1296. Genomic Analysis of Human-Associated Outbreak Caused by Salmonella enterica serovar Infantis in Cali, Colombia

Abstract Background Salmonella enterica serovar Infantis is emerging as a leading cause of foodborne infections. The Colombian National Health Institute reported 263 Infantis among all received Salmonella(n=12,966) from 1997 to 2018 being the 5th most frequent serovar in human clinical samples during this period. In this study, Infantis outbreak-associated isolates were sequenced and collectively analysed with global strains from different sources to compare their genomic content and phylogeny Figure 1. Genomic Comparisons Methods Between September 15-20 of 2019, 160 patients with gastroenteric symptoms resulting from the ingestion of a common food, arrived at Fundación Valle del Lilí. Salmonella spp were cultured from stool specimens of patients and 15 isolates were sent to the Genomic Unit of Agrosavia for whole-genome sequencing. Genomic DNA was sequenced using an Illumina®MiSeqX10 platform. Genome assembly was performed with standardized bioinformatics pipelines and in-silico serotyping with SISTR. Genomic comparisons included newly-sequenced isolates of Infantis(n=6) from a Colombian poultry farms as well as datasets from Patric(n=441) and EnteroBase(n=54). Results The 15 outbreak isolates were identified by in silico serotyping as S. Infantis, these isolates showed phenotypic sensitivity to all tested antibiotics except by tetracycline. Antimicrobial resistance plasmids IncFIBKpn3, IncX4 and the host-environment persistence plasmid pSL483 were only detected in 2 outbreak-related and 1 in poultry isolates. Out of a total of 511 high-quality sequences, ST32 was the most prevalent and were phylogenetically grouped into a single non-host specific clade. Outbreak-isolates were included in a monophyletic group with some genomes from the US and Chile, suggesting that the parent strain could have originated in those countries. Conclusion The magnitude of the outbreak(288 informed-cases) evidenced a high-virulent potential of outbreak-isolates. Routine sequencing of S.enterica and availability of genomes in Colombia can improve outbreak detection and resolution in the future. The presence of plasmids, although with low frequency, suggests a risk of the appearance of resistant clones. Disclosures All Authors: No reported disclosures

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Multidrug Antimicrobial Resistance and Molecular Detection of mcr-1 Gene in Salmonella Species Isolated from Chicken

Animals ◽

10.3390/ani11010206 ◽

2021 ◽

Vol 11 (1) ◽

pp. 206

Author(s):

Md Bashir Uddin ◽

S.M. Bayejed Hossain ◽

Mahmudul Hasan ◽

Mohammad Nurul Alam ◽

Mita Debnath ◽

...

Keyword(s):

Functional Analysis ◽

Antimicrobial Resistance ◽

In Silico ◽

Salmonella Enterica ◽

Molecular Mechanisms ◽

Antimicrobial Agents ◽

Genetic Relationships ◽

Evolutionary Relationship ◽

Salmonella Spp ◽

Gram Negative

Colistin (polymyxin E) is widely used in animal and human medicine and is increasingly used as one of the last-resort antibiotics against Gram-negative bacilli. Due to the increased use of colistin in treating infections caused by multidrug-resistant Gram-negative bacteria, resistance to this antibiotic ought to be monitored. The study was undertaken to elucidate the molecular mechanisms, genetic relationships and phenotype correlations of colistin-resistant isolates. Here, we report the detection of the mcr-1 gene in chicken-associated Salmonella isolates in Bangladesh and its in-silico functional analysis. Out of 100 samples, 82 Salmonella spp. were isolated from chicken specimens (liver, intestine). Phenotypic disc diffusion and minimum inhibitory concentration (MIC) assay using different antimicrobial agents were performed. Salmonella isolates were characterized using PCR methods targeting genus-specific invA and mcr-1 genes with validation for the functional analysis. The majority of the tested Salmonella isolates were found resistant to colistin (92.68%), ciprofloxacin (73.17%), tigecycline (62.20%) and trimethoprim/sulfamethoxazole (60.98%). When screened using PCR, five out of ten Salmonella isolates were found to carry the mcr-1 gene. One isolate was confirmed for Salmonella enterica subsp. enterica serovar Enteritidis, and other four isolates were confirmed for Salmonella enterica subsp. enterica serovar Typhimurium. Sequencing and phylogenetic analysis revealed a divergent evolutionary relationship between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, rendering them resistant to colistin. Three-dimensional homology structural analysis of MCR-1 proteins and molecular docking interactions suggested that MCR-1 and LptA share a similar substrate binding cavity, which could be validated for the functional analysis. The comprehensive molecular and in-silico analyses of the colistin resistance mcr-1 gene of Salmonella spp. of chicken origin in the present study highlight the importance of continued monitoring and surveillance for antimicrobial resistance among pathogens in food chain animals.

