Exploring Foodborne Pathogen Ecology and Antimicrobial Resistance in the Light of Shotgun Metagenomics

2018 ◽  
pp. 229-245
Author(s):  
Arnaud Bridier
Keyword(s):  
Antimicrobial Resistance ◽  
Foodborne Pathogen ◽  
Shotgun Metagenomics

First identification and Limited Dissemination of mcr-1 Colistin Resistance in Salmonella Isolates in Jiaxing

2021 ◽  
Author(s):  
Ping Li ◽  
Li Zhan ◽  
Henghui Wang ◽  
Wenjie Gao ◽  
Lei Gao ◽  
...  
Keyword(s):  
Public Health ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Gastrointestinal Disease ◽  
Foodborne Pathogen ◽  
Multidrug Resistant ◽  
Colistin Resistance ◽  
Antimicrobial Resistance Genes ◽  
Genetic Features ◽  
Multidrug Resistant Strain

Salmonella , a major foodborne pathogen, causes severe gastrointestinal disease in people and animals worldwide. Plasmid-borne mcr-1 , which confers colistin resistance in Salmonella, has significant epidemiological interest for public health safety. Here, we report the first evidence of mcr-1 -mediated colistin resistance in one multidrug-resistant strain，namely 16062 in this study, from 355 Salmonella isolates collected for Jiaxing foodborne pathogen monitoring in Zhejiang Province in 2015–2019. In addition to colistin, 16062 displayed multidrug resistance to various antimicrobials (β-lactams, quinolone, sulfonamide, florfenicol, ampicillin, streptomycin, nalidixic acid, aminoglycoside, and trimethoprim-sulfamethox). The mcr-1 -carrying IncX4 plasmid (p16062-MCR) in this study shares a conserved structure with other mcr -IncX4 plasmids. We found that other antimicrobial-resistance genes ( aac(6')-Ib-cr , aadA1 , aadA2 , aph(3')-Ia , oqxA , oqxB , sul1 , and cmlA1 ) are located on p16062-cmlA, an atypical IncHI2 plasmid, in isolate 16062. This is the first identification of transferable colistin resistance in foodborne Salmonella isolate collected in Jiaxing city, the 5-year monitoring of which revealed limited dissemination. By determining the genetic features of the plasmid vehicle, the characteristics of transferable mcr genes circulating in isolates from Jiaxing are now clearer.

scholarly journals Draft Genome Sequences of Multidrug-Resistant Campylobacter jejuni Strains Isolated from Chickens in Central China

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Yiluo Cheng ◽  
Wenting Zhang ◽  
Qin Lu ◽  
Guoyuan Wen ◽  
Qingping Luo ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Draft Genome ◽  
Foodborne Pathogen ◽  
Multidrug Resistant ◽  
Central China ◽  
Genome Sequences ◽  
Genetic Characteristics ◽  
Content Type

Campylobacter jejuni is a major foodborne pathogen that plays an important role in spreading drug resistance. We report the draft genome sequences of two multidrug-resistant C. jejuni isolates which contained similar mutations in the CmeR box. This will improve the understanding of C. jejuni antimicrobial resistance and genetic characteristics.

scholarly journals Comparison of the distribution and diversity of antimicrobial resistance genes between wild and commercially available Atlantic Mackerel

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Daniel Mompel ◽  
Joy Watts ◽  
Michelle Hale
Keyword(s):  
Antimicrobial Resistance ◽  
Farming Systems ◽  
Aquatic Organism ◽  
Intestinal Content ◽  
Livestock Farming ◽  
Shotgun Metagenomics ◽  
Atlantic Mackerel ◽  
Livestock Farming Systems ◽  
Antimicrobial Resistance Genes ◽  
Seawater Samples

The global uncontrolled rise of antimicrobial resistance (AMR) is a major societal threat and it is well documented that AMR is already negatively affecting healthcare and intensive livestock farming systems. Nonetheless, capture fisheries are still essential to the global food supply providing over 50% of the world’s aquatic organism production. To facilitate improved management, it is therefore imperative that we better understand reservoirs of AMR and how gene transmission occurs in the aquatic environment. In order to discern which AMR bacteria and genes are present in the marine environment, sediment and seawater samples were collected and Atlantic Mackerel were captured at the beginning of summer and autumn in the Solent Strait (Portsmouth, U.K). In addition, commercially available Atlantic mackerel were purchased at a local fish market. Using culture-dependent techniques we obtained more than 700 bacterial and 20 fungal isolates from skin, intestinal lining, and intestinal content. Ten different cefotaxime-resistant Pseudomonas spp. were isolated from the seawater and market fish skin samples, and one cefotaxime-resistant Rhanella sp. was isolated from wild fish digesta. Results from ongoing whole-genome shotgun metagenomics analysis will be discussed, as well as the connection between AMR bacteria and AMR gene presence within the marine coastal environment and the local fish markets, which are the last link between capture fisheries and consumers.

