A unified approach to molecular epidemiology investigations: tools and patterns in California as a case study for endemic shigellosis

<p>Abstract</p> <p>Background</p> <p>Shigellosis causes diarrheal disease in humans from both developed and developing countries, and multi-drug resistance is an emerging problem. The objective of this study is to present a unified approach that can be used to characterize endemic and outbreak patterns of shigellosis using use a suite of epidemiologic and molecular techniques. The approach is applied to a California case study example of endemic shigellosis at the population level.</p> <p>Methods</p> <p>Epidemiologic patterns were evaluated with respect to demographics, multi-drug resistance, antimicrobial resistance genes, plasmid profiles, and pulsed-field gel electrophoresis (PFGE) fingerprints for the 43 <it>Shigella </it>isolates obtained by the Monterey region health departments over the two year period from 2004-2005.</p> <p>Results</p> <p>The traditional epidemiologic as well as molecular epidemiologic findings were consistent with endemic as compared to outbreak shigellosis in this population. A steady low level of cases was observed throughout the study period and high diversity was observed among strains. In contrast to most studies in developed countries, the predominant species was <it>Shigella flexneri </it>(51%) followed closely by <it>S. sonnei </it>(49%). Over 95% of <it>Shigella </it>isolates were fully resistant to three or more antimicrobial drug subclasses, and 38% of isolates were resistant to five or more subclasses. More than half of <it>Shigella </it>strains tested carried the <it>tetB</it>, <it>catA</it>, or <it>bla</it>_TEMgenes for antimicrobial resistance to tetracycline, chloramphenicol, and ampicillin, respectively.</p> <p>Conclusion</p> <p>This study shows how epidemiologic patterns at the host and bacterial population levels can be used to investigate endemic as compared to outbreak patterns of shigellosis in a community. Information gathered as part of such investigations will be instrumental in identifying emerging antimicrobial resistance, for developing treatment guidelines appropriate for that community, and to provide baseline data with which to compare outbreak strains in the future.</p

Frequency of isolation of various subtypes and antimicrobial resistance of Shigella from urban slums of Karachi, Pakistan

Objectives: Shigellosis remains a major public health problem in developing countries. Antimicrobial resistance has complicated the empirical treatment. Knowledge of serotypes is crucial in vaccine development, as cross-protection between various serotypes is limited. Therefore we conducted a prospective study to determine the frequency of isolation of Shigella serotypes and antimicrobial resistance. Methods: Stool samples from 8155 individuals, collected through a surveillance study conducted in four slums of Karachi from January 2002 to March 2004, were cultured. Results: Shigella was isolated in 394 (4.8%) of 8155 Patients presenting with diarrhea. Two hundred and forty-two (62%) isolates were Shigella flexneri, 72 (18%) were Shigella sonnei, 43 (11%) were Shigella boydii, and 37 (9%) were Shigella dysenteriae. Thirteen S. flexneri serotypes were identified, of which the most frequent were 2a (38), 6 (37), and 1b (25), followed by 2b (23). Only 22 (5.6%) Shigella isolates were found to be pan-susceptible. Large proportions of isolates were resistant to cotrimoxazole (89% S. flexneri, 81% S. dysenteriae, 80% S. sonnei, and 56% S. boydii) and ampicillin (87% S. flexneri, 68% S dysenteriae, 35% S. boydii, and 4% S. sonnei). Conclusion: Concurrent circulation of multiple strains with high resistance is worrying and mandates surveillance at the national level to facilitate the control of shigellosis

Towards Rational Use of Antibiotics for Suspected Secondary Infections in Buruli Ulcer Patients

<p>Background: The emerging disease Buruli ulcer is treated with streptomycin and rifampicin and surgery if necessary. Frequently other antibiotics are used during treatment.</p><p>Methods/Principal Findings: Information on prescribing behavior of antibiotics for suspected secondary infections and for prophylactic use was collected retrospectively. Of 185 patients that started treatment for Buruli ulcer in different centers in Ghana and Benin 51 were admitted. Forty of these 51 admitted patients (78%) received at least one course of antibiotics other than streptomycin and rifampicin during their hospital stay. The median number (IQR) of antibiotic courses for admitted patients was 2 (1, 5). Only twelve patients received antibiotics for a suspected secondary infection, all other courses were prescribed as prophylaxis of secondary infections extended till 10 days on average after excision, debridement or skin grafting. Antibiotic regimens varied considerably per indication. In another group of BU patients in two centers in Benin, superficial wound cultures were performed. These cultures from superficial swabs represented bacteria to be expected from a chronic wound, but 13 of the 34 (38%) S. aureus were MRSA.</p><p>Conclusions/Significance: A guide for rational antibiotic treatment for suspected secondary infections or prophylaxis is needed. Adherence to the guideline proposed in this article may reduce and tailor antibiotic use other than streptomycin and rifampicin in Buruli ulcer patients. It may save costs, reduce toxicity and limit development of further antimicrobial resistance. This topic should be included in general protocols on the management of Buruli ulcer.</p>

Enteric bacterial pathogens in children with diarrhea in Niger: diversity and antimicrobial resistance.

Although rotavirus is the leading cause of severe diarrhea among children in sub-Saharan Africa, better knowledge of circulating enteric pathogenic bacteria and their antimicrobial resistance is crucial for prevention and treatment strategies.As a part of rotavirus gastroenteritis surveillance in Maradi, Niger, we performed stool culture on a sub-population of children under 5 with moderate-to-severe diarrhea between April 2010 and March 2012. Campylobacter, Shigella and Salmonella were sought with conventional culture and biochemical methods. Shigella and Salmonella were serotyped by slide agglutination. Enteropathogenic Escherichia coli (EPEC) were screened by slide agglutination with EPEC O-typing antisera and confirmed by detection of virulence genes. Antimicrobial susceptibility was determined by disk diffusion. We enrolled 4020 children, including 230 with bloody diarrhea. At least one pathogenic bacterium was found in 28.0% of children with watery diarrhea and 42.2% with bloody diarrhea. Mixed infections were found in 10.3% of children. EPEC, Salmonella and Campylobacter spp. were similarly frequent in children with watery diarrhea (11.1%, 9.2% and 11.4% respectively) and Shigella spp. were the most frequent among children with bloody diarrhea (22.1%). The most frequent Shigella serogroup was S. flexneri (69/122, 56.5%). The most frequent Salmonella serotypes were Typhimurimum (71/355, 20.0%), Enteritidis (56/355, 15.8%) and Corvallis (46/355, 13.0%). The majority of putative EPEC isolates was confirmed to be EPEC (90/111, 81.1%). More than half of all Enterobacteriaceae were resistant to amoxicillin and co-trimoxazole. Around 13% (46/360) Salmonella exhibited an extended-spectrum beta-lactamase phenotype.This study provides updated information on enteric bacteria diversity and antibiotic resistance in the Sahel region, where such data are scarce. Whether they are or not the causative agent of diarrhea, bacterial infections and their antibiotic resistance profiles should be closely monitored in countries like Niger where childhood malnutrition pre-disposes to severe and invasive infections