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Evaluation of Genomic Typing Methods in the Salmonella Reference Laboratory in Public Health, England, 2012-2020. Pathogens 2023; 12:pathogens12020223. [PMID: 36839496 PMCID: PMC9966477 DOI: 10.3390/pathogens12020223] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/12/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
We aim to provide an evidence-based evaluation of whole genome sequence (WGS) methods, employed at the Salmonella reference laboratory in England, in terms of its impact on public health and whether these methods remain a fit for purpose test under UKAS ISO 15189. The evaluation of the genomic methods were mapped against the value of detecting microbiological clusters to support the investigation of food-borne outbreaks of Salmonella in England between 2012-2020. The analysis of WGS with both SNP- and allelic-based methods provided an unprecedented level of strain discrimination and detection of additional clusters when comparing to all of the previous typing methods. The robustness of the routine genomic sequencing at the reference laboratory ensured confidence in the microbiological identifications, even in large outbreaks with complex international food distribution networks. There was evidence that the phylogeny derived from the WGS data can be used to inform the provenance of strains and support discrimination between domestic and non-domestic transmission events. Further insight on the evolutionary context of the emerging pathogenic strains was enabled with a deep dive of the phylogenetic data, including the detection of nested clusters. The public availability of the WGS data linked to the clinical, epidemiological and environmental context of the sequenced strains has improved the trace-back investigations during outbreaks. The global expansion in the use of WGS-based typing in reference laboratories has shown that the WGS methods are a fit for purpose test in public health as it has ensured the rapid implementation of interventions to protect public health, informed risk assessment and has facilitated the management of national and international food-borne outbreaks of Salmonella.
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2
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Konishi N, Obata H, Yokoyama K, Sadamasu K, Kai A. Comparison of the Serovars and Characteristics of Salmonella Isolated from Human Feces and Foods in the 1990s and 2010s in Tokyo. Jpn J Infect Dis 2023; 76:14-19. [PMID: 36047177 DOI: 10.7883/yoken.jjid.2022.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Salmonella foodborne disease outbreaks have markedly decreased in recent years, and different Salmonella serovars have been isolated. To clarify the characteristics of Salmonella strains causing annual epidemics and to estimate the source, we conducted a serotyping test on 1,132 human-derived Salmonella isolates in the 1990s and 2010s, and 1,061 food-derived Salmonella isolates in the 2010s in Tokyo. The serovars commonly isolated from human feces in the 1990s and after 2012 were S. Enteritidis, S. Typhimurium, S. Infantis, S. Thompson, and S. Agona. The new main serovars isolated after 2012 were S. Schwarzengrund, S. Enterica serovar 4:i:-, and S. Chester. In contrast, the main serovars detected from foods after 2012 were S. Infantis, S. Schwarzengrund, S. Agona, S. Manhattan, S. Typhimurium, and S. enterica serovar UT: r:1,5. S. Schwarzengrund has recently been frequently isolated. These strains were mainly isolated from chicken meat and offal. It was suggested that the same serovars of human-derived isolates were also isolated from foods, especially chicken meat and offal, and that these were recently an important causative food of Salmonellosis.
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Affiliation(s)
- Noriko Konishi
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Japan
| | - Hiromi Obata
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Japan
| | - Keiko Yokoyama
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Japan
| | - Akemi Kai
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Japan
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3
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Jansson Mörk M, Karamehmedovic N, Hansen A, Nederby Öhd J, Lindblad M, Östlund E, Rehn M, Jernberg C. Outbreak of Salmonella Newport linked to imported frozen cooked crayfish in dill brine, Sweden, July to November 2019. EURO SURVEILLANCE : BULLETIN EUROPEEN SUR LES MALADIES TRANSMISSIBLES = EUROPEAN COMMUNICABLE DISEASE BULLETIN 2022; 27. [PMID: 35656829 PMCID: PMC9164673 DOI: 10.2807/1560-7917.es.2022.27.22.2100918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In autumn 2019, the Public Health Agency of Sweden identified a cluster of Salmonella Newport cases by whole genome sequencing (WGS). Cases’ distribution in place and time indicated a nation-wide ongoing outbreak. An investigation was initiated to identify the source and prevent further cases. We conducted a case–case study based on notified salmonellosis cases and a Salmonella trawling questionnaire, comparing 20 outbreak cases and 139 control cases. Food exposures were compared by adjusted odds ratios (aOR) with 95% confidence interval (CI) using logistic regression. Implicated foods were sampled. Outbreak cases were more likely to have consumed crayfish (aOR = 26; 95% CI: 6.3–105). One specific brand of imported frozen, pre-cooked whole crayfish in dill brine was identified as the source. Salmonella Newport was later detected in different batches from retail and in one sample from border control. Isolates from food samples clustered with the human outbreak strain by WGS. Although the retailer made a complete recall, two more cases were identified long afterwards. This investigation demonstrated the successful use of a case–case study and targeted microbiological testing to identify the source. The immediate action taken by the retailer was important to confirm the source and stop the outbreak.
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Affiliation(s)
- Marie Jansson Mörk
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden.,Public Health Agency of Sweden, Solna, Sweden
| | | | | | - Joanna Nederby Öhd
- County Council Department of Communicable Disease Control and Prevention, Stockholm Region, Stockholm, Sweden
| | | | | | - Moa Rehn
- Public Health Agency of Sweden, Solna, Sweden
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Zahli R, Soliveri J, Abrini J, Copa-Patiño JL, Nadia A, Scheu AK, Nadia SS. Prevalence, typing and antimicrobial resistance of Salmonella isolates from commercial shellfish in the North coast of Morocco. World J Microbiol Biotechnol 2021; 37:170. [PMID: 34487261 DOI: 10.1007/s11274-021-03136-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
Salmonellosis is one of the most common foodborne illnesses in the world. The irrational use of antibiotics in medicine and in animal nutrition has greatly favored the emergence and spread of resistant strains of non-typhoid Salmonella. This study aims the determination of the prevalence of Salmonella in bivalve mollusks in Northern Morocco, as well as the molecular typing and antibiotic susceptibility testing of the strains isolated from positive samples. In total, 150 samples from shellfish composed of mussels (Mytilus galloprovincialis), clams (Callista chione and Ruditapes descussatus) and oysters (Magallana gigas). Isolated Salmonella were characterized by Molecular techniques PCR, MLST and MLVA, phylogenetically grouped by MLSA, and susceptibilities were determined for 30 antimicrobial drugs using microdilution method by the BD Phoenix Automated Microbiology System. Prevalence of Salmonella enterica subsp. enterica was 12.67%, grouped in four serovars identified as Chester, Hadar, Typhimurium and Kentucky. Five different MLST STs (sequence types) were detected, ST1954 being the most common, which was mostly found in Chester isolates. Forty-two percent of the isolates showed resistance to more than one antibiotic, especially trimethoprim, sulfa drugs, quinolones and β-lactam. There was a marked change in the serovars and antimicrobial resistance profiles of the Salmonella isolates in this study compared to those in previous studies.