Prevalence and Characterization of Campylobacter jejuni Isolated from Retail Chicken in Tianjin, China

2017 ◽  
Vol 80 (6) ◽  
pp. 1032-1040 ◽  
Author(s):  
Hui Ma ◽  
Yulan Su ◽  
Luyao Ma ◽  
Lina Ma ◽  
Ping Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Foodborne Pathogen ◽  
Multidrug Resistant ◽  
Antibiotic Resistant ◽  
Central Cities ◽  
Republic Of China ◽  
Lack Of Information ◽  
Great Genetic Diversity

ABSTRACT Campylobacter jejuni is an important foodborne pathogen worldwide; however, there is a lack of information on the prevalence and antibiotic-resistant profile of C. jejuni in the People's Republic of China. We determined the prevalence and characteristics of C. jejuni on the retail level in Tianjin, one of the five national central cities in China. A total of 227 samples of chicken wings, legs, and breasts were collected from supermarkets and wet markets; 42 of these samples were confirmed to be positive for Campylobacter contamination. The contamination rates of C. jejuni and other Campylobacter species were 13.7% (31 of 227 samples) and 5.7% (13 of 227 samples), respectively. A group of 31 C. jejuni isolates was subjected to antimicrobial susceptibility testing. All (100%) the selected isolates were resistant to ciprofloxacin and nalidixic acid; 77.4% were resistant to tetracycline, 67.7% to doxycycline, 35.5% to gentamicin, 25.8% to clindamycin and florfenicol, 19.4% to chloramphenicol, and 12.9% to erythromycin and azithromycin. A remarkably high proportion (41.9%) of multidrug-resistant isolates was identified. Multilocus sequence typing was conducted to study the population structure of the C. jejuni strains and their relationship to human isolates. The correlation between antimicrobial resistance traits and certain sequence types (STs) or clonal complexes was determined as well. A great genetic diversity of poultry isolates was identified, with 11 STs belonging to 6 clonal complexes and 11 singleton STs. The novel STs accounted for 40.9% (n = 9) of the 22 STs. ST-21, ST-353, ST-354, ST-443, ST-607, and ST-828 complexes had been previously identified from human isolates. This study revealed an extensive level of antimicrobial resistance and genetic diversity in C. jejuni isolated from chicken products in Tianjin, highlighting the necessity of performing enforced interventions to reduce Campylobacter prevalence in China.

scholarly journals A Microbiome-Based Solution to Address Alarming Levels of Drug-Resistant Bacteria in the Newborn Infant Gut

2020 ◽  
Vol 41 (S1) ◽  
pp. s439-s439
Author(s):  
Giorgio Casaburi ◽  
Rebbeca Duar ◽  
Bethany Henrick ◽  
Steven Frese
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Bacterial Species ◽  
The United States ◽  
Resistant Bacteria ◽  
Delivery Mode ◽  
Term Infants ◽  
Shotgun Metagenomics ◽  
Single Strain ◽  
Breastfed Infants

