Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period

AbstractThis study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. − 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbiomes and AMR determinants were observed at D.8 when Prevotella (20.9%) was the major genus, whereas at D. − 3–D.3, Alistipes (6.9–12.7%) and Bacteroides (5.2–8.5%) were the major genera. Lactobacillus and Escherichia were notably observed at D. − 3 (1.2%) and D. − 3–D.3 (0.2–0.4%), respectively. For AMR, a distinct cluster of AMR determinants was observed at D.8, mainly conferring resistance to macrolide–lincosamide–streptogramin (mefA), β-lactam (cfxA6 and aci1) and phenicol (rlmN). In contrast, at D. − 3–D.3, a high abundance of determinants with aminoglycoside (AMG) (sat, aac(6')-aph(2''), aadA and acrF), β-lactam (fus-1, cepA and mrdA), multidrug resistance (MDR) (gadW, mdtE, emrA, evgS, tolC and mdtB), phenicol (catB4 and cmlA4), and sulfonamide patterns (sul3) was observed. Canonical correlation analysis (CCA) plot associated Escherichia coli with aac(6')-aph(2''), emrA, mdtB, catB4 and cmlA4 at D. − 3, D.0 and/or D.3 whereas at D.8 associations between Prevotella and mefA, cfxA6 and aci1 were identified. The weaning age and diet factor played an important role in the microbial community composition.

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Effect of Lactobacillus plantarum on intestinal microbial community composition and response to enterotoxigenic Escherichia coli challenge in weaning piglets

Livestock Science ◽

10.1016/j.livsci.2010.06.034 ◽

2010 ◽

Vol 133 (1-3) ◽

pp. 98-100 ◽

Cited By ~ 12

Author(s):

Robert Pieper ◽

Pawel Janczyk ◽

Vladimir Urubschurov ◽

Zhenping Hou ◽

Ulrich Korn ◽

...

Keyword(s):

Escherichia Coli ◽

Microbial Community ◽

Lactobacillus Plantarum ◽

Community Composition ◽

Microbial Community Composition ◽

Enterotoxigenic Escherichia Coli ◽

Intestinal Microbial Community ◽

Weaning Piglets

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Plasmid-Borne and Chromosomal ESBL/AmpC Genes in Escherichia coli and Klebsiella pneumoniae in Global Food Products

Frontiers in Microbiology ◽

10.3389/fmicb.2021.592291 ◽

2021 ◽

Vol 12 ◽

Author(s):

Paula Kurittu ◽

Banafsheh Khakipoor ◽

Maria Aarnio ◽

Suvi Nykäsenoja ◽

Michael Brouwer ◽

...

Keyword(s):

