Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections

Leekitcharoenphon, Pimlapas; Raufu, Ibrahim A.; Nielsen, Mette Thorup; Lund, Birthe S. Rosenqvist; Ameh, J. A.; Ambali, A. G.; Sørensen, Gitte; Hello, Simon Le; Aarestrup, Frank Møller; Hendriksen, René S.

doi:10.1371/journal.pone.0156212

Cited by 9 publications

(18 citation statements)

References 24 publications

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“…Non-typhoidal Salmonella is one of the most common causes of food-borne diseases worldwide. It has been estimated to cause 93.8 million human infections and 155,000 deaths annually [1,2]. Contaminated poultry products, especially undercooked meat and raw eggs are important sources of human salmonellosis [3,4].…”

Section: Introductionmentioning

confidence: 99%

“…By this method, prediction of serotypes can be done using freely available in silico pipelines, such as SeqSero, which utilizes surface antigen-encoding genes for predicting serotypes, and Salmonella In Silico Typing Resources (SISTR), which infers serovars from core genome MLST (cgMLST) and surface antigens [ 9 , 11 , 12 ]. Several studies have now used WGS in Salmonella surveillance and outbreak investigation [ 2 , 13 – 15 ], and 91.9% concordance has been found between reported serovars by WKL scheme and predicted serovars using in silico resource [ 16 ], and 94.8% and 88.2% similarity was reported for SISTR and SeqSero, respectively [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

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Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria

et al. 2020

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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% (CI 95 [40.3-55.5]) for Salmonella was observed, with a sample level prevalence of 15.9% (CI 95 [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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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria

et al. 2020

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“…While in the developed countries, the majority of human Salmonella infection are foodborne (Jackson, Griffin, Cole, Walsh, & Chai, ; Majowicz et al., ), the relative importance of the transmission routes in Africa is poorly understood (Dione et al., ; Kariuki et al., ). Source attribution studies based on genomic subtyping have the potential to provide valuable information (Onsari & MacLennan, ) but are scarcely performed in Nigeria (Leekitcharoenphon et al., ); serotyping, which might not translate to genetic similarity, has been used (Raufu et al., ).…”

Section: Introductionmentioning

confidence: 99%

“…Food animals (like cattle) play a significant role in the epidemiology of Salmonella , because they act as reservoirs and excrete salmonellae in their faeces (Rodriguez‐Rivera et al., ); therefore, the meat and meat products can be contaminated during slaughter and processing, posing health risks; infections can also result from cattle contact (Cummings et al., ; Leekitcharoenphon et al., ). Beef cattle are an important potential source of salmonellae in Nigeria as they are widely consumed.…”

Section: Introductionmentioning

confidence: 99%

Phenotypic and genotypic comparison of salmonellae from diarrhoeic and healthy humans and cattle, Nigeria

Fashae

Leekitcharoenphon

Hendriksen

2017

Zoonoses and Public Health

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SummaryThe sources and modes of transmission of non-typhoidal Salmonella particularly zoonotic transmission are poorly understood in Africa. This study compared phenotypic and genotypic characteristics of Salmonellae isolated from cattle and humans. Faecal samples of diarrhoeic patients (n = 234), and a healthy population (n = 160), beef cattle at slaughter (n = 250), farms (n = 72) and market (n = 100) were cultured for salmonellae and serotyping and antimicrobial susceptibility were determined. Whole-genome sequence typing (WGST) of selected isolates and bioinformatic analysis were used to identify the multilocus sequence type (MLST), plasmid replicons, antimicrobial resistance genes and genetic relatedness by single nucleotide polymorphism (SNP) analysis.The Salmonella isolates, diarrhoeic patients (n = 17), healthy population (n = 13), cattle Rubislaw and S. Urbana, respectively. Clonal cluster shared by cattle and human WGST isolates was not found. Antimicrobial resistance rates were generally low and towards only chloramphenicol, ampicillin, gentamicin, ciprofloxacin, tetracycline and streptomycin, range 2.7% (chloramphenicol) to 8.9% (streptomycin). Multiply resistant isolates included serovars Kentucky, 4,5,12:i:-and Typhimurium. The study presents a baseline description of the prevalence, serotypes, antimicrobial resistance phenotypes and genetic relatedness of Salmonella isolated from healthy and diarrhoeic humans, and cattle at harvest, on farm and at market. Cattle are a reservoir of diverse salmonellae with shared serovars with humans, but WGST does not support zoonotic transmission. Further study with larger samples is recommended to determine whether epidemiological link exists between cattle and humans.

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“…In recent years, the decrease of the cost combined with high speed have made this approach an opportunity for it becomes more utilized in large bacterial outbreak investigations, including the use in public health microbiology and diagnostic, such as identification, typing, resistance detection, and virulence gene detection (Didelot et al, 2012 ; Wilson, 2012 ; Kwong et al, 2015 ). Salmonella genotyping based on WGS is replacing traditional methods and has proven very effective in identifying the source of outbreaks (Allard et al, 2012 ; Hoffmann et al, 2016 ), improved trace-back studies (Octavia et al, 2015a ; Hoffmann et al, 2016 ), predicted antimicrobial resistance (Zankari et al, 2013 ; McDermott et al, 2016 ) and elucidating the evolution of some Salmonella sub-types (Okoro et al, 2012 ; Zankari et al, 2013 ; Dimovski et al, 2014 ; Leekitcharoenphon et al, 2014 , 2016 ; Deng et al, 2015 ; Kariuki and Onsare, 2015 ; Fu et al, 2016 ; Phillips et al, 2016 ). In addition, WGS also provides ways to analyze more specific differentiation of strains focusing in genome adaptation.…”

Section: Genotypic Methodsmentioning

confidence: 99%

Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

2017

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Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST) has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models). Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.

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Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections

Cited by 9 publications

References 24 publications

Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria

Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria

Phenotypic and genotypic comparison of salmonellae from diarrhoeic and healthy humans and cattle, Nigeria

Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

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