Background: Recent studies have focused on the early infant gut microbiome, indicating that antibiotic resistance genes (ARGs) can be acquired in early life and may have long-term sequelae. Limiting the spread of antimicrobial resistance without triggering the development of additional resistance mechanisms would be of immense clinical value. Here, we present 2 analyses that highlight the abundance of ARGs in preterm and term infants and a proof of concept for modulating the microbiome to promote early stabilization and reduction in ARGs in term infants. Methods: Large-scale metagenomic analysis was performed on 2,141 microbiome samples (90% from pre-term infants) from 10 countries; most were from the United States (87%) and were obtained from the Comprehensive Antibiotic Resistance Database (CARD). We assessed the abundance and specific types of ARGs present. In the second study, healthy, breastfed infants were fed B. infantis EVC001 for 3 weeks starting at postnatal day 7. Stool samples were collected at day 21 and were processed utilizing shotgun metagenomics. Selected antimicrobial-resistant bacterial species were isolated, sequenced, and tested for minimal inhibitory concentrations to clinically relevant antibiotics. Results: In the first study, globally, 417 distinct ARGs were identified. The most abundant gene among all samples was annotated as msrE, a plasmid gene known to confer resistance to macrolide-lincosamide-streptogramin B (MLSB) antibiotics. The remaining most-abundant ARGs were efflux-pump genes associated with multidrug resistance. No significant association in antimicrobial resistance was found when considering delivery mode or antibiotic treatment in the first month of life. In the second study, the EVC001-fed group showed a significant decrease (90%) in ARGs compared to controls (P < .0001). ARGs that differed significantly between groups were predicted to confer resistance to β-lactams, fluoroquinolones, or multiple drug classes. Minimal inhibitory concentration assays confirmed resistance phenotypes among isolates Notably, we found resistance to extended-spectrum β-lactamases among healthy, vaginally delivered breastfed infants who had never been exposed to antibiotics. Conclusions: In this study, we show that the term and preterm infant microbiome contains alarming levels of ARGs associated with clinically relevant antibiotics harbored by bacteria commonly responsible for nosocomial infections. Colonization of the breastfed infant gut by a single strain of B. longum subsp infantis had profound impacts on the fecal metagenome, including reduction in ARGs and reduction of potential pathogens. These findings highlight the importance of developing novel approaches to limit the spread of ARGs among clinically relevant bacteria and the relevance of an additional approach in the effort to solve AR globally.Funding: Evolve BioSystems provided Funding: for this study.Disclosures: Giorgio Casaburi reports salary from Evolve BioSystems.

Prevalence and Multidrug Resistance Pattern of Salmonella Carrying Extended-Spectrum β-Lactamase in Frozen Chicken Meat in Bangladesh

2020 ◽  
Vol 83 (12) ◽  
pp. 2107-2121
Author(s):  
MST. SONIA PARVIN ◽  
MD. MEHEDI HASAN ◽  
MD. YAMIN ALI ◽  
EMDADUL HAQUE CHOWDHURY ◽  
MD. TANVIR RAHMAN ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Foodborne Pathogen ◽  
Multidrug Resistant ◽  
Chicken Meat ◽  
Resistance Pattern ◽  
Salmonella Spp ◽  
Policy Makers ◽  
Disk Diffusion Test ◽  
Extended Spectrum ◽  
Meat Samples

ABSTRACT Salmonella is an important foodborne pathogen that causes public health problems globally, and the increase of antimicrobial resistance in Salmonella has intensified the problem. Chicken meat is an important reservoir and disseminator of Salmonella to humans. This study aimed at estimating the burden of Salmonella carrying extended-spectrum β-lactamase (ESBL) and their antimicrobial resistance pattern in 113 domestic frozen chicken meat samples purchased from supershops available in five divisional megacities of Bangladesh. The study also focused on the determination of β-lactamase–, and plasmid-mediated quinolone resistance–encoding genes. All samples were analyzed for the presence of Salmonella using selective media and PCR assay. Antimicrobial susceptibility test was done by disk diffusion test, and ESBL screening was performed by double-disk synergy tests. Resistance genes were detected using multiplex PCR. Of samples, 65.5% were positive for Salmonella spp., and, of these, 58.1% isolates were ESBL producers. All the isolates were multidrug resistant (MDR): 40.5% were resistant to both three to five and six to eight antimicrobial classes; 17.6% were resistant to 9 to 11 classes, and 1.4% isolates to 12 to 15 classes. The highest rates of resistance were observed against oxytetracycline (100%), followed by trimethoprim-sulfamethoxazole (89.2%), tetracycline (86.5%), nalidixic acid (83.8%), amoxicillin (74.3%), and pefloxacin (70.3%). Notably, 48.6% of isolates demonstrated resistance to imipenem. One (1.4%) isolate was possibly extensively drug resistant. All the isolates were positive for the blaTEM gene, 2.7% were positive for blaCTX-M-1, and 20.3% for blaNDM-1. The prevalence of qnrA and qnrS genes was 4.1 and 6.8%, respectively. This study shows that ESBL-producing Salmonella are widespread in frozen chicken meat in Bangladesh, which puts greater responsibility on food processors and policy makers to ensure food safety. HIGHLIGHTS

Spatial and temporal patterns in antimicrobial resistance ofSalmonellaTyphimurium in cattle in England and Wales

2012 ◽  
Vol 140 (11) ◽  
pp. 2062-2073 ◽  
Author(s):  
R. COX ◽  
T. SU ◽  
H. CLOUGH ◽  
M. J. WOODWARD ◽  
C. SHERLOCK
Keyword(s):  
Antimicrobial Resistance ◽  
Spatial Model ◽  
Foodborne Pathogen ◽  
Temporal Patterns ◽  
Spatial And Temporal Patterns ◽  
Sharp Drop ◽  
England And Wales ◽  
North Wales ◽  
Common Peak ◽  
Resistant Strains