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DETECTION OF VIRULENCE GENES phoP AND phoQ IN Salmonella spp. USING IN SILICO POLYMERASE CHAIN REACTION

RESEARCH FAIR UNISRI ◽

10.33061/rsfu.v4i1.3414 ◽

2020 ◽

Vol 4 (1) ◽

Author(s):

Stalis Norma Ethica ◽

Hayatun Fuad ◽

Nur Hidayah ◽

Sri Sinto Dewi ◽

Aditya Rahman Ernanto ◽

...

Keyword(s):

In Silico ◽

Salmonella Enterica ◽

Virulence Genes ◽

Gene Detection ◽

Chain Reaction ◽

Salmonella Spp ◽

Detection Tool ◽

In Silico Study ◽

Polymerase Chain ◽

In Silico Pcr

Detection of Salmonella bacteria based on their virulence genes is among essential steps in the eradication of clinical infection by bacteria. In this study, two pair of primers, PhoPF-PhoPR: 5’- CCGCGCAGGAAAAACTCAAA-3’ and 5’-ATCTGTTCCAGCATCACCGG -3’ as well as PhoQF-PhoQR: 5’-AGAGATGATGCGCGTACTGG-3’ and 5’- CAGACGCCCCATGAGAACAT-3’, had been successfully designed using Primer3Plus to detect the presence of phoP and phoQ genes in Salmonella spp. Using genomic DNA of 44 genomic data of Salmonella spp. as templates, PhoPF-PhoPR could produce 520-bp amplicon, while PhoQF-PhoQR could result in 598-bp amplicon. Results of in silico PCR showed that both pairs of primers PhoPF-PhoPR and PhoQF-PhoQR could detect only Salmonella enterica species, and no Salmonella bongori species could be detected based on phoP and phoQ sequences. Both pairs of PhoPF-PhoPR and PhoQF-PhoQR primers were also able to detect the virulence genes in most of the studied subspecies of Salmonella enterica available in silico database unless Arizona subspecies. As conclusion, based on this in silico study, phoP and phoQ genes appeared to be biomarkers for Salmonella enterica species. Both pairs of primers designed in this study has potential to be used as detection tool to differentiate species Salmonella enterica from Salmonella bongori, and also to distinguish S.enterica subsp. enterica from subsp. Arizonae.Keywords: Gene detection, bacterial virulence, phoP, phoQ, Salmonella spp.

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Isolation, identification and some characteristics of two lytic bacteriophages against Salmonella enterica serovar Paratyphi B and S. enterica serovar Typhimurium from various food sources

FEMS Microbiology Letters ◽

10.1093/femsle/fnab037 ◽

2021 ◽

Vol 368 (7) ◽

Author(s):

Somaieh Sabzali ◽

Majid Bouzari

Keyword(s):

