Construction of a Pan-Genome Allele Database of Salmonella enterica Serovar Enteritidis for Molecular Subtyping and Disease Cluster Identification

Whole-genome sequence analysis of Clostridium chauvoei isolated from clinical case of black quarter (BQ) from India

Black quarter (BQ) is an infectious disease affecting cattle and small ruminants worldwide caused by Gram-positive anaerobic bacterium Clostridium chauvoei. In this study, a draft genome sequence of C. chauvoei NIVEDIBQ1 strain isolated from clinical case of black quarter was analyzed. Sequence analysis indicated that genome had 2653 predicted coding DNA sequences, harbored numerous genes, mobile genetic elements for pathogenesis, and virulence factors. Computational analysis revealed that strain contained 30 virulence-associated genes. An intact genomic region highly similar to the Clostridium phage was present in the genome. Presence of CRISPR systems and the transposon components likely contribute to the genome plasticity. Strain encode diverse spectrum of degradative carbohydrate-active enzymes (CAZymes). Comparative SNP analysis revealed that the genomes of the C. chauvoei strains analyzed were highly conserved. Phylogenetic analysis of strains and available genome (n = 21) based on whole-genome multi-locus sequence typing (wgMLST) and core orthologous genes showed the clustering of strains into two different clusters suggesting geographical links.

Bacteriophages: A weapon against mixed-species biofilms in the food processing environment

Mixed-species biofilms represent the most frequent actual lifestyles of microorganisms in food processing environments, and they are usually more resistant to control methods than single-species biofilms. The persistence of biofilms formed by foodborne pathogens is believed to cause serious human diseases. These challenges have encouraged researchers to search for novel, natural methods that are more effective towards mixed-species biofilms. Recently, the use of bacteriophages to control mixed-species biofilms have grown significantly in the food industry as an alternative to conventional methods. This review highlights a comprehensive introduction of mixed-species biofilms formed by foodborne pathogens and their enhanced resistance to anti-biofilm removal strategies. Additionally, several methods for controlling mixed-species biofilms briefly focused on applying bacteriophages in the food industry have also been discussed. This article concludes by suggesting that using bacteriophage, combined with other 'green' methods, could effectively control mixed-species biofilms in the food industry.

Serotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004-2019

Salmonella enterica (S. enterica) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health. Salmonella typing is essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250 S. enterica isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All S. enterica isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in dnaN. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,[5],12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree. In conclusion, we sorted out the phenotyping and genotyping diversity of S. enterica isolates in China during 2004-2019 and clarified the temporal and spatial distribution characteristics of Salmonella from different hosts in China in the recent 16 years. These results greatly supplement Salmonella strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of Salmonella; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China.

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

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.

Characterization of antimicrobial-resistant Escherichia coli causing urinary tract infections in dogs: Passive surveillance in Saskatchewan, Canada 2014 to 2018

BACKGROUND

Urinary tract infections (UTIs) are common in dogs and can be caused by multidrug-resistant Escherichia coli (E coli).

OBJECTIVE

To describe the frequency and mechanisms of antimicrobial resistance (AMR) among E coli causing UTIs in dogs in Western Canada during a 4-year surveillance period.

ANIMALS

Urine from 516 dogs.

METHODS

From November 2014 to 2018, 516 nonduplicate E coli isolates from the urine of dogs were collected from a diagnostic laboratory. Susceptibility testing was determined for a panel of 14 antimicrobials belonging to 7 drug classes. Resistant isolates were screened for the presence of extended-spectrum beta-lactamases (ESBLs), AmpC β-lactamases, and plasmid-mediated quinolone resistance (PMQR) genes. Epidemiological relationships were assessed by MLST.