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Affiliation(s)
- Rajae Zahli
- Biotechnology and Applied Microbiology Laboratory (BMA), Department of Biology, Abdelmalek Essadi University, Tétouan, Morocco.
| | - Juan Soliveri
- Department of Biomedicine and Biotechnology, Faculty of Farmacy, University of Alcalá, 28805, Madrid, Spain
| | - Jamal Abrini
- Biotechnology and Applied Microbiology Laboratory (BMA), Department of Biology, Abdelmalek Essadi University, Tétouan, Morocco
| | - José L Copa-Patiño
- Department of Biomedicine and Biotechnology, Faculty of Farmacy, University of Alcalá, 28805, Madrid, Spain
| | - Amajoud Nadia
- Regional Environmental Laboratory of the Urban Community of Tetouan, Tétouan, Morocco
| | - Ann-Karolin Scheu
- Department of Biomedicine and Biotechnology, Faculty of Farmacy, University of Alcalá, 28805, Madrid, Spain
| | - Skali Senhaji Nadia
- Biotechnology and Applied Microbiology Laboratory (BMA), Department of Biology, Abdelmalek Essadi University, Tétouan, Morocco
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Ando N, Sekizuka T, Yokoyama E, Aihara Y, Konishi N, Matsumoto Y, Ishida K, Nagasawa K, Jourdan-Da Silva N, Suzuki M, Kimura H, Le Hello S, Murakami K, Kuroda M, Hirai S, Fukaya S. Whole Genome Analysis Detects the Emergence of a Single Salmonella enterica Serovar Chester Clone in Japan's Kanto Region. Front Microbiol 2021; 12:705679. [PMID: 34385991 PMCID: PMC8354586 DOI: 10.3389/fmicb.2021.705679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/05/2021] [Indexed: 11/18/2022] Open
Abstract
In Japan's Kanto region, the number of Salmonella enterica serovar Chester infections increased temporarily between 2014 and 2016. Concurrently with this temporal increase in the Kanto region, S. Chester isolates belonging to one clonal group were causing repetitive outbreaks in Europe. A recent study reported that the European outbreaks were associated with travelers who had been exposed to contaminated food in Morocco, possibly seafood. Because Japan imports a large amount of seafood from Morocco, we aimed to establish whether the temporal increase in S. Chester infections in the Kanto region was associated with imported Moroccan seafood. Short sequence reads from the whole-genome sequencing of 47 S. Chester isolates from people in the Kanto region (2014-2016), and the additional genome sequences from 58 isolates from the European outbreaks, were analyzed. The reads were compared with the complete genome sequence from a S. Chester reference strain, and 347 single nucleotide polymorphisms (SNPs) were identified. These SNPs were used in this study. Cluster and Bayesian cluster analyses showed that the Japanese and European isolates fell into two different clusters. Therefore, Φ PT and I A S values were calculated to evaluate genetic differences between these clusters. The results revealed that the Japanese and European isolates were genetically distinct populations. Our root-to-tip analysis showed that the Japanese isolates originating from one clone had accumulated mutations, suggesting that an emergence of this organism occurred. A minimum spanning tree analysis demonstrated no correlation between genetic and geographical distances in the Japanese isolates, suggesting that the emergence of the serovar in the Kanto region did not involve person-to-person contact; rather, it occurred through food consumption. The d N /d S ratio indicated that the Japanese strain has evolved under positive selection pressure. Generally, a population of bacterial clones in a reservoir faces negative selection pressure. Therefore, the Japanese strain must have existed outside of any reservoir during its emergence. In conclusion, S. Chester isolates originating from one clone probably emerged in the Kanto region via the consumption of contaminated foods other than imported Moroccan seafood. The emerging strain may have not established a reservoir for survival in the food supply chain resulting in its disappearance after 2017.
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Affiliation(s)
- Naoshi Ando
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Yoshiyuki Aihara
- Division of Bacteriology, Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Noriko Konishi
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Yuko Matsumoto
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, Yokohama, Japan
| | | | - Koo Nagasawa
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | | | - Motoi Suzuki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Faculty of Health Science, School of Medical Technology, Gunma Paz University, Takasaki, Japan
| | - Simon Le Hello
- French National Reference Center for E. coli, Shigella and Salmonella, Institute Pasteur, Paris, France
- Groupe de Recherche sur l’Adaptation Microbienne (GRAM 2.0, EA2656), Normandy University, UNICAEN, UNIROUEN, Caen, France
| | - Koichi Murakami
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashi-Murayama, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Setsuko Fukaya
- Division of Bacteriology, Ibaraki Prefectural Institute of Public Health, Mito, Japan
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Mokgophi TM, Gcebe N, Fasina F, Jambwa K, Adesiyun AA. Prevalence, Serovars, and Factors Associated with Salmonella Contamination of Chicken Carcasses Sold in Outlets of the Informal Market in Gauteng Province, South Africa. J Food Prot 2021; 84:991-999. [PMID: 33428739 DOI: 10.4315/jfp-20-416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/05/2021] [Indexed: 02/05/2023]
Abstract
ABSTRACT Salmonella has been linked to many foodborne illnesses and epidemics in both humans and animals. This cross-sectional study determined the prevalence, serovars, and factors associated with Salmonella contamination of chickens slaughtered in informal market outlets in Gauteng Province, South Africa. A total of 151 chicken carcasses were randomly collected from 47 outlets. Standard bacteriological and molecular methods were used to isolate, identify, and determine the serovar of Salmonella isolates. The prevalence of Salmonella in carcass swabs, cloacal swabs, and carcass drips was 29.1% (44 of 151), 27.2% (41 of 151), and 43.7% (66 of 151), respectively, and the differences were statistically significant (P = 0.004). Only 5 (township locations of outlet, throughput, carcass evisceration, location of carcass for sale, and outlet sanitation) of 10 factors investigated for the contamination of carcasses by Salmonella were statistically significantly (P < 0.05) associated with the isolation of Salmonella. Of the 268 isolates of Salmonella, 157 (58.6%) were typeable using a limited molecular PCR technique, and nine serovars were identified. The predominant Salmonella enterica serovars were Bovismorbificans (31.0%), Enteritidis (7.5%), and Hadar (6.7%). The five important factors found to be significantly associated with the isolation of Salmonella at these outlets offer opportunities for the reduction of Salmonella contamination. There is a need for further investigation of the probable causes of the predominant isolation of Salmonella serovar Bovismorbificans in chickens and its potential implications for human infections in South Africa. It is concluded that chickens purchased from the informal market in Gauteng Province can be a source for salmonellosis in humans if improperly cooked before consumption.
