Infectious disease epidemiology

Mapping populations a risk: improving spatial demographic data for infectious disease modeling and metric derivation

by Audrey Dorelien

Comparison of community-acquired pneumonia due to methicillin-resistant and methicillin-susceptible Staphylococcus aureus producing the Panton-Valentine …

by Dimitrios Matthaiou

Respiratory infections-Incidence, characteristics and outcomes of patients with severe community acquired-MRSA pneumonia

by Dimitrios Matthaiou

Worldwide prevalence of head lice

by Dimitrios Matthaiou

A Social Network Analysis Approach to the Examination of Algonquian and Iroquois Political and Kinship Organization

by Brian Jones

Based on paper delivered at the SAA 2009

This paper utilizes recent advantages in Social Network Analysis software to examine differences in the structures... more This paper utilizes recent advantages in Social Network Analysis software to examine differences in the structures (topology) of Algonquian and Iroquois social networks.  These social networks were modeled in a simplified manner by looking at just two core variables that define connections between actors in the society: kinship and political organization.  The actors consist not of individuals, but of core family units that have both political and kinship relations with other family units.  The models examine 4,096 actor family units representing approximately 33,000 individuals.  This number is arbitrary, but likely represents the coastal population of Native southern New England, and perhaps three-fourths the population of the League of the Iroquois.  After establishing the general characteristics of these networks, I model the effects of population loss on their structural integrity by randomly removing a proportion of families from each.  The results of the Social Network Analysis strongly suggest that the underlying political and kinship organizations of these two societies resulted in significant differences in their ability to maintain cohesiveness in the face of population loss.

Microevolution of Pandemic Vibrio parahaemolyticus Assessed by the Number of Repeat Units in Short Sequence Tandem Repeat Regions

by Ronnie Gavilan

Katherine García, Ronnie G. Gavilán, Manfred G. Höfle, Jaime Martínez-Urtaza, Romilio T. Espejo. 2012 PlosONE

The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea... more The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea outbreaks related to seafood consumption in Southeast Asia, and later worldwide. Isolates of this strain constitutes a clonal complex, and their effectual differentiation is possible by comparison of their variable number tandem repeats (VNTRs). The differentiation of the isolates by the differences in VNTRs will allow inferring the population dynamics and microevolution of this strain but this requires knowing the rate and mechanism of VNTRs' variation. Our study of mutants obtained after serial cultivation of clones showed that mutation rates of the six VNTRs examined are on the order of 10−4 mutant per generation and that difference increases by stepwise addition of single mutations. The single stepwise mutation (SSM) was deduced because mutants with 1, 2, 3, or more repeat unit deletions or insertions follow a geometric distribution. Plausible phylogenetic trees are obtained when, according to SSM, the genetic distance between clusters with different number of repeats is assessed by the absolute differences in repeats. Using this approach, mutants originated from different isolates of pandemic V. parahaemolyticus after serial cultivation are clustered with their parental isolates. Additionally, isolates of pandemic V. parahaemolyticus from Southeast Asia, Tokyo, and northern and southern Chile are clustered according their geographical origin. The deepest split in these four populations is observed between the Tokyo and southern Chile populations. We conclude that proper phylogenetic relations and successful tracing of pandemic V. parahaemolyticus requires measuring the differences between isolates by the absolute number of repeats in the VNTRs considered.

Comparison of Mathematical Models and Development of a Hybrid Approach for the Simulation and Forecast of Influenza Epidemics within Heterogeneous …

by štefan emrich

Risk factors for sporadic shigellosis, FoodNet 2005

by Sanghyuk Shin

Foodborne Pathogens and Disease
Published in Volume: 7 Issue 7: July 4, 2010

Background: An estimated 450,000 cases of shigellosis occur annually in the United States. Outbreaks have been... more Background: An estimated 450,000 cases of shigellosis occur annually in the United States. Outbreaks have been associated with food, water, child daycare centers, and men who have sex with men. However, for sporadic infections, which account for the majority of cases, risk exposures are poorly characterized.

Methods: Foodborne Diseases Active Surveillance Network (FoodNet) conducts active, laboratory-based shigellosis surveillance in 10 US sites. We interviewed cases with illness onset during 2005 about exposures during the week before symptom onset using a standardized questionnaire. The proportion of patients who denied nonfood risks was used to estimate the burden attributable to foodborne transmission.

Results: Overall, 1494 cases were identified. The approximate incidence was 3.9/100,000, with the highest rates among children aged 1–4 years (16.4) and Hispanics (8.4). Of the 929 cases interviewed, 223 (24%) reported international travel in the week before symptom onset. Of the 626 nontraveling cases with complete risk factor information, 298 (48%) reported exposure to daycare or a household member with diarrhea; 99 (16%) reported drinking untreated water or recreational exposure to water; and 16 (3%) reported sexual contact with a person with diarrhea. Two hundred and fifty-nine (41%) denied all nonfood exposures examined.

