1
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Kim S, Kim S, Choi BY, Park B. Trends for Syndromic Surveillance of Norovirus in Emergency Department Data Based on Chief Complaints. J Infect Dis 2024; 230:103-108. [PMID: 39052697 DOI: 10.1093/infdis/jiad437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/04/2023] [Accepted: 09/22/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND This study compared trends in norovirus cases to determine whether chief complaint-based emergency department (ED) visit data could reflect trends of norovirus in Korea. METHODS The ED visits from the National Emergency Department Information System database and the weekly reported number of noroviruses from the sentinel surveillance system were collected between August 2017 and December 2020. The correlation between weekly norovirus cases and weekly ED visits considering the chief complaint and discharge diagnosis code was estimated using a 3-week moving average. RESULTS In total, 6 399 774 patients with chief complaints related to digestive system disease visited an ED. A higher correlation between reported norovirus cases and ED visit with chief complaint of vomiting and discharge diagnosis code of gastroenteritis and colitis of unspecified origin or other and unspecified gastroenteritis and colitis of infectious origin was observed (R = 0.88, P < .0001). The correlation was highest for the age group 0-4 years (R = 0.89, P < .0001). However, no correlation was observed between the reported norovirus cases and the number of ED visits with norovirus identified as a discharge diagnosis code. CONCLUSIONS ED visit data considering a combination of chief complaints and discharged diagnosis code would be useful for early detection of infectious disease trends.
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Affiliation(s)
- Soyeoun Kim
- Department of Preventive Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Sohee Kim
- Department of Social Administration Science, School of Pharmacy, University of Wisconsin-Madison
| | - Bo Youl Choi
- Department of Preventive Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Boyoung Park
- Department of Preventive Medicine, Hanyang University College of Medicine, Seoul, Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University
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2
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Clay B, Fisher BG. Rehydration strategies in infants and children with acute gastroenteritis refusing or not tolerating an oral fluid challenge. Arch Dis Child 2024; 109:515-519. [PMID: 38182270 DOI: 10.1136/archdischild-2023-326449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/20/2023] [Indexed: 01/07/2024]
Affiliation(s)
- Benjamin Clay
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Benjamin Gordon Fisher
- Department of Paediatrics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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3
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Liu J, Yuan Y, Feng L, Lin C, Ye C, Liu J, Li H, Hao L, Liu H. Intestinal pathogens detected in cockroach species within different food-related environment in Pudong, China. Sci Rep 2024; 14:1947. [PMID: 38253647 PMCID: PMC10803747 DOI: 10.1038/s41598-024-52306-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Cockroaches are considered mechanical transmitters of infectious diseases, posing a threat to human health. This study assessed the potential of cockroaches in food-related environments to mechanically transmit intestinal pathogens. Cockroaches captured with traps were placed together into a low temperature refrigerator at - 80° for 2 h. Standard taxonomic keys and Fluorescent quantitative PCR techniques were applied for species identification and digestive tract etiological examination. A total of 360 cockroach traps were placed, with a positive rate of 20.8%, and 266 cockroaches were captured. In general, compared with other places and areas, the degree of infestation of cockroaches was more serious in catering places and kitchens. Blattella germanica were most found in catering places (40.2%), followed by Periplaneta fuliginosa in schools (22.2%). According to the life stage, among the 128 cockroach samples, 23 were positive for nymphs and 13 were positive for adults. There were statistically significant differences in the intestinal pathogen detection rates between nymphs and adults (P < 0.05). A total of eight intestinal pathogens were detected, and enterovirus infections were the main ones, with sapovirus being the most detected in Blattella germanica or nymph. Shiga toxin-producing Escherichia coli (STEC) was the most frequently isolated bacterium. Blastocystis hominis had the highest isolation rate. In contrast, 12 diarrhoeal disease pathogens were isolated, and the viruses and bacteria with the highest frequencies were norovirus and E. coli, respectively; no parasites were found. Blattella germanica and Periplaneta fuliginosa in food-related environments can act as potential vectors for the spread of intestinal pathogens and may pose a significant threat to public health.
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Affiliation(s)
- Jun Liu
- Pudong New Area Center for Disease Control and Prevention, Shanghai, 200136, China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136, China
| | - Yongting Yuan
- Pudong New Area Center for Disease Control and Prevention, Shanghai, 200136, China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136, China
| | - Lei Feng
- Pudong New Area Center for Disease Control and Prevention, Shanghai, 200136, China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136, China
| | - Chen Lin
- Pudong New Area Center for Disease Control and Prevention, Shanghai, 200136, China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136, China
| | - Chuchu Ye
- Pudong New Area Center for Disease Control and Prevention, Shanghai, 200136, China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136, China
| | - Jingyi Liu
- Pudong New Area Center for Disease Control and Prevention, Shanghai, 200136, China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136, China
| | - Huihui Li
- Pudong New Area Center for Disease Control and Prevention, Shanghai, 200136, China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136, China
| | - Lipeng Hao
- Pudong New Area Center for Disease Control and Prevention, Shanghai, 200136, China.
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136, China.
| | - Hanzhao Liu
- Pudong New Area Center for Disease Control and Prevention, Shanghai, 200136, China.
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, 200136, China.
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4
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Sharif N, Ahmed SN, Khandaker S, Monifa NH, Abusharha A, Vargas DLR, Díez IDLT, Castilla AGK, Talukder AA, Parvez AK, Dey SK. Multidrug resistance pattern and molecular epidemiology of pathogens among children with diarrhea in Bangladesh, 2019-2021. Sci Rep 2023; 13:13975. [PMID: 37634040 PMCID: PMC10460387 DOI: 10.1038/s41598-023-41174-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023] Open
Abstract
Antimicrobial and multidrug resistance (MDR) pathogens are becoming one of the major health threats among children. Integrated studies on the molecular epidemiology and prevalence of AMR and MDR diarrheal pathogens are lacking. A total of 404 fecal specimens were collected from children with diarrhea in Bangladesh from January 2019 to December 2021. We used conventional bacteriologic and molecular sequence analysis methods. Phenotypic and genotypic resistance were determined by disk diffusion and molecular sequencing methods. Fisher's exact tests with 95% confidence intervals (CIs) was performed. Prevalence of bacterial infection was 63% (251 of 404) among children with diarrhea. E. coli (29%) was the most prevalent. E. coli, Shigella spp., V. cholerae, and Salmonella spp., showed the highest frequency of resistance against ceftriaxone (75-85%), and erythromycin (70-75%%). About 10-20% isolates of E. coli, V. cholerae and Shigella spp. showed MDR against cephem, macrolides, and quinolones. Significant association (p value < 0.05) was found between the phenotypic and genotypic resistance. The risk of diarrhea was the highest among the patients co-infected with E. coli and rotavirus [OR 3.6 (95% CI 1.1-5.4) (p = 0.001)] followed by Shigella spp. and rotavirus [OR 3.5 (95% CI 0.5-5.3) (p = 0.001)]. This study will provide an integrated insight of molecular epidemiology and antimicrobial resistance profiling of bacterial pathogens among children with diarrhea in Bangladesh.
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Affiliation(s)
- Nadim Sharif
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Shamsun Nahar Ahmed
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Shamim Khandaker
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Nuzhat Haque Monifa
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Ali Abusharha
- Optometry Department. Applied Medical Sciences Collage, King Saud University, P. O. Box 145111, Riyadh, Saudi Arabia
| | | | | | | | - Ali Azam Talukder
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Anowar Khasru Parvez
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Shuvra Kanti Dey
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh.
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5
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Llorente MT, Escudero R, Ramiro R, Remacha MA, Martínez-Ruiz R, Galán-Sánchez F, de Frutos M, Elía M, Onrubia I, Sánchez S. Enteroaggregative Escherichia coli as etiological agent of endemic diarrhea in Spain: A prospective multicenter prevalence study with molecular characterization of isolates. Front Microbiol 2023; 14:1120285. [PMID: 37065134 PMCID: PMC10100739 DOI: 10.3389/fmicb.2023.1120285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/01/2023] [Indexed: 03/22/2023] Open
Abstract
BackgroundEnteroaggregative Escherichia coli (EAEC) is increasingly associated with domestically acquired diarrheal episodes in high-income countries, particularly among children. However, its specific role in endemic diarrhea in this setting remains under-recognized and information on molecular characteristics of such EAEC strains is limited. We aimed to investigate the occurrence of EAEC in patients with non-travel related diarrhea in Spain and molecularly characterize EAEC strains associated with illness acquired in this high-income setting.MethodsIn a prospective multicenter study, stool samples from diarrheal patients with no history of recent travel abroad (n = 1,769) were collected and processed for detection of EAEC and other diarrheagenic E. coli (DEC) pathotypes by PCR. An additional case–control study was conducted among children ≤5 years old. Whole-genome sequences (WGS) of the resulting EAEC isolates were obtained.ResultsDetection of DEC in the study population. DEC was detected in 23.2% of patients aged from 0 to 102 years, with EAEC being one of the most prevalent pathotypes (7.8%) and found in significantly more patients ≤5 years old (9.8% vs. 3.4%, p < 0.001). Although not statistically significant, EAEC was more frequent in cases than in controls. WGS-derived characterization of EAEC isolates. Sequence type (ST) 34, ST200, ST40, and ST10 were the predominant STs. O126:H27, O111:H21, and O92:H33 were the predominant serogenotypes. Evidence of a known variant of aggregative adherence fimbriae (AAF) was found in 89.2% of isolates, with AAF/V being the most frequent. Ten percent of isolates were additionally classified as presumptive extraintestinal pathogenic E. coli (ExPEC), uropathogenic E. coli (UPEC), or both, and belonged to clonal lineages that could be specifically associated with extraintestinal infections.ConclusionEAEC was the only bacterial enteric pathogen detected in a significant proportion of cases of endemic diarrhea in Spain, especially in children ≤5 years old. In particular, O126:H27-ST200, O111:H21-ST40, and O92:H33-ST34 were the most important subtypes, with all of them infecting both patients and asymptomatic individuals. Apart from this role as an enteric pathogen, a subset of these domestically acquired EAEC strains revealed an additional urinary/systemic pathogenic potential.
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Affiliation(s)
- María Teresa Llorente
- Reference and Research Laboratory on Food and Waterborne Bacterial Infections, National Center for Microbiology, Institute of Health Carlos III, Madrid, Spain
- Reference and Research Laboratory on Special Pathogens, National Center for Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - Raquel Escudero
- Reference and Research Laboratory on Special Pathogens, National Center for Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - Raquel Ramiro
- Reference and Research Laboratory on Food and Waterborne Bacterial Infections, National Center for Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - María Antonia Remacha
- Servicio de Microbiología Clínica, Complejo Asistencial Universitario de León, León, Spain
| | - Rocío Martínez-Ruiz
- Servicio de Microbiología y Parasitología, Hospital Puerta de Hierro Majadahonda, Majadahonda, Spain
| | | | - Mónica de Frutos
- Servicio de Microbiología, Hospital Universitario del Río Hortega, Valladolid, Spain
| | - Matilde Elía
- Servicio de Microbiología Clínica, Hospital Universitario de Navarra, Pamplona, Spain
| | - Isabel Onrubia
- Pediatría, Centro de Salud Valle de la Oliva, Majadahonda, Spain
| | - Sergio Sánchez
- Reference and Research Laboratory on Food and Waterborne Bacterial Infections, National Center for Microbiology, Institute of Health Carlos III, Madrid, Spain
- *Correspondence: Sergio Sánchez,
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6
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Goldshtein R, Sharon N, Yana M, Rubinstein U, Amir AZ. Bacterial resistance to commonly prescribed antibiotics was rare among children hospitalised for clinical dysentery. Acta Paediatr 2023; 112:1067-1073. [PMID: 36802093 DOI: 10.1111/apa.16717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/20/2023]
Abstract
AIM Temporal changes in common pathogens that cause clinical dysentery have been described in Europe. We aimed to describe the distribution of pathogens and their antibiotic resistance in hospitalised Israeli children. METHODS This study retrospectively studied children hospitalised for clinical dysentery, with or without a positive stool culture, from 1 January 2016 to 31 December 2019. RESULTS We diagnosed 137 patients (65% males), with clinical dysentery at a median age of 3.7 (interquartile range 1.5-8.2) years. Stools were cultured in 135 patients (99%), and the results were positive in 101 (76%). These comprised Campylobacter (44%), Shigella sonnei (27%), non-typhoid Salmonella (18%) and enteropathogenic Escherichia coli (12%). Only one of the 44 Campylobacter cultures was resistant to erythromycin and one of the 12 enteropathogenic Escherichia coli cultures was resistant to ceftriaxone. None of the Salmonella and Shigella cultures were resistant to ceftriaxone or erythromycin. We did not find any pathogens that were associated with a typical clinical presentation or laboratory results on admission. CONCLUSION The most common pathogen was Campylobacter, in line with recent European trends. Bacterial resistance for commonly prescribed antibiotics was rare, and these findings support the current European recommendations.