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Affiliation(s)
- Thelma M Mokgophi
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Nomakorinte Gcebe
- Bacteriology Department, Onderstepoort Veterinary Research, Agricultural Research Council, South Africa
| | - Folorunso Fasina
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Sciences, University of Pretoria, South Africa
- Emergency Center for Transboundary Animal Diseases, Food and Agriculture Organization, Dar es Salaam, Tanzania
| | - Kudakhwashe Jambwa
- Bacteriology Department, Onderstepoort Veterinary Research, Agricultural Research Council, South Africa
| | - Abiodun A Adesiyun
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
- Department of Basic Veterinary Sciences, Sciences, School of Veterinary Medicine, The University of West Indies, St. Augustine, Trinidad and Tobago
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Al-Tawfiq JA, Memish ZA. The Emergence, Persistence, and Dissemination of Antimicrobial-Resistant Bacteria in Environmental Hajj Settings and Implications for Public Health. Trop Med Infect Dis 2021; 6:33. [PMID: 33802167 PMCID: PMC8005974 DOI: 10.3390/tropicalmed6010033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 11/21/2022] Open
Abstract
The emergence of antimicrobial resistance is causing the loss of what was once considered the miracle cure. The transmission of antimicrobial resistance during mass gathering is a potential threat in addition to other infectious diseases. Here, we review the English language literature on the rate and the acquisition of antimicrobial resistance during the Hajj. There is a variable incidence of methicillin-resistant Staphylococcus aureus, Escherichia coli, and Enterobacteriaceae. There had been no report of multi-drug-resistant Mycobacterium tuberculosis. Continued surveillance of antimicrobial resistance coupled with public health measures are needed to decrease the rate of emergence of resistance.
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Affiliation(s)
- Jaffar A. Al-Tawfiq
- Specialty Internal Medicine and Quality Division, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia;
- Infectious Disease Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Infectious Disease Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21093, USA
| | - Ziad A. Memish
- Director Research and Innovation Center, King Saud Medical City, Ministry of Health, Riyadh 12746, Saudi Arabia
- Al-Faisal University, Riyadh 11533, Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
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Mokgophi TM, Gcebe N, Fasina F, Adesiyun AA. Antimicrobial Resistance Profiles of Salmonella Isolates on Chickens Processed and Retailed at Outlets of the Informal Market in Gauteng Province, South Africa. Pathogens 2021; 10:pathogens10030273. [PMID: 33804304 PMCID: PMC8000370 DOI: 10.3390/pathogens10030273] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 02/05/2023] Open
Abstract
The study determined the antimicrobial resistance profiles of Salmonella on chickens processed and retailed at outlets of the informal markets in Gauteng province, South Africa. The study also investigated the relationship of antimicrobial resistant Salmonella to the source and type of samples and their serotypes. Carcass swabs, cloacal swabs and carcass drips were randomly collected from each of 151 slaughtered chickens from six townships. Isolation and identification were performed using standard and polymerase chain reaction (PCR) methods. The disc diffusion method was used to determine the resistance of Salmonella isolates to 16 antimicrobial agents and PCR to determine their serovars. Ninety-eight (64.9%) of the 151 chickens were contaminated with Salmonella of which 94.9% (93/98) were resistant serovars. The frequency of antimicrobial resistance of Salmonella isolates was high to erythromycin (94.9%) and spectinomycin (82.7%) but was low to ciprofloxacin (1.0%) and norfloxacin (1.0%) (p < 0.05). All 170 isolates of Salmonella tested exhibited resistance to one or more antimicrobial agents and the frequency varied significantly (p < 0.05) across the townships, the type of samples and the serovars. The prevalence of multidrug resistance (MDR) in Salmonella was 81.8% (139/170). Our findings pose zoonotic, food safety and therapeutic risks to workers and consumers of undercooked, contaminated chickens from these outlets.
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Affiliation(s)
- Thelma M. Mokgophi
- Department of Production Animal Studies, University of Pretoria, Private Bag X 04, Onderstepoort, Pretoria 0110, South Africa;
| | - Nomakorinte Gcebe
- Agricultural Research Council–Bacteriology and Zoonotic Diseases Diagnostic Laboratory, Onderstepoort Veterinary Research, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa;
| | - Folorunso Fasina
- ECTAD, Food and Agriculture Organization of the UN, Dar es Salaam 14111, Tanzania & Department of Vet-erinary Tropical Diseases, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa;
| | - Abiodun A. Adesiyun
- Department of Production Animal Studies, University of Pretoria, Private Bag X 04, Onderstepoort, Pretoria 0110, South Africa;
- Department of Paraclinical Sciences, School of Veterinary Medicine, University of the West Indies, St. Augustine, Trinidad and Tobago
- Correspondence:
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Park J, Shin E, Park AK, Kim S, Jeong HJ, Kim JS, Jin YH, Park NJ, Chun JH, Hwang K, Lee KJ, Kim J. Co-infection With Chromosomally-Located bla CTX-M-14 and Plasmid-Encoding bla CTX-M-15 in Pathogenic Escherichia coli in the Republic of Korea. Front Microbiol 2020; 11:545591. [PMID: 33262742 PMCID: PMC7686028 DOI: 10.3389/fmicb.2020.545591] [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: 03/25/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
The emergence of third-generation cephalosporin resistance in Escherichia coli is increasing at an alarming rate in many countries. Thus, the aim of this study was to analyze co-infecting bla CTX-M-producing pathogenic E. coli isolates linked to three school outbreaks. Among 66 E. coli isolates, 44 were identified as ETEC O25, an ETEC isolate serotype was O2, and the other 21 were confirmed as EAEC O44. Interestingly, six patients were co-infected with EAEC O44 and ETEC O25. For these isolates, molecular analysis [antibiotic susceptibility testing, identification of the β-lactamase gene, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE)] was performed for further characterization. In addition, the transmission capacity of bla CTX-M genes was examined by conjugation experiments. Whole-genome sequencing (WGS) was performed on representative EAEC O44 and ETEC O25 isolates associated with co-infection and single-infection. All isolates were resistant to cefotaxime and ceftriaxone. All EAEC isolates carried the bla CTX-M-14 gene and all ETEC isolates the bla CTX-M-15 gene, as detected by multiplex PCR and sequencing analysis. Sequence type and PFGE results indicated three different patterns depending on the O serotype. WGS results of representative isolates revealed that the ETEC O25 strains harbored bla CTX-M-15 located on IncK plasmids associated with the Δbla TEM-bla CTX-M-15-orf477 transposon. The representative EAEC O44 isolates carried bla CTX-M-14 on the chromosome, which was surrounded by the ISEcp1-bla CTX-M-14-IS903 transposon. To the best of our knowledge, this is the first report of co-infection with chromosomally located bla CTX-M-14 and plasmid-encoding bla CTX-M-15 in pathogenic E. coli. Our findings indicate that resistance genes in clinical isolates can spread through concurrent combinations of chromosomes and plasmids.
