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Biomedical subjects

Robert H Gilman

Publications and source records attributed to Robert H Gilman.

At least 19 recordsLinked to original sources
PubMed2025

Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.

BACKGROUND: The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where antibiotic consumption is exceptionally common. OBJECTIVES: We characterized the effects of antibiotics commonly used by Peruvian children (i.e. amoxicillin, azithromycin, cefalexin, trimethoprim/sulfamethoxazole) on the α-diversity, β-diversity and abundance of gut genera and antibiotic resistance genes (ARGs) from 3 to 16 months. METHODS: This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-19. Stools collected at 3, 6, 7, 9, 12 and 16 months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40 662 observations) to tabulate the number of antibiotic courses consumed in the 30 days prior to stool sampling. Using linear mixed models, we examined associations of recent antibiotic use with richness, diversity and abundance of gut genera and ARGs over time. RESULTS: Each additional recent antibiotic course decreased Bifidobacterium and Dialister abundance and increased Veillonella abundance, although gut richness and diversity were not affected. Recent use of amoxicillin, azithromycin, cefalexin or trimethoprim/sulfamethoxazole, specifically, did not impact gut microbiome measures. Amoxicillin, azithromycin and trimethoprim/sulfamethoxazole significantly enriched multiple ARGs and amoxicillin use significantly increased total ARGs. CONCLUSIONS: Common antibiotics like amoxicillin and azithromycin appear to be key drivers of the paediatric gut resistome. Resistome perturbations appeared to be stronger, or persist for longer, than gut microbiome effects in this middle-income country setting.

Humans↗
PubMed2025

Detection and characterization of neonatal cytomegalovirus through nanopore sequencing using flongle flow cells: Pilot study in Philadelphia, Pennsylvania.

BACKGROUND: Cytomegalovirus (CMV) remains a significant infection in neonates and its early detection can aid with further treatment (antiviral, audiology). However, current diagnostics do not provide genetic information. OBJECTIVE: We explored the use of the portable and comprehensive sequencing method from Oxford Nanopore Technologies, utilizing low-cost Flongle flow cells to detect and perform sequence-level characterization of neonatal urine samples that tested positive for CMV by PCR. STUDY DESIGN: We performed a pilot study based on a retrospective cohort study of neonates who were positive for CMV by PCR, who were admitted at two birth hospitals in Philadelphia, PA. We leveraged deep and long-read sequencing results to analyze the reads in two forms: by comparing them against a reference-based strain and by reconstructing the genome through de novo assembly with phylogenetic tree analysis. RESULTS: We assayed seven clinical samples, including a positive and negative control sample, from newborns ranging from 23 weeks' gestation to term, with testing performed for microcephaly, hearing test results, small gestational age, and thrombocytopenia. Each sample showed multiple differences compared to the reference strain, and the phylogenetic tree analysis of the de novo assembly depicted the genetic diversity of the samples. CONCLUSION: This pilot study shows that nanopore sequencing with low-cost Flongle flow cells can detect and characterize CMV strains from clinical neonatal urine samples. This, coupled with current screening and diagnostic criteria, could further our genomic understanding of neonatal CMV, such as viral genome diversity, genotype-phenotype associations, and spread of strains.

Humans↗
PubMed2007

Prevalence of sexually transmitted infections and high-risk sexual behaviors in heterosexual couples attending sexually transmitted disease clinics in Peru.