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Affiliation(s)
- Regina Goldshtein
- Department of Pediatrics, Laniado Hospital, Netanya, Israel.,Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Nechama Sharon
- Department of Pediatrics, Laniado Hospital, Netanya, Israel.,Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Moshe Yana
- Department of Pediatrics, Laniado Hospital, Netanya, Israel
| | - Uri Rubinstein
- Department of Pediatrics, Laniado Hospital, Netanya, Israel.,Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Achiya Z Amir
- Department of Pediatrics, Laniado Hospital, Netanya, Israel.,Institute of Pediatric Gastroenterology, Hepatology & Nutrition, Dana-Dwek Children's Hospital, Tel-Aviv Medical Center, Affiliated to Tel-Aviv University, Tel-Aviv, Israel
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7
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Umair M, Rehman Z, Haider SA, Usman M, Rana MS, Ikram A, Salman M. First report of coinfection and whole-genome sequencing of norovirus and sapovirus in an acute gastroenteritis patient from Pakistan. J Med Virol 2023; 95:e28458. [PMID: 36597899 DOI: 10.1002/jmv.28458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/20/2022] [Accepted: 01/01/2023] [Indexed: 01/05/2023]
Abstract
Acute gastroenteritis is one of the most common diseases in infants and children in developing countries including Pakistan. In Pakistan, rotavirus (RVA) is known to contribute significantly to pediatric diarrheal illness, but the contribution of other viruses is still unclear. In the current study we have identified a case of mixed infection of norovirus (NoV) and sapovirus (SaV) in a 2-year-old child with acute gastroenteritis. The sample was initially processed for the detection of group A RVA through ELISA followed by NoV using RT-PCR assay. The sample tested positive for NoV RNA and was later subjected to whole-genome sequencing using meta-genome approach on Miseq (Illumina) platform. Sequencing results revealed GII.15 genotype of NoV that clustered with viruses from China and USA from 2017 to 2021. We also retrieved the complete genome of SaV (GI.1 genotype) from the same sample and phylogenetic analysis showed clustering with strains reported from Japan, South Korea, US, and Taiwan during 2012-2016. This is the first report from Pakistan that confirms coinfection of NoV and SaV and elucidates their whole genomes. We recommend initiation of NoV and SaV surveillance program to ascertain disease burden and explore genetic diversity, especially as RVA vaccines have been included in national immunization program.
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Affiliation(s)
- Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Zaira Rehman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Syed Adnan Haider
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Usman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | | | - Aamer Ikram
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
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8
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Mitchell HD, Whitlock G, Zdravkov J, Olsson J, Silalang P, Bardsley M, Blomquist PB, Jenkins C, Thomson NR, Field N, Hughes G. Prevalence and risk factors of bacterial enteric pathogens in men who have sex with men: A cross-sectional study at the UK's largest sexual health service. J Infect 2023; 86:33-40. [PMID: 36343788 PMCID: PMC10564623 DOI: 10.1016/j.jinf.2022.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/05/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Outbreaks of bacterial enteric pathogens (BEPs) in men who have sex with men (MSM) associated with antimicrobial resistance are a public health concern. We investigated the prevalence and risk factors of BEPs in MSM to inform infection control. METHODS We conducted a cross-sectional study at a London sexual health clinic between 20/12/2017 and 06/02/2018. Residual rectal swabs from MSM attending for sexually transmitted infection (STI) testing were anonymously tested for a range of BEPs using real-time PCR. A sub-set of samples were tested for the mphA gene (a marker of azithromycin resistance). Results were linked to electronic health records. RESULTS BEPs were detected in 207 of 2116 participants, giving an overall prevalence of 9.8% (95% CI 8.5%-11.1%) ranging from 0.8% (0.4%-1.2%) for Shigella to 4.9% (4.0%-5.9%) for Enteroaggregative E. coli. MSM with BEPs were more likely to have a history of bacterial STIs (p = 0.010), to report more sexual partners (p<0.001), and among HIV-negative MSM, to report current HIV pre-exposure prophylaxis use (p<0.001). Gastrointestinal symptoms were rare (1.7%) and not associated with BEPs. 41.3% of MSM with BEPs and 14.1% of those without BEPs carried mphA (p<0.001). Among the former, this was associated with a history of bacterial STIs (51.5% vs 31.1%, p = 0.003). CONCLUSIONS One in ten MSM had a BEP detected and most did not report symptoms. MphA carriage was common, particularly among those with BEPs. Bacterial STI treatment might contribute to selection of resistant gut organisms, emphasising the need for better antimicrobial stewardship.
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Affiliation(s)
- Holly D Mitchell
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, University College London, Mortimer Market Centre, Off Capper Street, London, WC1E 6JB, UK; The National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections at University College London, UK.
| | - Gary Whitlock
- 56 Dean Street, Chelsea and Westminster Hospital National Health Service Foundation Trust, London, W1D 6AQ, UK
| | - Jey Zdravkov
- 56 Dean Street, Chelsea and Westminster Hospital National Health Service Foundation Trust, London, W1D 6AQ, UK
| | - Jenny Olsson
- 56 Dean Street, Chelsea and Westminster Hospital National Health Service Foundation Trust, London, W1D 6AQ, UK; Imperial College School of Medicine, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Panida Silalang
- Clinical and Public Health Group, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Megan Bardsley
- The National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections at University College London, UK; Clinical and Public Health Group, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Paula B Blomquist
- The National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections at University College London, UK; Clinical and Public Health Group, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Claire Jenkins
- Clinical and Public Health Group, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK; The National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool, UK
| | - Nicholas R Thomson
- Parasites and Microbes, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1SA, UK; Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Nigel Field
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, University College London, Mortimer Market Centre, Off Capper Street, London, WC1E 6JB, UK
| | - Gwenda Hughes
- The National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections at University College London, UK; Clinical and Public Health Group, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK
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9
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Benshak JA, Strachan N, Lopes B, Ramjee M, Macrae M, Forbes K. Identifying the Sources of Human Campylobacteriosis in Nigeria. Acta Trop 2022; 237:106702. [DOI: 10.1016/j.actatropica.2022.106702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/19/2022] [Accepted: 09/27/2022] [Indexed: 11/01/2022]
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10
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Donaldson AL, Harris JP, Vivancos R, O'Brien SJ. Can cases and outbreaks of norovirus in children provide an early warning of seasonal norovirus infection: an analysis of nine seasons of surveillance data in England UK. BMC Public Health 2022; 22:1393. [PMID: 35858892 PMCID: PMC9301858 DOI: 10.1186/s12889-022-13771-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/27/2022] [Indexed: 11/30/2022] Open
Abstract
Background Children are important transmitters of norovirus infection and there is evidence that laboratory reports in children increase earlier in the norovirus season than in adults. This raises the question as to whether cases and outbreaks in children could provide an early warning of seasonal norovirus before cases start increasing in older, more vulnerable age groups. Methods This study uses weekly national surveillance data on reported outbreaks within schools, care homes and hospitals, general practice (GP) consultations for infectious intestinal disease (IID), telehealth calls for diarrhoea and/or vomiting and laboratory norovirus reports from across England, UK for nine norovirus seasons (2010/11–2018/19). Lagged correlation analysis was undertaken to identify lead or lag times between cases in children and those in adults for each surveillance dataset. A partial correlation analysis explored whether school outbreaks provided a lead time ahead of other surveillance indicators, controlling for breaks in the data due to school holidays. A breakpoint analysis was used to identify which surveillance indicator and age group provided the earliest warning of the norovirus season each year. Results School outbreaks occurred 3-weeks before care home and hospital outbreaks, norovirus laboratory reports and NHS 111 calls for diarrhoea, and provided a 2-week lead time ahead of NHS 111 calls for vomiting. Children provided a lead time ahead of adults for norovirus laboratory reports (+ 1–2 weeks), NHS 111 calls for vomiting (+ 1 week) and NHS 111 calls for diarrhoea (+ 1 week) but occurred concurrently with adults for GP consultations. Breakpoint analysis revealed an earlier seasonal increase in cases among children compared to adults for laboratory, GP and NHS 111 data, with school outbreaks increasing earlier than other surveillance indicators in five out of nine surveillance years. Conclusion These findings suggest that monitoring cases and outbreaks of norovirus in children could provide an early warning of seasonal norovirus infection. However, both school outbreak data and syndromic surveillance data are not norovirus specific and will also capture other causes of IID. The use of school outbreak data as an early warning indicator may be improved by enhancing sampling in community outbreaks to confirm the causative organism.
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Affiliation(s)
- Anna L Donaldson
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK. .,Institute of Population Health, University of Liverpool, 2nd Floor, Block F, Waterhouse Buildings, 1-5 Brownlow Street, Liverpool, L69 3GL, UK. .,Field Epidemiology Service, Public Health England, Liverpool, UK.
| | - John P Harris
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK.,Institute of Population Health, University of Liverpool, 2nd Floor, Block F, Waterhouse Buildings, 1-5 Brownlow Street, Liverpool, L69 3GL, UK.,Cumbria and Lancashire Health Protection Team, Public Health England, Preston, UK
| | - Roberto Vivancos
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK.,Field Epidemiology Service, Public Health England, Liverpool, UK
| | - Sarah J O'Brien
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK.,Institute of Population Health, University of Liverpool, 2nd Floor, Block F, Waterhouse Buildings, 1-5 Brownlow Street, Liverpool, L69 3GL, UK
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11
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Mouftah SF, Pascoe B, Calland JK, Mourkas E, Tonkin N, Lefevre C, Deuker D, Smith S, Wickenden H, Hitchings MD, Sheppard SK, Elhadidy M. Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance. Microb Genom 2022; 8. [PMID: 35675117 PMCID: PMC9455717 DOI: 10.1099/mgen.0.000834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Campylobacter is the most common cause of bacterial gastroenteritis worldwide, and diarrhoeal disease is a major cause of child morbidity, growth faltering and mortality in low- and middle-income countries. Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries. In this study, we aimed to quantify the extent of gene sharing in local and global populations. We characterized the genetic diversity and accessory-genome content of a collection of Campylobacter isolates from the Cairo metropolitan area, Egypt. In total, 112 Campylobacter isolates were collected from broiler carcasses (n=31), milk and dairy products (n=24), and patients suffering from gastroenteritis (n=57). Among the most common sequence types (STs), we identified the globally disseminated host generalist ST-21 clonal complex (CC21) and the poultry specialists CC206, CC464 and CC48. Notably, CC45 and the cattle-specialist CC42 were under-represented, with a total absence of CC61. Core- and accessory-genome sharing was compared among isolates from Egypt and a comparable collection from the UK (Oxford). Lineage-specific accessory-genome sharing was significantly higher among isolates from the same country, particularly CC21, which demonstrated greater local geographical clustering. In contrast, no geographical clustering was noted in either the core or accessory genome of CC828, suggesting a highly admixed population. A greater proportion of Campylobacter coli isolates were multidrug resistant compared to Campylobacter jejuni. Our results suggest that there is more horizontal transfer of accessory genes between strains in Egypt. This has strong implications for controlling the spread of antimicrobial resistance among this important pathogen.
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Affiliation(s)
- Shaimaa F Mouftah
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Ben Pascoe
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Chiang Mai University, Chiang Mai, Thailand
| | - Jessica K Calland
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Evangelos Mourkas
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Naomi Tonkin
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Charlotte Lefevre
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Present address: Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Danielle Deuker
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Present address: Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, UK
| | - Sunny Smith
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Harry Wickenden
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | | | - Samuel K Sheppard
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.,Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
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12
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Rangaraju V, Malla BA, Milton AAP, Madesh A, Madhukar KB, Kadwalia A, Vinodhkumar OR, Kumar MS, Dubal ZB. Occurrence, antimicrobial resistance and virulence properties of thermophilic Campylobacter coli originating from two different poultry settings. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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A Hierarchical Genotyping Framework Using DNA Melting Temperatures Applied to Adenovirus Species Typing. Int J Mol Sci 2022; 23:ijms23105441. [PMID: 35628251 PMCID: PMC9141461 DOI: 10.3390/ijms23105441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 02/05/2023] Open
Abstract
Known genetic variation, in conjunction with post-PCR melting curve analysis, can be leveraged to provide increased taxonomic detail for pathogen identification in commercial molecular diagnostic tests. Increased taxonomic detail may be used by clinicians and public health decision-makers to observe circulation patterns, monitor for outbreaks, and inform testing practices. We propose a method for expanding the taxonomic resolution of PCR diagnostic systems by incorporating a priori knowledge of assay design and sequence information into a genotyping classification model. For multiplexed PCR systems, this framework is generalized to incorporate information from multiple assays to increase classification accuracy. An illustrative hierarchical classification model for human adenovirus (HAdV) species was developed and demonstrated ~95% cross-validated accuracy on a labeled dataset. The model was then applied to a near-real-time surveillance dataset in which deidentified adenovirus detected patient test data from 2018 through 2021 were classified into one of six adenovirus species. These results show a marked change in both the predicted prevalence for HAdV and the species makeup with the onset of the COVID-19 pandemic. HAdV-B decreased from a pre-pandemic predicted prevalence of up to 40% to less than 5% in 2021, while HAdV-A and HAdV-F species both increased in predicted prevalence.