Salmonella Enterica ◽

Phage Therapy ◽

Multidrug Resistant ◽

Food Sources ◽

Salmonella Spp ◽

Extended Spectrum ◽

Food Borne ◽

Serovar Typhimurium ◽

Paratyphi B ◽

Different Sources

ABSTRACT Salmonellosis is an important worldwide food-borne disease. Increasing resistance to Salmonella spp. has been reported in recent years, and now the prevalence of multidrug-resistant Salmonella spp. is a worldwide problem. This necessitates alternative approaches like phage therapy. This study aimed to isolate bacteriophages specific for Salmonella enterica serovar Paratyphi B and S. enterica serovar Typhimurium isolated from different sources (chicken meat, beef and eggshells). The antibiotic resistance profiles of the bacteria were determined by phenotypic and genotypic methods. The prevalence of extended-spectrum β-lactamase genes was examined by polymerase chain reaction. In total, 75% of the isolated Salmonella strains were resistant to tetracycline, whereas 70% of them were resistant to azithromycin. All of the isolates from beef were resistant to nalidixic acid. The most common extended-spectrum β-lactamase genes among the isolates were blaSHV (15%) followed by blaTEM (10%) and blaCTX (5%). Two specific bacteriophages were isolated and characterized. The host range for vB_SparS-ui was Salmonella Paratyphi B, S. enterica serovar Paratyphi A and S. enterica, while that for vB_StyS-sam phage was Salmonella Typhimurium and S. enterica serovar Enteritidis. The characteristics of the isolated phages indicate that they are proper candidates to be used to control some foodstuff contaminations and also phage therapy of infected animals.

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Linfonodos y carne molida de res como reservorios de Salmonella spp. de importancia en salud pública

Revista Mexicana de Ciencias Pecuarias ◽

10.22319/rmcp.v11i3.5516 ◽

2020 ◽

Vol 11 (3) ◽

pp. 795-810 ◽

Cited By ~ 1

Author(s):

Tania Palós Gutiérrez ◽

María Salud Rubio Lozano ◽

Enrique Jesús Delgado Suárez ◽

Naisy Rosi Guzmán ◽

Orbelin Soberanis Ramos ◽

...

Keyword(s):

In Silico ◽

Salmonella Enterica ◽

Salmonella Spp ◽

De Se

El objetivo fue estimar la frecuencia de contaminación, diversidad de serotipos y tipificación por multilocus (MLST) de Salmonella enterica (SE) en linfonodos y carne molida de bovino. Para ello, se analizaron 1545 muestras provenientes de 400 canales bovinas. El muestreo incluyó linfonodos superficiales (LNS) y profundos, carne molida magra y con grasa, obtenidas en estación cálida (abril-julio) y fría (septiembre-diciembre) durante 2017 y 2018. Los aislamientos puros se sometieron a secuenciación completa del genoma. Con estos datos, se realizó la predicción in silico de serotipos y del perfil de MLST. En total, se obtuvieron 78 aislamientos de SE (5% del total de muestras analizadas). La frecuencia de contaminación se asoció con el tipo de muestra (2=23.7, P<0.0001) y con la época del año (2=20.3, P<0.0001), siendo mayor en LNS (9.7%) y en estación cálida (7.0%). Los serotipos predominantes fueron Anatum y Reading (n=23 cada uno), Typhimurium (n=11) y London (n=9). El perfil de MLST de cepas de los serotipos Typhimurium (ST 19 y 34) y Kentucky (ST 198) se ha reportado previamente en aislamientos involucrados en casos clínicos. Se concluye que los linfonodos y la carne molida de res son reservorios de SE de importancia en salud pública, especialmente durante los meses cálidos del año. Por tanto, es necesario establecer medidas encaminadas a prevenir la diseminación, a lo largo de la cadena productiva, de las cepas asociadas con animales aparentemente sanos.

