International lineages, such as Salmonella Typhimurium sequence type (ST) 19, are most often associated with foodborne diseases and deaths in humans. In this study, we compared the whole-genome ...sequences of five S. Typhimurium strains belonging to ST19 recovered from clinical human stool samples in North Carolina, United States. Overall, S. Typhimurium strains displayed multidrug-resistant profile, being resistance to critically and highly important antimicrobials including ampicillin, ticarcillin/clavulanic acid, streptomycin and sulfisoxazole, chloramphenicol, tetracycline, respectively. Interestingly, all S. Typhimurium strains carried class 1 integron (intl1) and we were able to describe two genomic regions surrounding blaCARB-2 gene, size 4,062 bp and 4,422 bp for S. Typhimurium strains (HS5344, HS5437, and HS5478) and (HS5302 and HS5368), respectively. Genomic analysis for antimicrobial resistome confirmed the presence of clinically important genes, including blaCARB-2, aac(6')-Iaa, aadA2b, sul1, tetG, floR, and biocide resistance genes (qacEΔ1). S. Typhimurium strains harbored IncFIB plasmid containing spvRABCD operon, as well as rck and pef virulence genes, which constitute an important apparatus for spreading the virulence plasmid. In addition, we identified several virulence genes, chromosomally located, while the phylogenetic analysis revealed clonal relatedness among these strains with S. enterica isolated from human and non-human sources obtained in European and Asian countries. Our results provide new insights into this unusual class 1 integron in virulent S. Typhimurium strains that harbors a pool of genes acting as potential hotspots for horizontal gene transfer providing readily adaptation to new surrounds, as well as being crucially required for virulence in vivo. Therefore, continuous genomic surveillance is an important tool for safeguarding human health.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Multiple interlinked factors are associated with the global resistome, whereas multidrug-resistant (MDR) pathogens have been related to increased mortality rates in humans and animals. CTX-M-type is ...the most prevalent extended-spectrum β-lactamase (ESBL) among
Enterobacteriaceae
, which raises concern worldwide. Zoological gardens have a high density of animals that live very close to each other and to humans. Therefore, this study aimed to investigate through the whole-genome sequencing (WGS) MDR
Escherichia coli
lineages obtained from captivity wild animals in a zoo. Genetic background showed a wide resistome for antimicrobials (e.g.,
bla
CTX-M-65
,
bla
CTX-M-8
,
bla
CMY-2
,
qnrB19
), metals (e.g.,
pcoABCDERS
,
silABCEP
,
merACDEPRT
), and antibacterial biocides (e.g.,
sugE
,
mdfA
) among MDR CTX-M-producing
E. coli
belonging to CC155 and CC156. Mobilome analysis revealed several plasmids, and eight of them were completely characterized, which showed different backbone-encoding genes. Comparative analysis of plasmids
bla
CTX-M-65
/IncHI2-ST3,
bla
CTX-M-8
/IncI1-ST113, and IncQ1 showed a high identity among plasmids obtained from humans and animals worldwide distributed. Besides, several virulence genes, CRISPR, and prophage-related sequences were also detected. The occurrence of MDR
E. coli
belonging to CCs closely related to humans and food-producing animals and the high similarity among the plasmids from MDR
E. coli
carrying clinically significant antimicrobial resistance genes may indicate intercontinental dissemination of these lineages and plasmids. Therefore, these findings contribute to the monitoring of antimicrobial resistance and the human-animal-environment interface worldwide.
Key Points
• Wide resistome for antimicrobials, metals, and antibacterial biocides.
• Multidrug resistance plasmids (bla
CTX-M-65
/IncHI2-ST3, bla
CTX-M-8
/IncI1-ST113).
• Co-occurrence of plasmid-mediated resistance and virulence genes.
The pandemic
Escherichia coli
sequence type 131 (ST131) carrying plasmid-mediated colistin resistance
mcr
genes has emerged worldwide causing extraintestinal infections, with lineages belonging to ...three major clades (A, B, and C). Clade B is the most prevalent in animals, contaminating associated meat products, and can be transmitted zoonotically. However, the
bla
CTX–M–15
gene has only been associated with C2 subclade so far. In this study, we performed a genomic investigation of an
E. coli
(strain S802) isolated from a kale crop in Brazil, which exhibited a multidrug-resistant (MDR) profile to clinically significant antimicrobials (i.e., polymyxin, broad-spectrum cephalosporins, aminoglycosides, and fluoroquinolones). Whole-genome sequencing analysis revealed that the S802 strain belonged to serotype O25:H4, ST131/CC131, phylogenetic group B2, and virotype D5. Furthermore, S802 carried the clade B-associated
fimH22
allele, genes encoding resistance to clinically important antimicrobials, metals, and biocides, and was phylogenetically related to human, avian, and swine ST131-
H
22 strains. Additionally, IncHI2-IncQ1, IncF F2:A-:B1, and ColE1-like plasmids were identified harboring
mcr-1.1
,
bla
CTX–M–15
, and
qnrB19
, respectively. The emergence of the
E. coli
ST131-
H
22 sublineage carrying
mcr-1.1
,
bla
CTX–M–15
, and
qnrB19
in agricultural soil represents a threat to food and environmental safety. Therefore, a One Health approach to genomic surveillance studies is required to effectively detect and limit the spread of antimicrobial-resistant bacteria and their resistance genes.