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14
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Mitra S, Lo M, Saha R, Deb AK, Debnath F, Miyoshi S, Dutta S, Chawla‐Sarkar M. Epidemiology of major entero‐pathogenic viruses and genetic characterization of Group A rotaviruses among children (≤5 years) with acute gastroenteritis in eastern India, 2018‐2020. J Appl Microbiol 2022; 133:758-783. [DOI: 10.1111/jam.15594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Suvrotoa Mitra
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
| | - Mahadeb Lo
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
| | - Ritubrita Saha
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
| | - Alok K. Deb
- Division of Epidemiology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Falguni Debnath
- Division of Epidemiology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Shin‐Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences Okayama University Okayama Japan
- Collaborative Research Centre of Okayama University for Infectious Disease ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Shanta Dutta
- Regional Virus Research and Diagnostic Laboratory, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road Scheme‐XM, Beliaghata Kolkata India
| | - Mamta Chawla‐Sarkar
- Division of Virology, ICMR‐National Institute of Cholera and Enteric Diseases, P‐33, C.I.T. Road, Scheme‐XM, Beliaghata Kolkata India
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15
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Sultanoğlu H, Safi Y, Demirel ME, Demir MC, Altinsoy HB, Boğan M, Gümüşboğa H. Comparison of paracetamol and hyoscine-N-butylbromide in the treatment of abdominal pain and cramps due to acute gastroenteritis. IMC JOURNAL OF MEDICAL SCIENCE 2021. [DOI: 10.55010/imcjms.16.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background and objective: Hyoscine-N-butyl bromide (HBB) and paracetamol (acetaminophen)are widely used in emergency departments for abdominal pain and cramps. However, there is not enough data on the efficacy, safety, and superiority of each other in treating acute gastroenteritis (AGE) related abdominal pain and cramps. In this study HBB and paracetamol were compared for the treatment of abdominal pain and cramps related to acute gastroenteritis.
Materials and methods: The study was conducted in a tertiary university hospital emergency department as a prospective, randomized-controlled, and double-blind study. Intravenous (IV) 1000 mg paracetamol and IV 20 mg hyoscine-N-butyl bromide (HBB) were used to treat abdominal pain and cramps related to AGE. Visual analogue scale (VAS) was used to evaluate the degree of abdominal pain before and after treatment.
Results: HBB and paracetamol groups consisted of 123 and 158 cases respectively. In both groups, it was observed that the VAS score gradually decreased from the 0th hour to the 1st and 2nd hours (p<0.001).When comparing each time within itself, it was observed that HBB and paracetamol measurements had similar values (p>0.05). No severe side effects were observed in any of the patients.
Conclusion: HBB and paracetamol were used for symptomatic treatment in AGE patients presenting with abdominal pain and cramps. A significant reduction in pain and cramps was achieved in both patient groups. There was no difference between the two drugs in terms of treatment efficacy and side effects.
IMC J Med Sci 2022; 16(1): 009
*Correspondence: Hasan Gümüşboğa, Department of Emergency, Şehitkamil State Hospital, Gaziantep, Turkey, Posta code: 27500; Email: profhasan@hotmail.com; ORCID:0000-0003-2097-7102.
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Affiliation(s)
- Hasan Sultanoğlu
- Department of Emergency, School of Medicine, Düzce University, Düzce,Turkey
| | - Yılmaz Safi
- Department of Emergency, Necip Fazıl City Hospital, Kahramanmaraş,Turkey
| | - Mustafa Enes Demirel
- Department of Emergency, School of Medicine, Bolu Abant İzzet Baysal University,Turkey
| | - Mehmet Cihat Demir
- Department of Emergency, School of Medicine, Düzce University, Düzce,Turkey
| | - Hasan Baki Altinsoy
- Department of Radiology, School of Medicine, Düzce, Düzce University, Turkey
| | - Mustafa Boğan
- Department of Emergency, School of Medicine, Düzce University, Düzce,Turkey
| | - Hasan Gümüşboğa
- Department of Emergency, Şehitkamil State Hospital, Gaziantep, Turkey
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16
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Ondrikova N, Clough HE, Douglas A, Iturriza-Gomara M, Larkin L, Vivancos R, Harris JP, Cunliffe NA. Differential impact of the COVID-19 pandemic on laboratory reporting of norovirus and Campylobacter in England: A modelling approach. PLoS One 2021; 16:e0256638. [PMID: 34432849 PMCID: PMC8386829 DOI: 10.1371/journal.pone.0256638] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Background The COVID-19 pandemic has impacted surveillance activities for multiple pathogens. Since March 2020, there was a decline in the number of reports of norovirus and Campylobacter recorded by England’s national laboratory surveillance system. The aim is to estimate and compare the impact of the COVID-19 pandemic on norovirus and Campylobacter surveillance data in England. Methods We utilised two quasi-experimental approaches based on a generalised linear model for sequential count data. The first approach estimates overall impact and the second approach focuses on the impact of specific elements of the pandemic response (COVID-19 diagnostic testing and control measures). The following time series (27, 2015–43, 2020) were used: weekly laboratory-confirmed norovirus and Campylobacter reports, air temperature, conducted Sars-CoV-2 tests and Index of COVID-19 control measures stringency. Results The period of Sars-CoV-2 emergence and subsequent sustained transmission was associated with persistent reductions in norovirus laboratory reports (p = 0.001), whereas the reductions were more pronounced during pandemic emergence and later recovered for Campylobacter (p = 0.075). The total estimated reduction was 47% - 79% for norovirus (12–43, 2020). The total reduction varied by time for Campylobacter, e.g. 19% - 33% in April, 1% - 7% in August. Conclusion Laboratory reporting of norovirus was more adversely impacted than Campylobacter by the COVID-19 pandemic. This may be partially explained by a comparatively stronger effect of behavioural interventions on norovirus transmission and a relatively greater reduction in norovirus testing capacity. Our study underlines the differential impact a pandemic may have on surveillance of gastrointestinal infectious diseases.
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Affiliation(s)
- Nikola Ondrikova
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Institute for Risk & Uncertainty, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
| | - Helen E. Clough
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
| | - Amy Douglas
- Gastrointestinal Pathogens Unit, National Infection Service, Public Health England, London, United Kingdom
| | | | - Lesley Larkin
- Gastrointestinal Pathogens Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Roberto Vivancos
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
- Field Service, National Infection Service, Public Health England, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, United Kingdom
| | - John P. Harris
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- North West Health Protection Team, Public Health England, Liverpool, United Kingdom
| | - Nigel A. Cunliffe
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
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17
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Cleary E, Boudou M, Garvey P, Aiseadha CO, McKeown P, O'Dwyer J, Hynds P. Spatiotemporal Dynamics of Sporadic Shiga Toxin-Producing Escherichia coli Enteritis, Ireland, 2013-2017. Emerg Infect Dis 2021; 27:2421-2433. [PMID: 34424163 PMCID: PMC8386769 DOI: 10.3201/eid2709.204021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Republic of Ireland regularly reports the highest annual crude incidence rates of Shiga toxin–producing Escherichia coli (STEC) enteritis in the European Union, ≈10 times the average. We investigated spatiotemporal patterns of STEC enteritis in Ireland using multiple statistical tools. Overall, we georeferenced 2,755 cases of infection during January 2013–December 2017; we found >1 case notified in 2,340 (12.6%) of 18,641 Census Small Areas. We encountered the highest case numbers in children 0–5 years of age (n = 1,101, 39.6%) and associated with serogroups O26 (n = 800, 29%) and O157 (n = 638, 23.2%). Overall, we identified 17 space-time clusters, ranging from 2 (2014) to 5 (2017) clusters of sporadic infection per year; we detected recurrent clustering in 3 distinct geographic regions in the west and mid-west, all of which are primarily rural. Our findings can be used to enable targeted epidemiologic intervention and surveillance.
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18
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Diez Valcarce M, Kambhampati AK, Calderwood LE, Hall AJ, Mirza SA, Vinjé J. Global distribution of sporadic sapovirus infections: A systematic review and meta-analysis. PLoS One 2021; 16:e0255436. [PMID: 34411109 PMCID: PMC8376006 DOI: 10.1371/journal.pone.0255436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/15/2021] [Indexed: 02/04/2023] Open
Abstract
Acute gastroenteritis (AGE), characterized by diarrhea and vomiting, is an important cause of global mortality, accounting for 9% of all deaths in children under five years of age. Since the reduction of rotavirus in countries that have included rotavirus vaccines in their national immunization programs, other viruses such as norovirus and sapovirus have emerged as more common causes of AGE. Due to widespread use of real-time RT-PCR testing, sapovirus has been increasingly reported as the etiologic agent in both AGE outbreaks and sporadic AGE cases. We aimed to assess the role of sapovirus as a cause of endemic AGE worldwide by conducting a systematic review of published studies that used molecular diagnostics to assess the prevalence of sapovirus among individuals with AGE symptoms. Of 106 articles included, the pooled sapovirus prevalence was 3.4%, with highest prevalence among children <5 years of age (4.4%) and among individuals in community settings (7.1%). Compared to studies that used conventional RT-PCR, RT-qPCR assays had a higher pooled prevalence (5.6%). Among individuals without AGE symptoms, the pooled sapovirus prevalence was 2.7%. These results highlight the relative contribution of sapovirus to cases of AGE, especially in community settings and among children <5 years of age.
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Affiliation(s)
- Marta Diez Valcarce
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Emory University Rollins School of Public Health, Atlanta, GA, United States of America
| | - Anita K. Kambhampati
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Laura E. Calderwood
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Cherokee Nation Assurance, Arlington, VA, United States of America
| | - Aron J. Hall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Sara A. Mirza
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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19
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Carroll KJ, Jenkins C, Harvey-Vince L, Mohan K, Balasegaram S. Shiga toxin-producing Escherichia coli diagnosed by Stx PCR: assessing the public health risk of non-O157 strains. Eur J Public Health 2021; 31:576-582. [PMID: 33411922 DOI: 10.1093/eurpub/ckaa232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The implementation by diagnostic laboratories in England of polymerase chain reaction (PCR) to screen faecal specimens for Shiga toxin-producing Escherichia coli (STEC) has resulted in a significant increase in notifications mainly due to non-O157 strains. The purpose of this study was to develop an approach to public health risk assessment that prioritizes follow-up to cases caused by haemolytic uraemic syndrome (HUS) associated E. coli (HUSEC) strains and minimizes unnecessary actions. METHODS Epidemiological and microbiological data were prospectively collected from 1 November 2013 to 31 March 2017 and used to compare three risk assessment approaches. RESULTS A history of HUS/bloody diarrhoea/age under 6 years and faecal specimens positive for stx-predicted HUSEC with a diagnostic accuracy of 84% (95% CI; 81-88%). STEC isolated by Gastrointestinal Bacteria Reference Unit (GBRU) and stx2 and eae positive predicted HUSEC with a diagnostic accuracy of 99% (95% CI; 98-100%). Risk assessment combining these two tests predicts the most efficient use of resources, predicting that 18% (97/552) of cases would be eligible for follow-up at some stage, 16% (86/552) following local stx PCR results, 1% (7/552) following GBRU results of stx2 and eae status and 0.7% (4/552) following whole-genome sequencing. Follow-up could be stopped in 78% (76/97) of these cases, 97% (74/76) following second stage risk assessment. CONCLUSIONS This three-stage risk assessment approach prioritizes follow-up to HUSEC and minimizes unnecessary public health actions. We developed it into the algorithm for public health actions included in the updated PHE Guidance for management of STEC published in August 2018.
