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| Sequence alignment of the multidrug-resistant chromosomally integrated plasmid (MRCP), its progeny, and pOYZ4. The highlighted GCATTGGG nucleotides represent the duplicated DRs that flanked MRCP. Regions of > 99% identity are marked by gray shading. The positions of the genetic structures iU-A, TU-B, iU-C, and TU-D were marked. iU, inversion unit; TU, translocatable unit.
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IncHI2 plasmids, possessing high flexibility and genetic plasticity, play a vital role in the acquisition and transmission of resistance determinants. Polymorphic mobile genetic elements (MGEs) generated by a chromosomally integrated IncHI2 plasmid in an individual Salmonella isolate have not yet been detected, and the mechanisms of the formation,...
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... clusters including 14 subtypes were obtained by clustering analysis on the S1-PFGE profiles (Supplementary Figure 3A). Considering the size error margin of S1-PFGE prediction, plasmids showing a similar size (± 20-kb) were regarded as belonging to the same subtype. ...
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... the size error margin of S1-PFGE prediction, plasmids showing a similar size (± 20-kb) were regarded as belonging to the same subtype. Cluster B (circular plasmid, sizes < 260-kb) had the highest yields, while cluster A (circular factors, size > 260-kb) were more frequently detected after conjugation at 30 • C. Cluster C (the re-formation of plasmid-chromosomal cointegrates in E. coli J53) only seemed to occur at a very low rate at 37 • C (Supplementary Figure 3A). Moreover, siiF was detected on pPJ-T1-452kb and pPJ-T15-320kb of cluster A by southern hybridization (Supplementary Figure 3B). ...
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... B (circular plasmid, sizes < 260-kb) had the highest yields, while cluster A (circular factors, size > 260-kb) were more frequently detected after conjugation at 30 • C. Cluster C (the re-formation of plasmid-chromosomal cointegrates in E. coli J53) only seemed to occur at a very low rate at 37 • C (Supplementary Figure 3A). Moreover, siiF was detected on pPJ-T1-452kb and pPJ-T15-320kb of cluster A by southern hybridization (Supplementary Figure 3B). Interestingly, the siiABCDEF gene cluster is present in Salmonella sp. but not in E. coli (Morgan et al., 2004;Barlag and Hensel, 2015). ...
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... although the two strains belonged to different serotypes and XbaI-PFGE profiles ( Zhang et al., 2019), pOYZ4 shared a surprisingly high degree of homology (88.46% coverage; 99.71% identity) with MRCP (Supplementary Figure 4 and Figure 2). Similar to pOYZ4, MRCP also possessed an intact IncHI2-ST2 backbone (190-kb), which contained genes for replication (repHIA and repHI2), partition (parAB and parMR), conjugation (tra, trh, and htd), complete or partial toxin-antitoxin systems (hipA/hipB and higB), an SOS mutagenesis correlative operon (umuCD), and two tellurite resistance operons (terY3Y2XY1W and terZABCDEF) (Figure 3 and Supplementary Figure 4). Interestingly, the backbone was flanked by two variable regions (VRs) containing multi-resistance genes and four genes encoding site-specific recombinase (Figure 2). ...
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... circular plasmid pPJ-T0-230kb in J53-transconjugant PJ-T0 was 236,068-bp with 46% GC and 311 predicted CDSs (Figures 1, 3 and Supplementary Figure 4). Similarly, the pPJ-T16-250kb in PJ-T16 was 247,473-bp with 47% GC and 298 CDSs, and the pPJ-T17-213kb in PJ-T17 was 213,369-bp with 46% GC and 247 CDSs. ...
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... the pPJ-T16-250kb in PJ-T16 was 247,473-bp with 47% GC and 298 CDSs, and the pPJ-T17-213kb in PJ-T17 was 213,369-bp with 46% GC and 247 CDSs. All the plasmids showed a high homology with the MRCP (100% identity with 95.17, 97.35, and 90.83% coverage, respectively), and they all shared the same IncHI2-ST2 backbone as expected (Figures 1, 3 and Supplementary Figure 4). Interestingly, the fragment PJ-T13-chr250kb inserted into the J53 chromosomal gene bglH was the same as pPJ-T16-250kb (Figures 1, 3 and Supplementary Figure 4). ...
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... the plasmids showed a high homology with the MRCP (100% identity with 95.17, 97.35, and 90.83% coverage, respectively), and they all shared the same IncHI2-ST2 backbone as expected (Figures 1, 3 and Supplementary Figure 4). Interestingly, the fragment PJ-T13-chr250kb inserted into the J53 chromosomal gene bglH was the same as pPJ-T16-250kb (Figures 1, 3 and Supplementary Figure 4). That is, the SHfr HI2 R strain could not only form free IncHI2 plasmids but also directly integrate into the chromosome of the recipient, giving place to a new MRCP in E. coli. ...
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Background:
Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most seque...
Citations
The fourth mobile sulfonamide resistance gene sul4 has been discovered in many metagenomic datasets. However, there is no reports of it in cultured bacteria. In this study, a sul4 positive clinical Salmonella enterica SC2020597 was obtained by conventional Salmonella isolation methods and characterized by species identification and antimicrobial susceptibility testing. Meanwhile, the genomic DNA was sequenced using both long-read and short-read methods. Following that, the complete genome was analyzed by bioinformatic methods. The sul4 gene in S. enterica SC2020597 differed from the sul4 identified in metagenomic data by one amino acid and could confer full resistance to sulfamethoxazole. Genetic location analysis showed that the sul4 in SC2020597 was carried by a complex chromosomally integrated hybrid plasmid. IS CR20 -like was strongly associated with the mobilization of sul4 by core genetic context analysis. To the best of our knowledge, this is the first report of the emergence of sul4 in clinically cultured S. enterica . More important, the sul4 has the potential to spread to other bacteria with the help of mobile elements.