Conclusions: Sporadic shigellosis is most common among young children and Hispanics. Common exposures include international travel and contact with ill persons or daycare. However, more than one-third of US shigellosis cases annually might be due to food consumed in the United States.

Risk factors for sporadic shigellosis, FoodNet 2005

by Sanghyuk Shin

Foodborne Pathogens and Disease
Published in Volume: 7 Issue 7: July 4, 2010

Background: An estimated 450,000 cases of shigellosis occur annually in the United States. Outbreaks have been... more Background: An estimated 450,000 cases of shigellosis occur annually in the United States. Outbreaks have been associated with food, water, child daycare centers, and men who have sex with men. However, for sporadic infections, which account for the majority of cases, risk exposures are poorly characterized.

Methods: Foodborne Diseases Active Surveillance Network (FoodNet) conducts active, laboratory-based shigellosis surveillance in 10 US sites. We interviewed cases with illness onset during 2005 about exposures during the week before symptom onset using a standardized questionnaire. The proportion of patients who denied nonfood risks was used to estimate the burden attributable to foodborne transmission.

Results: Overall, 1494 cases were identified. The approximate incidence was 3.9/100,000, with the highest rates among children aged 1–4 years (16.4) and Hispanics (8.4). Of the 929 cases interviewed, 223 (24%) reported international travel in the week before symptom onset. Of the 626 nontraveling cases with complete risk factor information, 298 (48%) reported exposure to daycare or a household member with diarrhea; 99 (16%) reported drinking untreated water or recreational exposure to water; and 16 (3%) reported sexual contact with a person with diarrhea. Two hundred and fifty-nine (41%) denied all nonfood exposures examined.

Conclusions: Sporadic shigellosis is most common among young children and Hispanics. Common exposures include international travel and contact with ill persons or daycare. However, more than one-third of US shigellosis cases annually might be due to food consumed in the United States.

Gender-specific association of smoking and latent tuberculosis infection among marginalized populations in Tijuana, Mexico

by Sanghyuk Shin

more http://www.bc.lung.ca/association_and_services/documents/02Shin-Gender-SpecificAssocationofSmokingandLatentTuberculosisInfectionAmong.pdf

Shin SS1,2, Laniado-Laborin R3, Lozada R4, Cuevas-Mota J2, Burgos JL2, Rodwell TC2, Novotny TE1, Garfein RS2

1San Diego State University, San Diego, CA, USA
2University of California San Diego, San Diego, California, USA
3Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico
4Patronato Pro-COMUSIDA, Tijuana, Baja California, Mexico

BACKGROUND: We investigated the association between smoking and latent tuberculosis infection (LTBI) among groups at risk for HIV in Tijuana, Mexico.
DESIGN/METHODS: We conducted a cross-sectional survey among injection drug users (IDUs), drug users who never injected (DUs), homeless persons, and female sex workers (FSWs) aged >18 years. Interferon-gamma release assays and clinical measures were used to determine LTBI.
RESULTS: Of 503 participants, 300 (60.0%) were men; and 232 (46.1%), 207 (41.2%), 280 (55.7%), and 115 (22.9%) reported being IDU, DU, homeless and FSW, respectively. Overall, 148 (72.9%) women and 248 (82.7%) men reported smoking daily during the past six months, and smoked a mean of 13.1 and 12.2 cigarettes per day, respectively. LTBI prevalence was 49.3% among women and 62.0% among men. Smokers had higher LTBI prevalence compared to non-smokers among women (Prevalence Ratio [PR]=1.81; 95% CI=1.19, 2.76) but not among men (PR=0.87; 95% CI=0.71, 1.07). LTBI prevalence increased with the number of cigarettes smoked per day among women (p=0.002) but not among men (p=0.245). Using multivariate regression to control for age and incarceration history, LTBI prevalence remained higher for smokers compared with non-smokers among women (PR=1.65; 95% CI=1.09, 2.52) but not among men (PR=0.93; 95% CI=0.77, 1.13).
CONCLUSION: Smoking and LTBI were common among marginalized populations in Tijuana. Tuberculosis control efforts in these populations should include LTBI treatment and smoking cessation. Additional research is needed to understand gender differences in smoking and LTBI.

Hydro-epidemiology: the emergence of a research agenda

by Roger Falconer - Cardiff University

Paper 113:  Kay, D. and Falconer, R. A. 2008. Hydro-epidemiology: the emergence of a research agenda. Environmental Fluid Mechanics. 8(5-6), 451-459.