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Affiliation(s)
- Jungsun Park
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Eunkyung Shin
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Ae Kyung Park
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Soojin Kim
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Hyun Ju Jeong
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Jin Seok Kim
- Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Seoul, South Korea
| | - Young-Hee Jin
- Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Seoul, South Korea
| | - Nan Joo Park
- Microbiology Team, Gyeonggi-do Institute of Health and Environment, Suwon, South Korea
| | - Jeong-Hoon Chun
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Kyujam Hwang
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Kwang Jun Lee
- Division of Antimicrobial Resistance, National Institute of Health, Center for Infectious Diseases Research, Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea
| | - Junyoung Kim
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
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10
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Jibril AH, Okeke IN, Dalsgaard A, Kudirkiene E, Akinlabi OC, Bello MB, Olsen JE. Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria. PLoS One 2020; 15:e0238190. [PMID: 32966297 PMCID: PMC7510976 DOI: 10.1371/journal.pone.0238190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 08/11/2020] [Indexed: 12/22/2022] Open
Abstract
Salmonella is an important human pathogen and poultry products constitute an important source of human infections. This study investigated prevalence; identified serotypes based on whole genome sequence, described spatial distribution of Salmonella serotypes and predicted risk factors that could influence the prevalence of Salmonella infection in commercial poultry farms in Nigeria. A cross sectional approach was employed to collect 558 pooled shoe socks and dust samples from 165 commercial poultry farms in North West Nigeria. On-farm visitation questionnaires were administered to obtain information on farm management practices in order to assess risk factors for Salmonella prevalence. Salmonella was identified by culture, biotyping, serology and polymerase chain reaction (PCR). PCR confirmed isolates were paired-end Illumina- sequenced. Following de novo genome assembly, draft genomes were used to obtain serotypes by SeqSero2 and SISTR pipeline and sequence types by SISTR and Enterobase. Risk factor analysis was performed using the logit model. A farm prevalence of 47.9% (CI95 [40.3-55.5]) for Salmonella was observed, with a sample level prevalence of 15.9% (CI95 [12.9-18.9]). Twenty-three different serotypes were identified, with S. Kentucky and S. Isangi as the most prevalent (32.9% and 11%). Serotypes showed some geographic variation. Salmonella detection was strongly associated with disposal of poultry waste and with presence of other livestock on the farm. Salmonella was commonly detected on commercial poultry farms in North West Nigeria and S. Kentucky was found to be ubiquitous in the farms.
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Affiliation(s)
- Abdurrahman Hassan Jibril
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Sokoto, Nigeria
| | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Egle Kudirkiene
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Olabisi Comfort Akinlabi
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Muhammad Bashir Bello
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University Sokoto, Sokoto, Nigeria
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Ung A, Baidjoe AY, Van Cauteren D, Fawal N, Fabre L, Guerrisi C, Danis K, Morand A, Donguy MP, Lucas E, Rossignol L, Lefèvre S, Vignaud ML, Cadel-Six S, Lailler R, Jourdan-Da Silva N, Le Hello S. Disentangling a complex nationwide Salmonella Dublin outbreak associated with raw-milk cheese consumption, France, 2015 to 2016. ACTA ACUST UNITED AC 2020; 24. [PMID: 30670140 PMCID: PMC6344836 DOI: 10.2807/1560-7917.es.2019.24.3.1700703] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
On 18 January 2016, the French National Reference Centre for Salmonella reported to Santé publique France an excess of Salmonella enterica serotype Dublin (S. Dublin) infections. We investigated to identify the source of infection and implement control measures. Whole genome sequencing (WGS) and multilocus variable-number tandem repeat analysis (MLVA) were performed to identify microbiological clusters and links among cases, animal and food sources. Clusters were defined as isolates with less than 15 single nucleotide polymorphisms determined by WGS and/or with identical MLVA pattern. We compared different clusters of cases with other cases (case–case study) and controls recruited from a web-based cohort (case–control study) in terms of food consumption. We interviewed 63/83 (76%) cases; 2,914 controls completed a questionnaire. Both studies’ findings indicated that successive S. Dublin outbreaks from different sources had occurred between November 2015 and March 2016. In the case–control study, cases of distinct WGS clusters were more likely to have consumed Morbier (adjusted odds ratio (aOR): 14; 95% confidence interval (CI): 4.8–42) or Vacherin Mont d’Or (aOR: 27; 95% CI: 6.8–105), two bovine raw-milk cheeses. Based on these results, the Ministry of Agriculture launched a reinforced control plan for processing plants of raw-milk cheeses in the production region, to prevent future outbreaks.
