrim, FLASh, Bowtie2, an Samtools) were used for assembly, SNP detection and clustering. Laboratory capacity, throughput, and response time were assessed. RESULTS: From 2009 through 2015, 27,000 multidrug-resistant Gram-negative isolates were submitted. 225 contained carbapenemase-encoding genes (most commonly blaKPC, blaNDM, and blaOXA23). These were found in 15 species from 146 inpatients in 19 facilities. Genetically related CPB were found in more than one hospital. Other clusters or outbreaks were not clonal and involved genetically related plasmids, while some involved several unrelated plasmids. Relatedness depended on the clustering algorithm used. Transmission patterns of plasmids and other mobile genetic elements could not be determined without ultra-long read, single-molecule real-time sequencing. 80% of carbapenem-resistant phenotypes retained susceptibility to aminoglycosides, and 70% retained susceptibility to fluoroquinolones. However, among the CPB-confirmed genotypes, fewer than 25% retained susceptibility to aminoglycosides or fluoroquinolones. CONCLUSION: Although NGS is increasingly acclaimed to revolutionize clinical practice, resource-constrained environments, large or geographically dispersed healthcare networks, and military or government-funded public health laboratories are likely to encounter constraints and challenges as they implement NGS across their health systems. These include lack of standardized definitions and quality control metrics, limitations of short-read sequencing, insufficient bandwidth, and the current limited availability of very expensive and scarcely available sequencing platforms. Possible solutions and mitigations are also proposed.

Use of quadrivalent human papillomavirus vaccine and the prevalence of antibodies to vaccine-targeted strains among female service members before and after vaccination.

The quadrivalent human papillomavirus vaccine (HPV4) has been shown to generate a robust immune response among fully vaccinated individuals; however, among U.S. service members, HPV vaccine completion rates are low. This study compared the immunogenicity of HPV4 vaccine among partially and fully vaccinated service members at 4-6 years post-vaccination. A random sample was obtained of 2,091 female service members, aged 17-26 years, who received 1-3 HPV4 doses during 2006-2012, stratified by number of doses (one, two, or three). Pre- and post-immunization sera from these service members were tested for antibodies to the HPV strains covered by the vaccine. Prior to immunization 42% were seropositive for HPV strain 6; 34% for strain 11; 29% for strain 16; and 16% for strain 18. Among those naive to all four strains prior to immunization, there was 100% seroconversion after one, two, or three doses. The results indicate that many service members had already been exposed to strains of HPV prior to receiving the vaccine; however, seropositivity prevalence was lower for the oncogenic HPV strains 16 and 18. The data demonstrate sustained immunogenicity after a single dose of vaccine, with modest improvement with successive doses for all strains except 18.

Incident and recurrent Chlamydia trachomatis and Neisseria gonorrhoeae infections, active component, U.S. Armed Forces, 2010-2014.

Chlamydia trachomatis and Neisseria gonorrhoeae infections impose a significant clinical and public health burden on the Military Health System. Repeat infections contribute significantly to that burden. This report summarizes rates and relative risks of true incident (i.e., initial or "first time ever") and recurrent (i.e., repeat) chlamydia and gonorrhea infections among active component members between 1 January 2010 and 31 December 2014. During the surveillance period, a total of 66,396 initial chlamydia and 9,138 initial gonorrhea cases were diagnosed. Annual crude rates of initial chlamydia infections increased by 23%. Crude rates of initial gonorrhea infections remained stable overall, but female rates decreased by 28.3% over the period. Among the incident cohorts, 11,699 cases of repeat chlamydia, and 1,138 cases of repeat gonorrhea were diagnosed over the period, accounting for 15.0% and 11.1% of overall cohort chlamydia and gonorrhea infections, respectively. The Army branch, those aged 17-19 years, females, non-Hispanic black service members, junior enlisted ranks, and single/never-married service members had the highest crude rates of initial chlamydia and gonorrhea infection, and (single/never-married service members excepted) highest adjusted relative risk of repeat chlamydia infection.

Postdeployment Respiratory Health Care Encounters Following Deployment to Kabul, Afghanistan: A Retrospective Cohort Study.

Inhalational hazards are numerous in operational environments. A retrospective cohort study was conducted to investigate associations between deployment to Kabul, Afghanistan and subsequent respiratory health among U.S. military personnel. The study population consisted of personnel who deployed to Kabul, select Operation Enduring Freedom locations, personnel stationed in the Republic of Korea, and U.S.-stationed personnel. Incidence rate ratios (IRRs) were estimated for respiratory symptoms, signs, and ill-defined conditions, asthma, and chronic obstructive pulmonary disease. A significantly elevated rate of symptoms, signs, and ill-defined conditions was observed among Kabul-deployed personnel compared to personnel deployed or stationed in Bagram (IRR 1.12; 95% confidence interval [CI], 1.05-1.19), Republic of Korea (IRR 1.20; 95% CI, 1.10-1.31), and the United States (IRR 1.52; 95% CI, 1.43-1.62). A statistically elevated rate of asthma was observed among personnel deployed to Kabul, relative to U.S.-stationed personnel (IRR 1.61; 95% CI, 1.22-2.12). Statistically significant rates were not observed for chronic obstructive pulmonary disease among Kabul-deployed personnel compared to other study groups. These findings suggest that deployment to Kabul is associated with an elevated risk of postdeployment respiratory symptoms and new-onset asthma.