1
|
Kapulu MC, Muthumbi E, Otieno E, Rossi O, Ferruzzi P, Necchi F, Acquaviva A, Martin LB, Orindi B, Mwai K, Kibet H, Mwanzu A, Bigogo GM, Verani JR, Mbae C, Nyundo C, Agoti CN, Nakakana UN, Conti V, Bejon P, Kariuki S, Scott JAG, Micoli F, Podda A. Age-dependent acquisition of IgG antibodies to Shigella serotypes-a retrospective analysis of seroprevalence in Kenyan children with implications for infant vaccination. Front Immunol 2024; 15:1340425. [PMID: 38361949 PMCID: PMC10867106 DOI: 10.3389/fimmu.2024.1340425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
Background Shigellosis mainly affects children under 5 years of age living in low- and middle-income countries, who are the target population for vaccination. There are, however, limited data available to define the appropriate timing for vaccine administration in this age group. Information on antibody responses following natural infection, proxy for exposure, could help guide vaccination strategies. Methods We undertook a retrospective analysis of antibodies to five of the most prevalent Shigella serotypes among children aged <5 years in Kenya. Serum samples from a cross-sectional serosurvey in three Kenyan sites (Nairobi, Siaya, and Kilifi) were analyzed by standardized ELISA to measure IgG against Shigella sonnei and Shigella flexneri 1b, 2a, 3a, and 6. We identified factors associated with seropositivity to each Shigella serotype, including seropositivity to other Shigella serotypes. Results A total of 474 samples, one for each participant, were analyzed: Nairobi (n = 169), Siaya (n = 185), and Kilifi (n = 120). The median age of the participants was 13.4 months (IQR 7.0-35.6), and the male:female ratio was 1:1. Geometric mean concentrations (GMCs) for each serotype increased with age, mostly in the second year of life. The overall seroprevalence of IgG antibodies increased with age except for S. flexneri 6 which was high across all age subgroups. In the second year of life, there was a statistically significant increase of antibody GMCs against all five serotypes (p = 0.01-0.0001) and a significant increase of seroprevalence for S. flexneri 2a (p = 0.006), S. flexneri 3a (p = 0.006), and S. sonnei (p = 0.05) compared with the second part of the first year of life. Among all possible pairwise comparisons of antibody seropositivity, there was a significant association between S. flexneri 1b and 2a (OR = 6.75, 95% CI 3-14, p < 0.001) and between S. flexneri 1b and 3a (OR = 23.85, 95% CI 11-54, p < 0.001). Conclusion Children living in low- and middle-income settings such as Kenya are exposed to Shigella infection starting from the first year of life and acquire serotype-specific antibodies against multiple serotypes. The data from this study suggest that Shigella vaccination should be targeted to infants, ideally at 6 or at least 9 months of age, to ensure children are protected in the second year of life when exposure significantly increases.