Escherichia Coli ◽

Multidrug Resistance ◽

Virulence Genes ◽

Food Products ◽

Whole Genome ◽

Beta Lactamase ◽

Broiler Meat ◽

E Coli ◽

Meat Samples ◽

Global Food

Plasmid-mediated extended-spectrum beta-lactamase (ESBL), AmpC, and carbapenemase producing Enterobacteriaceae, in particular Escherichia coli and Klebsiella pneumoniae, with potential zoonotic transmission routes, are one of the greatest threats to global health. The aim of this study was to investigate global food products as potential vehicles for ESBL/AmpC-producing bacteria and identify plasmids harboring resistance genes. We sampled 200 food products purchased from Finland capital region during fall 2018. Products originated from 35 countries from six continents and represented four food categories: vegetables (n = 60), fruits and berries (n = 50), meat (n = 60), and seafood (n = 30). Additionally, subsamples (n = 40) were taken from broiler meat. Samples were screened for ESBL/AmpC-producing Enterobacteriaceae and whole genome sequenced to identify resistance and virulence genes and sequence types (STs). To accurately identify plasmids harboring resistance and virulence genes, a hybrid sequence analysis combining long- and short-read sequencing was employed. Sequences were compared to previously published plasmids to identify potential epidemic plasmid types. Altogether, 14 out of 200 samples were positive for ESBL/AmpC-producing E. coli and/or K. pneumoniae. Positive samples were recovered from meat (18%; 11/60) and vegetables (5%; 3/60) but were not found from seafood or fruit. ESBL/AmpC-producing E. coli and/or K. pneumoniae was found in 90% (36/40) of broiler meat subsamples. Whole genome sequencing of selected isolates (n = 21) revealed a wide collection of STs, plasmid replicons, and genes conferring multidrug resistance. blaCTX–M–15-producing K. pneumoniae ST307 was identified in vegetable (n = 1) and meat (n = 1) samples. Successful IncFII plasmid type was recovered from vegetable and both IncFII and IncI1-Iγ types from meat samples. Hybrid sequence analysis also revealed chromosomally located beta-lactamase genes in two of the isolates and indicated similarity of food-derived plasmids to other livestock-associated sources and also to plasmids obtained from human clinical samples from various countries, such as IncI type plasmid harboring blaTEM–52C from a human urine sample obtained in the Netherlands which was highly similar to a plasmid obtained from broiler meat in this study. Results indicate certain foods contain bacteria with multidrug resistance and pose a possible risk to public health, emphasizing the importance of surveillance and the need for further studies on epidemiology of epidemic plasmids.

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Three cases of mcr-1-positive colistin-resistant Escherichia coli bloodstream infections in Italy, August 2016 to January 2017

Eurosurveillance ◽

10.2807/1560-7917.es.2017.22.16.30517 ◽

2017 ◽

Vol 22 (16) ◽

Cited By ~ 17

Author(s):

Marta Corbella ◽

Bianca Mariani ◽

Carolina Ferrari ◽

Francesco Comandatore ◽

Erika Scaltriti ◽

...

Keyword(s):

Escherichia Coli ◽

Multidrug Resistance ◽

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Bloodstream Infections ◽

Tertiary Hospital ◽

Whole Genome ◽

E Coli ◽

Sequence Types

We describe three cases of bloodstream infection caused by colistin-resistant Escherichia coli in patients in a tertiary hospital in Italy, between August 2016 and January 2017. Whole genome sequencing detected the mcr-1 gene in three isolated strains belonging to different sequence types (STs). This occurrence of three cases with mcr-1-positive E. coli belonging to different STs in six months suggests a widespread problem in settings where high multidrug resistance is endemic such as in Italy.

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Whole genome shotgun sequencing revealed highly polymorphic genome regions and genes in Escherichia coli O157:H7 isolates collected from a single feedlot

PLoS ONE ◽

10.1371/journal.pone.0202775 ◽

2018 ◽

Vol 13 (8) ◽

pp. e0202775

Author(s):

Xin Gao ◽

Xun Yang ◽

Lance Noll ◽

Xiaorong Shi ◽

Jay Worley ◽

...

Keyword(s):

Escherichia Coli ◽

Shotgun Sequencing ◽

Whole Genome Shotgun ◽

Whole Genome ◽

Escherichia Coli O157 ◽

Whole Genome Shotgun Sequencing

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Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information

mBio ◽

10.1128/mbio.00431-19 ◽

2019 ◽

Vol 10 (2) ◽

Cited By ~ 6

Author(s):

Ana Georgina Cobián Güemes ◽

Yan Wei Lim ◽

Robert A. Quinn ◽

Douglas J. Conrad ◽

Sean Benler ◽

...

Keyword(s):

Escherichia Coli ◽

Cystic Fibrosis ◽

Microbial Community ◽

Life Span ◽

Microbial Community Composition ◽

Rapid Response ◽

Metabolomics Data ◽

Content Type ◽

Pulmonary Exacerbations

ABSTRACTPulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient’s lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenicEscherichia coli(STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF.IMPORTANCEProper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient’s microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenicEscherichia coli. The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.

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