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Affiliation(s)
- Aymeric Ung
- These authors contributed equally to this article and share first authorship.,European Programme for Intervention Epidemiology Training (EPIET), European Centre of Disease Prevention and Control (ECDC), Stockholm, Sweden.,Santé publique France (SpFrance), the French national public health agency, Saint-Maurice, France
| | - Amrish Y Baidjoe
- Institut Pasteur, Enteric Bacterial Pathogens Unit, National Reference Center (NRC) for E. coli, Shigella and Salmonella, Paris, France.,European Programme for Public Health Microbiology Training (EUPHEM), European Centre of Disease Prevention and Control (ECDC), Stockholm, Sweden.,These authors contributed equally to this article and share first authorship
| | - Dieter Van Cauteren
- Santé publique France (SpFrance), the French national public health agency, Saint-Maurice, France
| | - Nizar Fawal
- Institut Pasteur, Enteric Bacterial Pathogens Unit, National Reference Center (NRC) for E. coli, Shigella and Salmonella, Paris, France
| | - Laetitia Fabre
- Institut Pasteur, Enteric Bacterial Pathogens Unit, National Reference Center (NRC) for E. coli, Shigella and Salmonella, Paris, France
| | - Caroline Guerrisi
- Sorbonne Université, UPMC, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Kostas Danis
- European Programme for Intervention Epidemiology Training (EPIET), European Centre of Disease Prevention and Control (ECDC), Stockholm, Sweden.,Santé publique France (SpFrance), the French national public health agency, Saint-Maurice, France
| | - Anne Morand
- French Directorate General for Food (DGAL), Ministry of Agriculture and Food, Paris, France
| | - Marie-Pierre Donguy
- French Directorate General for Food (DGAL), Ministry of Agriculture and Food, Paris, France
| | - Etienne Lucas
- Santé publique France (SpFrance), the French national public health agency, Saint-Maurice, France
| | - Louise Rossignol
- Sorbonne Université, UPMC, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Sophie Lefèvre
- Institut Pasteur, Enteric Bacterial Pathogens Unit, National Reference Center (NRC) for E. coli, Shigella and Salmonella, Paris, France
| | - Marie-Léone Vignaud
- Université Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Sabrina Cadel-Six
- Université Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Renaud Lailler
- Université Paris-Est, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Nathalie Jourdan-Da Silva
- These authors contributed equally to this article and share last authorship.,Santé publique France (SpFrance), the French national public health agency, Saint-Maurice, France
| | - Simon Le Hello
- These authors contributed equally to this article and share last authorship.,Institut Pasteur, Enteric Bacterial Pathogens Unit, National Reference Center (NRC) for E. coli, Shigella and Salmonella, Paris, France
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Spatial and space-time clustering and demographic characteristics of human nontyphoidal Salmonella infections with major serotypes in Toronto, Canada. PLoS One 2020; 15:e0235291. [PMID: 32609730 PMCID: PMC7329108 DOI: 10.1371/journal.pone.0235291] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/11/2020] [Indexed: 01/04/2023] Open
Abstract
Nontyphoidal Salmonella enterica (NTS) causes a substantial health burden to human populations in Canada and worldwide. Exposure sources and demographic factors vary by location and can therefore have a major impact on salmonellosis clustering. We evaluated major NTS serotypes: S. Enteritidis (n = 620), S. Typhimurium (n = 150), S. Thompson (n = 138), and S. Heidelberg (n = 136) reported in the city of Toronto, Canada, between January 1, 2015, and December 31, 2017. Cases were analyzed at the forward sortation area (FSA)—level (an area indicated by the first three characters of the postal code). Serotype-specific global and local clustering of infections were evaluated using the Moran's I method. Spatial and space-time clusters were investigated using Poisson and multinomial scan statistic models. Case-case analyses using a multinomial logistic regression model was conducted to compare seasonal and demographic factors among the different serotypes. High infection rate FSAs clustered in the central region of Toronto for S. Enteritidis, in the south-central region for S. Typhimurium, in north-west region for S. Thompson, and in the south-east region for S. Heidelberg. The relative risk ratio of S. Enteritidis infections was significantly higher in cases who reported travel outside of Ontario. The relative risk ratio of infections was significantly higher in summer for S. Typhimurium, and in fall for S. Thompson. The relative risk ratio of infection was highest for the 0–9 age group for S. Typhimurium, and the 20–39 age group for S. Heidelberg. Our study will aid public health stakeholders in designing serotype-specific geographically targeted disease prevention programs.
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13
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Genetic diversity of clinical Salmonella enterica serovar Typhimurium in a university hospital of south Tunisia, 2000-2013. INFECTION GENETICS AND EVOLUTION 2020; 85:104436. [PMID: 32569743 DOI: 10.1016/j.meegid.2020.104436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/28/2020] [Accepted: 06/16/2020] [Indexed: 01/06/2023]
Abstract
Typhimurium is one of the main Salmonella serovar responsible for non-typhoidal gastro-enteritis in Tunisia. Here, we aimed to assess the genetic diversity of 88 clinical Salmonella Typhimurium strains recovered during 14 years from 2000 to 2013. Phage typing, CRISPR polymorphisms (CRISPOL), pulsed-field gel electrophoresis (PFGE), multi-locus variable-number tandem repeat analysis (MLVA) and Whole genome sequencing (WGS) were used to study the relatedness and spatio-temporal evolution of Salmonella Typhimurium populations (Typhimurium (n = 81), monophasic (n = 3) and nonmotile (n = 4) variants). Seven-locus MLST from whole genome assemblies showed that all isolates, except one, belonged to ST19. The isolates were divided into 10 definitive phage (DT) types, dominated by DT104-L (39.8%), DT41 (14.8%), DT116 (11.4%) and DT120 (5.7%). Fifty-seven MLVA patterns (DI, 0.978) were obtained compared to 11 different CRISPOL types and 15 PFGE types (DI,0.845). For cgMLST analysis, 20 profiles were found. A total of 3056 SNPs were identified from the whole genome of the 88 Salmonella Typhimurium isolates. These SNPs resolved these isolates into 86 SNP haplotypes. The phylogeny result allocated most Salmonella Typhimurium isolates into four distinct clades and seven subclades. Genetic diversity between the four clades ranged in the order of 249 to 720 nucleotide changes. The prevalent phage type DT104L formed a major clade on the phylogenetic tree. Pairwise SNP differences between the strains of this clade ranged between 0 and 59. SNP-based WGS typing seems to be the most valuable molecular markers for studying the evolutionary relationships of homogeneous serovar Typhimurium isolates.
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14
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Aoki Y, Watanabe Y, Kitazawa K, Ando N, Hirai S, Yokoyama E. Emergence of Salmonella enterica subsp. enterica serovar Chester in a rural area of Japan. J Vet Med Sci 2020; 82:580-584. [PMID: 32188802 PMCID: PMC7273606 DOI: 10.1292/jvms.20-0033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In Japan, only one outbreak of Salmonella enterica subsp. enterica serovar Chester (S. Chester) has been confirmed in 1999. We performed a single-center retrospective case review of S. Chester infections that occurred in a rural area of Japan in 2016 (n=8). Case 5 and 6 occurred in twin infants who had contact with a pet dog. The dog's stool culture was positive for S. Chester. Pulsed-field gel electrophoresis and cluster analysis of S. Chester strains revealed that all the isolates appeared to be derived from the same genetic clone. Emergence of Salmonella infection can be overlooked if cases are not reported to health authorities; therefore, core hospitals should play a role to alert the occurrence of public health issue.
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Affiliation(s)
- Yoshihiro Aoki
- Department of Pediatrics, Asahi General Hospital, 1326 I, Asahi, Chiba 289-2511, Japan.,Department of Emergency and Critical Care Medicine, Aizawa Hospital, 2-5-1 Honjo, Matsumoto, Nagano 390-8510, Japan
| | - Yudai Watanabe
- Department of Clinical Laboratory, Asahi General Hospital, 1326 I, Asahi, Chiba 289-2511, Japan
| | - Katsuhiko Kitazawa
- Department of Pediatrics, Asahi General Hospital, 1326 I, Asahi, Chiba 289-2511, Japan
| | - Naoshi Ando
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba 260-8715, Japan
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba 260-8715, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba 260-8715, Japan
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15
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Van Goethem N, Descamps T, Devleesschauwer B, Roosens NHC, Boon NAM, Van Oyen H, Robert A. Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79. [PMID: 31409417 PMCID: PMC6692930 DOI: 10.1186/s13012-019-0930-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist's perspective. METHODS In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. RESULTS Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. CONCLUSIONS For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist's perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.