Collapse
Affiliation(s)
- Melissa C. Kapulu
- KEMRI-Wellcome Trust Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Esther Muthumbi
- KEMRI-Wellcome Trust Programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Omar Rossi
- GSK Vaccines Institute for Global Health, Siena, Italy
| | | | | | | | | | | | - Kennedy Mwai
- KEMRI-Wellcome Trust Programme, Kilifi, Kenya
- Epidemiology and Biostatistics Division, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Godfrey M. Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Jennifer R. Verani
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Cecilia Mbae
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | | | | | | | - Philip Bejon
- KEMRI-Wellcome Trust Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - J. Anthony G. Scott
- KEMRI-Wellcome Trust Programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Audino Podda
- GSK Vaccines Institute for Global Health, Siena, Italy
| |
Collapse
|
2
|
Ahn Y, Jin S, Park G, Lee HY, Lee H, Shin E, Kim J, Yoo J, Kim Y. Epidemiological analysis and prevention strategies in response to a shigellosis cluster outbreak: a retrospective case series in an alternative school in the Republic of Korea, 2023. Osong Public Health Res Perspect 2024; 15:68-76. [PMID: 38481051 PMCID: PMC10982656 DOI: 10.24171/j.phrp.2023.0298] [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: 10/14/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND In March 2023, an alternative school in the Republic of Korea reported 12 cases of shigellosis. This study aims to analyze the epidemiological characteristics in order to determine the cause of the cluster outbreak of shigellosis and to develop prevention strategies. METHODS This study focused on 12 patients with confirmed Shigella infection and investigated their demographics, clinical features, epidemiology, diagnostics, and antimicrobial susceptibility. Following the identification of Shigella, we conducted follow-up rectal smear cultures to manage patients, implementing isolation and control measures. RESULTS This study investigated the emergence of multidrug-resistant Shigella following missionary activities in Cambodia, documenting a cluster infection within an alternative school in Daejeon, the Republic of Korea. The outbreak affected 56 participants, resulting in the confirmation of 12 cases. The incidence rates varied by gender and occupation, with higher rates among males and teachers. All 12 cases demonstrated multidrug resistance. Challenges included delayed pathogen confirmation and suboptimal adherence to isolation criteria. The incident prompted revisions in the criteria for isolation release, focusing on symptom resolution. The study underscores the necessity for strengthened surveillance, educational initiatives focusing on prevention in endemic areas, and improved oversight of unlicensed educational establishments. CONCLUSION Successful response strategies included swift situation assessment, collaborative efforts, effective infection control measures, and modified criteria for isolation release. Continued surveillance of multidrug-resistant strains is recommended, especially in regions with a high prevalence.
Collapse
Affiliation(s)
- Yeongseo Ahn
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Sunmi Jin
- Yuseong-gu Health Center, Daejeon, Republic of Korea
| | - Gemma Park
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Hye Young Lee
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Hyungyong Lee
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Eunkyung Shin
- Division of Bacterial Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Junyoung Kim
- Division of Bacterial Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jaeil Yoo
- Division of Bacterial Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Yuna Kim
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| |
Collapse
|
3
|
Stenhouse GE, Keddy KH, Bengtsson RJ, Hall N, Smith AM, Thomas J, Iturriza-Gómara M, Baker KS. The genomic epidemiology of shigellosis in South Africa. Nat Commun 2023; 14:7715. [PMID: 38001075 PMCID: PMC10673971 DOI: 10.1038/s41467-023-43345-5] [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: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.
Collapse
Affiliation(s)
- George E Stenhouse
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
| | | | - Rebecca J Bengtsson
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Miren Iturriza-Gómara
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Kate S Baker
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
- Department of Genetics, University of Cambridge, CB23EH, Cambridge, UK.
| |
Collapse
|
4
|
