Outbreak of <i>Salmonella</i> Newport Infections with Decreased Susceptibility to Azithromycin Linked to Beef Obtained in the United States and Soft Cheese Obtained in Mexico — United States, 2018–2019

Plumb, Ian D.; Schwensohn, Colin; Gieraltowski, Laura; Tecle, Selam; Schneider, Zachary; Freiman, Jennifer; Cote, Andrea; Noveroske, Douglas; Kolsin, Jonathan; Brandenburg, Joshua; Chen, Jessica C.; Tagg, Kaitlin A.; White, Porscha Bumpus; Shah, Hazel J; Watkins, Louise Francois; Wise, Matthew E.; Friedman, Cindy R.

doi:10.15585/mmwr.mm6833a1

Cited by 43 publications

(29 citation statements)

References 6 publications

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“…Similarly, Mather et al (2013) demonstrated that S. Typhimurium DT104 and its antimicrobial resistance genes were maintained largely separately within animal and human populations in Scotland, with little transmission between animals and humans and vice versa. Overall, these data suggest that the transmission of Salmonella between bovine and human hots may be less frequent than sometimes assumed, even though there have been cases of AMR S. Dublin (Harvey et al, 2017), S. Newport (Centers for Disease Control and Prevention, 2002;Plumb et al, 2019) and S. Typhimurium (Olsen et al, 2004;McLaughlin et al, 2006) outbreaks in humans linked to raw milk, raw beef or cheese. Our findings are also consistent with some studies that indicated geographical association with different Salmonella clonal groups; for example, Kovac et al (2017) reported that S. Cerro found in Texas and NY represents largely distinct clonal groups.…”

Section: Discussionmentioning

confidence: 80%

Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial‐resistant Salmonella enterica

Liao

Orsi

Carroll

2020

Environmental Microbiology

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Summary Genetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco‐evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York and Washington states to understand host‐ and geographic‐associated population structure. Results revealed distinct presence/absence profiles of functional genes and pseudogenes (e.g., virulence genes) associated with bovine and human isolates. Notably, bovine isolates contained significantly more transposase genes but fewer transposase pseudogenes than human isolates, suggesting the occurrence of large‐scale transposition in genomes of bovine and human isolates at different times. The high correlation between transposase genes and AMR genes, as well as plasmid replicons, highlights the potential role of horizontally transferred transposons in promoting adaptation to antibiotics. By contrast, a number of potentially geographic‐associated single‐nucleotide polymorphisms (SNPs), rather than geographic‐associated genes, were identified. Interestingly, 38% of these SNPs were in genes annotated as cell surface protein‐encoding genes, including some essential for antibiotic resistance and host colonization. Overall, different evolutionary forces and limited recent inter‐population transmission appear to shape AMR S. enterica population structure in different hosts and geographic origins.

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Section: Discussionmentioning

confidence: 80%

Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial‐resistant Salmonella enterica

Liao

Orsi

Carroll

2020

Environmental Microbiology

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“…Some examples include MDR S. enterica ser. Newport associated with exposure to dairy cattle and beef in the United States (Holmberg et al, 1984; Centers for Disease Control and Prevention [CDC], 2002;Butaye et al, 2006;Schneider et al, 2011;Plumb, 2019), MDR S. enterica ser. Heidelberg is frequently associated with poultry in both Canada and the United States (Dutil et al, 2010;Routh et al, 2015;Gieraltowski et al, 2016), and MDR S. enterica ser.…”

Section: Discussionmentioning

confidence: 99%

Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance

et al. 2020

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Whole-genome sequencing (WGS) is used increasingly in public-health laboratories for typing and characterizing foodborne pathogens. To evaluate the performance of existing bioinformatic tools for in silico prediction of antimicrobial resistance (AMR) and serotypes of Salmonella enterica, WGS-based genotype predictions were compared with the results of traditional phenotyping assays. A total of 111 S. enterica isolates recovered from a Canadian baseline study on broiler chicken conducted in 2012-2013 were selected based on phenotypic resistance to 15 different antibiotics and isolates were subjected to WGS. Both SeqSero2 and SISTR accurately determined S. enterica serotypes, with full matches to laboratory results for 87.4 and 89.2% of isolates, respectively, and partial matches for the remaining isolates. Antimicrobial resistance genes (ARGs) were identified using several bioinformatics tools including the Comprehensive Antibiotic Resistance Database-Resistance Gene Identifier (CARD-RGI), Center for Genomic Epidemiology (CGE) ResFinder web tool, Short Read Sequence Typing for Bacterial Pathogens (SRST2 v 0.2.0), and k-mer alignment method (KMA v 1.17). All ARG identification tools had ≥ 99% accuracy for predicting resistance to all antibiotics tested except streptomycin (accuracy 94.6%). Evaluation of ARG detection in assembled versus raw-read WGS data found minimal observable differences that were gene-and coverage-dependent. Where initial phenotypic results indicated isolates were sensitive, yet ARGs were detected, repeat AMR testing corrected discrepancies. All tools failed to find resistance-determining genes for one gentamicinand two streptomycin-resistant isolates. Further investigation found a single nucleotide polymorphism (SNP) in the nuoF coding region of one of the isolates which may be responsible for the observed streptomycin-resistant phenotype. Overall, WGS-based predictions of AMR and serotype were highly concordant with phenotype determination regardless of computational approach used.

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“…Other serotypes exhibiting MDR includes Salmonella Newport, which has recently been reported by the Centers for Disease Control and Prevention as having ciprofloxacin and azithromycin resistance in the US; the origin was soft cheese and beef from the US and Mexico, respectively [20]. Globally, MDR has also been reported for DT104 S. Typhimurium [21,22].…”

Section: Discussionmentioning

confidence: 99%

International lineages of Salmonella enterica serovars isolated from chicken farms, Wakiso District, Uganda

et al. 2020

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The growing occurrence of multidrug-resistant (MDR) Salmonella enterica in poultry has been reported with public health concern worldwide. We reported, recently, the occurrence of Escherichia coli and Salmonella enterica serovars carrying clinically relevant resistance genes in dairy cattle farms in the Wakiso District, Uganda, highlighting an urgent need to monitor food-producing animal environments. Here, we present the prevalence, antimicrobial resistance, and sequence type of 51 Salmonella isolates recovered from 379 environmental samples from chicken farms in Uganda. Among the Salmonella isolates, 32/51 (62.7%) were resistant to at least one antimicrobial, and 10/51 (19.6%) displayed multiple drug resistance. Through PCR, five replicon plasmids were identified among chicken Salmonella isolates including IncFIIS 17/51 (33.3%), IncI1α 12/51 (23.5%), IncP 8/51 (15.7%), IncX1 8/51 (15.7%), and IncX2 1/51 (2.0%). In addition, we identified two additional replicons through WGS (Whole Genome Sequencing; ColpVC and IncFIB). A significant seasonal difference between chicken sampling periods was observed (p = 0.0017). We conclude that MDR Salmonella highlights the risks posed to animals and humans. Implementing a robust, integrated surveillance system will aid in monitoring MDR zoonotic threats.

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Outbreak of Salmonella Newport Infections with Decreased Susceptibility to Azithromycin Linked to Beef Obtained in the United States and Soft Cheese Obtained in Mexico — United States, 2018–2019

Cited by 43 publications

References 6 publications

Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial‐resistant Salmonella enterica

Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial‐resistant Salmonella enterica

Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance

International lineages of Salmonella enterica serovars isolated from chicken farms, Wakiso District, Uganda

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