Antimicrobial resistance analysis and whole-genome sequencing of Salmonella enterica serovar Indiana isolate from ducks

ABSTRACTAlthoughSalmonella entericacan produce life-threatening colitis in horses, certain serotypes are more commonly associated with clinical disease. Our aim was to evaluate the proportional morbidity attributed to different serotypes, as well as the phenotypic and genotypic antimicrobial resistance (AMR) ofSalmonellaisolates from patients at an equine referral hospital in the southern United States. A total of 255Salmonellaisolates was obtained from clinical samples of patients admitted to the hospital between 2007 and 2015. Phenotypic resistance to 14 antibiotics surveilled by the U.S. National Antimicrobial Resistance Monitoring System was determined using a commercially available panel. Whole-genome sequencing was used to identify serotypes and genotypic AMR. The most common serotypes wereSalmonella entericaserotype Newport (18%),Salmonella entericaserotype Anatum (15.2%), andSalmonella entericaserotype Braenderup (11.8%). Most (n= 219) of the isolates were pansusceptible, while 25 were multidrug resistant (≥3 antimicrobial classes). Genes encoding beta-lactam resistance, such asblaCMY-2,blaSHV-12,blaCTX-M-27, andblaTEM-1B, were detected. TheqnrB2 andaac(6′)-Ib-crgenes were present in isolates with reduced susceptibility to ciprofloxacin. Genes encoding resistance to gentamicin (aph(3′)-Ia,aac(6′)-IIc), streptomycin (strA andstrB), sulfonamides (sul1), trimethoprim (dfrA), phenicols (catA), tetracyclines [tet(A) andtet(E)], and macrolides [ere(A)] were also identified. The main predicted incompatibility plasmid type was I1 (10%). Core genome-based analyses revealed phylogenetic associations between isolates of common serotypes. The presence of AMRSalmonellain equine patients increases the risk of unsuccessful treatment and causes concern for potential zoonotic transmission to attending veterinary personnel, animal caretakers, and horse owners. Understanding the epidemiology ofSalmonellain horses admitted to referral hospitals is important for the prevention, control, and treatment of salmonellosis.IMPORTANCEIn horses, salmonellosis is a leading cause of life-threatening colitis. At veterinary teaching hospitals, nosocomial outbreaks can increase the risk of zoonotic transmission, lead to restrictions on admissions, impact hospital reputation, and interrupt educational activities. The antimicrobials most often used in horses are included in the 5th revision of the World Health Organization's list of critically important antimicrobials for human medicine. Recent studies have demonstrated a trend of increasing bacterial resistance to drugs commonly used to treatSalmonellainfections. In this study, we identify temporal trends in the distribution ofSalmonellaserotypes and their mechanisms of antimicrobial resistance; furthermore, we are able to determine the likely origin of several temporal clusters of infection by using whole-genome sequencing. These data can be used to focus strategies to better contain the dissemination and enhance the mitigation ofSalmonellainfections and to provide evidence-based policies and guidelines to steward antimicrobial use in veterinary medicine.

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Whole genome sequencing (WGS) fails to detect antimicrobial resistance (AMR) from heteroresistant subpopulation of Salmonella enterica

Food Microbiology ◽

10.1016/j.fm.2020.103530 ◽

2020 ◽

Vol 91 ◽

pp. 103530

Author(s):

Ye Htut Zwe ◽

Seow Fong Chin ◽

Gurjeet Singh Kohli ◽

Kyaw Thu Aung ◽

Liang Yang ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Whole Genome

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Whole-genome sequencing and antimicrobial resistance analysis of a multidrug-resistant strain Aeromonas veronii JC529 from a common carp

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2021.08.007 ◽

2021 ◽

Author(s):

Tiange Sheng ◽

Gege Song ◽

Taotao Yue ◽

Junhui Zhang ◽

Wendong Wang ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Common Carp ◽

Resistant Strain ◽

Multidrug Resistant ◽

Whole Genome ◽

Resistance Analysis ◽

Aeromonas Veronii ◽

Multidrug Resistant Strain

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Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife

Gut Pathogens ◽

10.1186/s13099-017-0213-x ◽

2017 ◽

Vol 9 (1) ◽

Cited By ~ 15

Author(s):

Milton Thomas ◽

Gavin John Fenske ◽

Linto Antony ◽

Sudeep Ghimire ◽

Ronald Welsh ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Whole Genome

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Whole-Genome Sequencing Analysis of Salmonella Enterica Serotype Enteritidis Isolated from Poultry Sources in South Korea, 2010–2017

Pathogens ◽

10.3390/pathogens10010045 ◽

2021 ◽

Vol 10 (1) ◽

pp. 45

Author(s):

Ji-Yeon Hyeon ◽

Shaoting Li ◽

David A. Mann ◽

Shaokang Zhang ◽

Kyu-Jik Kim ◽

...