Wang L, Zhang Y, Liu L, Huang F, Dong B. Effects of Three-Layer Encapsulated Tea Tree Oil on Growth Performance, Antioxidant Capacity, and Intestinal Microbiota of Weaned Pigs. Front Vet Sci 2021; 8:789225. [PMID: 34926648 PMCID: PMC8674471 DOI: 10.3389/fvets.2021.789225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Tea tree oil (TTO) exerts key roles in improving growth performance of pigs. However, knowledge is limited regarding comparative effects of Encp TTO and Un-encp TTO supplementation on growth performance of pigs. A study determined the effects of TTO or its capsulation on growth performance, antioxidant capacity, and intestinal microbiome of weaned pigs. A total of 144 healthy pigs (8.5 ± 0.24 kg) were subjected to four treatments for a 28-d trial with six replicates per treatment and six pigs per pen: negative control, NC; positive control, PC (antibiotic supplemented); Un-encp TTO (supplemented with unencapsulated TTO); Encp TTO (supplemented with encapsulated TTO). NC, TTO, and PC treatments were compared with regard to improved average daily gain (ADG), average daily feed intake (ADFI), feed conversion rate, nutrient digestibility, and intestinal morphology (p < 0.05) and decreased diarrhea rate. TTO- and PC-treated pigs had higher levels of serum superoxide dismutase, glutathione peroxidase, and immunoglobulin G; lower levels of liver aspartate aminotransferase and alanine aminotransferase; and improved concentrations of interleukin 10 (IL-10), tumor necrosis factor α, and IL-1β (p < 0.05). TTO- and PC-treated pigs had higher abundance of beneficial bacterial species Subdoligranulum and lower abundance of diarrhea associated species Escherichia-Shigella in cecal and colonic digesta (p < 0.05). Encapsulation of TTO preserved more activities of TTO than its unencapsulated counterpart by showing higher ADG, ADFI, and feed conversion rate during day 1 (d1) to d14 (p < 0.05) and tended to lower diarrhea rate (p = 0.083) and improve villous height/crypt depth (VH/CD) ratio (p = 0.089) in jejunum. Encapsulation of TTO also improved antioxidant indexes and decreased liver injury and inflammation accordingly (p < 0.05). Encapsulated TTO-treated pigs had higher abundance of beneficial Clostridium_sensu_stricto_1 and lower the abundance of harmful Escherichia-Shigella in cecal and colonic digesta (p < 0.05). Our results demonstrated TTO benefits on improving growth performance of weaned pigs and further proved that encapsulation of TTO was superior to its unencapsulated counterpart at multiples. Encapsulated TTO was similar to the PC group and could be potentially an alternative of feed antibiotics for weaned pigs.
Collapse
Affiliation(s)
| | | | | | | | - Bing Dong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
5
|
Li XH, Huang YY, Lu LM, Zhao LJ, Luo XK, Li RJ, Dai YY, Qin C, Huang YQ, Chen H. Early genetic diagnosis of clarithromycin resistance in Helicobacter pylori. World J Gastroenterol 2021; 27:3595-3608. [PMID: 34239272 PMCID: PMC8240046 DOI: 10.3748/wjg.v27.i24.3595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/13/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The drug resistance rate of clinical Helicobacter pylori (H. pylori) isolates has increased. However, the mechanism of drug resistance remains unclear. In this study, drug-resistant H. pylori strains were isolated from different areas and different populations of Chinese for genomic analysis.
AIM To investigate drug-resistant genes in H. pylori and find the genes for the early diagnosis of clarithromycin resistance.
METHODS Three drug-resistant H. pylori strains were isolated from patients with gastritis in Bama County, China. Minimal inhibitory concentrations of clarithromycin, metronidazole, and levofloxacin were determined and complete genome sequencing was performed with annotation. Hp1181 and hp1184 genes were found in these strains and then detected by reverse transcription polymerase chain reaction. The relationships between hp1181 or hp1184 and clarithromycin resistance were ascertained with gene mutant and drug-resistant strains. The homology of the strains with hp26695 was assessed through complete genome detection and identification. Differences in genome sequences, gene quantity, and gene characteristics were detected amongst the three strains. Prediction and analysis of the function of drug-resistant genes indicated that the RNA expression of hp1181 and hp1184 increased in the three strains, which was the same in the artificially induced clarithromycin-resistant bacteria. After gene knockout, the drug sensitivity of the strains was assessed.
RESULTS The strains showing a high degree of homology with hp26695, hp1181, and hp1184 genes were found in these strains; the expression of the genes hp1184 and hp1181 was associated with clarithromycin resistance.
CONCLUSION Hp1181 and hp1184 mutations may be the earliest and most persistent response to clarithromycin resistance, and they may be the potential target genes for the diagnosis, prevention, and treatment of clarithromycin resistance.