OBJECTIVES: The objectives of this study were to determine the prevalence of sexually transmitted infection (STIs) in heterosexual couples and the sexual behaviors associated with their acquisition. GOAL: The goal of this study was to better direct educational efforts to decrease STI among heterosexual couples in Lima, Peru. STUDY DESIGN: We conducted a case-control study in 195 heterosexual couples without HIV infection who attended 2 sexually transmitted disease clinics in Lima, Peru. A case was defined as an individual with one or more newly diagnosed STIs such as gonorrhea, chlamydia, trichomoniasis, herpes simplex, syphilis, mycoplasma, or ureaplasma. RESULTS: Thirty-three percent of individuals (41 men and 89 women) had at least one STI and 26 couples (13%) had the same STI detected. Men who have sex with men (MSM) accounted for 13% of all men, had higher rate of STIs and higher risk behaviors than non-MSM. Ureaplasma infection was the most prevalent STI found in both men and women and was associated with oral sexual contact. In heterosexual pairs, condom use during anal sex occurred less than 10% of the time. CONCLUSIONS: The heterosexual couples in sexually transmitted disease clinics have high-risk behaviors and STIs are frequent. The educational effort concerning prevention of STIs requires higher effort.

Adolescent↗
PubMed2006

Microscopic-observation drug-susceptibility assay for the diagnosis of TB.

BACKGROUND: New diagnostic tools are urgently needed to interrupt the transmission of tuberculosis and multidrug-resistant tuberculosis. Rapid, sensitive detection of tuberculosis and multidrug-resistant tuberculosis in sputum has been demonstrated in proof-of-principle studies of the microscopic-observation drug-susceptibility (MODS) assay, in which broth cultures are examined microscopically to detect characteristic growth. METHODS: In an operational setting in Peru, we investigated the performance of the MODS assay for culture and drug-susceptibility testing in three target groups: unselected patients with suspected tuberculosis, prescreened patients at high risk for tuberculosis or multidrug-resistant tuberculosis, and unselected hospitalized patients infected with the human immunodeficiency virus. We compared the MODS assay head-to-head with two reference methods: automated mycobacterial culture and culture on Löwenstein-Jensen medium with the proportion method. RESULTS: Of 3760 sputum samples, 401 (10.7%) yielded cultures positive for Mycobacterium tuberculosis. Sensitivity of detection was 97.8% for MODS culture, 89.0% for automated mycobacterial culture, and 84.0% for Löwenstein-Jensen culture (P<0.001); the median time to culture positivity was 7 days, 13 days, and 26 days, respectively (P<0.001), and the median time to the results of susceptibility tests was 7 days, 22 days, and 68 days, respectively. The incremental benefit of a second MODS culture was minimal, particularly in patients at high risk for tuberculosis or multidrug-resistant tuberculosis. Agreement between MODS and the reference standard for susceptibility was 100% for rifampin, 97% for isoniazid, 99% for rifampin and isoniazid (combined results for multidrug resistance), 95% for ethambutol, and 92% for streptomycin (kappa values, 1.0, 0.89, 0.93, 0.71, and 0.72, respectively). CONCLUSIONS: A single MODS culture of a sputum sample offers more rapid and sensitive detection of tuberculosis and multidrug-resistant tuberculosis than the existing gold-standard methods used.

Adult↗
PubMed2006

Postmortem findings and opportunistic infections in HIV-positive patients from a public hospital in Peru.

There is a paucity of HIV autopsy data from South America and none that document the postmortem findings in patients with HIV/AIDS in Peru. The purpose of this autopsy study was to determine the spectrum of opportunistic infections and the causes of mortality in HIV-positive patients at a public hospital in Lima. Clinico-epidemiological information regarding HIV infection in Peru is also reviewed. Sixteen HIV-related hospital postmortems, performed between 1999 and 2004, were included in this retrospective analysis. The primary cause of death was established in 12 patients: one died of neoplasia and 11 of infectious diseases, including 3 from pulmonary infection, 7 from disseminated infection, and 2 from central nervous system infection (one case had dual pathology). Opportunistic infections were identified in 14 cases, comprising cytomegalovirus, histoplasmosis, cryptococcosis, toxoplasmosis, Pneumocystis pneumonia, aspergillosis, tuberculosis, varicella zoster virus, and cryptosporidiosis. Fourteen patients had at least one AIDS-related disease that had been neither clinically suspected nor diagnosed premortem. Moreover, 82% of the diagnoses considered to be of important clinical significance had not been suspected antemortem. The spectrum and frequency of certain opportunistic infections differed from other South American autopsy studies, highlighting the importance of performing HIV/AIDS postmortems in resource-limited countries where locally specific disease patterns may be observed.