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Evaluation of Whole Genome Sequencing for outbreak detection of Salmonella enterica serovar Enteritidis

10.26226/morressier.5f4ccc57648d3d8b3f362bad ◽

2020 ◽

Author(s):

Ainhoa Arrieta-Gisasola ◽

Aitor Atxaerandio Landa ◽

Javier Garaizar ◽

Joseba Bikandi ◽

José Karkamo ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Outbreak Detection ◽

Whole Genome ◽

Salmonella Enterica Serovar Enteritidis

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Prevalence and Antimicrobial Resistances of Salmonella spp. Isolated from Wild Boars in Liguria Region, Italy

Pathogens ◽

10.3390/pathogens10050568 ◽

2021 ◽

Vol 10 (5) ◽

pp. 568

Author(s):

Elisabetta Razzuoli ◽

Valeria Listorti ◽

Isabella Martini ◽

Laura Migone ◽

Lucia Decastelli ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Wild Boar ◽

Antimicrobial Susceptibility ◽

Potential Risk ◽

Salmonella Enterica ◽

Intestinal Tract ◽

Wild Boar Population ◽

Salmonella Spp ◽

Wild Boars ◽

In The Wild

Salmonella spp. is an important zoonotic agent. Wild boars might host this pathogen in the intestinal tract and might represent a risk for Salmonella spp. transmission to humans. Wild boars are widely spread in Liguria, due to the environmental characteristics of the region. The aim of the study was the isolation, typing, and investigation of antimicrobial susceptibility of the isolated strains of Salmonella spp. During the 2013–2017 hunting seasons, 4335 livers of wild boars were collected and analyzed for the presence of Salmonella spp. A total of 260 strains of Salmonella spp. were isolated and characterized, with a prevalence of 6%. The isolated strains belonged to all six Salmonella enterica subspecies. Most of them were identified as Salmonella enterica subs. enterica of which 31 different serotypes were identified. The dominating serotype identified was S. Enteritidis. The antimicrobial resistance profiles of the isolated strains were analyzed against sixteen molecules. Of the isolated strains, 94.6% were resistant to at least one of the tested antimicrobials. This study showed the circulation of resistant Salmonella spp. strains in the wild boar population living in this area of Italy, underling the potential risk for these animals to disseminate this pathogen and its antimicrobial resistances.

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Virulence and Antimicrobial Resistance Profiles of Salmonella enterica Serovars Isolated from Chicken at Wet Markets in Dhaka, Bangladesh

Microorganisms ◽

10.3390/microorganisms9050952 ◽

2021 ◽

Vol 9 (5) ◽

pp. 952

Author(s):

Nure Alam Siddiky ◽

Md Samun Sarker ◽

Md. Shahidur Rahman Khan ◽

Ruhena Begum ◽

Md. Ehsanul Kabir ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Salmonella Enterica ◽

Virulence Genes ◽

Health Concern ◽

Production Cycle ◽

Salmonella Spp ◽

Native Chicken ◽

Resistance Patterns ◽

Research Findings ◽

Native Chickens

Virulent and multi drug resistant (MDR) Salmonellaenterica is a foremost cause of foodborne diseases and had serious public health concern globally. The present study was undertaken to identify the pathogenicity and antimicrobial resistance (AMR) profiles of Salmonellaenterica serovars recovered from chicken at wet markets in Dhaka, Bangladesh. A total of 870 cecal contents of broiler, sonali, and native chickens were collected from 29 wet markets. The overall prevalence of S. Typhimurium, S. Enteritidis, and untyped Salmonella spp., were found to be 3.67%, 0.57%, and 1.95% respectively. All isolates were screened by polymerase chain reaction (PCR) for eight virulence genes, namely invA, agfA, IpfA, hilA, sivH, sefA, sopE, and spvC. S. Enteritidis isolates carried all virulence genes whilst S. Typhimurium isolates carried six virulence genes except sefA and spvC. A diverse phenotypic and genotypic AMR pattern was found. Harmonic descending trends of resistance patterns were observed among the broiler, sonali, and native chickens. Interestingly, virulent and MDR Salmonella enterica serovars were found in native chicken, although antimicrobials were not used in their production cycle. The research findings anticipate that virulent and MDR Salmonella enterica are roaming in the wet markets which can easily anchor to the vendor, consumers, and in the food chain.