Collapse
Affiliation(s)
- Xiao-Hua Li
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Yong-Yi Huang
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Lin-Ming Lu
- Department of Pathology, Wannan Medical College, Wuhu 241002, Anhui Province, China
| | - Li-Juan Zhao
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Xian-Ke Luo
- Department of Gastroenterology, National Hospital of Guangxi Zhuang Autonomous Region, Nanning Guangxi Zhuang Autonomous Region, 530001, China
| | - Ru-Jia Li
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Yuan-Yuan Dai
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Chun Qin
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Yan-Qiang Huang
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Hao Chen
- Department of Pathology, Wannan Medical College, Wuhu 241002, Anhui Province, China
| |
Collapse
|
6
|
Shigella sonnei: virulence and antibiotic resistance. Arch Microbiol 2020; 203:45-58. [PMID: 32929595 PMCID: PMC7489455 DOI: 10.1007/s00203-020-02034-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/21/2022]
Abstract
Shigella sonnei is the emerging pathogen globally, as it is the second common infectious species of shigellosis (bloody diarrhoea) in low- and middle-income countries (LMICs) and the leading one in developed world. The multifactorial processes and novel mechanisms have been identified in S. sonnei, that are collectively playing apart a substantial role in increasing its prevalence, while replacing the S. flexneri and other Gram-negative gut pathogens niche occupancy. Recently, studies suggest that due to improvement in sanitation S. sonnei has reduced cross-immunization from Plesiomonas shigelliodes (having same O-antigen as S. sonnei) and also found to outcompete the two major species of Enterobacteriaceae family (Shigella flexneri and Escherichia coli), due to encoding of type VI secretion system (T6SS). This review aimed to highlight S. sonnei as an emerging pathogen in the light of recent research with pondering aspects on its epidemiology, transmission, and pathogenic mechanisms. Additionally, this paper aimed to review S. sonnei disease pattern and related complications, symptoms, and laboratory diagnostic techniques. Furthermore, the available treatment reigns and antibiotic-resistance patterns of S. sonnei are also discussed, as the ciprofloxacin and fluoroquinolone-resistant S. sonnei has already intensified the global spread and burden of antimicrobial resistance. In last, prevention and controlling strategies are briefed to limit and tackle S. sonnei and possible future areas are also explored that needed more research to unravel the hidden mysteries surrounding S. sonnei.
Collapse
|
7
|
Ingle DJ, Easton M, Valcanis M, Seemann T, Kwong JC, Stephens N, Carter GP, Gonçalves da Silva A, Adamopoulos J, Baines SL, Holt KE, Chow EPF, Fairley CK, Chen MY, Kirk MD, Howden BP, Williamson DA. Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia. Clin Infect Dis 2020; 69:1535-1544. [PMID: 30615105 DOI: 10.1093/cid/ciz005] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/04/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND In urban Australia, the burden of shigellosis is either in returning travelers from shigellosis-endemic regions or in men who have sex with men (MSM). Here, we combine genomic data with comprehensive epidemiological data on sexual exposure and travel to describe the spread of multidrug-resistant Shigella lineages. METHODS A population-level study of all cultured Shigella isolates in the state of Victoria, Australia, was undertaken from 1 January 2016 through 31 March 2018. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analyses of 545 Shigella isolates were performed at the Microbiological Diagnostic Unit Public Health Laboratory. Risk factor data on travel and sexual exposure were collected through enhanced surveillance forms or by interviews. RESULTS Rates of antimicrobial resistance were high, with 17.6% (95/541) and 50.6% (274/541) resistance to ciprofloxacin and azithromycin, respectively. There were strong associations between antimicrobial resistance, phylogeny, and epidemiology. Specifically, 2 major MSM-associated lineages were identified: a Shigellasonnei lineage (n = 159) and a Shigella flexneri 2a lineage (n = 105). Of concern, 147/159 (92.4%) of isolates within the S. sonnei MSM-associated lineage harbored mutations associated with reduced susceptibility to recommended oral antimicrobials: namely, azithromycin, trimethoprim-sulfamethoxazole, and ciprofloxacin. Long-read sequencing demonstrated global dissemination of multidrug-resistant plasmids across Shigella species and lineages, but predominantly associated with MSM isolates. CONCLUSIONS Our contemporary data highlight the ongoing public health threat posed by resistant Shigella, both in Australia and globally. Urgent multidisciplinary public health measures are required to interrupt transmission and prevent infection.