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Affiliation(s)
- K J Carroll
- Surrey and Sussex Health Protection Team, Public Health England South East, Horsham, UK
| | - C Jenkins
- National Infection Service, Public Health England, London, UK
| | - L Harvey-Vince
- Surrey County Council Public Health Department, Kingston-Upon-Thames, UK
| | - K Mohan
- Thames Valley Health Protection Team, Public Health England South East, Chilton, UK
| | - S Balasegaram
- Field Service South East & London, Public Health England, London, UK
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20
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Arnold M, Smith RP, Tang Y, Guzinski J, Petrovska L. Bayesian Source Attribution of Salmonella Typhimurium Isolates From Human Patients and Farm Animals in England and Wales. Front Microbiol 2021; 12:579888. [PMID: 33584605 PMCID: PMC7876086 DOI: 10.3389/fmicb.2021.579888] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
The purpose of the study was to apply a Bayesian source attribution model to England and Wales based data on Salmonella Typhimurium (ST) and monophasic variants (MST), using different subtyping approaches based on sequence data. The data consisted of laboratory confirmed human cases and mainly livestock samples collected from surveillance or monitoring schemes. Three different subtyping methods were used, 7-loci Multi-Locus Sequence Typing (MLST), Core-genome MLST, and Single Nucleotide Polymorphism distance, with the impact of varying the genetic distance over which isolates would be grouped together being varied for the latter two approaches. A Bayesian frequency matching method, known as the modified Hald method, was applied to the data from each of the subtyping approaches. Pigs were found to be the main contributor to human infection for ST/MST, with approximately 60% of human cases attributed to them, followed by other mammals (mostly horses) and cattle. It was found that the use of different clustering methods based on sequence data had minimal impact on the estimates of source attribution. However, there was an impact of genetic distance over which isolates were grouped: grouping isolates which were relatively closely related increased uncertainty but tended to have a better model fit.
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Affiliation(s)
- Mark Arnold
- Department of Epidemiological Sciences, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Richard Piers Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Yue Tang
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Jaromir Guzinski
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
| | - Liljana Petrovska
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Addlestone, United Kingdom
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21
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de Oliveira-Tozetto S, Santiso-Bellón C, Ferrer-Chirivella JM, Navarro-Lleó N, Vila-Vicent S, Rodríguez-Díaz J, Buesa J. Epidemiological and Genetic Characterization of Sapovirus in Patients with Acute Gastroenteritis in Valencia (Spain). Viruses 2021; 13:v13020184. [PMID: 33530573 PMCID: PMC7911121 DOI: 10.3390/v13020184] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/16/2021] [Accepted: 01/24/2021] [Indexed: 02/08/2023] Open
Abstract
Sapovirus is a common cause of acute gastroenteritis in all age groups. Sapovirus infections are seldom investigated in Spain, and its epidemiology in the country is not well known. The use of molecular diagnostic procedures has allowed a more frequent detection of sapoviruses in patients with diarrhea. A total of 2545 stool samples from patients with acute gastroenteritis attended from June 2018 to February 2020 at the Clinic University Hospital in Valencia, Spain, were analyzed by reverse transcription (RT) and real-time multiplex PCR (RT-PCR) to investigate the etiology of enteric infections. Sapovirus was the second enteric virus detected with a positive rate of 8%, behind norovirus (12.2%) and ahead of rotavirus (7.1%), astrovirus (4.9%) and enteric adenoviruses (2.9%). Most sapovirus infections occurred in infants and young children under 3 years of age (74%) with the highest prevalence in autumn and early winter. Coinfections were found in 25% of the patients with sapovirus diarrhea, mainly with other enteric viruses. Genotyping demonstrated the circulation of seven different genotypes during the study period, with a predominance of genotypes GI.1, GI.2, and GII.1. Phylogenetic analysis showed that genogroup GII strains form a cluster separated from genogroup GI and GV, being genotype GV.1 strains related to genotype GI.1 and GI.2 strains.
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Affiliation(s)
- Sibele de Oliveira-Tozetto
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Cristina Santiso-Bellón
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
- Correspondence: (C.S.-B.); (J.B.)
| | - Josep M. Ferrer-Chirivella
- Microbiology Service, INCLIVA Health Research Institute, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
| | - Noemi Navarro-Lleó
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Susana Vila-Vicent
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Jesús Rodríguez-Díaz
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Javier Buesa
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
- Microbiology Service, INCLIVA Health Research Institute, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
- Correspondence: (C.S.-B.); (J.B.)
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22
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Probst V, Datyner EK, Haddadin Z, Rankin DA, Hamdan L, Rahman HK, Spieker A, Stewart LS, Guevara C, Yepsen E, Schmitz JE, Halasa NB. Human adenovirus species in children with acute respiratory illnesses. J Clin Virol 2021; 134:104716. [PMID: 33360858 PMCID: PMC8324062 DOI: 10.1016/j.jcv.2020.104716] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/21/2020] [Accepted: 12/06/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Human adenovirus (HAdV) species B, C, and E are commonly associated with acute respiratory illnesses (ARI). We sought to determine the association between HAdV species and ARI severity in children over one respiratory season at Monroe Carell Jr. Children's Hospital at Vanderbilt. METHODS We conducted a retrospective cohort study of children with HAdV from a provider-ordered BioFire® FilmArray Respiratory Pathogen Panel 2.0 (RPP) from 05/2018-06/2019. Type-specific PCR assays for HAdV-B3, B7, B11, B14, B16, B21, HAdV-C1, C2, C5, C6, and HAdV-E4 were performed. Demographics, clinical characteristics, and outcome data were compared between HAdV species. RESULTS Of 4514 respiratory specimens collected, 2644 (59 %) had at least one pathogen detected by RPP, and 384 (15 %) were HAdV-positive; 342 (89 %) were available for research testing with 306 (89 %) specimens from unique symptomatic individuals; 237 (77 %) were positive for the following species: 104 (44 %) HAdV-B, 114 (48 %) HAdV-C, 9 (4%) HAdV-E, and 10 (4%) with co-detection between species. The majority with identified HAdV species were seen in the ED (62 %), and approximately one-third were hospitalized. Patients with HAdV-C were more likely to be younger, hospitalized, and have a higher frequency of seizures compared to HAdV-B. CONCLUSION HAdV-C and HAdV-B were the most common species detected, with differences in clinical characteristics and outcomes noted. Additional studies with larger sample sizes focusing on a high-risk pediatric population are necessary to determine if differences in illness severity across individual HAdV types exist to guide further type-specific HAdV vaccine development.
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Affiliation(s)
- Varvara Probst
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA.
| | - Emily K Datyner
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Zaid Haddadin
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Danielle A Rankin
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA; Vanderbilt Epidemiology PhD Program, Vanderbilt University School of Medicine, 1161 21st Ave S, Nashville, TN, 37232, USA
| | - Lubna Hamdan
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Herdi K Rahman
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Andrew Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, 2525 West End Ave #1100, Nashville, TN, 37203, USA
| | - Laura S Stewart
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Claudia Guevara
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Erin Yepsen
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Jonathan E Schmitz
- Departments of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1211 Medical Center Dr, Nashville, TN, 37232, USA
| | - Natasha B Halasa
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
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Mare A, Man A, Toma F, Ciurea CN, Coșeriu RL, Vintilă C, Maier AC. Hemolysin-Producing Strains among Diarrheagenic Escherichia coli Isolated from Children under 2 Years Old with Diarrheal Disease. Pathogens 2020; 9:pathogens9121022. [PMID: 33291609 PMCID: PMC7761922 DOI: 10.3390/pathogens9121022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/20/2022] Open
Abstract
Even if serotyping based on O antigens is still routinely used by most laboratories for the detection of diarrheagenic Escherichia coli, this method can provide false-positive reactions, due to the high diversity of O antigens. Molecular methods represent a valuable tool that clarifies these situations. In the Bacteriology Laboratory of Mureș County Hospital, between May 2016 and July 2019, 160 diarrheagenic E. coli strains were isolated from children under 2 years old with diarrheic disease. The strains were identified as Shiga toxin-producing E. coli (STEC)/enteropathogenic Escherichia coli (EPEC) via agglutination with polyvalent sera. STEC strains were serotyped using monovalent sera for serogroup O157. Simplex PCR was performed on the strains to determine the presence of the hlyA gene, and, for the positive ones, the hemolytic activity was tested. Antibiotic susceptibility of the identified diarrheagenic E. coli strains was also investigated. STEC strains were the most frequently identified (49.1%), followed by EPEC (40.2%). The hlyA gene was identified in 12 cases, representing 18.2% of the STEC strains. Even if the extended-spectrum β-lactamase (ESBL)-producing strains represented only 10%, a relevant percentage of multidrug-resistant (MDR) strains (24%) was identified.
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Affiliation(s)
- Anca Mare
- Department of Microbiology, Pharmacy, Sciences and Technology, George Emil Palade University of Medicine, 540142 Târgu Mureș, Romania; (A.M.); (A.M.); (F.T.)
| | - Adrian Man
- Department of Microbiology, Pharmacy, Sciences and Technology, George Emil Palade University of Medicine, 540142 Târgu Mureș, Romania; (A.M.); (A.M.); (F.T.)
| | - Felicia Toma
- Department of Microbiology, Pharmacy, Sciences and Technology, George Emil Palade University of Medicine, 540142 Târgu Mureș, Romania; (A.M.); (A.M.); (F.T.)
| | - Cristina Nicoleta Ciurea
- Department of Microbiology, Pharmacy, Sciences and Technology, George Emil Palade University of Medicine, 540142 Târgu Mureș, Romania; (A.M.); (A.M.); (F.T.)
- Correspondence: ; Tel.: +40-07-5908-3638
| | - Răzvan Lucian Coșeriu
- Infectious Diseases Laboratory, Mureș County Clinical Hospital, 540233 Târgu Mureș, Romania; (R.L.C.); (C.V.)
| | - Camelia Vintilă
- Infectious Diseases Laboratory, Mureș County Clinical Hospital, 540233 Târgu Mureș, Romania; (R.L.C.); (C.V.)
| | - Adrian Cornel Maier
- Department of Urology, Faculty of Medicine, University “Dunarea de Jos” Galați, 800008 Galați, Romania;
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Barker CR, Painset A, Swift C, Jenkins C, Godbole G, Maiden MCJ, Dallman TJ. Microevolution of Campylobacter jejuni during long-term infection in an immunocompromised host. Sci Rep 2020; 10:10109. [PMID: 32572150 PMCID: PMC7308304 DOI: 10.1038/s41598-020-66771-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/18/2020] [Indexed: 02/04/2023] Open
Abstract
Campylobacteriosis typically manifests as a short-lived, self-limiting gastrointestinal infection in humans, however prolonged infection can be seen in cases with underlying immunodeficiency. Public Health England received 25 isolates of Campylobacter jejuni from an individual with combined variable immunodeficiency over a period of 15 years. All isolates were typed and archived at the time of receipt. Whole genome sequencing (WGS) and antimicrobial susceptibility testing were performed to examine the relatedness of the isolates and to investigate the changes in the genome that had taken place over the course of the infection. Genomic typing methods were compared to conventional phenotypic methods, and revealed that the infection was caused by a single, persistent strain of C. jejuni belonging to clonal complex ST-45, with evidence of adaptation and selection in the genome over the course of the infection. Genomic analysis of sequence variants associated with antimicrobial resistance identified the genetic background behind rRNA gene mutations causing variable levels of resistance to erythromycin. This application of WGS to examine a persistent case of campylobacteriosis provides insight into the mutations and selective pressures occurring over the course of an infection, some of which have important clinical relevance.
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Affiliation(s)
- Clare R Barker
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, UK
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK
| | - Anaïs Painset
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK
| | - Craig Swift
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK
| | - Gauri Godbole
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - Martin C J Maiden
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK
| | - Timothy J Dallman
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK.
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK.
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
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25
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Mehat JW, La Ragione RM, van Vliet AHM. Campylobacter jejuni and Campylobacter coli autotransporter genes exhibit lineage-associated distribution and decay. BMC Genomics 2020; 21:314. [PMID: 32306949 PMCID: PMC7168839 DOI: 10.1186/s12864-020-6704-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/27/2020] [Indexed: 11/17/2022] Open
Abstract
Background Campylobacter jejuni and Campylobacter coli are major global causes of bacterial gastroenteritis. Whilst several individual colonisation and virulence factors have been identified, our understanding of their role in the transmission, pathogenesis and ecology of Campylobacter has been hampered by the genotypic and phenotypic diversity within C. jejuni and C. coli. Autotransporter proteins are a family of outer membrane or secreted proteins in Gram-negative bacteria such as Campylobacter, which are associated with virulence functions. In this study we have examined the distribution and predicted functionality of the previously described capC and the newly identified, related capD autotransporter gene families in Campylobacter. Results Two capC-like autotransporter families, designated capC and capD, were identified by homology searches of genomes of the genus Campylobacter. Each family contained four distinct orthologs of CapC and CapD. The distribution of these autotransporter genes was determined in 5829 C. jejuni and 1347 C. coli genomes. Autotransporter genes were found as intact, complete copies and inactive formats due to premature stop codons and frameshift mutations. Presence of inactive and intact autotransporter genes was associated with C. jejuni and C. coli multi-locus sequence types, but for capC, inactivation was independent from the length of homopolymeric tracts in the region upstream of the capC gene. Inactivation of capC or capD genes appears to represent lineage-specific gene decay of autotransporter genes. Intact capC genes were predominantly associated with the C. jejuni ST-45 and C. coli ST-828 generalist lineages. The capD3 gene was only found in the environmental C. coli Clade 3 lineage. These combined data support a scenario of inter-lineage and interspecies exchange of capC and subsets of capD autotransporters. Conclusions In this study we have identified two novel, related autotransporter gene families in the genus Campylobacter, which are not uniformly present and exhibit lineage-specific associations and gene decay. The distribution and decay of the capC and capD genes exemplifies the erosion of species barriers between certain lineages of C. jejuni and C. coli, probably arising through co-habitation. This may have implications for the phenotypic variability of these two pathogens and provide opportunity for new, hybrid genotypes to emerge.