Salmonella is one of the most important zoonotic pathogens and a major cause of foodborne illnesses, posing a serious global public health hazard. The emergence of plasmid-mediated mcr genes in Salmonella has greatly reduced the clinical choice of salmonellosis treatment. The aim of this study was to investigate the plasmid characteristics of mcr-positive Salmonella identified from patients in Sichuan, China during 2014 to 2017 by whole genomes sequencing. In this study, a total of 12 mcr-positive isolates (1.15%, ; mcr-1, n=10; mcr-3, n=2) were identified from 1046 Salmonella isolates using PCR. Further characterization of these isolates was performed through antimicrobial susceptibility testing, conjugation assays, whole genome sequencing, and bioinformatics analysis. The mcr-1 gene in these isolates were carried by three types of typical mcr-1-bearing plasmids widely distributed in Enterobacteriaceae (IncX4, IncI2 and IncHI2). Of note, two mcr-1-harboring IncHI2 plasmids were integrated into chromosomes by insertion sequences. Two mcr-3-bearing plasmids were IncC and IncFIB broad-host-range plasmids respectively. Genetic context analysis found that mcr-1 was mainly located in Tn6330 or truncated Tn6300, and mcr-3 shared a common genetic structure tnpA-mcr-3-dgkA-ISKpn40. Overall, we found that mcr gene in clinical Salmonella were commonly carried by broad-host plasmids and have potential to transfer into other bacteria by these plasmids. Continuous surveillance of MDR Salmonella in humans and investigation the underlying transmission mechanisms of ARGs are vital to curb the current severe AMR concern.
Salmonella is a major foodborne pathogen that poses a substantial risk to food safety and public health. This study aimed to assess the prevalence, antibiotic susceptibility, and genomic features of Salmonella isolates recovered from 600 retail meat samples (300 pork, 150 chicken and 150 beef) from August 2018 to October 2019 in Shaanxi, China. Overall, 40 (6.67 %) of 600 samples were positive to Salmonella, with the highest prevalence in chicken (21.33 %, 32/150), followed in pork (2.67 %, 8/300), while no Salmonella was detected in beef. A total of 10 serotypes and 11 sequence types (STs) were detected in 40 Salmonella isolates, with the most common being ST198 S. Kentucky (n = 15), ST13 S. Agona (n = 6), and ST17 S. Indiana (n = 5). Resistance was most commonly found to tetracycline (82.50 %), followed by to ampicillin (77.50 %), nalidixic acid (70.00 %), kanamycin (57.50 %), ceftriaxone (55.00 %), cefotaxime (52.50 %), cefoperazone (52.50 %), chloramphenicol (50.00 %), levofloxacin (57.50 %), cefotaxime (52.50 %), kanamycin (52.50 %), chloramphenicol (50.00 %), ciprofloxacin (50.00 %), and levofloxacin (50.00 %). All ST198 S. Kentucky isolates showed multi-drug resistance (MDR; ≥3 antimicrobial categories) pattern. Genomic analysis showed 56 distinct antibiotic resistance genes (ARGs) and 6 target gene mutations of quinolone resistance determining regions (QRDRs) in 40 Salmonella isolates, among which, the most prevalent ARG types were related to aminoglycosides and β-lactams resistance, and the most frequent mutation in QRDRs was GyrA (S83F) (47.5 %). The number of ARGs in Salmonella isolates showed a significant positive correlation with the numbers of insert sequences (ISs) and plasmid replicons. Taken together, our findings indicated retail chickens were seriously contaminated, while pork and beef are rarely contaminated by Salmonella. Antibiotic resistance determinants and genetic relationships of the isolates provide crucial data for food safety and public health safeguarding.
Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) are plasmid-encoded genes that threaten the clinical utility of colistin (COL), one of the highest-priority and critically-important antibiotics (HP-CIAs), used in treating infections caused by multidrug-resistant and extensively-drug resistant bacteria in humans and animals. For more than six decades, COL has been used largely unregulated in the poultry sector in low- and middle-income countries (LMICs) and this led to the development/spread of mcr gene-containing bacteria (MGCB). The prevalence rates of mcr-positive organisms from the poultry sector in LMICs between January 1970 and May 2023 range between 0.51% and 58.8%. By horizontal gene transfer, conjugative plasmids possessing insertion sequences (ISs) especially ISApl1, transposons predominantly Tn6330 and integrons have enhanced the spread of mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8, mcr-9 and mcr-10 in the poultry sector of LMICs. These genes are harboured by Escherichia, Klebsiella, Proteus, Salmonella, Cronobacter, Enterobacter, Shigella, Providencia, Aeromonas, Raoultella, Pseudomonas and Acinetobacter species, belonging to diverse clones. The mcr-1, mcr-3 and mcr-10 have been integrated also into the chromosome of these bacteria and are mobilizable by ISs and integrative conjugative elements. These bacteria often co-express mcr with virulence genes and other genes conferring resistance to HP-CIAs, such as extended-spectrum cephalosporins, carbapenems, fosfomycin, fluoroquinolone and tigecycline. The transmission routes and dynamics of MGCB from the poultry sector in LMICs within the One Heath triad include: contacts with poultry birds, feed/drinking water, manure, poultry farmers and their farm wears, farming equipment, consumption and sale of contaminated poultry meat/egg and associated products, etc. Use of pre/probiotics/other non-antimicrobial alternatives in raising birds, judicious use of non-critically-important antibiotics for therapy, banning of non-therapeutic COL use, improved vaccination, biosecurity, hand hygiene and sanitization, development of rapid diagnostic test kits, and intensified surveillance of mcr gene among others, could effectively control the spread of MGCB from the poultry sector in LMICs.