RESULTS

80.2% (414/516) of isolates were susceptible to all antimicrobials tested. There was no significant increase in the proportion of isolates resistant to any of the tested antimicrobials during the study period. Resistance to ampicillin was the most common (14.9%, 77/516). Overall, 12 isolates had blaCMY-2 -type AmpC β-lactamases, and 7 produced CTX-M-type ESBLs. A single isolate had the aac(6')-Ib-cr PMQR gene. The qnr and qepA determinants were not detected. A single isolate belonging to the pandemic lineage ST131 was identified.

CONCLUSION

Escherichia coli isolated from the urine of dogs in our region remain susceptible to first-line therapies, though resistance, particularly to the aminopenicillins, warrants monitoring. This is the first description of E coli ST131 from a companion animal in Canada.

Acquisition and carriage of multidrug-resistant organisms in dogs and cats presented to small animal practices and clinics in Switzerland

BACKGROUND

The emergence and spread of multidrug-resistant organisms (MDRO) present a threat to human and animal health.

OBJECTIVES

To assess acquisition, prevalence of and risk factors for MDRO carriage in dogs and cats presented to veterinary clinics or practices in Switzerland.

ANIMALS

Privately owned dogs (n = 183) and cats (n = 88) presented to 4 veterinary hospitals and 1 practice.

METHODS

Prospective, longitudinal, observational study. Oronasal and rectal swabs were collected at presentation and 69% of animals were sampled again at discharge. Methicillin-resistant (MR) staphylococci and macrococci, cephalosporinase-, and carbapenemase-producing (CP) Enterobacterales were isolated. Genetic relatedness of isolates was assessed by repetitive sequence-based polymerase chain reaction and multilocus sequence typing. Risk factors for MDRO acquisition and carriage were analyzed based on questionnaire-derived and hospitalization data.

RESULTS

Admission prevalence of MDRO carriage in pets was 15.5% (95% confidence interval [CI], 11.4-20.4). The discharge prevalence and acquisition rates were 32.1% (95% CI, 25.5-39.3) and 28.3% (95% CI, 22-35.4), respectively. Predominant hospital-acquired isolates were extended spectrum β-lactamase-producing Escherichia coli (ESBL-E coli; 17.3%) and β-lactamase-producing Klebsiella pneumoniae (13.7%). At 1 institution, a cluster of 24 highly genetically related CP (bla_oxa181 and bla_oxa48 ) was identified. Multivariate analysis identified hospitalization at clinic 1 (odds ratio [OR], 5.1; 95% CI, 1.6-16.8) and days of hospitalization (OR 3-5 days, 4.4; 95% CI, 1.8-10.9; OR > 5 days, 6.2; 95% CI, 1.3-28.8) as risk factors for MDRO acquisition in dogs.

CONCLUSIONS

Veterinary hospitals play an important role in the selection and transmission of MDRO among veterinary patients.

Integrated Whole-Genome Sequencing Infrastructure for Outbreak Detection and Source Tracing of Salmonella enterica Serotype Enteritidis

As an important foodborne pathogen, Salmonella enterica serotype Enteritidis is recognized as one of the most common causes of human salmonellosis globally. Outbreak detection for this highly homogenous serotype, however, has remained challenging. Rapid advances in sequencing technologies have presented whole-genome sequencing (WGS) as a significant advancement for source tracing and molecular typing of foodborne pathogens. A retrospective analysis was conducted using Salmonella Enteritidis isolates (n = 65) from 11 epidemiologically confirmed outbreaks and a collection of contemporaneous sporadic isolates (n = 258) during 2007-2017 to evaluate the performance of WGS in delineating outbreak-associated isolates. Whole-genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis revealed well-supported clades in concordance with epidemiological evidence and pairwise distances of ≤3 SNPs for all outbreaks. WGS-based framework of outbreak detection was thus proposed and applied prospectively to investigate isolates (n = 66) from nine outbreaks during 2018-2019. We further demonstrated the superior discriminatory power and accuracy of WGS to resolve and delineate outbreaks for pragmatic food source tracing. The proposed integrated WGS framework is the first in China for Salmonella Enteritidis and has the potential to serve as a paradigm for outbreak detection and source tracing of Salmonella throughout the stages of food production, as well as expanded to other foodborne pathogens.