AIDS-Related Opportunistic Infections↗
PubMed2006

Improved recovery of Mycobacterium tuberculosis from children using the microscopic observation drug susceptibility method.

OBJECTIVE: The diagnosis of pulmonary tuberculosis presents challenges in children, because symptoms are nonspecific, sputa are not accessible, and Mycobacterium tuberculosis cultures and smears often are negative. The Microscopic Observation Drug Susceptibility technique is a simple, inexpensive method for Mycobacterium tuberculosis isolation with superior speed and sensitivity over Lowenstein-Jensen culture in studies of adults with pulmonary tuberculosis. The objective of this study was to determine whether Microscopic Observation Drug Susceptibility culture can improve the sensitivity and the speed of Mycobacterium tuberculosis recovery among Peruvian children with symptoms suggestive of pulmonary tuberculosis. METHODS: Two specimens of each type (gastric aspirate, nasopharyngeal aspirate, and stool specimens) were collected from each patient, examined by auramine stain, and cultured by Microscopic Observation Drug Susceptibility and Lowenstein-Jensen techniques. Patients (n = 165) were enrolled between April 2002 and February 2004 at the Instituto de Salud del Niño, the major pediatric hospital in Lima, Peru. Inclusion criteria were age < or = 12 years, Stegen-Toledo clinical score > or = 5 points, and absence of antituberculous therapy. The main outcome measurements were (1) proportion of specimens that were culture positive by Microscopic Observation Drug Susceptibility versus Lowenstein-Jensen and (2) days required for positive culture result, stratified by specimen type and auramine stain result. RESULTS: Fifteen (9%) patients had at least 1 positive Mycobacterium tuberculosis culture (from stool in 3 cases, nasopharyngeal aspirate in 8 cases, and gastric aspirate in 15 cases). Thirty-eight culture-positive specimens were obtained (22 gastric aspirate, 12 nasopharyngeal aspirates, and 4 stools). Microscopic Observation Drug Susceptibility provided significantly more positive cultures than Lowenstein-Jensen (33 of 38 specimens culture positive by Microscopic Observation Drug Susceptibility vs 21 of 38 by Lowenstein-Jensen). This was attributed to enhanced recovery of Mycobacterium tuberculosis from auramine-negative specimens (19 of 23 by Microscopic Observation Drug Susceptibility vs 9 of 23 by Lowenstein-Jensen), in contrast to similar detection rates for the 2 tests with auramine-positive samples. Similar results were found for analyses that were limited to gastric aspirates. Isolation was faster by Microscopic Observation Drug Susceptibility than Lowenstein-Jensen. CONCLUSIONS: Isolation of Mycobacterium tuberculosis from children with suspected pulmonary tuberculosis by Microscopic Observation Drug Susceptibility demonstrated greater yield and faster recovery than by Lowenstein-Jensen method, significantly improving local capabilities to detect pediatric tuberculosis in resource-poor settings.

Bacteriological Techniques↗
PubMed2006

Infrequent MODS TB culture cross-contamination in a high-burden resource-poor setting.

One obstacle to wider use of rapid liquid culture-based tuberculosis diagnostics such as the microscopic observation drug susceptibility (MODS) assay is concern about cross-contamination. We investigated the rate of laboratory cross-contamination in MODS, automated MBBacT, and Lowenstein-Jensen (LJ) cultures performed in parallel, through triangulation of microbiologic (reculturing stored samples), molecular (spoligotype/RFLP), and clinical epidemiologic data. At least 1 culture was positive for Mycobacterium tuberculosis for 362 (11%) of 3416 samples; 53 were regarded as potential cross-contamination suspects. Cross-contamination accounted for 17 false-positive cultures from 14 samples representing 0.41% (14/3416) and 0.17% (17/10248) of samples and cultures, respectively. Positive predictive values for MODS, MBBacT (bioMérieux, Durham, NC), and LJ were 99.1%, 98.7%, and 99.7%, and specificity was 99.9% for all 3. Low rates of cross-contamination are achievable in mycobacterial laboratories in resource-poor settings even when a large proportion of samples are infectious and highly sensitive liquid culture-based diagnostics such as MODS are used.