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Affiliation(s)
- Jai W Mehat
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, UK.
| | - Roberto M La Ragione
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Arnoud H M van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, UK.
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26
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Vilcu AM, Blanchon T, Sabatte L, Souty C, Maravic M, Hanslik T, Steichen O. Cross-validation of an algorithm detecting acute gastroenteritis episodes from prescribed drug dispensing data in France: comparison with clinical data reported in a primary care surveillance system, winter seasons 2014/15 to 2016/17. BMC Med Res Methodol 2019; 19:110. [PMID: 31151387 PMCID: PMC6545010 DOI: 10.1186/s12874-019-0745-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/29/2019] [Indexed: 12/15/2022] Open
Abstract
Background This study compares an algorithm to detect acute gastroenteritis (AG) episodes from drug dispensing data to the validated data reported in a primary care surveillance system in France. Methods We used drug dispensing data collected in a drugstore database and data collected by primary care physicians involved in a French surveillance network, from season 2014/15 to 2016/17. We used an adapted version of an AG discrimination algorithm to identify AG episodes from the drugstore database. We used Pearson’s correlation coefficient to evaluate the agreement between weekly AG signals obtained from the two data sources during winter months, in the overall population, by specific age-groups and by regions. Results Correlations between AG signals for all ages were 0.84 [95%CI 0.69; 0.92] for season 2014/15, 0.87 [95%CI 0.75; 0.93] for season 2015/16 and 0.94 [95%CI 0.88; 0.97] for season 2016/17. The association between AG signals estimated from two data sources varied significantly across age groups in season 2016/17 (p-value < 0.01), and across regions in all three seasons studied (p-value < 0.01). Conclusions There is a strong agreement between the dynamic of AG activity estimated from drug dispensing data and from validated primary care surveillance data collected during winter months in the overall population but the agreement is poorer in several age groups and in several regions. Once automated, the reuse of drug dispensing data, already collected for reimbursement purposes, could be a cost-efficient method to monitor AG activity at the national level. Electronic supplementary material The online version of this article (10.1186/s12874-019-0745-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana-Maria Vilcu
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France.
| | - Thierry Blanchon
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France
| | - Laure Sabatte
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France
| | - Cécile Souty
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France
| | - Milka Maravic
- Real World Insight, IQVIA, F-92099, La Défense Cedex, France.,Assistance Publique - Hôpitaux de Paris (APHP), hôpital Lariboisière, Service de Rhumatologie, F-75010, Paris, France
| | - Thomas Hanslik
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France.,Université de Versailles Saint-Quentin-en-Yvelines, UVSQ, UFR de Médecine, F-78000, Versailles, France.,Assistance Publique - Hôpitaux de Paris (APHP), hôpital Ambroise Paré, Service de Médecine Interne, F-92100, Boulogne Billancourt, France
| | - Olivier Steichen
- Sorbonne Université, Inserm, université Paris 13, Laboratoire d'informatique médicale et d'ingénierie des connaissances en e-santé, LIMICS, F-75006, Paris, France.,Assistance Publique - Hôpitaux de Paris (APHP), hôpital Tenon, Service de Médecine Interne, F-75020, Paris, France
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27
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Carroll KJ, Harvey-Vince L, Jenkins C, Mohan K, Balasegaram S. The epidemiology of Shiga toxin-producing Escherichia coli infections in the South East of England: November 2013-March 2017 and significance for clinical and public health. J Med Microbiol 2019; 68:930-939. [PMID: 30994441 DOI: 10.1099/jmm.0.000970] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE This study describes the epidemiology of Shiga toxin-producing Escherichia coli (STEC) infections in a population in the South East of England. METHODS From 1 November 2013 to 31 March 2017 participating diagnostic laboratories reported Shiga toxin gene (stx) positive real-time PCR results to local public health teams. Stx positive faecal samples/isolates were referred to the Gastrointestinal Bacteria Reference Unit (GBRU) for confirmation by culture and typing by whole genome sequencing (WGS). Key clinical information was collected by public health teams.Results/Key findings. Altogether, 548 faecal specimens (420 were non-travel associated) were stx positive locally, 535 were submitted to the GBRU. STEC were isolated from 42 %, confirmed by stx PCR in 21 % and 37 % were PCR negative. The most common non-travel associated STEC serogroups were O157, O26, O146 and O91. The annualized incidence of confirmed STEC infections (PCR or culture) was 5.8 per 100 000. The ratio of O157 to non-O157 STEC serogroups was 1:7. The annualized incidence of non-O157 haemolytic uraemic syndrome-associated Escherichia coli (HUSEC) strains was 0.4 per 100 000. Bloody diarrhoea was reported by 58 % of cases infected with E. coli O157, 33 % of cases infected with non-O157 HUSEC strains and 12 % of other lower risk non-O157 strains. Overall, 76 % of non-O157 HUSEC isolates possessed the eae virulence gene. CONCLUSIONS HUSEC including serogroup O157 were uncommon and more likely to cause bloody diarrhoea than other STEC. The routine use of stx PCR testing can influence clinical management. Understanding the local epidemiology facilitates a proportionate public health response to STEC, based on clinical and microbiological characteristics including stx subtype(s).
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Affiliation(s)
- Kevin J Carroll
- 1 PHE South East, Surrey and Sussex HPT, Parkside, Chart Way, Horsham RH12 1XA, UK
| | - Lisa Harvey-Vince
- 1 PHE South East, Surrey and Sussex HPT, Parkside, Chart Way, Horsham RH12 1XA, UK
| | - Claire Jenkins
- 2 Gastrointestinal Bacteria Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5HT, UK
| | - Keerthi Mohan
- 3 PHE South East, Thames Valley HPT, Chilton, Oxon, OX11 0RQ, UK
| | - Sooria Balasegaram
- 4 Field Services, National Infection Service, Public Health England, London, UK
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28
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Pietsch C, Liebert UG. Intrahost viral evolution during chronic sapovirus infections. J Clin Virol 2019; 113:1-7. [DOI: 10.1016/j.jcv.2019.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/22/2018] [Accepted: 02/04/2019] [Indexed: 12/27/2022]
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29
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Human Sapovirus among Outpatients with Acute Gastroenteritis in Spain: A One-Year Study. Viruses 2019; 11:v11020144. [PMID: 30744057 PMCID: PMC6409837 DOI: 10.3390/v11020144] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/06/2019] [Accepted: 02/07/2019] [Indexed: 02/06/2023] Open
Abstract
Viral agents of human gastroenteritis affect people of all ages across the globe. As a mainly self-limiting disease, it is difficult to evaluate the real prevalence of etiological agents circulating in each region. Many of the analyzed outbreaks are caused by viruses of the family Caliciviridae, especially the genus Norovirus (NoV). Most studies have focused on other enteric viruses, leaving sapovirus (SaV) underestimated as an important emerging human threat. This one-year study analyzed clinical samples from hospital outpatients with acute gastroenteritis in Spain, with the aim of revealing the importance of human SaV as an emerging viral pathogen. A total of 2667 stools were tested using reverse transcription (RT)-qPCR to detect and quantify SaV. Sapovirus was detected in all age groups, especially in infants, children, and the elderly. The prevalence was 15.64% (417/2667), and was slightly higher in 0–2- and 3–5-year-olds (19.53% and 17.95%, respectively) and much lower in 13–18-year-olds (9.86%). Positive samples were detected throughout the year, with peaks of detection during autumn and the late winter to early spring months. The mean value for the quantified samples was 6.5 × 105 genome copies per gram of stool (GC/g) (range 2.4 × 103–6.6 × 1011 GC/g). RT-nested PCR and sequencing were used for further genotyping. Genetic characterization showed a predominance of genogroup I (GI), followed by GII and GIV. The detection of multiple genotypes suggests the circulation of different strains without any clear tendency. The results obtained suggest SaV as the second major gastroenteritis agent after NoV in the region.
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30
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Dirani G, Zannoli S, Paesini E, Farabegoli P, Dalmo B, Vocale C, Liguori G, Varani S, Sambri V. Easyscreen™ Enteric Protozoa Assay for the Detection of Intestinal Parasites: A Retrospective Bi-Center Study. J Parasitol 2019. [DOI: 10.1645/18-52] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Giorgio Dirani
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Piazzale della Liberazione 60, 47522 Pi
| | - Silvia Zannoli
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Piazzale della Liberazione 60, 47522 Pi
| | - Elena Paesini
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Piazzale della Liberazione 60, 47522 Pi
| | - Patrizia Farabegoli
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Piazzale della Liberazione 60, 47522 Pi
| | - Barbara Dalmo
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Piazzale della Liberazione 60, 47522 Pi
| | - Caterina Vocale
- Regional Reference Center for Microbiological Emergencies (CRREM), Unit of Microbiology, St. Orsola
| | - Giovanna Liguori
- Regional Reference Center for Microbiological Emergencies (CRREM), Unit of Microbiology, St. Orsola
| | - Stefania Varani
- Regional Reference Center for Microbiological Emergencies (CRREM), Unit of Microbiology, St. Orsola
| | - Vittorio Sambri
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Piazzale della Liberazione 60, 47522 Pi
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31
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Hungerford D, Vivancos R, Read JM, Bonnett LJ, Bar-Zeev N, Iturriza-Gómara M, Cunliffe NA, French N. Mitigating bias in observational vaccine effectiveness studies using simulated comparator populations: Application to rotavirus vaccination in the UK. Vaccine 2018; 36:6674-6682. [PMID: 30293764 DOI: 10.1016/j.vaccine.2018.09.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/18/2018] [Accepted: 09/21/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Measuring vaccine effectiveness (VE) relies on the use of observational study designs. However, achieving robust estimates of direct and indirect VE is frequently compromised by bias, particularly when using syndromic diagnoses of low-specificity. METHODS In order to mitigate confounding between the measured outcome and vaccine uptake, we developed a method to balance comparator populations using individual-level propensity scoring derived from the vaccine-exposed population, and applied it to the unexposed comparator population. Indirect VE was estimated by comparing the unvaccinated vaccine-exposed group with a propensity score-simulated unvaccinated, unexposed group. Direct VE was derived by removing indirect VE from the overall VE. We applied this method to an evaluation of the effectiveness of infant rotavirus vaccination in the UK. Using a general practice cohort of 45,259 live births between May 2010 and December 2015, we calculated indirect and direct VE against consultations for acute gastroenteritis using conventional and vaccination-propensity adjustment comparator populations. RESULTS The overall VE during the rotavirus-season (January-May) calculated using mixed-effects Cox regression was 30% [95% confidence intervals (95% CI: 25,35%)]. Use of conventional comparator populations resulted in implausible VE estimates -14% (95% CI: -41,7%) for direct and 29% (95% CI: 14,42%) for indirect effects. Applying our alternative method, direct VE was 26% (95% CI: 1,45%) and indirect VE was 8% (95% CI: -19,29%). CONCLUSIONS Estimating VE using propensity score simulated comparator populations, particularly for studies using routine health data with syndromic, low-specificity endpoints will aid accurate measurement of the broader public health impact of a vaccine programme.
