Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations

Salmonella entericaserovar Heidelberg is the second most frequently occurring serovar in Quebec and the third-most prevalent in Canada. Given that conventional pulsed-field gel electrophoresis (PFGE) subtyping for commonSalmonellaserovars, such asS. Heidelberg, yields identical subtypes for the majority of isolates recovered, public health laboratories are desperate for new subtyping tools to resolve highly clonalS. Heidelberg strains involved in outbreak events. As PFGE was unable to discriminate isolates from three epidemiologically distinct outbreaks in Quebec, this study was conducted to evaluate whole-genome sequencing (WGS) and phylogenetic analysis as an alternative to conventional subtyping tools. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013, and 2014) supported by strong epidemiological evidence were sequenced and analyzed using a high-quality core genome single-nucleotide variant (hqSNV) bioinformatics approach (SNV phylogenomics [SNVphyl] pipeline). Outbreaks were indistinguishable by conventional PFGE subtyping, exhibiting the same PFGE pattern (SHEXAI.0001/SHEBNI.0001). Phylogenetic analysis based on hqSNVs extracted from WGS separated the outbreak isolates into three distinct groups, 100% concordant with the epidemiological data. The minimum and maximum number of hqSNVs between isolates from the same outbreak was 0 and 4, respectively, while >59 hqSNVs were measured between 2 previously indistinguishable outbreaks having the same PFGE and phage type, thus corroborating their distinction as separate unrelated outbreaks. This study demonstrates that despite the previously reported high clonality of this serovar, the WGS-based hqSNV approach is a superior typing method, capable of resolving events that were previously indistinguishable using classic subtyping tools.

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Comparison between Salmonella enterica Serotype Enteritidis Genotyping Methods and Phage Type

Journal of Clinical Microbiology ◽

10.1128/jcm.01122-15 ◽

2015 ◽

Vol 53 (9) ◽

pp. 3021-3031 ◽

Cited By ~ 3

Author(s):

Alessandra De Cesare ◽

Keshav Krishnamani ◽

Antonio Parisi ◽

Antonia Ricci ◽

Ida Luzzi ◽

...

Keyword(s):

Salmonella Enterica ◽

Phage Type ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Quantitative Comparison ◽

Pulsed Field Gel Electrophoresis ◽

Typing Method ◽

Content Type ◽

Repeat Analysis ◽

Automated Ribotyping

A quantitative comparison between discriminatory indexes and concordance among multilocus variable-number tandem-repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE), automated ribotyping, and phage typing has been performed, testing 238Salmonella entericaserotype Enteritidis isolates not epidemiologically correlated. The results show that MLVA is the best choice, but each typing method provides a piece of information for establishing clonal relationships between the isolates.

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Comparative Analysis of Extended-Spectrum-β-Lactamase CTX-M-65-Producing Salmonella enterica Serovar Infantis Isolates from Humans, Food Animals, and Retail Chickens in the United States

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00488-17 ◽

2017 ◽

Vol 61 (7) ◽

Cited By ~ 45

Author(s):

Heather Tate ◽

Jason P. Folster ◽

Chih-Hao Hsu ◽

Jessica Chen ◽

Maria Hoffmann ◽

...

Keyword(s):

United States ◽

Antimicrobial Resistance ◽

Salmonella Enterica ◽

One Health ◽

The United States ◽

Nucleotide Polymorphism ◽

High Quality ◽

Single Nucleotide ◽

Content Type ◽

High Quality Snps

ABSTRACT We sequenced the genomes of 10 Salmonella enterica serovar Infantis isolates containing bla CTX-M-65 obtained from chicken, cattle, and human sources collected between 2012 and 2015 in the United States through routine National Antimicrobial Resistance Monitoring System (NARMS) surveillance and product sampling programs. We also completely assembled the plasmids from four of the isolates. All isolates had a D87Y mutation in the gyrA gene and harbored between 7 and 10 resistance genes [aph(4)-Ia, aac(3)-IVa, aph(3′)-Ic, bla CTX-M-65, fosA3, floR, dfrA14, sul1, tetA, aadA1] located in two distinct sites of a megaplasmid (∼316 to 323 kb) similar to that described in a bla CTX-M-65-positive S. Infantis isolate from a patient in Italy. High-quality single nucleotide polymorphism (hqSNP) analysis revealed that all U.S. isolates were closely related, separated by only 1 to 38 pairwise high-quality SNPs, indicating a high likelihood that strains from humans, chickens, and cattle recently evolved from a common ancestor. The U.S. isolates were genetically similar to the bla CTX-M-65-positive S. Infantis isolate from Italy, with a separation of 34 to 47 SNPs. This is the first report of the bla CTX-M-65 gene and the pESI (plasmid for emerging S. Infantis)-like megaplasmid from S. Infantis in the United States, and it illustrates the importance of applying a global One Health human and animal perspective to combat antimicrobial resistance.

