Dataset Information

Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya.

ABSTRACT: Understanding the dynamics of infection and carriage of typhoid in endemic settings is critical to finding solutions to prevention and control. In a 3-year case-control study, we investigated typhoid among children aged <16 years (4670 febrile cases and 8549 age matched controls) living in an informal settlement, Nairobi, Kenya. 148 S. Typhi isolates from cases and 95 from controls (stool culture) were identified; a carriage frequency of 1 %. Whole-genome sequencing showed 97% of cases and 88% of controls were genotype 4.3.1 (Haplotype 58), with the majority of each (76% and 88%) being multidrug-resistant strains in three sublineages of the H58 genotype (East Africa 1 (EA1), EA2, and EA3), with sequences from cases and carriers intermingled. The high rate of multidrug-resistant H58 S. Typhi, and the close phylogenetic relationships between cases and controls, provides evidence for the role of carriers as a reservoir for the community spread of typhoid in this setting. National Institutes of Health (R01AI099525); Wellcome Trust (106158/Z/14/Z); European Commission (TyphiNET No 845681); National Institute for Health Research (NIHR); Bill and Melinda Gates Foundation (OPP1175797).

SUBMITTER: Kariuki S

PROVIDER: S-EPMC8494480 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya.

Kariuki Samuel S Dyson Zoe A ZA Mbae Cecilia C Ngetich Ronald R Kavai Susan M SM Wairimu Celestine C Anyona Stephen S Gitau Naomi N Onsare Robert Sanaya RS Ongandi Beatrice B Duchene Sebastian S Ali Mohamed M Clemens John David JD Holt Kathryn E KE Dougan Gordon G

eLife 20210913

<h4>Background</h4>Understanding the dynamics of infection and carriage of typhoid in endemic settings is critical to finding solutions to prevention and control.<h4>Methods</h4>In a 3-year case-control study, we investigated typhoid among children aged <16 years (4670 febrile cases and 8549 age matched controls) living in an informal settlement, Nairobi, Kenya.<h4>Results</h4>148 <i>S</i>. Typhi isolates from cases and 95 from controls (stool culture) were identified; a carriage frequency of 1 ...[more]

PMID: 34515028

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Project description:Background: We employed DNA microarray technology to investigate the host response to Streptococcus pneumoniae in a mouse model of asymptomatic carriage. Over a period of six weeks, we profiled transcript abundance and complexity in the Nasal Associated Lymphoid Tissue (NALT) to identify genes whose expression differed between pneumococcal-colonized and uncolonized states. Results: Colonization with S. pneumoniae altered the expression of hundreds of genes over the course of the study, demonstrating that carriage is a dynamic process characterized by increased expression of a set of early inflammatory responses, including induction of a Type 1 Interferon response, and the production of several antimicrobial factors. Subsequent to this initial inflammatory response, we observed increases in transcripts associated with T cell development and activation, as well as wounding, basement membrane remodeling, and cell proliferation. Our analysis suggests that microbial colonization induced expression of genes encoding components critical for controlling JAK/STAT signaling, including stat1, stat2, socs3, and mapk1, as well as induction of several Type 1 Interferon-inducible genes and other antimicrobial factors at the earliest stages of colonization. Conclusions: Examining multiple time points over six weeks of colonization demonstrated that asymptomatic carriage stimulates a dynamic host response characterized by temporal waves with distinct biological programs. Our data suggest that the usual response to the presence of the pneumocccus is an initial controlled inflammatory response followed by activation of host physiological processes such as response to wounding, basement membrane remodeling, and increasing cellular numbers that ultimately allow the host to maintain an intact epithelium and eventually mount a preventive adaptive immune response. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.

Project description:BackgroundTransmission of multidrug-resistant Candida auris infection has been reported in the USA. To better understand its emergence and transmission dynamics and to guide clinical and public health responses, we did a molecular epidemiological investigation of C auris cases in the USA.MethodsIn this molecular epidemiological survey, we used whole-genome sequencing to assess the genetic similarity between isolates collected from patients in ten US states (California, Connecticut, Florida, Illinois, Indiana, Maryland, Massachusetts, New Jersey, New York, and Oklahoma) and those identified in several other countries (Colombia, India, Japan, Pakistan, South Africa, South Korea, and Venezuela). We worked with state health departments, who provided us with isolates for sequencing. These isolates of C auris were collected during the normal course of clinical care (clinical cases) or as part of contact investigations or point prevalence surveys (screening cases). We integrated data from standardised case report forms and contact investigations, including travel history and epidemiological links (ie, patients that had shared a room or ward with a patient with C auris). Genetic diversity of C auris within a patient, a facility, and a state were evaluated by pairwise differences in single-nucleotide polymorphisms (SNPs).FindingsFrom May 11, 2013, to Aug 31, 2017, isolates that corresponded to 133 cases (73 clinical cases and 60 screening cases) were collected. Of 73 clinical cases, 66 (90%) cases involved isolates related to south Asian isolates, five (7%) cases were related to South American isolates, one (1%) case to African isolates, and one (1%) case to east Asian isolates. Most (60 [82%]) clinical cases were identified in New York and New Jersey; these isolates, although related to south Asian isolates, were genetically distinct. Genomic data corroborated five (7%) clinical cases in which patients probably acquired C auris through health-care exposures abroad. Among clinical and screening cases, the genetic diversity of C auris isolates within a person was similar to that within a facility during an outbreak (median SNP difference three SNPs, range 0-12).InterpretationIsolates of C auris in the USA were genetically related to those from four global regions, suggesting that C auris was introduced into the USA several times. The five travel-related cases are examples of how introductions can occur. Genetic diversity among isolates from the same patients, health-care facilities, and states indicates that there is local and ongoing transmission.FundingUS Centers for Disease Control and Prevention.

Project description:OBJECTIVE To determine incidence of and risk factors for readmissions with multidrug-resistant organism (MDRO) infections among patients with previous MDRO infection. DESIGN Retrospective cohort of patients admitted between January 1, 2006, and October 1, 2015. SETTING Barnes-Jewish Hospital, a 1,250-bed academic tertiary referral center in St Louis, Missouri. METHODS We identified patients with MDROs obtained from the bloodstream, bronchoalveolar lavage (BAL)/bronchial wash, or other sterile sites. Centers for Disease Control and prevention (CDC) and European CDC definitions of MDROs were utilized. All readmissions ≤1 year from discharge from the index MDRO hospitalization were evaluated for bloodstream, BAL/bronchial wash, or other sterile site cultures positive for the same or different MDROs. RESULTS In total, 4,429 unique patients had a positive culture for an MDRO; 3,453 of these (78.0%) survived the index hospitalization. Moreover, 2,127 patients (61.6%) were readmitted ≥1 time within a year, for a total of 5,849 readmissions. Furthermore, 512 patients (24.1%) had the same or a different MDRO isolated from blood, BAL/bronchial wash, or another sterile site during a readmission. Bone marrow transplant, end-stage renal disease, lymphoma, methicillin-resistant Staphylococcus aureus, or carbapenem-resistant Pseudomonas aeruginosa during index hospitalization were factors associated with increased risk of having an MDRO isolated during a readmission. MDROs isolated during readmissions were in the same class of MDRO as the index hospitalization 9%-78% of the time, with variation by index pathogen. CONCLUSIONS Readmissions among patients with MDRO infections are frequent. Various patient and organism factors predispose to readmission. When readmitted patients had an MDRO, it was often a pathogen in the same class as that isolated during the index admission, with the exception of Acinetobacter (~9%). Infect Control Hosp Epidemiol 2018;39:12-19.

Dataset Information

Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya.

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Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya.

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