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Affiliation(s)
- Nina Van Goethem
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
| | - Tine Descamps
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Brecht Devleesschauwer
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Nele A. M. Boon
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Herman Van Oyen
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Public Health and Primary Care, Faculty of Medicine, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
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16
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Bourouache M, Mimouni R, Nejmeddine M, Chadli S, Benlmeliani F, Sardi J, Malmoussi M, Ouagari Z, Basbassi ME, Aghrouch M. The prevalence of syphilis in HIV-seropositive patients: a retrospective study at the regional hospital in Agadir, Morocco. Pan Afr Med J 2019; 33:252. [PMID: 31692814 PMCID: PMC6814908 DOI: 10.11604/pamj.2019.33.252.15781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/15/2019] [Indexed: 12/18/2022] Open
Abstract
Introduction HIV and syphilis are major public health problems in Morocco. The region of Souss-Massa, south-west of the country, hold more than 24% of HIV seropositive cases registered in Morocco during 2009. The aim of this study is to evaluate the seroprevalence of syphilis among HIV seropositive patients in the region of Souss-Massa, south-west of Morocco. Methods To evaluate the seroprevalence of syphilis and neurosyphilis among HIV seropositive patients, we retrospectively investigated the medical records of HIV-infected patients attending the regional hospital located in the city of Agadir, during the period comprised between 2011 and 2016. Results The population studied involved 1381 males (49.18%) and 1427 females (50.82%) HIV seropositive patients. Among them, 481 patients were seropositive for syphilis and three cases were diagnosed with neurosyphilis. The sex ratio distribution was 243 male (52.71%) and 218 female (47.29%). The prevalence of syphilis among the studied population was estimated to 16.42% with a slight dominance in male (17.63%) compared to female (15.28%). By contrast, neurosyphilis was only detected in male patients, with a prevalence estimated to 0.11%. Conclusion Even if the prevalence of HIV and syphilis is stable in the region of Souss-Massa, the prevalence of syphilis among HIV seropositive patients remained high and correlated positively with that of HIV infection. We did not find a significant difference between the genders, in relation to the prevalence of HIV and syphilis. We concluded that it was essential to continue monitoring the population, in order to improve the prevention and the access to the medical care in the south-west of Morocco.
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Affiliation(s)
- Mohamed Bourouache
- Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Rachida Mimouni
- Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Mohamed Nejmeddine
- Infectious Diseases Group, Laboratory of Cell Biology and Molecular Genetics, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Smail Chadli
- Higher Institute for Nursing Professions and Health Techniques, Agadir, Morocco
| | - Fatima Benlmeliani
- Laboratory of Bio-Medical Analysis, Hassan II Regional Hospital, Agadir, Morocco
| | - Jamila Sardi
- Laboratory of Bio-Medical Analysis, Hassan II Regional Hospital, Agadir, Morocco
| | - Mourad Malmoussi
- Department of Infectious Diseases, Hassan II Regional Hospital, Agadir, Morocco
| | - Zineb Ouagari
- Department of Infectious Diseases, Hassan II Regional Hospital, Agadir, Morocco
| | - Maryam El Basbassi
- Laboratory of Bio-Medical Analysis, Hassan II Regional Hospital, Agadir, Morocco
| | - Mohamed Aghrouch
- Laboratory of Bio-Medical Analysis, Hassan II Regional Hospital, Agadir, Morocco
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17
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Epidemiological Survey and Retrospective Analysis of Salmonella Infections between 2000 and 2017 in Warmia and Masuria Voivodship in Poland. ACTA ACUST UNITED AC 2019; 55:medicina55030074. [PMID: 30897848 PMCID: PMC6473649 DOI: 10.3390/medicina55030074] [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: 11/19/2018] [Revised: 02/26/2019] [Accepted: 03/15/2019] [Indexed: 11/17/2022]
Abstract
Background and Objectives: Salmonellosis is a major foodborne bacterial infection throughout the world. Epidemiological surveillance is one of the key factors to reduce the number of infections caused by this pathogen in both humans and animals. The first outcome measure was the prevalence of non-typhoid Salmonella (NTS) infections between 2000 and 2017 among the population of the predominantly agricultural and touristic Polish region of Warmia and Masuria (WaM). The second outcome measure was the comparison of the NTS hospitalization rate of all registered NTS cases, an investigation of the monthly reports of infections, and the exploration of the annual minimal and maximal NTS infection number in WaM in the above-mentioned time period. The last outcome was a comparison of the prevalence of NTS infections in the region and in its administrative districts by considering both rural and urban municipalities three years before and three years after the accession of Poland into the European Union (EU) in 2004. Materials and Methods: The total number of infections and hospitalizations in the 19 districts of the WaM voivodship in Poland was registered monthly between 2000–2017 by the Provincial Sanitary-Epidemiological Station in Olsztyn, Poland. Results: Between 2000 and 2017, the number of diagnosed salmonellosis cases decreased significantly in WaM; the decrease was higher in urban districts than in rural ones, and the ratio of hospitalizations and the total number of NTS cases increased significantly across all districts. The lowest number of cases was reported in the winter months and was stable from 2007, whereas the highest number was reported in the summer months with a higher tendency of outbreaks. Conclusion: The falling number of salmonellosis cases in 2000–2017 in WaM reflects the general trend in Poland and Europe. The decrease of NTS infections in WaM is related to the accession of Poland into the EU.
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18
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Jourdan-da Silva N, Fabre L, Robinson E, Fournet N, Nisavanh A, Bruyand M, Mailles A, Serre E, Ravel M, Guibert V, Issenhuth-Jeanjean S, Renaudat C, Tourdjman M, Septfons A, de Valk H, Le Hello S. Ongoing nationwide outbreak of Salmonella Agona associated with internationally distributed infant milk products, France, December 2017. ACTA ACUST UNITED AC 2019; 23. [PMID: 29338811 PMCID: PMC5770849 DOI: 10.2807/1560-7917.es.2018.23.2.17-00852] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
On 1 December 2017, an outbreak of Salmonella Agona infections among infants was identified in France. To date, 37 cases (median age: 4 months) and two further international cases have been confirmed. Five different infant milk products manufactured at one facility were implicated. On 2 and 10 December, the company recalled the implicated products; on 22 December, all products processed at the facility since February 2017. Trace-forward investigations indicated product distribution to 66 countries.