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Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections

Journal of Clinical Microbiology ◽

10.1128/jcm.00517-18 ◽

2018 ◽

Vol 56 (9) ◽

Cited By ~ 15

Author(s):

Anna Janowicz ◽

Fabrizio De Massis ◽

Massimo Ancora ◽

Cesare Cammà ◽

Claudio Patavino ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Multilocus Sequence Typing ◽

Core Genome ◽

Brucella Melitensis ◽

Reference Sequence ◽

Snp Analysis ◽

Phylogenetic Distance ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Content Type

ABSTRACT The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome multilocus sequence typing (cgMLST) has not been explored so far. The current study developed an allele-based cgMLST method and compared its performance to that of the genome-wide SNP approach and the traditional multilocus variable-number tandem repeat analysis (MLVA) on a defined sample collection. The data set was comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 isolates with unknown epidemiological status, composed of human and animal samples collected in Italy. The cgMLST scheme generated in this study contained 2,704 targets of the B. melitensis 16M reference genome. We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be ≤6 loci in the cgMLST and ≤7 in WGS SNP analysis. Higher phylogenetic distance resolution was achieved with cgMLST and SNP analysis than with MLVA, particularly for strains belonging to the same lineage, thereby allowing diverse and unrelated genotypes to be identified with greater confidence. The application of a cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen, and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.

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Influence of SOS-inducing agents on the expression of ArtAB toxin gene in Salmonella enterica and Salmonella bongori

Microbiology ◽

10.1099/mic.0.000939 ◽

2020 ◽

Vol 166 (8) ◽

pp. 785-793

Author(s):

Shou Miura ◽

Yukino Tamamura ◽

Mariko Takayasu ◽

Miwa Sasaki ◽

Natsuko Nishimura ◽

...

Keyword(s):

Salmonella Enterica ◽

Type Species ◽

Phage Type ◽

Sos Response ◽

Toxin Gene ◽

Efficient Production ◽

Prophage Induction ◽

Content Type ◽

Link Type ◽

Quinolone Antibiotics

Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) definitive phage type 104 (DT104), S. enterica subspecies enterica serovar Worthington (S. Worthington) and S. bongori produce ArtA and ArtB (ArtAB) toxin homologues, which catalyse ADP-ribosylation of pertussis toxin-sensitive G protein. ArtAB gene (artAB) is encoded on prophage in DT104 and its expression is induced by mitomycin C (MTC) and hydrogen peroxide (H2O2) that trigger the bacterial SOS response. Although the genetic regulatory mechanism associated with artAB expression is not characterized, it is thought to be associated with prophage induction, which occurs when the RecA-mediated SOS response is triggered. Here we show that subinhibitory concentration of quinolone antibiotics that are SOS-inducing agents, also induce ArtAB production in these Salmonella strains. Both MTC and fluoroquinolone antibiotics such as enrofloxacin-induced artA and recA transcription and artAB-encoding prophage (ArtAB-prophage) in DT104 and S. Worthington. However, in S. bongori , which harbours artAB genes on incomplete prophage, artA transcription was induced by MTC and enrofloxacin, but prophage induction was not observed. Taken together, these results suggest that SOS response followed by induction of artAB transcription is essential for ArtAB production. H2O2-mediated induction of ArtAB prophage and efficient production of ArtAB was observed in DT104 but not in S. Worthington and S. bongori . Therefore, induction of artAB expression with H2O2 is strain-specific, and the mode of action of H2O2 as an SOS-inducing agent might be different from those of MTC and quinolone antibiotics.