Cost of Illness↗
PubMed2006

Understandings of reproductive tract infections in a peri-urban pueblo joven in Lima, Peru.

BACKGROUND: Control programs for Reproductive Tract Infections (RTIs) typically focus on increasing awareness of risks associated with different forms of sexual contact, and pay little attention to how or why people may link RTIs to other features of their physical or social environments. This paper describes how women in a peri-urban pueblo joven located in the coastal desert surrounding Lima, Peru conceptualize the links between RTIs, sexual behaviour, personal hygiene, and the adverse environment in which they live. METHODS: We combined qualitative interviews and a participatory voting exercise to examine social and physical environmental influences on RTIs and gynaecologic symptom interpretation. RESULTS: Knowledge of RTIs in general was limited, although knowledge of AIDS was higher. Perceived causes of RTIs fell into three categories: sexual contact with infected persons, personal hygiene and exposure to the contaminated physical environment, with AIDS clearly related to sexual contact. The adverse environment is thought to be a major contributor to vaginal discharge, "inflamed ovaries" and urinary tract infection. The more remote parts of this periurban squatter settlement, characterized by blowing sand and dust and limited access to clean water, are thought to exhibit higher rates of RTIs as a direct result of the adverse environment found there. Stigma associated with RTIs often keeps women from seeking care or obtaining information about gynaecologic symptoms, and favours explanations that avoid mention of sexual practices. CONCLUSION: The discrepancy between demonstrated disease risk factors and personal explanations influenced by local environmental conditions and RTI-related stigma poses a challenge for prevention programs. Effective interventions need to take local understandings of RTIs into account as they engage in dialogue with communities about prevention and treatment of RTIs.

Journal Article↗
PubMed2006

Neurocysticercal antigens stimulate chemokine secretion from human monocytes via an NF-kappaB-dependent pathway.

Neurocysticercosis, infection with larval Taenia solium, is a common, serious neuroparasitic infection. Larval degeneration results in inflammatory cell influx and granuloma formation which leads to clinical symptomatology. The role of chemokines in such cell influx is unknown. We demonstrate that monocyte stimulation by T. solium larval antigen (TsAg) results in a differential profile of CXCL8/IL-8 (146.5+/-8.5ng/ml after 24h), CCL2/MCP-1 (267+/-4 ng/ml after 48 h) and CCL3/MIP-1alpha (1.72+/-0.43 ng/ml after 8 h) secretion. There was coordinate mRNA accumulation reaching maximum at 1h for CCL3 and 2 h for CXCL8 and CCL2. TsAg induced maximal nuclear binding of p65, p50 and c-rel subunits of the transcriptional regulator NF-kappaB by 2 h. IkappaBalpha but not IkappaBbeta was degraded within 10 min before resynthesis by 2 h. Pre-treatment with the broad-spectrum NF-kappaB inhibitor pyrrolidine dithiocarbamate caused complete abrogation of TsAg-induced CCL2 secretion (p=0.005) and 91% reduction of CXCL8 secretion (p=0.0003). TsAg was unable to induce CXCL8 promoter activity in Toll-like receptor (TLR)-2 or TLR-4/MD-2 transfected HeLa cells in the absence of lectins or other adaptor molecules. In summary, our data demonstrate that TsAg induces chemokine secretion via specific pathways dependent on NF-kappaB but not TLR-4/TLR-2, and indicate a potential mechanism whereby larval degeneration results in brain inflammation.

Animals↗
PubMed2006

La cuerda dulce--a tolerability and acceptability study of a novel approach to specimen collection for diagnosis of paediatric pulmonary tuberculosis.