Prospective Salmonella Enteritidis surveillance and outbreak detection using whole genome sequencing, Minnesota 2015-2017

Clusters of Salmonella Enteritidis cases were identified by the Minnesota Department of Health using both pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) single nucleotide polymorphism analysis from 1 January 2015 through 31 December 2017. The median turnaround time for obtaining WGS results was 11 days longer than for PFGE (12 vs. 1 day). WGS analysis more than doubled the number of clusters compared to PFGE analysis, but reduced the total number of cases included in clusters by 34%. The median cluster size was two cases for WGS compared to four for PFGE, and the median duration of WGS clusters was 27 days shorter than PFGE clusters. While the percentage of PFGE clusters with a confirmed source (46%) was higher than WGS clusters (32%), a higher percentage of cases in clusters that were confirmed as outbreaks reported the vehicle or exposure of interest for WGS (78%) than PFGE (46%). WGS cluster size was a significant predictor of an outbreak source being confirmed. WGS data have enhanced S. Enteritidis cluster investigations in Minnesota by improving the specificity of cluster case definitions and has become an integral part of the S. Enteritidis surveillance process.

Molecular Characterization of Carbapenem-Resistant Serratia marcescens Clinical Isolates in a Tertiary Hospital in Hangzhou, China

INTRODUCTION

Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most commonly associated with clinical infections, data on Serratia marcescens are inadequate and superficial.

METHODS

In this study, we characterized 36 carbapenem-resistant Serratia marcescens (CRSM) isolates in our hospital from April 2018 to March 2019 by analysing whole-genome sequencing (WGS) data. The molecular typing of the isolates was performed using both pulsed-field gel electrophoresis (PFGE) and core genome multilocus sequence typing (cgMLST).

RESULTS

Thirty-three of the 36 isolates showed carbapenem resistance conferred by a bla KPC-2-harbouring plasmid, while the remaining three isolates were characterized by overexpression of beta-lactamase combined with porin loss. The bla KPC-2 genes in all the isolates were located on a plasmid of ~103 kb, except one, which was on a plasmid of ~94 kb. The gene structure surrounding bla KPC-2 in the plasmids was confirmed by integration of a partial Tn4401 structure and an intact IS26 as previously reported. Most of the plasmids also contained a mobile genetic element (MGE) comprising qnr and ISKpn19, which provided evidence of horizontal transfer of antibiotic resistance genes.

CONCLUSION

The thirty-six CRSM isolates were mainly clonally disseminated with a bla KPC-2-harbouring plasmid in our hospital. The gene structure surrounding bla KPC-2 as an MGE, as well as the qnr segment, might be acquired by horizontal gene transfer, and it could aggravate the infection and increase the difficulty of clinical treatment.

Characterization and Genome Analysis of a Novel Salmonella Phage vB_SenS_SE1

Salmonella is a significant food-borne pathogen that infects a large number of people worldwide. In this study, a lytic bacteriophage vB_SenS_SE1 capable of infecting Salmonella is isolated from municipal wastewater in Beijing, and its biological and genomic features are analyzed. Transmission electron micrograph shows that vB_SenS_SE1 is likely a Siphoviridae virus, with an icosahedral head and a long non-contracted tail. The stability test in vitro reveals that it is stable at 4-50 °C and pH 4-12. Based on the one-step growth curve, vB_SenS_SE1 has a 60-min exponential phase and a low burst size (19 PFU per cell). Bioinformatics analysis reveals that vB_SenS_SE1 consists of a circular, double-stranded DNA molecule of 40,987 bp with a GC content of 51.2%. Its genome carries 63 predicted open reading frames (orfs), with 22 orfs encoding known proteins. Phylogenetic analysis of the large terminase subunit shows that vB_SenS_SE1 exhibits strong homology to Salmonella phage St161, St162, VSiP, and FSL SP-031. The CoreGenes analysis shows that it is a member of the virus genus Cornellvirus. The features of phage vB_SenS_SE1 suggest that it has the potential to be an agent to control Salmonella.

