Antimicrobial resistance and related gene analysis of Salmonella from egg and chicken sources by whole-genome sequencing

In response to new stringent regulations in Canada regarding the use of antibiotics in animal production, many farms have implemented practices to produce animals that are raised without antibiotics (RWA) from birth to slaughter. This study aims to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, the occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance of farms that adopted the RWA program and conventional farms using antibiotics in accordance with the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week-old pigs and composite manure from the barn over six time points and applying whole-genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug use records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced the frequency of AMR genes in piglet feces and in-barn manure. However, metagenomic analyses showed that RWA barns had a significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.

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Serotype Diversity and Antimicrobial Resistance amongSalmonella entericaIsolates from Patients at an Equine Referral Hospital

Applied and Environmental Microbiology ◽

10.1128/aem.02829-17 ◽

2018 ◽

Vol 84 (13) ◽

pp. e02829-17 ◽

Cited By ~ 3

Author(s):

I. M. Leon ◽

S. D. Lawhon ◽

K. N. Norman ◽

D. S. Threadgill ◽

N. Ohta ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Referral Hospital ◽

Whole Genome ◽

Content Type ◽

Genes Encoding ◽

Life Threatening ◽

Common Serotypes

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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Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

Nature Communications ◽

10.1038/s41467-020-16322-5 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Silvia Argimón ◽

Melissa A. L. Masim ◽

June M. Gayeta ◽

Marietta L. Lagrada ◽

Polle K. V. Macaranas ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

The Philippines ◽

Surveillance Program ◽

Whole Genome ◽

Antimicrobial Resistance Surveillance

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Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges

Frontiers in Microbiology ◽

10.3389/fmicb.2019.01107 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 20

Author(s):

Lucie Collineau ◽

Patrick Boerlin ◽

Carolee A. Carson ◽

Brennan Chapman ◽

Aamir Fazil ◽

...

Keyword(s):

Risk Assessment ◽

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Quantitative Risk Assessment ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data

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Comparative Whole-Genome Phylogeny of Animal, Environmental, and Human Strains Confirms the Genogroup Organization and Diversity of the Stenotrophomonas maltophilia Complex

Applied and Environmental Microbiology ◽

10.1128/aem.02919-19 ◽

2020 ◽

Vol 86 (10) ◽

Author(s):

Mélanie Mercier-Darty ◽

Guilhem Royer ◽

Brigitte Lamy ◽

Chadly Charron ◽

Olivier Lemenand ◽

...

Keyword(s):

Genetic Diversity ◽

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Resistance Genes ◽

Stenotrophomonas Maltophilia ◽

Whole Genome ◽

Content Type ◽

Genetic Organization ◽

Animal Strains

ABSTRACT The Stenotrophomonas maltophilia complex (Smc) comprises opportunistic environmental Gram-negative bacilli responsible for a variety of infections in both humans and animals. Beyond its large genetic diversity, its genetic organization in genogroups was recently confirmed through the whole-genome sequencing of human and environmental strains. As they are poorly represented in these analyses, we sequenced the whole genomes of 93 animal strains to determine their genetic background and characteristics. Combining these data with 81 newly sequenced human strains and the genomes available from RefSeq, we performed a genomic analysis that included 375 nonduplicated genomes with various origins (animal, 104; human, 226; environment, 30; unknown, 15). Phylogenetic analysis and clustering based on genome-wide average nucleotide identity confirmed and specified the genetic organization of Smc in at least 20 genogroups. Two new genogroups were identified, and two previously described groups were further divided into two subgroups each. Comparing the strains isolated from different host types and their genogroup affiliation, we observed a clear disequilibrium in certain groups. Surprisingly, some antimicrobial resistance genes, integrons, and/or clusters of attC sites lacking integron-integrase (CALIN) sequences targeting antimicrobial compounds extensively used in animals were mainly identified in animal strains. We also identified genes commonly found in animal strains coding for efflux systems. The result of a large whole-genome analysis performed by us supports the hypothesis of the putative contribution of animals as a reservoir of Stenotrophomonas maltophilia complex strains and/or resistance genes for strains in humans. IMPORTANCE Given its naturally large antimicrobial resistance profile, the Stenotrophomonas maltophilia complex (Smc) is a set of emerging pathogens of immunosuppressed and cystic fibrosis patients. As it is group of environmental microorganisms, this adaptation to humans is an opportunity to understand the genetic and metabolic selective mechanisms involved in this process. The previously reported genomic organization was incomplete, as data from animal strains were underrepresented. We added the missing piece of the puzzle with whole-genome sequencing of 93 strains of animal origin. Beyond describing the phylogenetic organization, we confirmed the genetic diversity of the Smc, which could not be estimated through routine phenotype- or matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF)-based laboratory tests. Animals strains seem to play a key role in the diversity of Smc and could act as a reservoir for mobile resistance genes. Some genogroups seem to be associated with particular hosts; the genetic support of this association and the role of the determinants/corresponding genes need to be explored.

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