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Affiliation(s)
- Daniel Hungerford
- The Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool L69 7BE, UK; Field Epidemiology Services, National Infection Service, Public Health England, Suite 3b, Third Floor, The Cunard Building, Water Street, Liverpool L3 1DS, UK; NIHR Health Protection Research Unit in Gastrointestinal Infections, The Farr Institute@HeRC, University of Liverpool, 2nd Floor, Block F, Waterhouse Buildings, 1-5 Brownlow Street, Liverpool L69 3GL, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool L69 7BE, UK.
| | - Roberto Vivancos
- Field Epidemiology Services, National Infection Service, Public Health England, Suite 3b, Third Floor, The Cunard Building, Water Street, Liverpool L3 1DS, UK; NIHR Health Protection Research Unit in Gastrointestinal Infections, The Farr Institute@HeRC, University of Liverpool, 2nd Floor, Block F, Waterhouse Buildings, 1-5 Brownlow Street, Liverpool L69 3GL, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool L69 7BE, UK.
| | - Jonathan M Read
- NIHR Health Protection Research Unit in Gastrointestinal Infections, The Farr Institute@HeRC, University of Liverpool, 2nd Floor, Block F, Waterhouse Buildings, 1-5 Brownlow Street, Liverpool L69 3GL, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool L69 7BE, UK; Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YW, UK.
| | - Laura J Bonnett
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool, Block F, Waterhouse Buildings, 1-5 Brownlow Street, Liverpool L69 3GL, UK.
| | - Naor Bar-Zeev
- The Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool L69 7BE, UK; International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, 415 N Washington Street 5th Floor, Baltimore, MD 21231, USA
| | - Miren Iturriza-Gómara
- The Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool L69 7BE, UK; NIHR Health Protection Research Unit in Gastrointestinal Infections, The Farr Institute@HeRC, University of Liverpool, 2nd Floor, Block F, Waterhouse Buildings, 1-5 Brownlow Street, Liverpool L69 3GL, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool L69 7BE, UK.
| | - Nigel A Cunliffe
- The Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool L69 7BE, UK.
| | - Neil French
- The Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool L69 7BE, UK.
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CapC, a Novel Autotransporter and Virulence Factor of Campylobacter jejuni. Appl Environ Microbiol 2018; 84:AEM.01032-18. [PMID: 29915112 DOI: 10.1128/aem.01032-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Campylobacter jejuni is recognized as an important causative agent of bacterial gastroenteritis in the developed world. Despite the identification of several factors contributing to infection, characterization of the virulence strategies employed by C. jejuni remains a significant challenge. Bacterial autotransporter proteins are a major class of secretory proteins in Gram-negative bacteria, and notably, many autotransporter proteins contribute to bacterial virulence. The aim of this study was to characterize the C. jejuni 81116 C8J_1278 gene (capC), predicted to encode an autotransporter protein, and examine the contribution of this factor to virulence of C. jejuni The predicted CapC protein has a number of features that are consistent with autotransporters, including the N-terminal signal sequence and the C-terminal β-barrel domain and was determined to localize to the outer membrane. Inactivation of the capC gene in C. jejuni 81116 and C. jejuni M1 resulted in reduced insecticidal activity in Galleria mellonella larvae. Furthermore, C. jejuni capC mutants displayed significantly reduced adherence to and invasion of nonpolarized, partially differentiated Caco-2 and T84 intestinal epithelial cells. Gentamicin treatment showed that the reduced invasion of the capC mutant is primarily caused by reduced adherence to intestinal epithelial cells, not by reduced invasion capability. C. jejuni capC mutants caused reduced interleukin 8 (IL-8) secretion from intestinal epithelial cells and elicited a significantly diminished immune reaction in Galleria larvae, indicating that CapC functions as an immunogen. In conclusion, CapC is a new virulence determinant of C. jejuni that contributes to the integral infection process of adhesion to human intestinal epithelial cells.IMPORTANCECampylobacter jejuni is a major causative agent of human gastroenteritis, making this zoonotic pathogen of significant importance to human and veterinary public health worldwide. The mechanisms by which C. jejuni interacts with intestinal epithelial cells and causes disease are still poorly understood due, in part, to the heterogeneity of C. jejuni infection biology. Given the importance of C. jejuni to public health, the need to characterize novel and existing virulence mechanisms is apparent. The significance of our research is in demonstrating the role of CapC, a novel virulence factor in C. jejuni that contributes to adhesion and invasion of the intestinal epithelium, thereby in part, addressing the dearth of knowledge concerning the factors involved in Campylobacter pathogenesis and the variation observed in the severity of human infection.
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Kiseleva V, Faizuloev E, Meskina E, Marova A, Oksanich A, Samartseva T, Bakhtoyarov G, Bochkareva N, Filatov N, Linok A, Ammour Y, Zverev V. Molecular-Genetic Characterization of Human Rotavirus A Strains Circulating in Moscow, Russia (2009-2014). Virol Sin 2018; 33:304-313. [PMID: 30062589 DOI: 10.1007/s12250-018-0043-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
Abstract
Enteric viruses are the most common cause of acute gastroenteritis (AGE) in young children and a significant public health problem globally. Hospital admissions of children under 5 years of age with diarrhea are primarily associated with group A rotavirus (RVA) infection. In this retrospective study, the population structure of viruses linked to AGE etiology in young children hospitalized with AGE in Moscow was evaluated, and molecular characterization of RVA strains was performed. Fecal specimens were collected from children under 5 years old hospitalized with AGE between 2009 and 2014 in Moscow, Russia. Multiplex real-time reverse transcription PCR was used to detect enteric viruses and for G/[P]-genotyping of isolated RVAs. Sequencing of RVA VP7 and VP4 cDNA fragments was used to validate the data obtained by PCR-genotyping. The main causes for hospitalization of children with AGE were RVA (40.1%), followed by noroviruses (11.4%), while adenoviruses, astroviruses, sapoviruses, enteroviruses, and orthoreoviruses were detected in 4.7%, 1.9%, 1.4%, 1.2%, and 0.2% of samples tested, respectively. Nosocomial infections, predominantly associated with RVAs and noroviruses, were detected in 24.8% of cases and occurred significantly more frequently in younger infants. The predominant RVA genotype was G4P[8], detected in 38.7% of RVA-positive cases, whereas genotypes G1P[8], G9P[8], G3P[8], and G2P[4] were found in 11.8%, 6.6%, 4.2%, and 3.3% of cases, respectively. Together, the presence of circulating RVA strains with rare VP7 and VP4 gene variants (G6 and P[9]) highlights the need to conduct continuous epidemiological monitoring of RVA infection.
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Affiliation(s)
- Victoria Kiseleva
- Department of Virology, I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - Evgeny Faizuloev
- Department of Virology, I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia. .,Faculty of Preventive Medicine and Health Organization, Russian Medical Academy of Continuous Professional Education, Moscow, 125993, Russia.
| | - Elena Meskina
- M. Vladimirsky Moscow Regional Research Clinical Institute (MONIKI), Moscow, 129110, Russia
| | - Anna Marova
- Department of Virology, I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - Alexey Oksanich
- Department of Virology, I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - Tatiana Samartseva
- Department of Virology, I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - Georgy Bakhtoyarov
- Department of Virology, I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - Natalia Bochkareva
- M. Vladimirsky Moscow Regional Research Clinical Institute (MONIKI), Moscow, 129110, Russia
| | - Nikolay Filatov
- Department of Virology, I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia.,Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Andrey Linok
- Department of Virology, I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - Yulia Ammour
- Department of Virology, I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia
| | - Vitaly Zverev
- Department of Virology, I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia.,Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
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34
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Wang MD J, Li PhD Y, Kong MD X, Li PhD H, Zhang BA Q, Jin PhD M, Wang PhD Y, Duan PhD Z. Two gastroenteritis outbreaks caused by sapovirus in Shenzhen, China. J Med Virol 2018; 90:1695-1702. [DOI: 10.1002/jmv.25236] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 05/14/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Jinjin Wang MD
- College of Food Science and TechnologyShanghai Ocean UniversityShanghai China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and Prevention Beijing China
| | - Yuan Li PhD
- Shenzhen Baoan Center for Disease Control and Prevention Shenzhen Guangdong China
| | - Xiangxu Kong MD
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and Prevention Beijing China
| | - Huiying Li PhD
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and Prevention Beijing China
| | - Qing Zhang BA
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and Prevention Beijing China
| | - Miao Jin PhD
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and Prevention Beijing China
| | - Yongjie Wang PhD
- College of Food Science and TechnologyShanghai Ocean UniversityShanghai China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and PreservationMinistry of Agriculture (Shanghai) Shanghai China
| | - Zhaojun Duan PhD
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and Prevention Beijing China
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35
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Koskinen JM, Soukka JM, Meltola NJ, Koskinen JO. Microbial identification from faces and urine in one step by two-photon excitation assay technique. J Immunol Methods 2018; 460:113-118. [PMID: 30056941 DOI: 10.1016/j.jim.2018.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/15/2018] [Accepted: 06/28/2018] [Indexed: 01/03/2023]
Abstract
Two-photon excitation fluorometry (TPX) is a separation-free bioaffinity assay technique which enables accurate diagnostic testing in microvolumes. The technology is currently commercially applied in an automated mariPOC® test system for rapid phenotypic multi-microbe detection of pathogen antigens. The first TPX applications for diagnostics were intended for respiratory infection testing from nasopharyngeal and oropharyngeal samples. Feces and urine are more complex sample matrices and contain substances that may interfere with immunoassay binding or fluorescence detection. Our objective was to study the suitability of these complex matrices in the TPX technique. As expected, feces and urine elevated fluorescence levels but the methodology has the unique property of compensating for matrix effects. Compensation allows reliable separation of specific fluorescence from the fluorescence caused by the matrix. The studied clinical samples did not contain immunoassay inhibitors. The results suggest that the methodology is robust and may provide reliable testing of feces and urine samples with high accuracy.
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Affiliation(s)
- Juha M Koskinen
- ArcDia International Ltd, Lemminkäisenkatu 32, 20520 Turku, Finland; Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland.
| | - Jori M Soukka
- ArcDia International Ltd, Lemminkäisenkatu 32, 20520 Turku, Finland
| | - Niko J Meltola
- ArcDia International Ltd, Lemminkäisenkatu 32, 20520 Turku, Finland
| | - Janne O Koskinen
- ArcDia International Ltd, Lemminkäisenkatu 32, 20520 Turku, Finland
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36
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Van Cauteren D, Le Strat Y, Sommen C, Bruyand M, Tourdjman M, Da Silva NJ, Couturier E, Fournet N, de Valk H, Desenclos JC. Estimated Annual Numbers of Foodborne Pathogen-Associated Illnesses, Hospitalizations, and Deaths, France, 2008-2013. Emerg Infect Dis 2018; 23:1486-1492. [PMID: 28820137 PMCID: PMC5572882 DOI: 10.3201/eid2309.170081] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Estimates of the annual numbers of foodborne illnesses and associated hospitalizations and deaths are needed to set priorities for surveillance, prevention, and control strategies. The objective of this study was to determine such estimates for 2008–2013 in France. We considered 15 major foodborne pathogens (10 bacteria, 3 viruses, and 2 parasites) and estimated that each year, the pathogens accounted for 1.28–2.23 million illnesses, 16,500–20,800 hospitalizations, and 250 deaths. Campylobacter spp., nontyphoidal Salmonella spp., and norovirus accounted for >70% of all foodborne pathogen–associated illnesses and hospitalizations; nontyphoidal Salmonella spp. and Listeria monocytogenes were the main causes of foodborne pathogen–associated deaths; and hepatitis E virus appeared to be a previously unrecognized foodborne pathogen causing ≈68,000 illnesses in France every year. The substantial annual numbers of foodborne illnesses and associated hospitalizations and deaths in France highlight the need for food-safety policymakers to prioritize foodborne disease prevention and control strategies.
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37
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Neuert S, Nair S, Day MR, Doumith M, Ashton PM, Mellor KC, Jenkins C, Hopkins KL, Woodford N, de Pinna E, Godbole G, Dallman TJ. Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal Salmonella enterica. Front Microbiol 2018; 9:592. [PMID: 29636749 PMCID: PMC5880904 DOI: 10.3389/fmicb.2018.00592] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/15/2018] [Indexed: 11/13/2022] Open
Abstract
Surveillance of antimicrobial resistance (AMR) in non-typhoidal Salmonella enterica (NTS), is essential for monitoring transmission of resistance from the food chain to humans, and for establishing effective treatment protocols. We evaluated the prediction of phenotypic resistance in NTS from genotypic profiles derived from whole genome sequencing (WGS). Genes and chromosomal mutations responsible for phenotypic resistance were sought in WGS data from 3,491 NTS isolates received by Public Health England’s Gastrointestinal Bacteria Reference Unit between April 2014 and March 2015. Inferred genotypic AMR profiles were compared with phenotypic susceptibilities determined for fifteen antimicrobials using EUCAST guidelines. Discrepancies between phenotypic and genotypic profiles for one or more antimicrobials were detected for 76 isolates (2.18%) although only 88/52,365 (0.17%) isolate/antimicrobial combinations were discordant. Of the discrepant results, the largest number were associated with streptomycin (67.05%, n = 59). Pan-susceptibility was observed in 2,190 isolates (62.73%). Overall, resistance to tetracyclines was most common (26.27% of isolates, n = 917) followed by sulphonamides (23.72%, n = 828) and ampicillin (21.43%, n = 748). Multidrug resistance (MDR), i.e., resistance to three or more antimicrobial classes, was detected in 848 isolates (24.29%) with resistance to ampicillin, streptomycin, sulphonamides and tetracyclines being the most common MDR profile (n = 231; 27.24%). For isolates with this profile, all but one were S. Typhimurium and 94.81% (n = 219) had the resistance determinants blaTEM-1,strA-strB, sul2 and tet(A). Extended-spectrum β-lactamase genes were identified in 41 isolates (1.17%) and multiple mutations in chromosomal genes associated with ciprofloxacin resistance in 82 isolates (2.35%). This study showed that WGS is suitable as a rapid means of determining AMR patterns of NTS for public health surveillance.
