Long-term spatiotemporal variation of antimicrobial resistance genes within the Serratia marcescens population and transmission of S. marcescens revealed by public whole-genome datasets

Antimicrobial resistance has become a major public health threat. Food-related Staphylococcus species have received much attention due to their multidrug resistance. The cfr gene associated with multidrug resistance has been consistently detected in food-derived Staphylococcus species. In this retrospective study, we examined the prevalence of cfr-positive Staphylococcus strains isolated from poultry meat in different geographical areas of China from 2011 to 2016. Two cfr-positive Staphylococcus delphini strains were identified from poultry meat in China. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in the two S. delphini isolates 245-1 and 2794-1. Whole-genome sequencing showed that they both harbored a novel 20,258-bp cfr-carrying Tn558 transposon derivative on their chromosomes. The Tn558 derivative harbors multiple antimicrobial resistance genes, including the transferable multiresistance gene cfr, chloramphenicol resistance gene fexA, aminoglycoside resistance genes aacA-aphD and aadD, and bleomycin resistance gene ble. Surprisingly, within the Tn558 derivative, an active unconventional circularizable structure containing various resistance genes and a copy of a direct repeat sequence was identified by two-step PCR. Furthermore, core genome phylogenetic analysis revealed that the cfr-positive S. delphini strains were most closely related to S. delphini 14S03313-1 isolated from Japan in 2017 and 14S03319-1 isolated from Switzerland in 2017. This study is the first report of S. delphini harboring a novel cfr-carrying Tn558 derivative isolated from retail food. This finding raises further concerns regarding the potential threat to food safety and public health safety. The occurrence and dissemination of similar cfr-carrying transposons from diverse Staphylococcus species need further surveillance.

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Quantifying and predicting antimicrobials and antimicrobial resistance genes in waterbodies through a holistic approach: a study in Minnesota, United States

Scientific Reports ◽

10.1038/s41598-021-98300-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Irene Bueno ◽

Amanda Beaudoin ◽

William A. Arnold ◽

Taegyu Kim ◽

Lara E. Frankson ◽

...

Keyword(s):

Wastewater Treatment ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Wastewater Treatment Plants ◽

Spatial Scales ◽

Holistic Approach ◽

Antimicrobial Resistance Genes ◽

Study Power ◽

High Uncertainty

AbstractThe environment plays a key role in the spread and persistence of antimicrobial resistance (AMR). Antimicrobials and antimicrobial resistance genes (ARG) are released into the environment from sources such as wastewater treatment plants, and animal farms. This study describes an approach guided by spatial mapping to quantify and predict antimicrobials and ARG in Minnesota’s waterbodies in water and sediment at two spatial scales: macro, throughout the state, and micro, in specific waterbodies. At the macroscale, the highest concentrations across all antimicrobial classes were found near populated areas. Kernel interpolation provided an approximation of antimicrobial concentrations and ARG abundance at unsampled locations. However, there was high uncertainty in these predictions, due in part to low study power and large distances between sites. At the microscale, wastewater treatment plants had an effect on ARG abundance (sul1 and sul2 in water; blaSHV, intl1, mexB, and sul2 in sediment), but not on antimicrobial concentrations. Results from sediment reflected a long-term history, while water reflected a more transient record of antimicrobials and ARG. This study highlights the value of using spatial analyses, different spatial scales, and sampling matrices, to design an environmental monitoring approach to advance our understanding of AMR persistence and dissemination.

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Whole-Genome Sequences of 35 Incompatibility Group I1 Plasmid-Carrying Salmonella enterica Isolates from Food Animal and Clinical Sources

Microbiology Resource Announcements ◽

10.1128/mra.00831-19 ◽

2019 ◽

Vol 8 (35) ◽

Cited By ~ 2

Author(s):

Nesreen H. Aljahdali ◽

Pravin R. Kaldhone ◽

Steven L. Foley ◽

Bijay K. Khajanchi

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Salmonella Enterica ◽

Whole Genome ◽

Genome Sequences ◽

Incompatibility Group ◽

Content Type ◽

Food Animal ◽

Antimicrobial Resistance Genes ◽

Genotypic Characteristics

We sequenced 35 Salmonella enterica isolates carrying incompatibility group I1 (IncI1) plasmids from different serotypes to study their genotypic characteristics. The isolates originated from food animals (n = 32) and human patients (n = 3). All isolates carried IncI1 plasmids, and many had additional plasmids detected along with virulence and antimicrobial resistance genes.