Keyword(s):

Supply Chain ◽

Antimicrobial Resistance ◽

South Korea ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Resistance Genes ◽

Salmonella Enterica ◽

Snp Analysis ◽

Whole Genome ◽

Human Salmonellosis

Salmonella enterica subsp. enterica serotype Enteritidis (SE) is recognized as a major cause of human salmonellosis worldwide, and most human salmonellosis is due to the consumption of contaminated poultry meats and poultry byproducts. Whole-genome sequencing (data were obtained from 96 SE isolates from poultry sources, including an integrated broiler supply chain, farms, slaughterhouses, chicken transporting trucks, and retail chicken meats in South Korea during 2010–2017. Antimicrobial resistance and virulence genes were investigated using WGS data, and the phylogenetic relationship of the isolates was analyzed using single-nucleotide polymorphism (SNP) typing and core genome multilocus sequence typing (cgMLST). All isolates carried aminoglycoside resistance genes, aac(6’)-Iaa, and 56 isolates carried multiple antimicrobial resistance genes. The most frequent virulence gene profile, pef-fim-sop-inv.-org-sip-spa-sif-fli-flg-hil-ssa-sse-prg-pag-spv, was found in 90 isolates. The SNP analysis provided a higher resolution than the cgMLST analysis, but the cgMLST analysis was highly congruent with the SNP analysis. The phylogenetic results suggested the presence of resident SE within the facility of processing plants, environments of slaughterhouses, and the integrated broiler supply chain, and the phylogenetically related isolates were found in retail meats. In addition, the SE isolates from different origins showed close genetic relationships indicating that these strains may have originated from a common source. This study could be valuable reference data for future traceback investigations in South Korea.

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Monitoring the Antimicrobial Resistance Dynamics of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing

10.1101/2021.08.20.457169 ◽

2021 ◽

Author(s):

Laura M Carroll ◽

Ariel J Buehler ◽

Ahmed Gaballa ◽

Julie D Siler ◽

Kevin J Cummings ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Dairy Cattle ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

In Silico ◽

Salmonella Enterica ◽

Detection Methods ◽

Whole Genome ◽

The Individual ◽

Individual Farm

Livestock represent a possible reservoir for facilitating the transmission of the zoonotic foodborne pathogen Salmonella enterica to humans; there is also concern that strains can acquire resistance to antimicrobials in the farm environment. Here, we use whole-genome sequencing (WGS) to characterize Salmonella strains (n = 128) isolated from healthy dairy cattle and their associated environments on 13 New York State farms to assess the diversity and microevolution of this important pathogen at the level of the individual herd. Additionally, the accuracy and concordance of multiple in silico tools are assessed, including: (i) two in silico serotyping tools, (ii) combinations of five antimicrobial resistance (AMR) determinant detection tools and one to five AMR determinant databases, and (iii) one antimicrobial minimum inhibitory concentration (MIC) prediction tool. For the isolates sequenced here, in silico serotyping methods outperformed traditional serotyping and resolved all un-typable and/or ambiguous serotype assignments. Serotypes assigned in silico showed greater congruency with the Salmonella whole-genome phylogeny than traditional serotype assignments, and in silico methods showed high concordance (99% agreement). In silico AMR determinant detection methods additionally showed a high degree of concordance, regardless of the pipeline or database used (≥98% agreement between susceptible/resistant assignments for all pipeline/database combinations). For AMR detection methods that relied exclusively on nucleotide BLAST, accuracy could be maximized by using a range of minimum nucleotide identity and coverage thresholds, with thresholds of 75% nucleotide identity and 50-60% coverage adequate for most pipeline/database combinations. In silico characterization of the microevolution and AMR dynamics of each of six serotype groups (S. Anatum, Cerro, Kentucky, Meleagridis, Newport, Typhimurium/Typhimurium variant Copenhagen) revealed that some lineages were strongly associated with individual farms, while others were distributed across multiple farms. Numerous AMR determinant acquisition and loss events were identified, including the recent acquisition of cephalosporin resistance-conferring blaCMY- and blaCTX-M-type beta-lactamases. The results presented here provide high-resolution insight into the temporal dynamics of AMR Salmonella at the scale of the individual farm and highlight both the strengths and limitations of WGS in tracking zoonotic pathogens and their associated AMR determinants at the livestock-human interface.

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Whole-Genome Sequencing of Six Strains of Salmonella enterica Isolated from Imported Meat in Algeria

Microbiology Resource Announcements ◽

10.1128/mra.00615-19 ◽

2019 ◽

Vol 8 (35) ◽

Author(s):

A. Deriet ◽

M. Berrazeg ◽

S. C. J. De Keersmaecker ◽

N. Botteldoorn ◽

K. Vanneste ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Virulence Factors ◽

Salmonella Enterica ◽

Whole Genome ◽

Foodborne Disease ◽

Content Type

Nontyphoidal Salmonella (NTS) is one of the main causes of foodborne disease worldwide. In this report, we announce the first whole-genome sequencing of six strains of Salmonella enterica isolated from imported meat in Algeria. The genome sizes ranged from 4,601,209 to 4,958,962 bp. Antimicrobial resistance (AMR) genes, plasmids, and virulence factors were detected.

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