SUMMARYSalmonellais the second most commonly reported human foodborne pathogen in England and Wales, and antimicrobial-resistant strains ofSalmonellaare an increasing problem in both human and veterinary medicine. In this work we used a generalized linear spatial model to estimate the spatial and temporal patterns of antimicrobial resistance inSalmonellaTyphimurium in England and Wales. Of the antimicrobials considered we found a common peak in the probability that anS. Typhimurium incident will show resistance to a given antimicrobial in late spring and in mid to late autumn; however, for one of the antimicrobials (streptomycin) there was a sharp drop, over the last 18 months of the period of investigation, in the probability of resistance. We also found a higher probability of resistance in North Wales which is consistent across the antimicrobials considered. This information contributes to our understanding of the epidemiology of antimicrobial resistance inSalmonella.

scholarly journals Genome Sequence of an Emerging Salmonella enterica Serovar Infantis and Genomic Comparison with Other S. Infantis Strains

2020 ◽  
Vol 12 (3) ◽  
pp. 223-228 ◽  
Author(s):  
Emiliano Cohen ◽  
Galia Rahav ◽  
Ohad Gal-Mor
Keyword(s):  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Salmonella Enterica ◽  
Phenotypic Diversity ◽  
Foodborne Pathogen ◽  
Bacterial Pathogen ◽  
Pathogenicity Islands ◽  
Genomic Comparison ◽  
Human Infections ◽  
Salmonella Pathogenicity Islands

Abstract Salmonella enterica serovar Infantis (S. Infantis) is one of the dominant serovars of the bacterial pathogen S. enterica. In recent years, the number of human infections caused by S. Infantis has been increasing in many countries, and often the emerging population harbors a unique virulence-resistant megaplasmid called plasmid of emerging S. Infantis (pESI). Here, we report the complete gap-free genome sequence of the S. Infantis Israeli emerging clone and compare its chromosome and pESI sequences with other complete S. Infantis genomes. We show a conserved presence of the Salmonella pathogenicity islands 1–6, 9, 11, 12, and CS54 and a common integration of five bacteriophages in the S. Infantis chromosome. In contrast, we found variable presence of additionally three chromosomally integrated phages and eight modular regions in pESI, which contribute to the genetic and phenotypic diversity (including antimicrobial resistance) of this ubiquitous foodborne pathogen.

scholarly journals Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies

2021 ◽  
Vol 9 (1) ◽  
pp. 97
Author(s):  
J. Christopher Noone ◽  
Karin Helmersen ◽  
Truls Michael Leegaard ◽  
Inge Skråmm ◽  
Hege Vangstein Aamot
Keyword(s):  
Antimicrobial Resistance ◽  
University Hospital ◽  
Orthopaedic Implant ◽  
Metagenomic Sequencing ◽  
Pathogen Identification ◽  
Shotgun Metagenomics ◽  
Microbial Identification ◽  
Conventional Culture ◽  
Shotgun Metagenomic Sequencing ◽  
Antimicrobial Resistance Gene

Conventional culture-based diagnostics of orthopaedic-implant-associated infections (OIAIs) are arduous. Hence, the aim of this study was to evaluate a culture-independent, rapid nanopore-based diagnostic protocol with regard to (a) pathogen identification, (b) time to pathogen identification, and (c) identification of antimicrobial resistance (AMR). This prospective proof-of-concept study included soft tissue biopsies from 32 patients with OIAIs undergoing first revision surgery at Akershus University Hospital, Norway. The biopsies were divided into two segments. Nanopore shotgun metagenomic sequencing and pathogen and antimicrobial resistance gene identification using the EPI2ME analysis platform (Oxford Nanopore Technologies) were performed on one segment. Conventional culture-based diagnostics were performed on the other. Microbial identification matched in 23/32 OIAI patients (72%). Sequencing detected additional microbes in 9/32 patients. Pathogens detected by culturing were identified by sequencing within a median of 1 h of sequencing start [range 1–18 h]. Phenotypic AMR was explained by the detection of resistance genes in 11/23 patients (48%). Diagnostics of OIAIs using shotgun metagenomics sequencing are possible within 24 h from biopsy using nanopore technology. Sequencing outperformed culturing with respect to speed and pathogen detection where pathogens were at sufficient concentration, whereas culture-based methods had an advantage at lower pathogen concentrations. Sequencing-based AMR detection may not yet be a suitable replacement for culture-based antibiotic susceptibility testing.

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