The emergence and rapid dissemination of colistin-resistant
carrying the plasmid-mediated
gene have created an urgent need to develop specific screening methods. In this study, we evaluated four ...assays based on the inhibition of MCR-1 activity by EDTA: (i) a combined-disk test (CDT) comparing the inhibition zones of colistin and colistin (10 μg) plus EDTA (100 mM); (ii) reduction of colistin MIC (CMR) in the presence of EDTA (80 μg/ml); (iii) a modified rapid polymyxin Nordmann/Poirel test (MPNP); and (iv) alteration of zeta potential (R
= ZP
/ZP
). We obtained encouraging results for the detection of MCR-1 in
isolates recovered from human, food, and animal samples, using the following assay parameters: ≥3 mm difference in the inhibition zones between colistin disks without and with EDTA; ≥4-fold colistin MIC decrease in the presence of EDTA; R
of ≥2.5; and the absence of metabolic activity and proliferation, indicated by unchanged color of phenol red in the presence of colistin-EDTA, in the MPNP test. In this regard, the CDT, CMR, R
, and MPNP assays exhibited sensitivities of 96.7, 96.7, 95.1, and 96.7% and specificities of 89.6, 83.3, 100, and 100%, respectively, for detecting MCR-1-positive
Our results demonstrate that inhibition by EDTA and zeta potential assays may provide simple and inexpensive methods for the presumptive detection of MCR-1-producing
isolates in human and veterinary diagnostic laboratories.
Polyethylene-degrading bacteria have been emerging as a rational and safe alternative in bioremediation strategies. In this context, some
Paenibacillus
species produce enzymes involved in the ...biodegradation of pollutants. Among the enzymes involved in the biodegradation of polyethylene, the alkane hydroxylases, encoded by
alkB
homologous genes, play a key role in this process. Therefore, this study aimed to identify and perform a genomic investigation of the first polyethylene-degrading
Paenibacillus
sp. strain, named DK1. The whole-genome sequence-based analysis revealed that the DK1 strain belonged to the species
Paenibacillus aquistagni
and shared a total of 4327 CDSs with
P. aquistagni
strain 11. On the other hand, a comparison of the gene clusters showed that DK1 strain harbored a genetic context surrounding the
alkB-like
gene similar to that found in
Pseudomonas
sp. strains. The percentage of similarity ranged from 47.88 to 99.76% among all complete amino acid sequences of AlkB-
like
proteins analyzed. Nevertheless, the predicted amino acid sequences of AlkB-
like
contained typical structural motifs of alkane hydroxylases, such as His boxes and the HYG motif. These findings associated with the previously reported phenotypic results highlighted the potential of
P. aquistagni
strain DK1 to biodegrade polyethylene. Therefore, further studies focusing on the biochemical and structural properties of the AlkB-
like
protein from
Paenibacillus
may also contribute to the development of sustainable bioremediation strategies.
The global spread of antibiotic-resistant bacteria and their resistance genes is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving ...environmental and food safety. In this study, we have performed a microbiological and genomic investigation of critical priority pathogens resistant to broad-spectrum cephalosporins and showing endophytic lifestyles in fresh vegetables sold in a country with high endemicity of extended-spectrum β-lactamases (ESBLs). We report the isolation of international high-risk clones of CTX-M-15-producing
, belonging to clonal complexes CC38 and CC648, and
of complex CC307 from macerated tissue of surface-sterilized leaves of spinach, cabbage, arugula, and lettuce. Regardless of species, all ESBL-positive isolates were able to endophytically colonize common bean (
) seedlings, showed resistance to acid pH, and had a multidrug-resistant (MDR) profile to clinically relevant antibiotics (i.e., broad-spectrum cephalosporins, aminoglycosides, and fluoroquinolones). Genomic analysis of CTX-M-producing endophytic
revealed a wide resistome (antibiotics, biocides, disinfectants, and pesticides) and virulome, and genes for endophytic fitness and for withstanding acidic conditions. Transferable IncFIB and IncHI2A plasmids carried
genes and, additionally, an IncFIB plasmid (named pKP301cro) also harbored genes encoding resistance to heavy metals. These data support the hypothesis that fresh vegetables marketed for consumption can act as a figurative Trojan horse for the hidden spread of international clones of critical WHO priority pathogens producing ESBLs, and/or their resistance genes, to humans and other animals, which is a critical issue within a food safety and broader public and environmental health perspective.
Extended-spectrum β-lactamases (ESBL)-producing
are a leading cause of human and animal infections, being classified as critical priority pathogens by the World Health Organization. Epidemiological studies have shown that spread of ESBL-producing bacteria is not a problem restricted to hospitals, but also represents a growing problem involving environmental and food safety. In this regard, CTX-M-type β-lactamases have become the most widely distributed and clinically relevant ESBLs worldwide. Here, we have investigated the occurrence and genomic features of ESBL-producing
in surface-sterilized fresh vegetables. We have uncovered that international high-risk clones of CTX-M-15-producing
and
harboring a wide resistome and virulome, carry additional genes for endophytic fitness and resistance to acidic conditions. Furthermore, we have demonstrated that these CTX-M-15-positive isolates are able to endophytically colonize plant tissues. Therefore, we believe that fresh vegetables can act as a figurative Trojan horse for the hidden spread of critical priority pathogens exhibiting endophytic lifestyles.
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