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Affiliation(s)
| | - Laetitia Fabre
- Institut Pasteur, Centre National de Référence des Salmonella, Paris, France
| | - Eve Robinson
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Santé publique France, Saint-Maurice, France
| | | | | | | | | | - Estelle Serre
- Institut Pasteur, Centre National de Référence des Salmonella, Paris, France
| | - Magali Ravel
- Institut Pasteur, Centre National de Référence des Salmonella, Paris, France
| | - Véronique Guibert
- Institut Pasteur, Centre National de Référence des Salmonella, Paris, France
| | | | - Charlotte Renaudat
- Institut Pasteur, Centre National de Référence des Salmonella, Paris, France
| | | | | | | | - Simon Le Hello
- Institut Pasteur, Centre National de Référence des Salmonella, Paris, France
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19
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Siira L, Naseer U, Alfsnes K, Hermansen NO, Lange H, Brandal LT. Whole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016. Euro Surveill 2019; 24:1800186. [PMID: 30696528 PMCID: PMC6352000 DOI: 10.2807/1560-7917.es.2019.24.4.1800186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 11/06/2018] [Indexed: 11/20/2022] Open
Abstract
IntroductionDuring summer 2016, Norway observed an increase in Salmonella enterica subsp. enterica serovar Chester cases among travellers to Greece.AimOur aim was to investigate genetic relatedness of S. Chester for surveillance and outbreak detection by core genome multilocus sequence typing (cgMLST) and compare the results to genome mapping.MethodsWe included S. Chester isolates from 51 cases of salmonellosis between 2000 and 2016. Paired-end sequencing (2 × 250 bp) was performed on Illumina MiSeq. Genetic relatedness by cgMLST for Salmonella enterica subsp. enterica, including 3,002 genes and seven housekeeping genes, was compared by reference genome mapping with CSI Phylogeny version 1.4 and conventional MLST.ResultsConfirmed travel history was available for 80% of included cases, to Europe (n = 13), Asia (n = 12) and Africa (n = 16). Isolates were distributed into four phylogenetic clusters corresponding to geographical regions. Sequence type (ST) ST411 and a single-locus variant ST5260 (n = 17) were primarily acquired in southern Europe, ST1954 (n = 15) in Africa, ST343 (n = 11) and ST2063 (n = 8) primarily in Asia. Part of the European cluster was further divided into a Greek (n = 10) and a Cypriot (n = 4) cluster. All isolates in the African cluster displayed resistance to ≥ 1 class of antimicrobials, while resistance was rare in the other clusters.ConclusionWhole genome sequencing of S. Chester in Norway showed four geographically distinct clusters, with a possible outbreak occurring during summer 2016 related to Greece. We recommend public health institutes to implement cgMLST-based real-time Salmonella enterica surveillance for early and accurate detection of future outbreaks and further development of cluster cut-offs.
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Affiliation(s)
- Lotta Siira
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Umaer Naseer
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
| | - Kristian Alfsnes
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
| | - Nils Olav Hermansen
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Heidi Lange
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
| | - Lin T Brandal
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
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20
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Rincé A, Balière C, Hervio-Heath D, Cozien J, Lozach S, Parnaudeau S, Le Guyader FS, Le Hello S, Giard JC, Sauvageot N, Benachour A, Strubbia S, Gourmelon M. Occurrence of Bacterial Pathogens and Human Noroviruses in Shellfish-Harvesting Areas and Their Catchments in France. Front Microbiol 2018; 9:2443. [PMID: 30364306 PMCID: PMC6193098 DOI: 10.3389/fmicb.2018.02443] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/24/2018] [Indexed: 01/18/2023] Open
Abstract
During a 2-year study, the presence of human pathogenic bacteria and noroviruses was investigated in shellfish, seawater and/or surface sediments collected from three French coastal shellfish-harvesting areas as well as in freshwaters from the corresponding upstream catchments. Bacteria isolated from these samples were further analyzed. Escherichia coli isolates classified into the phylogenetic groups B2, or D and enterococci from Enterococcus faecalis and E. faecium species were tested for the presence of virulence genes and for antimicrobial susceptibility. Salmonella members were serotyped and the most abundant serovars (Typhimurium and its monophasic variants and Mbandaka) were genetically characterized by high discriminative subtyping methods. Campylobacter and Vibrio were identified at the species level, and haemolysin-producing Vibrio parahaemolyticus were searched by tdh- and trh- gene detection. Main results showed a low prevalence of Salmonella in shellfish samples where only members of S. Mbandaka were found. Campylobacter were more frequently isolated than Salmonella and a different distribution of Campylobacter species was observed in shellfish compared to rivers, strongly suggesting possible additional inputs of bacteria. Statistical associations between enteric bacteria, human noroviruses (HuNoVs) and concentration of fecal indicator bacteria revealed that the presence of Salmonella was correlated with that of Campylobacter jejuni and/or C. coli as well as to E. coli concentration. A positive correlation was also found between the presence of C. lari and the detection of HuNoVs. This study highlights the importance of simultaneous detection and characterization of enteric and marine pathogenic bacteria and human noroviruses not only in shellfish but also in catchment waters for a hazard assessment associated with microbial contamination of shellfish.
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Affiliation(s)
- Alain Rincé
- UNICAEN, U2RM, Normandie Université, Caen, France
| | - Charlotte Balière
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
| | - Dominique Hervio-Heath
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
| | - Joëlle Cozien
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
| | - Solen Lozach
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
| | - Sylvain Parnaudeau
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
| | | | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur,Paris, France
| | | | | | | | - Sofia Strubbia
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur,Paris, France
| | - Michèle Gourmelon
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
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21
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Cuypers WL, Jacobs J, Wong V, Klemm EJ, Deborggraeve S, Van Puyvelde S. Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing. Microb Genom 2018; 4. [PMID: 29975627 PMCID: PMC6113872 DOI: 10.1099/mgen.0.000195] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fluoroquinolone (FQ)-resistant Salmonella spp. were listed by the WHO in 2017 as priority pathogens for which new antibiotics were urgently needed. The overall global burden of Salmonella infections is high, but differs per region. Whereas typhoid fever is most prevalent in South and South-East Asia, non-typhoidal salmonellosis is prevalent across the globe and associated with a mild gastroenteritis. By contrast, invasive non-typhoidal Salmonella cause bloodstream infections associated with high mortality, particularly in sub-Saharan Africa. Most Salmonella strains from clinical sources are resistant to first-line antibiotics, with FQs now being the antibiotic of choice for treatment of invasive Salmonella infections. However, FQ resistance is increasingly being reported in Salmonella, and multiple molecular mechanisms are already described. Whole-genome sequencing (WGS) is becoming more frequently used to analyse bacterial genomes for antibiotic-resistance markers, and to understand the phylogeny of bacteria in relation to their antibiotic-resistance profiles. This mini-review provides an overview of FQ resistance in Salmonella, guided by WGS studies that demonstrate that WGS is a valuable tool for global surveillance.