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Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017

Microbiology ◽

10.1099/mic.0.000895 ◽

2020 ◽

Vol 166 (5) ◽

pp. 453-459

Author(s):

Arthur W. Pightling ◽

James Pettengill ◽

Yan Luo ◽

Errol Strain ◽

Hugh Rand

Keyword(s):

Phylogenetic Analysis ◽

Drug Administration ◽

Salmonella Enterica ◽

Type Species ◽

Food And Drug Administration ◽

Genomic Diversity ◽

Diverse Populations ◽

Content Type ◽

The Us ◽

Geographic Regions

In 2017, the US Food and Drug Administration investigated the sources of multiple outbreaks of salmonellosis. Epidemiologic and traceback investigations identified Maradol papayas as the suspect vehicles. During the investigations, the genomes of 55 Salmonella enterica that were isolated from papaya samples were sequenced. Serovar assignments and phylogenetic analysis placed the 55 isolates into ten distinct groups, each representing a different serovar. Within-serovar SNP differences are generally between 0 and 20 SNPs, while the median between-serovar distance is 51 812 SNPs. We observed two groups with SNP distances between 21 and 100 SNPs. These relatively large within-serovar SNP distances may indicate that the isolates represent either diverse populations or multiple, genetically distinct subpopulations. Further inspection of these cases with traceback evidence allowed us to identify an 11th population. We observed that high levels of genomic diversity from individual firms is possible, with one firm yielding five of the ten serovars. Also, high levels of diversity are possible within small geographic regions, as five of the serovars were isolated from papayas that originated from farms located in Armería and Tecomán, Colima. In addition, we identified AMR genes that are present in three of the serovars studied here (aph(3’)-lb, aph(6)-ld, tet(C), fosA7, and qnrB19) and we detected the presence of the plasmid IncHI2A among S. Urbana isolates.

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Rapid Increase of CTX-M-Producing Shigella sonnei Isolates in Switzerland Due to Spread of Common Plasmids and International Clones

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01057-20 ◽

2020 ◽

Vol 64 (10) ◽

Author(s):

Edgar I. Campos-Madueno ◽

Odette J. Bernasconi ◽

Aline I. Moser ◽

Peter M. Keller ◽

Francesco Luzzaro ◽

...

Keyword(s):

Core Genome ◽

The United States ◽

Sequence Type ◽

Shigella Sonnei ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Content Type ◽

Phylogenetic Comparison ◽

The United Kingdom ◽

Extended Spectrum

ABSTRACT The Swiss Centre for Antibiotic Resistance (ANRESIS) has recently noted an increase of extended-spectrum cephalosporin-resistant (ESC-R) Shigella sonnei isolates nationwide (3.8% in 2016 versus 37.5% in 2019). To understand this phenomenon, we analyzed 25 representative isolates (of which 14 were ESC-R) collected in Switzerland during 2016 to 2019. Whole-genome sequencing was achieved using both the Illumina and the Nanopore platforms. Both ESC-R and extended-spectrum cephalosporin-susceptible isolates belonged to sequence type 152 (ST152). The ESC-R isolates carried blaCTX-M-3 in IncI1-pST57 (n = 5), blaCTX-M-15 in IncFII (F2:A-:B-) (n = 5), blaCTX-M-15 in IncI1-pST16, and blaCTX-M-27, blaCTX-M-55, or blaCTX-M-134 in other IncFII plasmids (n = 1 each). Plasmids having the same bla and Inc group exhibited high degrees of genetic identity to each other but also to plasmids previously reported in other Enterobacterales. Core-genome analysis showed that there were 4 main clusters, each of which included strains that differed by <58 single nucleotide variants (SNVs) and that consisted of both blaCTX-M-positive and blaCTX-M-negative isolates. Moreover, most isolates belonging to the same cluster shared an identical core-genome sequence type (cgST). For instance, cluster 1 included 4 isolates of cgST113036, of which only 3 harbored the IncI1-pST57 blaCTX-M-3-positive plasmid. The 25 S. sonnei isolates were also subjected to phylogenetic comparison with deposited international strains. As a result, matching isolates (isolates that had the same cgST and that differed by <8 SNVs) have been reported in the United Kingdom, the United States, France, and the Netherlands. Overall, our results suggest that some common S. sonnei clusters can spread between continents and can be imported into other nations after international trips. Such clusters include, in part, isolates that do not possess blaESBL-harboring plasmids, indicating their tendency to acquire them from other Enterobacterales.