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Conjugal Transfer, Whole-Genome Sequencing, and Plasmid Analysis of Four mcr-1-Bearing Isolates from U.S. Patients

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02417-18 ◽

2019 ◽

Vol 63 (4) ◽

Cited By ~ 1

Author(s):

Wenming Zhu ◽

Adrian Lawsin ◽

Rebecca L. Lindsey ◽

Dhwani Batra ◽

Kristen Knipe ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Genome Sequencing ◽

Resistance Genes ◽

Whole Genome ◽

Colistin Resistance ◽

Content Type ◽

Plasmid Analysis ◽

Antimicrobial Resistance Genes

ABSTRACT Four Enterobacteriaceae clinical isolates bearing mcr-1 gene-harboring plasmids were characterized. All isolates demonstrated the ability to transfer colistin resistance to Escherichia coli; plasmids were stable in conjugants after multiple passages on nonselective media. mcr-1 was located on an IncX4 (n = 3) or IncN (n = 1) plasmid. The IncN plasmid harbored 13 additional antimicrobial resistance genes. Results indicate that the mcr-1-bearing plasmids in this study were highly transferable in vitro and stable in the recipients.

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The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain

Genes ◽

10.3390/genes9050268 ◽

2018 ◽

Vol 9 (5) ◽

pp. 268 ◽

Cited By ~ 41

Author(s):

Elena Oniciuc ◽

Eleni Likotrafiti ◽

Adrián Alvarez-Molina ◽

Miguel Prieto ◽

Jesús Santos ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Resistance Genes ◽

Food Chain ◽

Whole Genome ◽

Antimicrobial Resistance Genes ◽

Metagenome Sequencing

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Genomic Characterization of Fluoroquinolone-Resistant Thermophilic Campylobacter Strains Isolated from Layer Chicken Feces in Gangneung, South Korea by Whole-Genome Sequencing

Genes ◽

10.3390/genes12081131 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1131

Author(s):

Noel Gahamanyi ◽

Dae-Geun Song ◽

Kye-Yoon Yoon ◽

Leonard E. G. Mboera ◽

Mecky I. Matee ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Resistance Genes ◽

Virulence Genes ◽

Coli Strain ◽

Whole Genome ◽

Thermophilic Campylobacter ◽

Antimicrobial Resistance Genes ◽

Campylobacter Species

Thermophilic Campylobacter species of poultry origin have been associated with up to 80% of human campylobacteriosis cases. Layer chickens have received less attention as possible reservoirs of Campylobacter species. Initially, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of two archived Campylobacter isolates (Campylobacter jejuni strain 200605 and Campylobacter coli strain 200606) from layer chickens to five antimicrobials (ciprofloxacin, nalidixic acid, erythromycin, tetracycline, and gentamicin) were determined using broth microdilution while the presence of selected antimicrobial resistance genes was performed by polymerase chain reaction (PCR) using specific primers. Whole-genome sequencing (WGS) was performed by the Illumina HiSeq X platform. The analysis involved antimicrobial resistance genes, virulome, multilocus sequence typing (MLST), and phylogeny. Both isolates were phenotypically resistant to ciprofloxacin (MIC: 32 vs. 32 µg/mL), nalidixic acid (MIC: 128 vs. 64 µg/mL), and tetracycline (MIC: 64 vs. 64 µg/mL), but sensitive to erythromycin (MIC: 1 vs. 2 µg/mL) and gentamicin (MIC: 0.25 vs. 1 µg/mL) for C. jejuni strain 200605 and C. coli strain 200606, respectively. WGS confirmed C257T mutation in the gyrA gene and the presence of cmeABC complex conferring resistance to FQs in both strains. Both strains also exhibited tet(O) genes associated with tetracycline resistance. Various virulence genes associated with motility, chemotaxis, and capsule formation were found in both isolates. However, the analysis of virulence genes showed that C. jejuni strain 200605 is more virulent than C. coli strain 200606. The MLST showed that C. jejuni strain 200605 belongs to sequence type ST-5229 while C. coli strain 200606 belongs to ST-5935, and both STs are less common. The phylogenetic analysis clustered C. jejuni strain 200605 along with other strains reported in Korea (CP028933 from chicken and CP014344 from human) while C. coli strain 200606 formed a separate cluster with C. coli (CP007181) from turkey. The WGS confirmed FQ-resistance in both strains and showed potential virulence of both strains. Further studies are recommended to understand the reasons behind the regional distribution (Korea, China, and Vietnam) of such rare STs.

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