BACKGROUND: Recent data demonstrate the utility of the string test for the diagnosis of sputum-scarce HIV-associated TB in adults. We hypothesized that, if well-tolerated by children, this simple tool might offer a breakthrough in paediatric TB diagnosis. Thus the objective of this study, undertaken in the paediatric service of the Hospital Nacional Dos de Mayo, Lima, Perú, was to determine the tolerability and acceptability of the string test to paediatric TB suspects, their parents and nursing staff. METHODS: 22 paediatric subjects aged 3-14 years (median 8) under investigation for TB were invited to undergo 2 string tests (four-hour downtime each). Subjective and objective pain and discomfort rating scales were used to assess the perception of the subject, parent and attending nurse. RESULTS: Patients as young as 4 years tolerated the procedure extremely well with 84% willing to undergo a second procedure. Peak discomfort at the time of swallowing and of string retrieval was mild (30% of maximum possible score) and brief as judged by visual analogue ratings and objective indicators. Good concordance of parent/child and objective/subjective ratings strengthened the validity of these findings. CONCLUSION: The string test is well tolerated and achievable for most paediatric TB suspects as young as 4 years. A formal prospective paediatric efficacy study is now needed.

Adolescent↗
PubMed2006

Clinical correlates of tuberculosis co-infection in HIV-infected children hospitalized in Peru.

INTRODUCTION: In developing countries, tuberculosis (TB) is responsible for almost 250,000 deaths among children yearly. Active TB in children with human immunodeficiency virus (HIV) infection is difficult to diagnose and progresses rapidly to death. The aim of this preliminary study was to investigate the prevalence and clinical correlates of TB-related illness among HIV-infected children admitted to an infectious diseases ward in Peru, a country where TB is highly endemic. METHOD: Forty-seven HIV-infected children admitted for a suspected infectious process in a Peruvian hospital were investigated for evidence of clinical tuberculosis by auramine stain, culture, and polymerase chain reaction (PCR) of clinical specimens. RESULTS: Eight children (17%) had evidence of tuberculosis, including five with positive cultures and three with positive PCR tests only. Weight loss was the only feature associated with a positive test for tuberculosis. Radiological changes were very common in both TB-positive and TB-negative groups and these changes were not useful to identify TB-positive cases. CONCLUSIONS: Weight loss may be used to identify high-risk HIV positive children who require more aggressive evaluation for tuberculosis. Radiological changes were common in both TB-positive and TB-negative groups.

AIDS-Related Opportunistic Infections↗
PubMed2006

Taenia solium and Taenia ovis: stage-specific expression of the vaccine antigen genes, TSOL18, TSOL16, and homologues, in oncospheres.

Recombinant antigens that have been cloned from Taenia solium and Taenia ovis have been shown to be highly effective when used as vaccines against cysticercosis in the intermediate hosts. This study investigated the presence of mRNA encoding the TSOL18 and TSOL16 antigens in different life-cycle stages of T. solium, and their related homologues in T. ovis. Reverse transcription-PCR and Southern blotting demonstrated that the antigens are stage-specifically expressed in the oncosphere. The apparent absence of expression of TSOL18 in the metacestode life-cycle stage suggests that the vaccine based on this antigen targets exclusively the early stages in the development of the parasite.

Animals↗
PubMed2006

Characterization and cloning of T24, a Taenia solium antigen diagnostic for cysticercosis.

The third and final diagnostic antigen of the lentil lectin purified glycoproteins (LLGP) extracted from the larval stage of Taenia solium has been characterized, cloned, and expressed. T24 is an integral membrane protein that belongs to the tetraspanin superfamily. It migrates at a position corresponding to 24-kDa and as a homodimer at 42-kDa. Antibodies from cysticercosis patients recognize secondary structure epitopes that are dependent upon correctly formed disulfide bonds. A portion of T24, the large, extracellular loop domain, was expressed in an immunologically reactive form in insect cells. When tested in a Western blot assay with a large battery of serum samples, this protein, T24H, has a sensitivity of 94% (101/107), for detecting cases of cysticercosis with two or more viable cysts, and a specificity of 98% (284/290). The identification and expression of T24H sets the stage for the development of an ELISA suitable for testing single samples and for large-scale serosurveys that is not dependent upon the isolation and purification of antigens from parasite materials.