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Affiliation(s)
- Saskia Neuert
- National Institute for Health Research Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom.,Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
| | - Satheesh Nair
- Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
| | - Martin R Day
- Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
| | - Michel Doumith
- Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
| | - Philip M Ashton
- Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
| | - Kate C Mellor
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom.,London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Claire Jenkins
- National Institute for Health Research Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom.,Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
| | - Katie L Hopkins
- Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
| | - Neil Woodford
- Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
| | - Elizabeth de Pinna
- Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
| | - Gauri Godbole
- National Institute for Health Research Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom.,Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
| | - Timothy J Dallman
- National Institute for Health Research Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom.,Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kindom
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38
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Abstract
Norovirus is a leading cause of childhood vomiting and diarrhea in the United States and globally. Although most illnesses caused by norovirus are self-resolving, severe outcomes may occur from dehydration, including hospitalization and death. A vast majority of deaths from norovirus occur in developing countries. Immunocompromised children are at risk for more severe outcomes. Treatment of norovirus illness is focused on early correction of dehydration and maintenance of fluid status and nutrition. Hand hygiene, exclusion of ill individuals, and environmental cleaning are important for norovirus outbreak prevention and control, and vaccines to prevent norovirus illness are currently under development.
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Affiliation(s)
- Minesh P Shah
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road Northeast, Atlanta, GA 30329, USA.
| | - Aron J Hall
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road Northeast, Atlanta, GA 30329, USA
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39
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Hungerford D, Vivancos R, Read JM, Iturriza-Gόmara M, French N, Cunliffe NA. Rotavirus vaccine impact and socioeconomic deprivation: an interrupted time-series analysis of gastrointestinal disease outcomes across primary and secondary care in the UK. BMC Med 2018; 16:10. [PMID: 29375036 PMCID: PMC5787923 DOI: 10.1186/s12916-017-0989-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/08/2017] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Rotavirus causes severe gastroenteritis in infants and young children worldwide. The UK introduced the monovalent rotavirus vaccine (Rotarix®) in July 2013. Vaccination is free of charge to parents, with two doses delivered at 8 and 12 weeks of age. We evaluated vaccine impact across a health system in relation to socioeconomic deprivation. METHODS We used interrupted time-series analyses to assess changes in monthly health-care attendances in Merseyside, UK, for all ages, from July 2013 to June 2016, compared to predicted counterfactual attendances without vaccination spanning 3-11 years pre-vaccine. Outcome measures included laboratory-confirmed rotavirus gastroenteritis (RVGE) hospitalisations, acute gastroenteritis (AGE) hospitalisations, emergency department (ED) attendances for gastrointestinal conditions and consultations for infectious gastroenteritis at community walk-in centres (WIC) and general practices (GP). All analyses were stratified by age. Hospitalisations were additionally stratified by vaccine uptake and small-area-level socioeconomic deprivation. RESULTS The uptake of the first and second doses of rotavirus vaccine was 91.4% (29,108/31,836) and 86.7% (27,594/31,836), respectively. Among children aged < 5 years, the incidence of gastrointestinal disease decreased across all outcomes post-vaccine introduction: 80% (95% confidence interval [CI] 70-87%; p < 0.001) for RVGE hospitalisation, 44% (95% CI 35-53%; p < 0.001) for AGE hospitalisations, 23% (95% CI 11-33%; p < 0.001) for ED, 32% (95% CI 7-50%; p = 0.02) for WIC and 13% (95% CI -3-26%; p = 0.10) for GP. The impact was greatest during the rotavirus season and for vaccine-eligible age groups. In adults aged 65+ years, AGE hospitalisations fell by 25% (95% CI 19-30%; p < 0.001). The pre-vaccine risk of AGE hospitalisation was highest in the most socioeconomically deprived communities (adjusted incident rate ratio 1.57; 95% CI 1.51-1.64; p < 0.001), as was the risk for non-vaccination (adjusted risk ratio 1.54; 95% CI 1.34-1.75; p < 0.001). The rate of AGE hospitalisations averted per 1,000 first doses of vaccine was higher among infants in the most deprived communities compared to the least deprived in 2014/15 (28; 95% CI 25-31 vs. 15; 95% CI 12-17) and in 2015/16 (26; 95% CI 23-30 vs. 13; 95% CI 11-16). CONCLUSIONS Following the introduction of rotavirus vaccination, incidence of gastrointestinal disease reduced across the health-care system. Vaccine impact was greatest among the most deprived populations, despite lower vaccine uptake. Prioritising vaccine uptake in socioeconomically deprived communities should give the greatest health benefit in terms of population disease burden.
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Affiliation(s)
- Daniel Hungerford
- The Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, L69 7BE, Liverpool, UK. .,Field Epidemiology Services, Public Health England, L3 1DS, Liverpool, UK. .,NIHR Health Protection Research Unit in Gastrointestinal Infections, L69 3GL, Liverpool, UK. .,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, L69 3GL, Liverpool, UK.
| | - Roberto Vivancos
- Field Epidemiology Services, Public Health England, L3 1DS, Liverpool, UK.,NIHR Health Protection Research Unit in Gastrointestinal Infections, L69 3GL, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, L69 3GL, Liverpool, UK
| | - Jonathan M Read
- NIHR Health Protection Research Unit in Gastrointestinal Infections, L69 3GL, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, L69 3GL, Liverpool, UK.,Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Miren Iturriza-Gόmara
- The Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, L69 7BE, Liverpool, UK.,NIHR Health Protection Research Unit in Gastrointestinal Infections, L69 3GL, Liverpool, UK
| | - Neil French
- The Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, L69 7BE, Liverpool, UK
| | - Nigel A Cunliffe
- The Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, L69 7BE, Liverpool, UK.,Department of Microbiology, Alder Hey Children's NHS Foundation Trust, L12 2AP, Liverpool, UK
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40
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Newitt S, MacGregor V, Robbins V, Bayliss L, Chattaway MA, Dallman T, Ready D, Aird H, Puleston R, Hawker J. Two Linked Enteroinvasive Escherichia coli Outbreaks, Nottingham, UK, June 2014. Emerg Infect Dis 2018; 22:1178-84. [PMID: 27314432 PMCID: PMC4918187 DOI: 10.3201/eid2207.152080] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Enteroinvasive Escherichia coli (EIEC) outbreaks are uncommon in Europe. In June 2014, two EIEC outbreaks occurred in Nottingham, UK, within 2 days; outbreak A was linked to a takeaway restaurant and outbreak B to a wedding party. We conducted 2 analytical studies: a case-control study for outbreak A and a cohort study for outbreak B. We tested microbiological and environmental samples, including by using whole-genome sequencing. For both outbreaks combined, we identified 157 probable case-patients; 27 were laboratory-confirmed as EIEC O96:H19-positive. Combined epidemiologic, microbiological, and environmental findings implicated lettuce as the vehicle of infection in outbreak A, but the source of the organism remained unknown. Whole-genome sequencing identified the same organism in cases from both outbreaks, but no epidemiologic link was confirmed. These outbreaks highlight that EIEC has the capacity to cause large and severe gastrointestinal disease outbreaks and should be considered as a potential pathogen in foodborne outbreaks in Europe.
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41
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Bronowski C, Mustafa K, Goodhead I, James CE, Nelson C, Lucaci A, Wigley P, Humphrey TJ, Williams NJ, Winstanley C. Campylobacter jejuni transcriptome changes during loss of culturability in water. PLoS One 2017; 12:e0188936. [PMID: 29190673 PMCID: PMC5708674 DOI: 10.1371/journal.pone.0188936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/15/2017] [Indexed: 12/21/2022] Open
Abstract
Background Water serves as a potential reservoir for Campylobacter, the leading cause of bacterial gastroenteritis in humans. However, little is understood about the mechanisms underlying variations in survival characteristics between different strains of C. jejuni in natural environments, including water. Results We identified three Campylobacter jejuni strains that exhibited variability in their ability to retain culturability after suspension in tap water at two different temperatures (4°C and 25°C). Of the three, strains C. jejuni M1 exhibited the most rapid loss of culturability whilst retaining viability. Using RNAseq transcriptomics, we characterised C. jejuni M1 gene expression in response to suspension in water by analyzing bacterial suspensions recovered immediately after introduction into water (Time 0), and from two sampling time/temperature combinations where considerable loss of culturability was evident, namely (i) after 24 h at 25°C, and (ii) after 72 h at 4°C. Transcript data were compared with a culture-grown control. Some gene expression characteristics were shared amongst the three populations recovered from water, with more genes being up-regulated than down. Many of the up-regulated genes were identified in the Time 0 sample, whereas the majority of down-regulated genes occurred in the 25°C (24 h) sample. Conclusions Variations in expression were found amongst genes associated with oxygen tolerance, starvation and osmotic stress. However, we also found upregulation of flagellar assembly genes, accompanied by down-regulation of genes involved in chemotaxis. Our data also suggested a switch from secretion via the sec system to via the tat system, and that the quorum sensing gene luxS may be implicated in the survival of strain M1 in water. Variations in gene expression also occurred in accessory genome regions. Our data suggest that despite the loss of culturability, C. jejuni M1 remains viable and adapts via specific changes in gene expression.
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Affiliation(s)
- Christina Bronowski
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Kasem Mustafa
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Ian Goodhead
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Chloe E. James
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Charlotte Nelson
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Anita Lucaci
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Paul Wigley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Tom J. Humphrey
- Medical Microbiology and Infectious Diseases, School of Medicine, Swansea University, Swansea, United Kingdom
| | - Nicola J. Williams
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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Shane AL, Mody RK, Crump JA, Tarr PI, Steiner TS, Kotloff K, Langley JM, Wanke C, Warren CA, Cheng AC, Cantey J, Pickering LK. 2017 Infectious Diseases Society of America Clinical Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea. Clin Infect Dis 2017; 65:e45-e80. [PMID: 29053792 PMCID: PMC5850553 DOI: 10.1093/cid/cix669] [Citation(s) in RCA: 276] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 07/26/2017] [Indexed: 12/11/2022] Open
Abstract
These guidelines are intended for use by healthcare professionals who care for children and adults with suspected or confirmed infectious diarrhea. They are not intended to replace physician judgement regarding specific patients or clinical or public health situations. This document does not provide detailed recommendations on infection prevention and control aspects related to infectious diarrhea.
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Affiliation(s)
- Andi L Shane
- Division of Infectious Diseases, Department of Pediatrics, Emory University and Children’s Healthcare of Atlanta, Atlanta, Georgia
| | - Rajal K Mody
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John A Crump
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina; Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Phillip I Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Theodore S Steiner
- Nutrition, Washington University in St. Louis School of Medicine, St. Louis, MO; 5Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada
| | - Karen Kotloff
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, and the Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD
| | | | - Christine Wanke
- Division of Nutrition and Infection, Tufts University, Boston, Massachusetts,Cirle Alcantara Warren, MD
| | - Cirle Alcantara Warren
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia
| | - Allen C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Joseph Cantey
- Division of Infectious Diseases, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Larry K Pickering
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, Georgia
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43
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Infectious gastroenteritis and the need for strict contact precaution procedures in adults presenting to the emergency department: a Danish register-based study. J Hosp Infect 2017; 98:391-397. [PMID: 29128345 DOI: 10.1016/j.jhin.2017.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/03/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUND Acute infectious gastroenteritis requires contact precautions to prevent spread. On acute admission, the cause of diarrhoea is unknown, so the decision regarding which patients to isolate has to be made on clinical information with a risk of inexpedient use of contact precautions. AIM To investigate how often gastroenteritis occurs (and therefore how often the need for isolation has to be assessed) in Danish emergency departments, and how often patients have to remain on contact precautions according to the results of faecal samples. METHODS This Danish register-based retrospective cohort study on adults in Danish emergency departments used three data sources: discharge diagnoses from the Danish National Patient Register; microbiological results from faecal samples provided in the emergency department; and the causes of hospital admission based on the chief complaint. FINDINGS Among 66,885 acute admissions, 4.3% of patients had at least one feature of gastroenteritis: admission with diarrhoea as the chief complaint (1.6%); microbiological examination of faecal sample (2.8%); and discharged with a diagnosis of gastroenteritis (1.7%). Nineteen percent of those who had a faecal sample tested were found to have norovirus or Clostridium difficile, and needed to remain on strict contact precautions. CONCLUSION The initiation of contact precautions has to be assessed for 4.3% of all emergency department patients; 19% of the patients who had a faecal sample tested had highly contagious gastroenteritis and required strict contact precautions. Further studies are needed to develop tools to determine which patients to isolate.