Collapse
Affiliation(s)
- Danielle J Ingle
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.,National Centre for Epidemiology and Population Health, The Australian National University, Canberra
| | - Marion Easton
- Victorian Department of Health and Human Services, Melbourne
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.,Melbourne Bioinformatics Group, Victoria, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Jason C Kwong
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Nicola Stephens
- Victorian Department of Health and Human Services, Melbourne
| | - Glen P Carter
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne
| | | | - Sarah L Baines
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.,London School of Hygiene and Tropical Medicine, United Kingdom
| | - Eric P F Chow
- Melbourne Sexual Health Centre, Alfred Health, Carlton.,Central Clinical School, Monash University, Melbourne, Australia
| | - Christopher K Fairley
- Melbourne Sexual Health Centre, Alfred Health, Carlton.,Central Clinical School, Monash University, Melbourne, Australia
| | - Marcus Y Chen
- Melbourne Sexual Health Centre, Alfred Health, Carlton.,Central Clinical School, Monash University, Melbourne, Australia
| | - Martyn D Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| |
Collapse
|
8
|
Chung The H, Boinett C, Pham Thanh D, Jenkins C, Weill FX, Howden BP, Valcanis M, De Lappe N, Cormican M, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen TNT, Ha Thanh T, Voong VP, Duong VT, Nguyen PHL, Turner P, Wick R, Ceyssens PJ, Thwaites G, Holt KE, Thomson NR, Rabaa MA, Baker S. Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Nat Commun 2019; 10:4828. [PMID: 31645551 PMCID: PMC6811581 DOI: 10.1038/s41467-019-12823-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/25/2019] [Indexed: 02/08/2023] Open
Abstract
Shigella sonnei increasingly dominates the international epidemiological landscape of shigellosis. Treatment options for S. sonnei are dwindling due to resistance to several key antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolutionary history of the recently emergent fluoroquinolone-resistant S. sonnei. We reaffirm that extant resistant organisms belong to a single clonal expansion event. Our results indicate that sequential accumulation of defining mutations (gyrA-S83L, parC-S80I, and gyrA-D87G) led to the emergence of the fluoroquinolone-resistant S. sonnei population around 2007 in South Asia. This clone was then transmitted globally, resulting in establishments in Southeast Asia and Europe. Mutation analysis suggests that the clone became dominant through enhanced adaptation to oxidative stress. Experimental evolution reveals that under fluoroquinolone exposure in vitro, resistant S. sonnei develops further intolerance to the antimicrobial while the susceptible counterpart fails to attain complete resistance. Shigella sonnei is one of the main species causing shigellosis worldwide. Here the authors analyse nearly 400 S. sonnei genome sequences and carry out experimental evolution experiments to shed light into the evolutionary processes underlying the recent emergence of fluoroquinolone resistance in this pathogen.