Amino Acid Sequence↗
PubMed2006

Aegicerin, the first oleanane triterpene with wide-ranging antimycobacterial activity, isolated from Clavija procera.

An ethanol extract of the Peruvian plant Clavija procera, a member of the rare Theophrastaceae family, was fractionated using a colorimetric bioassay-guided protocol against Mycobacterium tuberculosis (MTB), yielding the oleanane triterpenoid aegicerin (1) as the active constituent. Its MIC values ranged between 1.6 and 3.12 microg/mL against 37 different sensitive and resistant MTB strains (1 H37Rv, 21 susceptible clinical isolates, 2 INH-resistant clinical isolates, and 13 MDR clinical isolates).

Animals↗
PubMed2006

Development of a normal human immunoglobulin G standard curve for enzyme-linked immunosorbent assay: use for comparison of antigen efficacy.

Internal standard reference curves are used in enzyme-linked immunosorbent assay (ELISA) plates to control for inter- and intra-assay variance. To compare the diagnostic potential of multiple T. solium antigens on an unbiased, universal scale, we have created a standard curve using normal, human immunoglobulin G (hIgG). The hIgG curve is inexpensive and simple to prepare, and remains stable at 5 degrees C for at least one year, with a coefficient of variance of less than 10%. The hIgG standard curve has proven a critical tool for the comparison of several diagnostic antigens slated for assay development.

Animals↗
PubMed2006

Effectiveness of enterobacterial repetitive intergenic consensus PCR and random amplified polymorphic DNA fingerprinting for Helicobacter pylori strain differentiation.

We compared the robustness and discriminatory power of the enterobacterial repetitive intergenic consensus (ERIC) and random amplified polymorphic DNA (RAPD) fingerprinting methods for detecting cases of mixed Helicobacter pylori infection in Peruvian shantytown residents. H. pylori isolates from 63 participants were cultured, and five single colonies and a pool of additional colonies from each participant were analyzed by ERIC-PCR and by RAPD tests with four 10-nucleotide primers (one primer per reaction). There was 94% agreement between the ERIC and RAPD profiles in classifying sets of isolates as uniform versus closely related but not identical versus probably unrelated, indicating a high kappa statistic of 0.8942. Subtle differences in related ERIC or RAPD patterns likely reflect gene transfer between strains, recombination, and/or mutation, whereas markedly different patterns reflect infection by unrelated strains. At least half of infected shantytown residents seemed to carry more than one H. pylori strain, although in 19 of 31 persons, the strains were closely related. Three RAPD tests, each with a different primer, were needed to achieve the sensitivity of one ERIC test. ERIC-PCR constitutes a resource- and time-efficient method for H. pylori strain differentiation.

Bacterial Typing Techniques↗
PubMed2006

Longitudinal analysis of cryptosporidium species-specific immunoglobulin G antibody responses in Peruvian children.

Cryptosporidium species are ubiquitous in the environment and are frequently detected in the stools of children who live where sanitation conditions are poor. To better characterize the immune response to these parasites, we monitored immunoglobulin G (IgG) antibody levels in a cohort of children from Lima, Peru. Two new enzyme-linked immunosorbent assays based on the C. parvum (bovine, subtype IIa) Iowa strain 17-kDa and 27-kDa antigens were used to measure IgG antibody levels in longitudinal serum samples. Antibody responses were detected during infections with C. parvum, C. felis, and C. meleagridis and with four different subtypes of C. hominis. We also noted that the magnitude of the antibody response was related to the number of previous infections and that older children generally had higher levels of antibodies to the two C. parvum antigens. Antibody responses were not associated with infections with either Cyclospora sp. or Giardia sp. We believe the antibody assays will be important tools for monitoring the success of future public health interventions.

Age Factors↗