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Kowada K, Takeuchi K, Hirano E, Toho M, Sada K. Development of a multiplex real-time PCR assay for detection of human enteric viruses other than norovirus using samples collected from gastroenteritis patients in Fukui Prefecture, Japan. J Med Virol 2017; 90:67-75. [PMID: 28845896 DOI: 10.1002/jmv.24926] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 07/27/2017] [Indexed: 11/09/2022]
Abstract
There are many varieties of gastroenteritis viruses, of which norovirus (NoV) accounts for over 90% of the viral food poisoning incidents in Japan. However, protocols for rapidly identifying other gastroenteritis viruses need to be established to investigate NoV-negative cases intensively. In this study, a multiplex real-time PCR assay targeting rotavirus A, rotavirus C, sapovirus, astrovirus, adenovirus, and enterovirus was developed using stool samples collected from gastroenteritis patients between 2010 and 2013 in Fukui Prefecture, Japan. Of the 126 samples collected sporadically from pediatric patients with suspected infectious gastroenteritis, 51 were positive for non-NoV target viruses, whereas 27 were positive for NoV, showing a high prevalence of non-NoV viruses in pediatric patients. In contrast, testing in 382 samples of 58 gastroenteritis outbreaks showed that non-NoV viruses were detected in 13 samples, with NoV in 267. Of the 267 NoV-positive patients, only two were co-infected with non-NoV target viruses, suggesting that testing for non-NoV gastroenteritis viruses in NoV-positive samples was mostly unnecessary in outbreak investigations. Given these results, multiplex real-time PCR testing for non-NoV gastroenteritis viruses, conducted separately from NoV testing, may be helpful to deal with two types of epidemiological investigations, regular surveillance of infectious gastroenteritis and urgent testing when gastroenteritis outbreaks occur.
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Affiliation(s)
- Kazuaki Kowada
- Fukui Prefectural Institute of Public Health and Environmental Science, Fukui, Japan.,University of Fukui, Fukui, Japan
| | | | - Eiko Hirano
- Fukui Prefectural Institute of Public Health and Environmental Science, Fukui, Japan
| | - Miho Toho
- Fukui Prefectural Institute of Public Health and Environmental Science, Fukui, Japan
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45
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García Vera C, García Ventura M, del Castillo Aguas G, Domínguez Aurrecoechea B, Esparza Olcina MJ, Martínez Rubio A, Mengual Gil JM. Acute bacterial gastroenteritis: 729 cases recruited by a Primary Care national network. An Pediatr (Barc) 2017. [DOI: 10.1016/j.anpede.2016.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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46
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García Vera C, García Ventura M, del Castillo Aguas G, Domínguez Aurrecoechea B, Esparza Olcina MJ, Martínez Rubio A, Mengual Gil JM. Gastroenteritis aguda bacteriana: 729 casos reclutados por una red nacional de atención primaria. An Pediatr (Barc) 2017; 87:128-134. [DOI: 10.1016/j.anpedi.2016.04.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/17/2016] [Accepted: 04/29/2016] [Indexed: 11/28/2022] Open
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47
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Hassard F, Sharp JH, Taft H, LeVay L, Harris JP, McDonald JE, Tuson K, Wilson J, Jones DL, Malham SK. Critical Review on the Public Health Impact of Norovirus Contamination in Shellfish and the Environment: A UK Perspective. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:123-141. [PMID: 28176295 PMCID: PMC5429388 DOI: 10.1007/s12560-017-9279-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 01/19/2017] [Indexed: 05/04/2023]
Abstract
We review the risk of norovirus (NoV) infection to the human population from consumption of contaminated shellfish. From a UK perspective, risk is apportioned for different vectors of NoV infection within the population. NoV spreads mainly by person-to-person contact or via unsanitary food handling. NoV also enters the coastal zone via wastewater discharges resulting in contamination of shellfish waters. Typically, NoV persists in the marine environment for several days, with its presence strongly linked to human population density, wastewater discharge rate, and efficacy of wastewater treatment. Shellfish bioaccumulate NoV and current post-harvest depuration is inefficient in its removal. While NoV can be inactivated by cooking (e.g. mussels), consumption of contaminated raw shellfish (e.g. oysters) represents a risk to human health. Consumption of contaminated food accounts for 3-11% of NoV cases in the UK (~74,000 cases/year), of which 16% are attributable to oyster consumption (11,800 cases/year). However, environmental and human factors influencing NoV infectivity remain poorly understood. Lack of standard methods for accurate quantification of infective and non-infective (damaged) NoV particles represent a major barrier, hampering identification of an appropriate lower NoV contamination limit for shellfish. Future management strategies may include shellfish quality assessment (at point of harvest or at point of supply) or harvesting controls. However, poor understanding of NoV inactivation in shellfish and the environment currently limits accurate apportionment and risk assessment for NoV and hence the identification of appropriate shellfish or environmental quality standards.
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Affiliation(s)
- Francis Hassard
- Centre for Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, UK
| | | | - Helen Taft
- School of Environment, Natural Resources & Geography, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Lewis LeVay
- Centre for Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, UK
| | - John P Harris
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, L69 3GL, UK
| | - James E McDonald
- School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Karen Tuson
- Centre for Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, UK
| | - James Wilson
- Bangor Mussel Producers Ltd., Victoria House, Plas Llwyd Terrace, Bangor, Gwynedd, LL57 1UB, UK
| | - David L Jones
- School of Environment, Natural Resources & Geography, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Shelagh K Malham
- Centre for Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, UK.
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48
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Hine JL, de Lusignan S, Burleigh D, Pathirannehelage S, McGovern A, Gatenby P, Jones S, Jiang D, Williams J, Elliot AJ, Smith GE, Brownrigg J, Hinchliffe R, Munro N. Association between glycaemic control and common infections in people with Type 2 diabetes: a cohort study. Diabet Med 2017; 34:551-557. [PMID: 27548909 DOI: 10.1111/dme.13205] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/19/2016] [Indexed: 01/03/2023]
Abstract
AIM To investigate the impact of glycaemic control on infection incidence in people with Type 2 diabetes. METHODS We compared infection rates during 2014 in people with Type 2 diabetes and people without diabetes in a large primary care cohort in the UK (the Royal College of General Practitioners Research and Surveillance Centre database). We performed multilevel logistic regression to investigate the impact of Type 2 diabetes on presentation with infection, and the effect of glycaemic control on presentation with upper respiratory tract infections, bronchitis, influenza-like illness, pneumonia, intestinal infectious diseases, herpes simplex, skin and soft tissue infections, urinary tract infections, and genital and perineal infections. People with Type 2 diabetes were stratified by good [HbA1c < 53 mmol/mol (< 7%)], moderate [HbA1c 53-69 mmol/mol (7-8.5%)] and poor [HbA1c > 69 mmol/mol (> 8.5%)] glycaemic control using their most recent HbA1c concentration. Infection incidence was adjusted for important sociodemographic factors and patient comorbidities. RESULTS We identified 34 278 people with Type 2 diabetes and 613 052 people without diabetes for comparison. The incidence of infections was higher in people with Type 2 diabetes for all infections except herpes simplex. Worsening glycaemic control was associated with increased incidence of bronchitis, pneumonia, skin and soft tissue infections, urinary tract infections, and genital and perineal infections, but not with upper respiratory tract infections, influenza-like illness, intestinal infectious diseases or herpes simplex. CONCLUSIONS Almost all infections analysed were more common in people with Type 2 diabetes. Infections that are most commonly of bacterial, fungal or yeast origin were more frequent in people with worse glycaemic control.
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Affiliation(s)
- J L Hine
- Section of Clinical Medicine and Ageing, University of Surrey, Guildford
| | - S de Lusignan
- Section of Clinical Medicine and Ageing, University of Surrey, Guildford
| | - D Burleigh
- Section of Clinical Medicine and Ageing, University of Surrey, Guildford
| | - S Pathirannehelage
- Section of Clinical Medicine and Ageing, University of Surrey, Guildford
| | - A McGovern
- Section of Clinical Medicine and Ageing, University of Surrey, Guildford
| | - P Gatenby
- Section of Clinical Medicine and Ageing, University of Surrey, Guildford
- Royal Surrey County Hospital, Guildford, Surrey, UK
| | - S Jones
- Section of Clinical Medicine and Ageing, University of Surrey, Guildford
| | - D Jiang
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - J Williams
- Section of Clinical Medicine and Ageing, University of Surrey, Guildford
| | | | - G E Smith
- Public Health England, Birmingham, UK
| | - J Brownrigg
- St George's Vascular Institute, Division of Cardiovascular Sciences, St George's University of London, London, UK
| | - R Hinchliffe
- St George's Vascular Institute, Division of Cardiovascular Sciences, St George's University of London, London, UK
| | - N Munro
- Section of Clinical Medicine and Ageing, University of Surrey, Guildford
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49
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Bergallo M, Galliano I, Montanari P, Brusin MR, Finotti S, Paderi G, Gabiano C. Development of a quantitative real-time PCR assay for sapovirus in children under 5-years-old in Regina Margherita Hospital of Turin, Italy. Can J Microbiol 2017; 63:296-302. [DOI: 10.1139/cjm-2016-0482] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gastroenteritis is a common disease in children. It is characterized by diarrhea, vomiting, abdominal pain, and fever. Sapovirus (SaV) is a causative agent of acute gastroenteritis, but it causes milder illness than do rotavirus and norovirus. There is high variability in the analytical performance of quantitative PCR-based assays among clinical laboratories. This study developed a reverse transcription real-time PCR method to detect SaV in fecal specimens collected from children under 5-years-old with acute gastroenteritis. Of 137 episodes of acute gastroenteritis, 15 (10.9%) were associated with SaV genomic detection, with a median viral load of 6.6(log10) ± 7.1(log10) genomes/mg fecal specimens. There was a significant difference in detection rate between males and females (9.48% (13/15) vs. 1.46% (2/15), p = 0.0232). Among the 15 SaV-positive cases, 6 were also positive for rotavirus. Viral RNA recovery rate ranged from 46% to 77% in the manual RNAzol protocol and from 31% to 90% in the automated Maxwell protocol. We also studied whether human genomic DNA influences the sensitivity of the assay: its presence caused a decrease in PCR sensitivity. The development of a laboratory-designed real-time PCR TaqMan assay for quantitative detection of SaV and the optimization and standardization of this assay, using stools of children with acute gastroenteritis, are described.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Martina Rosa Brusin
- Struttura Complessa, Pediatric University Regina Margherita Hospital, Piazza Polonia 94, 1016 Turin, Italy
| | - Serena Finotti
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Giulia Paderi
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Clara Gabiano
- Struttura Complessa, Pediatric University Regina Margherita Hospital, Piazza Polonia 94, 1016 Turin, Italy
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50
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Harris JP, Iturriza-Gomara M, O'Brien SJ. Re-assessing the total burden of norovirus circulating in the United Kingdom population. Vaccine 2017; 35:853-855. [PMID: 28094075 PMCID: PMC5287221 DOI: 10.1016/j.vaccine.2017.01.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/04/2017] [Accepted: 01/06/2017] [Indexed: 11/16/2022]
Abstract
Norovirus is the commonest cause of GI disease in the UK. Less stringent diagnostic threshold Increases previous estimate by 26%. Re-assessed estimate equates to burden of infection at 59 per 1000 person years.
The second Infectious Intestinal Diseases study (IID2) estimated the incidence of norovirus in the UK at 47/1000 population (three million cases annually). Clinically significant norovirus was defined using a cycle threshold (ct) value of <30; a more stringent cut-off than used in diagnostic laboratories. The low infectious dose of norovirus means asymptomatic individuals potentially contribute to ongoing transmission. Using a less stringent but diagnostically relevant threshold increases the estimation of the population burden of norovirus infection by around 26% to 59/1000 person years (95% CI 52.32–64.98), equating to 3.7 million norovirus infections annually (3.3–4.1 million). With possible vaccines on the horizon for norovirus, having a good estimate of the total burden of norovirus infection, as well as symptomatic disease will be useful in helping to guide vaccination policy when candidate vaccines become available.
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Affiliation(s)
- John P Harris
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at the University of Liverpool, Liverpool, UK.
| | - Miren Iturriza-Gomara
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at the University of Liverpool, Liverpool, UK
| | - Sarah J O'Brien
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at the University of Liverpool, Liverpool, UK
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