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Epidemiology of a Salmonella enterica subsp. enterica Serovar Typhimurium Strain Associated with a Songbird Outbreak

Applied and Environmental Microbiology ◽

10.1128/aem.01408-12 ◽

2012 ◽

Vol 78 (20) ◽

pp. 7290-7298 ◽

Cited By ~ 26

Author(s):

Sonia M. Hernandez ◽

Kevin Keel ◽

Susan Sanchez ◽

Eija Trees ◽

Peter Gerner-Smidt ◽

...

Keyword(s):

United States ◽

Salmonella Enterica ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Pfge Type ◽

Eastern United States ◽

Typing Method ◽

Content Type ◽

Typhimurium Strain ◽

Serovar Typhimurium

ABSTRACTSalmonella entericasubsp.entericaserovar Typhimurium is responsible for the majority of salmonellosis cases worldwide. ThisSalmonellaserovar is also responsible for die-offs in songbird populations. In 2009, there was anS. Typhimurium epizootic reported in pine siskins in the eastern United States. At the time, there was also a human outbreak with this serovar that was associated with contaminated peanuts. As peanuts are also used in wild-bird food, it was hypothesized that the pine siskin epizootic was related to this human outbreak. A comparison of songbird and humanS. Typhimurium pulsed-field gel electrophoresis (PFGE) patterns revealed that the epizootic was attributed not to the peanut-associated strain but, rather, to a songbird strain first characterized from an American goldfinch in 1998. This sameS. Typhimurium strain (PFGE type A3) was also identified in the PulseNet USA database, accounting for 137 of 77,941 totalS. Typhimurium PFGE entries. A second molecular typing method, multiple-locus variable-number tandem-repeat analysis (MLVA), confirmed that the same strain was responsible for the pine siskin epizootic in the eastern United States but was distinct from a genetically related strain isolated from pine siskins in Minnesota. The pine siskin A3 strain was first encountered in May 2008 in an American goldfinch and later in a northern cardinal at the start of the pine siskin epizootic. MLVA also confirmed the clonal nature ofS. Typhimurium in songbirds and established that the pine siskin epizootic strain was unique to the finch family. For 2009, the distribution of PFGE type A3 in passerines and humans mirrored the highest population density of pine siskins for the East Coast.

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Genomic Investigation of the Emergence of Invasive Multidrug-Resistant Salmonella enterica Serovar Dublin in Humans and Animals in Canada

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00108-19 ◽

2019 ◽

Vol 63 (6) ◽

Cited By ~ 2

Author(s):

Chand S. Mangat ◽

Sadjia Bekal ◽

Brent P. Avery ◽

Geneviève Côté ◽

Danielle Daignault ◽

...

Keyword(s):

Salmonella Enterica ◽

Bloodstream Infections ◽

The United States ◽

Multidrug Resistant ◽

Phylogenomic Analysis ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Content Type ◽

Human Infections ◽

Integrated Program

ABSTRACT Salmonella enterica subsp. enterica serovar Dublin is a zoonotic pathogen that often leads to invasive bloodstream infections in humans that are multidrug resistant. Described here are the results of Canadian national surveillance of S. Dublin from 2003 to 2015 in humans and bovines, principally collected through the Canadian Integrated Program for Antibiotic Resistance Surveillance (CIPARS). An increase in human infections due to multidrug-resistant (MDR) S. Dublin was observed in 2010, many of which were bloodstream infections. Phylogenomic analysis of human and bovine isolates revealed a closely related network that differed by only 0 to 17 single nucleotide variants (SNVs), suggesting some potential transmission between humans and bovines. Phylogenomic comparison of global publicly available sequences of S. Dublin showed that Canadian isolates clustered closely with those from the United States. A high correlation between phenotypic and genotypic antimicrobial susceptibility was observed in Canadian isolates. IS26 replication was widespread among U.S. and Canadian isolates and caused the truncation and inactivation of the resistance genes strA and blaTEM-1B. A hybrid virulence and MDR plasmid (pN13-01125) isolated from a Canadian S. Dublin isolate was searched against NCBI SRA data of bacteria. The pN13-01125 coding sequences were found in 13 Salmonella serovars, but S. Dublin appears to be a specific reservoir. In summary, we have observed the rise of invasive MDR S. Dublin in humans in Canada and found that they are closely related to bovine isolates and to American isolates in their mobile and chromosomal contents.

