John Crump | University of Otago (original) (raw)

Papers by John Crump

Nature genetics, Jan 11, 2015

The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many... more The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is appl...

Objectives. We evaluated the cost-effectiveness of fee-based and free testing strategies at an HI... more Objectives. We evaluated the cost-effectiveness of fee-based and free testing strategies at an HIV voluntary counseling and testing (VCT) program integrated into a community-based AIDS service organization in Moshi, Tanzania. Methods. We waived the usual fee schedule during a 2-week free, advertised VCT campaign; analyzed the number of clients testing per day during prefree, free, and postfree testing periods; and

Journal of the International Association of Physicians in AIDS Care (JIAPAC), 2007

Antiretroviral treatment literacy leads to greater HIV testing and treatment and antiretroviral t... more Antiretroviral treatment literacy leads to greater HIV testing and treatment and antiretroviral treatment adherence. Among northern Tanzanian subjects, antiretroviral treatment awareness was only 17%. Factors associated with low antiretroviral treatment literacy included having exchanged money or gifts for sex, living in rural areas, having more than 2 children, and having a primary education only. Previous HIV testing was protective against low antiretroviral treatment literacy. These results support refocusing HIV education efforts and increasing synergy between HIV prevention and treatment programs.

Credible measures of disease incidence are necessary to guide typhoid fever control efforts. In E... more Credible measures of disease incidence are necessary to guide typhoid fever control efforts. In Egypt, incidence estimates have been derived from hospital-based syndromic surveillance, which may not represent the popu- lation with typhoid fever. To determine the population-based incidence of typhoid fever in Fayoum Governorate (pop. 2,240,000), we established laboratory-based surveillance at five tiers of health care. Incidence estimates were

ABSTRACT Data on nontuberculous mycobacterial (NTM) disease in sub-Saharan Africa are limited. Du... more ABSTRACT Data on nontuberculous mycobacterial (NTM) disease in sub-Saharan Africa are limited. During 2006-2008, we identified 3 HIV-infected patients in northern Tanzania who had invasive NTM; 2 were infected with "Mycobacterium sherrisii" and 1 with M. avium complex sequevar MAC-D. Invasive NTM disease is present in HIV-infected patients in sub-Saharan Africa.

The American journal of tropical medicine and hygiene, 2007

We evaluated enteric infection serology as an alternative outcome measure to diarrhea prevalence ... more We evaluated enteric infection serology as an alternative outcome measure to diarrhea prevalence in a randomized controlled trial of household-based drinking water treatment; 492 households were randomly assigned to 5 household-based water treatment interventions or control. Individuals were followed weekly over 52 weeks to measure diarrhea prevalence. Study subjects of age <or= 6 months and < 24 months had blood drawn at entry and exit from the study or age cohort. Serologic assays for Cryptosporidium parvum, Giardia intestinalis, enterotoxigenic Escherichia coli (ETEC), and Norovirus were done. Of 343 subjects eligible for the study, the proportions of subjects experiencing serologic responses were 56% for Norovirus, 24% for C. parvum, 10% for ETEC, and 16% for G. intestinalis. Serologic response was associated with increased diarrhea prevalence only for G. intestinalis (P = 0.0134). Serologic response to the antigens tested for G. intestinalis but not for Norovirus, C. parv...

Genome research, 2014

Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in t... more Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI ("sequence-based ultrarapid pathogen…

Tropical Medicine & International Health, 2007

To investigate the risk factors for infection with endemic typhoid fever in the Samarkand region ... more To investigate the risk factors for infection with endemic typhoid fever in the Samarkand region of Uzbekistan. Case-control study of culture-confirmed bloodstream infection with Salmonella Typhi. Patients were compared to age-matched community controls. Salmonella Typhi isolates were tested for antimicrobial susceptibility. We enrolled 97 patients and 192 controls. The median age of patients was 19 years. In a conditional regression model, consumption of unboiled surface water outside the home [adjusted odds ratio (aOR)=3.0, 95% confidence interval (CI)=1.1-8.2], use of antimicrobials in the 2 weeks preceding onset of symptoms (aOR=12.2, 95% CI 4.0-37.0), and being a student (aOR=4.0, 95% CI 1.4-11.3) were independently associated with typhoid fever. Routinely washing vegetables (aOR 0.06, 95% CI 0.02-0.2) and dining at a tea-house (aOR 0.4, 95% CI 0.2-1.0) were associated with protection against illness. Salmonella Typhi resistant to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole was identified in 6 (15%) of 41 isolates tested. Endemic typhoid fever in Uzbekistan is transmitted by contaminated water. Recent use of antimicrobials also increased risk of infection. Targeted efforts at improving drinking water quality, especially for students and young adults, are likely to decrease transmission of typhoid fever. Measures to decrease the unnecessary use of antimicrobials would be expected to reduce the risk of typhoid fever and decrease the spread of multiple drug-resistant Salmonella Typhi.

Journal of Virological Methods, 2009

Journal of Clinical Microbiology, 2004

Serologic testing is essential for the diagnosis of some infectious diseases and yet is fraught w... more Serologic testing is essential for the diagnosis of some infectious diseases and yet is fraught with potential pitfalls. All parts of the diagnostic process must be optimized to ensure that serologic tests perform adequately. Recognizing that a lack of clinical data and correctly timed, paired sera frequently led to uninterpretable serology results at our laboratory, we developed and implemented simple acceptability criteria for serologic tests. We assessed the impact of these criteria by comparing submissions and results for the year before and the year after implementation of the criteria. The number of serologic tests performed declined by 25% after implementation of the acceptability criteria, despite an increase in requests for serologic tests. Inappropriate testing of acute-phase sera alone fell from 49 to 0% (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001) for the tests monitored. Appropriate submission of paired sera rose from 9 to 19% (P = 0.006). The proportion of results classified as interpretable rose from 52 to 100% (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001). We recommend that acceptability criteria be developed and applied to samples submitted to clinical microbiology laboratories for serologic testing.

Journal of Clinical Microbiology, 2003

Journal of Clinical Microbiology, 2008

Journal of Applied Microbiology, 2004

JAIDS Journal of Acquired Immune Deficiency Syndromes, 2009

Epidemiology and Infection, 2003

Escherichia coli O157 infections cause an estimated 60 deaths and 73000 illnesses annually in the... more Escherichia coli O157 infections cause an estimated 60 deaths and 73000 illnesses annually in the United States. A marked summer peak in incidence is largely unexplained. We investigated an outbreak of E. coli O157 infections at an agricultural fair in Ohio and implicated consumption of beverages made with fairground water and sold by a geographically localized group of vendors who were all on the same branch of the fairground water distribution system. To examine county fair attendance as a risk factor for infection, we conducted two further epidemiological studies. In the first, we enhanced surveillance for E. coli O157 infections in 15 Northeast Ohio counties during the 2000 agricultural fair season and showed increased risk of E. coli O157 infection among fair attendees. In the second study, we examined Ohio Public Health Laboratory Information Service (PHLIS) data for 1999 using a time-varying covariate proportional hazards model and demonstrated an association between agricult...