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Affiliation(s)
- Wim L Cuypers
- 1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium.,2Department of Mathematics and Computer Science, University of Antwerp, Antwerpen, Belgium
| | - Jan Jacobs
- 3Department of Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium.,4Department of Microbiology and Immunology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Vanessa Wong
- 5Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,6Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Stijn Deborggraeve
- 1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Sandra Van Puyvelde
- 6Wellcome Trust Sanger Institute, Hinxton, UK.,1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
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22
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Lawson B, Franklinos LHV, Rodriguez-Ramos Fernandez J, Wend-Hansen C, Nair S, Macgregor SK, John SK, Pizzi R, Núñez A, Ashton PM, Cunningham AA, M de Pinna E. Salmonella Enteritidis ST183: emerging and endemic biotypes affecting western European hedgehogs (Erinaceus europaeus) and people in Great Britain. Sci Rep 2018; 8:2449. [PMID: 29402927 PMCID: PMC5799193 DOI: 10.1038/s41598-017-18667-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/07/2017] [Indexed: 12/30/2022] Open
Abstract
The impacts of hedgehog (Erinaceus europaeus) Salmonella infection on public health and on animal welfare and conservation are unknown. We isolated Salmonella Enteritidis multi-locus sequence-type (ST)183 from 46/170 (27%) hedgehog carcasses (27 S. Enteritidis phage type (PT)11, 18 of a novel PT66 biotype and one with co-infection of these PTs) and from 6/208 (3%) hedgehog faecal samples (4 PT11, 2 PT66) from across Great Britain, 2012–2015. Whole genome phylogenetic analysis of the hedgehog isolates and ST183 from people in England and Wales found that PT11 and PT66 form two divergent clades. Hedgehog and human isolates were interspersed throughout the phylogeny indicating that infections in both species originate from a common population. PT11 was recovered from hedgehogs across England and Scotland, consistent with endemic infection. PT66 was isolated from Scotland only, possibly indicating a recent emergence event. People infected with ST183 were four times more likely to be aged 0–4 years than people infected by the more common ST11 S. Enteritidis. Evidence for human ST183 infection being non-foodborne included stronger correlation between geographic and genetic distance, and significantly increased likelihood of infection in rural areas, than for ST11. These results are consistent with hedgehogs acting as a source of zoonotic infection.
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Affiliation(s)
- Becki Lawson
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom.
| | - Lydia H V Franklinos
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom.,University College London, Gower Street, London, WC1E 6BT, UK
| | - Julia Rodriguez-Ramos Fernandez
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom.,IDEXX Laboratories Limited, Grange House, Sandbeck Way, Wetherby, West Yorkshire, LS22 7DN, UK
| | - Clare Wend-Hansen
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, NW9 5EQ, United Kingdom
| | - Satheesh Nair
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, NW9 5EQ, United Kingdom
| | - Shaheed K Macgregor
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Shinto K John
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Romain Pizzi
- Scottish SPCA National Wildlife Rescue Centre, Fishcross, Alloa, FK10 3AN, & Royal Zoological Society of Scotland, Edinburgh, EH12 6TS, United Kingdom
| | - Alejandro Núñez
- Animal and Plant Health Agency (APHA), APHA Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Philip M Ashton
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, NW9 5EQ, United Kingdom.
| | - Andrew A Cunningham
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Elizabeth M de Pinna
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, NW9 5EQ, United Kingdom
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23
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Revez J, Espinosa L, Albiger B, Leitmeyer KC, Struelens MJ. Survey on the Use of Whole-Genome Sequencing for Infectious Diseases Surveillance: Rapid Expansion of European National Capacities, 2015-2016. Front Public Health 2017; 5:347. [PMID: 29326921 PMCID: PMC5741818 DOI: 10.3389/fpubh.2017.00347] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/05/2017] [Indexed: 11/30/2022] Open
Abstract
Whole-genome sequencing (WGS) has become an essential tool for public health surveillance and molecular epidemiology of infectious diseases and antimicrobial drug resistance. It provides precise geographical delineation of spread and enables incidence monitoring of pathogens at genotype level. Coupled with epidemiological and environmental investigations, it delivers ultimate resolution for tracing sources of epidemic infections. To ascertain the level of implementation of WGS-based typing for national public health surveillance and investigation of prioritized diseases in the European Union (EU)/European Economic Area (EEA), two surveys were conducted in 2015 and 2016. The surveys were designed to determine the national public health reference laboratories’ access to WGS and operational WGS-based typing capacity for national surveillance of selected foodborne pathogens, antimicrobial-resistant pathogens, and vaccine-preventable diseases identified as priorities for European genomic surveillance. Twenty-eight and twenty-nine out of the 30 EU/EEA countries participated in the survey in 2015 and 2016, respectively. National public health reference laboratories in 22 and 25 countries had access to WGS-based typing for public health applications in 2015 and 2016, respectively. Reported reasons for limited or no access were lack of funding, staff, and expertise. Illumina technology was the most frequently used followed by Ion Torrent technology. The access to bioinformatics expertise and competence for routine WGS data analysis was limited. By mid-2016, half of the EU/EEA countries were using WGS analysis either as first- or second-line typing method for surveillance of the pathogens and antibiotic resistance issues identified as EU priorities. The sampling frame as well as bioinformatics analysis varied by pathogen/resistance issue and country. Core genome multilocus allelic profiling, also called cgMLST, was the most frequently used annotation approach for typing bacterial genomes suggesting potential bioinformatics pipeline compatibility. Further capacity development for WGS-based typing is ongoing in many countries and upon consolidation and harmonization of methods should enable pan-EU data exchange for genomic surveillance in the medium-term subject to the development of suitable data management systems and appropriate agreements for data sharing.
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Affiliation(s)
- Joana Revez
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Laura Espinosa
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Barbara Albiger
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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24
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Abstract
Foodborne pathogens are causing a great number of diseases with significant effects on human health and economy. The characteristics of the most common pathogenic bacteria (Bacillus cereus, Campylobacter jejuni, Clostridium botulinum, Clostridium perfringens, Cronobacter sakazakii, Esherichia coli, Listeria monocytogenes, Salmonella spp., Shigella spp., Staphylococccus aureus, Vibrio spp. and Yersinia enterocolitica), viruses (Hepatitis A and Noroviruses) and parasites (Cyclospora cayetanensis, Toxoplasma gondii and Trichinella spiralis), together with some important outbreaks, are reviewed. Food safety management systems based on to classical hazard-based approach has been proved to be inefficient, and risk-based food safety approach is now suggested from leading researchers and organizations. In this context, a food safety management system should be designed in a way to estimate the risks to human health from food consumption and to identify, select and implement mitigation strategies in order to control and reduce these risks. In addition, the application of suitable food safety education programs for all involved people in the production and consumption of foods is suggested.
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Affiliation(s)
- Thomas Bintsis
- Department of International Trade, TEI of West Macedonia, Kastoria, Greece
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