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Expansion of Vancomycin-ResistantEnterococcus faeciumin an Academic Tertiary Hospital in Southwest Germany: a Large-Scale Whole-Genome-Based Outbreak Investigation

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01978-18 ◽

2019 ◽

Vol 63 (5) ◽

Cited By ~ 16

Author(s):

Jan Liese ◽

Leonard Schüle ◽

Philipp Oberhettinger ◽

Leonie Tschörner ◽

Tran Nguyen ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Large Scale ◽

Medical Center ◽

Regional Scale ◽

Epidemiological Data ◽

Tertiary Hospital ◽

Sequence Type ◽

Whole Genome ◽

Content Type ◽

Health Care Networks

ABSTRACTVancomycin-resistantEnterococcus faecium(VREfm) is a frequent cause of nosocomial outbreaks. In the second half of 2015, a sharp increase in the incidence of VREfm was observed at our university medical center. Next-generation sequencing (NGS) was used to analyze the first isolates of VREfm recovered from patients between 2010 and 2016 (n = 773) in order to decipher epidemiological change, outbreak dynamics, and possible transmission routes. VREfm isolates were analyzed using whole-genome sequencing followed by sequence type extraction and phylogenetic analysis. We examined epidemiological data, room occupancy data, and patient transferals and calculated an intensity score for patient-to-patient contact. Phylogenetic analysis revealed the presence of 38 NGS clusters and 110 single clones. The increase of VREfm was caused mainly by the expansion of two newly introduced NGS clusters, comprising VanB-type strains determined by multilocus sequence typing (MLST) as sequence type 80 (ST80) and ST117. By combining phylogenetic information with epidemiological data, intrahospital transmission could be demonstrated, however to a lesser extent than initially expected based solely on epidemiological data. The outbreak clones were continuously imported from other hospitals, suggesting a change in the epidemiological situation at a regional scale. By tracking intrahospital patient transferals, two major axes could be identified that contributed to the spread of VREfm within the hospital. NGS-based outbreak analysis revealed a dramatic change in the local and regional epidemiology of VREfm, emphasizing the role of health care networks in the spread of VREfm.

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Temperature-Sensitive Salmonella enterica Serovar Enteritidis PT13a Expressing Essential Proteins of Psychrophilic Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.01953-15 ◽

2015 ◽

Vol 81 (19) ◽

pp. 6757-6766 ◽

Cited By ~ 3

Author(s):

Barry N. Duplantis ◽

Stephanie M. Puckett ◽

Everett L. Rosey ◽

Keith A. Ameiss ◽

Angela D. Hartman ◽

...

Keyword(s):

Salmonella Enterica ◽

Type Strain ◽

Wild Type Strain ◽

Phage Type ◽

The Body ◽

Temperature Sensitive ◽

Restrictive Temperature ◽

Wild Type ◽

Psychrophilic Bacteria ◽

Content Type

ABSTRACTSynthetic genes based on deduced amino acid sequences of the NAD-dependent DNA ligase (ligA) and CTP synthetase (pyrG) of psychrophilic bacteria were substituted for their native homologues in the genome ofSalmonella entericaserovar Enteritidis phage type 13a (PT13a). The resulting strains were rendered temperature sensitive (TS) and did not revert to temperature resistance at a detectable level. At permissive temperatures, TS strains grew like the parental strain in broth medium and in macrophage-like cells, but their growth was slowed or stopped when they were shifted to a restrictive temperature. When injected into BALB/c mice at the base of the tail, representing a cool site of the body, the strains with restrictive temperatures of 37, 38.5, and 39°C persisted for less than 1 day, 4 to 7 days, and 20 to 28 days, respectively. The wild-type strain persisted at the site of inoculation for at least 28 days. The wild-type strain, but not the TS strains, was also found in spleen-plus-liver homogenates within 1 day of inoculation of the tail and was detectable in these organs for at least 28 days. Intramuscular vaccination of White Leghorn chickens with the PT13a strain carrying the psychrophilicpyrGgene provided some protection against colonization of the reproductive tract and induced an anti-S. entericaantibody response.

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