Collapse
Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Christine Boinett
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, UK
| | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Niall De Lappe
- National Salmonella, Shigella, and Listeria monocytogenes Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Martin Cormican
- School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Sonam Wangchuk
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Ladaporn Bodhidatta
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Carl J Mason
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Phat Voong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thuy Duong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phu Huong Lan Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Ryan Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | | | - Guy Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK.,The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Maia A Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. .,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, The Department of Medicine, University of Cambridge, Cambridge, UK
| |
Collapse
|
9
|
Abstract
PURPOSE OF REVIEW Diarrhoea is a major global health problem, and recent studies have confirmed Shigella as a major contributor to this burden. Here, we review recent advances in Shigella research; focusing on their epidemiology, pathogenesis, antimicrobial resistance, and the role of the gut microbiome during infection. RECENT FINDINGS Enhanced epidemiological data, combined with new generation diagnostics, has highlighted a greater burden of Shigella disease than was previously estimated, which is not restricted to vulnerable populations in low-middle income countries. As we gain an ever more detailed insight into the orchestrated mechanisms that Shigella exploit to trigger infection, we can also begin to appreciate the complex role of the gut microbiome in preventing and inducing such infections. The use of genomics, in combination with epidemiological data and laboratory investigations, has unravelled the evolution and spread of various species. Such measures have identified resistance to antimicrobials as a key contributor to the success of specific clones. SUMMARY We need to apply novel findings towards sustainable approaches for treating and preventing Shigella infections. Vaccines and alternative treatments are under development and may offer an opportunity to reduce the burden of Shigella disease and restrict the mobility of antimicrobial resistant clones.
Collapse
|
10
|
Lobato‐Márquez D, Krokowski S, Sirianni A, Larrouy‐Maumus G, Mostowy S. A requirement for septins and the autophagy receptor p62 in the proliferation of intracellular Shigella. Cytoskeleton (Hoboken) 2019; 76:163-172. [PMID: 29752866 PMCID: PMC6519264 DOI: 10.1002/cm.21453] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/11/2018] [Accepted: 05/09/2018] [Indexed: 12/28/2022]
Abstract
Shigella flexneri, a Gram-negative enteroinvasive pathogen, causes inflammatory destruction of the human intestinal epithelium. During infection of epithelial cells, Shigella escape from the phagosome to the cytosol, where they reroute host cell glycolysis to obtain nutrients for proliferation. Septins, a poorly understood component of the cytoskeleton, can entrap cytosolic Shigella targeted to autophagy in cage-like structures to restrict bacterial proliferation. Although bacterial entrapment by septin caging has been the subject of intense investigation, the role of septins and the autophagy machinery in the proliferation of noncaged Shigella is mostly unknown. Here, we found that intracellular Shigella fail to efficiently proliferate in SEPT2-, SEPT7-, or p62/SQSTM1-depleted cells. Consistent with a failure to proliferate, single cell analysis of bacteria not entrapped in septin cages showed that the number of metabolically active Shigella in septin- or p62-depleted cells is reduced. Targeted metabolomic analysis revealed that host cell glycolysis is dysregulated in septin-depleted cells, suggesting a key role for septins in modulation of glycolysis. Together, these results suggest that septins and the autophagy machinery may regulate metabolic pathways that promote the proliferation of intracellular Shigella not entrapped in septin cages.
Collapse
Affiliation(s)
- Damián Lobato‐Márquez
- MRC Centre for Molecular Bacteriology and Infection, Department of MedicineSection of Microbiology, Imperial College LondonLondonUnited Kingdom
- Department of Immunology and InfectionLondon School of Hygiene and Tropical Medicine, Keppel StreetLondonUnited Kingdom
| | - Sina Krokowski
- MRC Centre for Molecular Bacteriology and Infection, Department of MedicineSection of Microbiology, Imperial College LondonLondonUnited Kingdom
- Department of Immunology and InfectionLondon School of Hygiene and Tropical Medicine, Keppel StreetLondonUnited Kingdom
| | - Andrea Sirianni
- MRC Centre for Molecular Bacteriology and Infection, Department of MedicineSection of Microbiology, Imperial College LondonLondonUnited Kingdom
| | - Gerald Larrouy‐Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural SciencesImperial College LondonLondonUnited Kingdom
| | - Serge Mostowy
- MRC Centre for Molecular Bacteriology and Infection, Department of MedicineSection of Microbiology, Imperial College LondonLondonUnited Kingdom
- Department of Immunology and InfectionLondon School of Hygiene and Tropical Medicine, Keppel StreetLondonUnited Kingdom
| |
Collapse
|