Association of Salmonella virulence factor alleles with intestinal and invasive serovars

BACKGROUND

The role of Salmonella virulence factor (VF) allelic variation in modulating pathogenesis or host specificity has only been demonstrated in a few cases, mostly through serendipitous findings. Virulence factor (VF) alleles from Salmonella enterica subsp. enterica genomes were compared to identify potential associations with the host-adapted invasive serovars Typhi, Dublin, Choleraesuis, and Gallinarum, and with the broad host-range intestinal serovars Typhimurium, Enteritidis, and Newport.

RESULTS

Through a bioinformatics analysis of 500 Salmonella genomes, we have identified allelic variants of 70 VFs, many of which are associated with either one of the four host-adapted invasive Salmonella serovars or one of the three broad host-range intestinal serovars. In addition, associations between specific VF alleles and intra-serovar clusters, sequence types (STs) and/or host-adapted FimH adhesins were identified. Moreover, new allelic VF associations with non-typhoidal S. Enteritidis and S. Typhimurium (NTS) or invasive NTS (iNTS) were detected.

CONCLUSIONS

By analogy to the previously shown association of specific FimH adhesin alleles with optimal binding by host adapted Salmonella serovars, lineages or strains, we predict that some of the identified association of other VF alleles with host-adapted serovars, lineages or strains will reflect specific contributions to host adaptation and/or pathogenesis. The identification of these allelic associations will support investigations of the biological impact of VF alleles and better characterize the role of allelic variation in Salmonella pathogenesis. Most relevant functional experiments will test the potential causal contribution of the detected FimH-associated VF variants in host adapted virulence.

Molecular analysis of clonally related Salmonella Typhi recovered from epidemiologically unrelated cases of typhoid fever, Brazil

BACKGROUND

The primary method of molecular subtyping for the identification and investigation of outbreaks has been pulsed-field gel electrophoresis (PFGE). In some cases, this technique has not been able to show discrimination between the unrelated strains that can be achieved by whole genome sequencing (WGS).

METHODS

The aim of this study was to determine the strengths and drawbacks of WGS using different analytic approaches compared to traditional typing method, PFGE, for retrospectively typing clusters cases of 28 S. Typhi.

RESULTS

We evaluated three analytical approaches on the WGS data set (Nucleotide Difference (ND), (SNPs) and Whole genome multi locus sequence typing (wgMLST) that identically classified the clusters-related strains into two clusters, cluster A (with strains from 2017), and Cluster B (with strains from 2007).

CONCLUSIONS

In this study WGS based typing, was able to compete with PFGE for differentiation of the clusters of S. Typhi strains.

Pangenome of Serratia marcescens strains from nosocomial and environmental origins reveals different populations and the links between them

Serratia marcescens is a Gram-negative bacterial species that can be found in a wide range of environments like soil, water and plant surfaces, while it is also known as an opportunistic human pathogen in hospitals and as a plant growth promoting bacteria (PGPR) in crops. We have used a pangenome-based approach, based on publicly available genomes, to apply whole genome multilocus sequence type schemes to assess whether there is an association between source and genotype, aiming at differentiating between isolates from nosocomial sources and the environment, and between strains reported as PGPR from other environmental strains. Most genomes from a nosocomial setting and environmental origin could be assigned to the proposed nosocomial or environmental MLSTs, which is indicative of an association between source and genotype. The fact that a few genomes from a nosocomial source showed an environmental MLST suggests that a minority of nosocomial strains have recently derived from the environment. PGPR strains were assigned to different environmental types and clades but only one clade comprised strains accumulating a low number of known virulence and antibiotic resistance determinants and was exclusively from environmental sources. This clade is envisaged as a group of promissory MLSTs for selecting prospective PGPR strains.

Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective

BACKGROUND

Rapid and accurate identification of Verotoxigenic Escherichia coli (VTEC) O157:H7 is dependent on well-established, standardized and highly discriminatory typing methods. Currently, conventional subtyping tests for foodborne bacterial pathogen surveillance are rapidly being replaced with whole-genome sequencing (WGS) in public health laboratories. The capacity of WGS to revolutionize global foodborne disease surveillance has positioned this tool to become the new gold standard; however, to ensure evidence standards for public health decision making can still be achieved, the performance of WGS must be thoroughly validated against current gold standard methods prior to implementation. Here we aim to verify the performance of WGS in comparison to pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem repeat analysis (MLVA) for eight retrospective outbreaks of VTEC O157:H7 from the Canadian perspective. Since real-time implementation and routine use of WGS in public health laboratories is highly reliant on standardized data analysis tools, we also provide a comparative analysis of two popular methodologies for WGS analyses; an in-house developed single nucleotide variant phylogenomics (SNVPhyl) pipeline and the BioNumerics whole genome multilocus sequence typing (wgMLST) tool. To provide a useful and consistent starting point for examining laboratory-based surveillance data for VTEC O157:H7 in Canada, we also aim to describe the number of genetic differences observed among outbreak-associated isolates.

RESULTS

WGS provided enhanced resolution over traditional subtyping methods, and accurately distinguished outbreak-related isolates from non-outbreak related isolates with high epidemiological concordance. WGS also illuminated potential linkages between sporadic cases of illness and contaminated food, and isolates spanning multiple years. The topologies generated by SNVPhyl and wgMLST were highly congruent with strong statistical support. Few genetic differences were observed among outbreak-related isolates (≤5 SNVs/ < 10 wgMLST alleles) unless the outbreak was suspected to be multi-strain.

CONCLUSIONS

This study validates the superiority of WGS and indicates the BioNumerics wgMLST schema is suitable for surveillance and cluster detection of VTEC O157:H7. These findings will provide a useful and consistent starting point for examining WGS data for prospective laboratory-based surveillance of VTEC O157:H7, but however, the data will continue to be interpreted according to context and in combination with epidemiological and food safety evidence to inform public-health decision making in Canada.

Molecular-based identification and detection of Salmonella in food production systems: current perspectives

Salmonella remains a prominent cause of foodborne illnesses and can originate from a wide range of food products. Given the continued presence of pathogenic Salmonella in food production systems, there is a consistent need to improve identification and detection methods that can identify this pathogen at all stages in food systems. Methods for subtyping have evolved over the years, and the introduction of whole genome sequencing and advancements in PCR technologies have greatly improved the resolution for differentiating strains within a particular serovar. This, in turn, has led to the continued improvement in Salmonella detection technologies for utilization in food production systems. In this review, the focus will be on recent advancements in these technologies, as well as potential issues associated with the application of these tools in food production. In addition, the recent and emerging research developments on Salmonella detection and identification methodologies and their potential application in food production systems will be discussed.

Salmonella in Foods: A Reemerging Problem

The number of human salmonellosis within the European Union tended to increase since 2013. One of the reasons might be Salmonella Enteritidis rising in laying hens flocks by around 17% in 2015 vs 2014 and by 57% in 2016 vs 2015. The most important sources of food-borne Salmonella outbreaks are still eggs and egg products as well as ready-to-eat foods having a long shelf life. Specific actions are suggested to restart decreasing the number of human salmonellosis: (1) revision of sampling schemes to solve pathogen under detection in both animals and foods; (2) integration of microbiological criteria with fit for purpose performance objectives and food safety objectives; and (3) improvement of epidemiological investigations of human, food, and animal isolates by using whole-genome sequencing in order to effectively track salmonellosis and verify which prevention measures are most effective.

A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis

The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.