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Salmonella enterica Subsp. houtenae Associated with an Abscess in Young Roe Deer (Capreolus capreolus)

Pathogens ◽

10.3390/pathogens10060654 ◽

2021 ◽

Vol 10 (6) ◽

pp. 654

Author(s):

Adriana Trotta ◽

Laura Del Sambro ◽

Michela Galgano ◽

Stefano Ciccarelli ◽

Erika Ottone ◽

...

Keyword(s):

Salmonella Enterica ◽

Roe Deer ◽

Capreolus Capreolus ◽

Epidemiological Data ◽

Resistance Pattern ◽

Salmonella Spp ◽

Antibiotic Resistant ◽

Biochemical Identification ◽

Salmonella Pathogenicity Islands ◽

Insight Into

Background: S. enterica subsp. houtenae has been rarely documented, and very limited genomic information is available. This report describes a rare case of primary extraintestinal salmonellosis in a young roe deer, associated with Salmonella enterica subsp. houtenae. Methods: A traditional cultural-based analysis was carried out from the contents of a neck abscess; biochemical identification and PCR assay were performed to isolate and identify the pathogen. Through whole-genome sequencing (WGS), multilocus sequence typing (MLST), core genome MLST (cgMLST), and the Salmonella pathogenicity islands (SPIs) survey, resistome and virulome genes were investigated to gain insight into the virulence and antimicrobial resistance of S. houtenae. Results: Biochemical identification and PCR confirmed the presence of Salmonella spp. in the swelling. The WGS analysis identified Salmonella enterica subspecies houtenae serovar 43:z4,z23:- and ST 958. The virulence study predicted a multidrug resistance pattern with resistance shown against aminoglycosides, tetracycline, beta-lactamase, fluoroquinolones, fosfomycin, nitroimidazole, aminocoumarin, and peptide. Fifty-three antibiotic-resistant genes were identified. No plasmids were detected. Conclusion: This study demonstrates the importance of continuous surveillance of pathogenic salmonellae. Biomolecular analyses combined with epidemiological data can provide important information about poorly described Salmonella strains and can help to improve animal welfare.

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A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer

Genome Medicine ◽

10.1186/s13073-020-00816-4 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Evangelina López de Maturana ◽

◽

Juan Antonio Rodríguez ◽

Lola Alonso ◽

Oscar Lao ◽

...

Keyword(s):

Pancreatic Cancer ◽

Functional Analysis ◽

Genetic Susceptibility ◽

In Silico ◽

Complex Disease ◽

Meta Analysis ◽

Low Frequency ◽

Acinar Cells ◽

Pancreatic Acinar Cells ◽

Phenotypic Variance

Abstract Background Pancreatic cancer (PC) is a complex disease in which both non-genetic and genetic factors interplay. To date, 40 GWAS hits have been associated with PC risk in individuals of European descent, explaining 4.1% of the phenotypic variance. Methods We complemented a new conventional PC GWAS (1D) with genome spatial autocorrelation analysis (2D) permitting to prioritize low frequency variants not detected by GWAS. These were further expanded via Hi-C map (3D) interactions to gain additional insight into the inherited basis of PC. In silico functional analysis of public genomic information allowed prioritization of potentially relevant candidate variants. Results We identified several new variants located in genes for which there is experimental evidence of their implication in the biology and function of pancreatic acinar cells. Among them is a novel independent variant in NR5A2 (rs3790840) with a meta-analysis p value = 5.91E−06 in 1D approach and a Local Moran’s Index (LMI) = 7.76 in 2D approach. We also identified a multi-hit region in CASC8—a lncRNA associated with pancreatic carcinogenesis—with a lowest p value = 6.91E−05. Importantly, two new PC loci were identified both by 2D and 3D approaches: SIAH3 (LMI = 18.24), CTRB2/BCAR1 (LMI = 6.03), in addition to a chromatin interacting region in XBP1—a major regulator of the ER stress and unfolded protein responses in acinar cells—identified by 3D; all of them with a strong in silico functional support. Conclusions This multi-step strategy, combined with an in-depth in silico functional analysis, offers a comprehensive approach to advance the study of PC genetic susceptibility and could be applied to other diseases.

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