Abstract
There is a growing international awareness of the health risks associated with water, and particularly... more Abstract
There is a growing international awareness of the health risks associated with water, and particularly in developing countries.  For example: (i) a child dies in Africa every 30s due to malaria - a disease related to stagnant water, (ii) every year flooding causes many deaths world-wide, with infant mortality due to diarrhea from contaminated flood waters posing the biggest threat, and (iii) poor sanitation and its relation to hepatitis A continues to be a serious problem.  A revealing measure of the extent of such global problems is that more than half of the hospital beds in the world today are occupied by people with water-related diseases.  Addressing these issues mandates an interdisciplinary approach by the world’s scientific and engineering community.  In this spirit a workshop was held in Phoenix to provide a forum where epidemiologists, hydraulics researchers and other stakeholders of varied backgrounds (e.g., policy makers, environmental groups etc.) could all participate in a debate on a future agenda for hydro-epidemiology.  The principal outcome of the workshop was a significant appreciation of the potential for interdisciplinary research and development in hydro-epidemiology and the major contribution that hydraulics professionals could offer, in partnership with the public health community, in addressing such water related disease control and prevention challenges.

Simulations of infectious diseases on networks

by Graham Poulter

Risk of infection from needle reuse at a phlebotomy center

by Tomás Aragón

Am J Public Health. 2001 Apr;91(4):636-8. PubMed PMID: 11291380; PubMed Central PMCID: PMC1446637.

Survival of meningococci outside of the host: implications for acquisition

by Claire Swain

Co-authored with Dr Diana Martin, published in Epidemiology and Infection

Plasmodium falciparum parasitaemia described by a new mathematical model

by Hans H. Diebner

Parasitology 122, 379-391 (2001). Coauthors: Louis Molineaux, Martin Eichner, William E. Collins, Geoffrey M. Jeffery and Klaus Dietz.

A new mathematical model of Plasmodium falciparum asexual parasitaemia is formulated and fitted to 35 malaria therapy... more A new mathematical model of Plasmodium falciparum asexual parasitaemia is formulated and fitted to 35 malaria therapy cases making a spontaneous recovery after primary inoculation. Observed and simulated case-histories are compared with respect to 9 descriptive statistics. The simulated courses of parasitaemia are more realistic than any previously published. The model uses a discrete time-step of 2 days. Its realistic behaviour was achieved by the following combination of features (i) intra-clonal antigenic variation, (ii) large variations of the variants' baseline growth rate, depending on both variant and case, (iii) innate autoregulation of the asexual parasite density, variable among cases, (iv) acquired variant-specific immunity and (v) acquired variant-transcending immunity, variable among cases. Aspects of the model's internal behaviour, concerning variant dynamics, as well as the respective contributions of the three control mechanisms (iii) ± (v), are displayed. Some implications for pathogenesis and control are discussed.

Genesis, sequestration and survival of Plasmodium falciparum gametocytes: parameter estimates from fitting a model to malariatherapy data

by Hans H. Diebner

Transactions of the Royal Society of Tropical Medicine and Hygiene 95, 497-501 (2001). Coauthors: Martin Eichner, Louis Molineaux, William E.Collins, Geoffrey M. Jeffery and Klaus Dietz.

Modelling the transition of asexual blood stages of Plasmodium falciparum to gametocytes

by Hans H. Diebner

J. Theo. Biol. 202, 113-127 (2000). Coauthors: Martin Eichner, Louis Molineaux, William E. Collins, Geoffrey M. Jeffery and Klaus Dietz.

Wealth inequality and tuberculosis elimination in Europe

by Jonathan Suk

Host age, sex, and reproductive seasonality affect nematode parasitism in wild Japanese macaques

by Andrew J. J. MacIntosh

Gram-positive Toxic Shock Syndromes: A Pathophysiological Review

by Andrew Ferguson

The Lancet Infectious Diseases,  Volume 9, Issue 5, Pages 281 - 290, May 2009 . doi:10.1016/S1473-3099(09)70066-0. Co-authored with Dr. E. Lappin

Toxic shock syndrome (TSS) is an acute, multi-system, toxin-mediated illness, often resulting in multi-organ failure.... more Toxic shock syndrome (TSS) is an acute, multi-system, toxin-mediated illness, often resulting in multi-organ failure. It represents the most fulminant expression of a spectrum of diseases caused by toxin-producing strains of Staphylococcus aureus and Streptococcus pyogenes (group A streptococcus). The importance of Gram-positive organisms as pathogens is increasing, and TSS is likely to be underdiagnosed in patients with staphylococcal or group A streptococcal infection who present with shock. TSS results from the ability of bacterial toxins to act as superantigens, stimulating immune-cell expansion and rampant cytokine expression in a manner that bypasses normal MHC-restricted antigen processing. A repetitive cycle of cell stimulation and cytokine release results in a cytokine avalanche that causes tissue damage, disseminated intravascular coagulation, and organ dysfunction. Specific therapy focuses on early identification of the illness, source control, and administration on antimicrobial agents including drugs capable of suppressing toxin production (eg, clindamycin, linezolid). Intravenous immunoglobulin has the potential to neutralise superantigen and to mitigate subsequent tissue damage.